From 8a8d5b265ae95cf394fdf13cdd8a171128da2389 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 27 May 2024 10:58:42 +0000 Subject: [PATCH] Add changes --- _data/packages-embeddings.csv | 5000 ++++++++--------- _data/repos.yml | 8401 ++++++++++++++-------------- assets/js/repos.js | 1323 +++-- data/package-distances.csv | 2 +- data/package-normalized-counts.csv | 2 +- data/package-pair-counts.csv | 2 +- 6 files changed, 7413 insertions(+), 7317 deletions(-) diff --git a/_data/packages-embeddings.csv b/_data/packages-embeddings.csv index 5f91b7a2..a15c44f9 100644 --- a/_data/packages-embeddings.csv +++ b/_data/packages-embeddings.csv @@ -1,2501 +1,2501 @@ name,x,y,norm,distinct -,-40.651867,-17.16247,1.4142135623730951,1 -$build_deps,-27.559982,-17.681393,4.358898943540674,19 -..,-35.983494,-17.894201,3.4641016151377544,4 -2decomp,-27.913486,-13.969868,4.242640687119285,9 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+zlib-api,-11.919001,-28.39143,5.0,25 +zlib-toolfile,-15.711088,39.75623,13.416407864998739,109 +zoltan,-15.511419,-15.338651,6.708203932499369,26 +zsh,6.6727986,6.799118,41.641325627314025,241 +zstd,30.334597,-11.337717,94.09038208021052,977 +zstd-toolfile,-17.403149,39.178055,10.44030650891055,109 +zstd:,-19.194063,-26.830334,4.795831523312719,10 diff --git a/_data/repos.yml b/_data/repos.yml index 1ca6df80..7bc6b5f5 100644 --- a/_data/repos.yml +++ b/_data/repos.yml @@ -293,359 +293,437 @@ ACCESS-NRI/ACCESS-OM2-BGC: subscribers_count: 4 topics: [] updated_at: 1710289078.0 -ACCESS-NRI/ACCESS-OM3: +AMReX-Microelectronics/artemis: data_format: 2 - description: ACCESS-OM3 repository for spack configuration information + description: ARTEMIS (Adaptive mesh Refinement Time-domain ElectrodynaMIcs Solver) + couples the Maxwell's equations implementation in WarpX with classical equations + that describe quantum material behavior (such as, LLG equation for micromagnetics + and London equation for superconducting materials) for quantifying the performance + of next-generation microelectronics. filenames: - - spack.yaml - full_name: ACCESS-NRI/ACCESS-OM3 + - Docs/spack.yaml + full_name: AMReX-Microelectronics/artemis + latest_release: null + readme: "

ARTEMIS

\n

ARTEMIS (Adaptive mesh Refinement Time-domain ElectrodynaMIcs\ + \ Solver) is a high-performance coupled electrodynamics\u2013micromagnetics solver\ + \ for full physical modeling of signals in microelectronic circuitry. The overall\ + \ strategy couples a finite-difference time-domain (FDTD) approach for Maxwell\u2019\ + s equations to a magnetization model described by the Landau\u2013Lifshitz\u2013\ + Gilbert (LLG) equation. The algorithm is implemented in the Exascale Computing\ + \ Project (ECP) software framework, AMReX, which provides effective scalability\ + \ on manycore and GPU-based supercomputing architectures. Furthermore, the code\ + \ leverages ongoing developments of the Exascale Application Code, WarpX, which\ + \ is primarily being developed for plasma wakefield accelerator modeling. Our\ + \ temporal coupling scheme provides second-order accuracy in space and time by\ + \ combining the integration steps for the magnetic field and magnetization into\ + \ an iterative sub-step that includes a trapezoidal temporal discretization for\ + \ the magnetization. The performance of the algorithm is demonstrated by the excellent\ + \ scaling results on NERSC multicore and GPU systems, with a significant (59\xD7\ + ) speedup on the GPU using a node-by-node comparison. The utility of our code\ + \ is validated by performing simulations of transmission lines, rectangle electromagnetic\ + \ waveguides, magnetically tunable filters, on-chip coplanar waveguides and resonators,\ + \ magnon-photon coupling circuits, and so on.

\n

Installation

\n\ +

Download AMReX Repository

\n

git\ + \ clone git@github.com:AMReX-Codes/amrex.git

\n

Download Artemis Repository

\n

git clone git@github.com:AMReX-Microelectronics/artemis.git

\n\ +

Build

\n\ +

Make sure that the AMReX and Artemis are cloned in the same location in their\ + \ filesystem. Navigate to the Exec folder of Artemis and execute\nmake -j\ + \ 4.
\nYou can turn on and off the LLG equation by specifying USE_LLG\ + \ during compilation.
\nThe following command compiles Artemis without LLG\n\ + make -j 4 USE_LLG=FALSE
\nThe following command compiles Artemis\ + \ with LLG\nmake -j 4 USE_LLG=TRUE
\nThe default value of USE_LLG\ + \ is TRUE.

\n

Running Artemis

\n

Example input scripts are\ + \ located in Examples directory.

\n

Simple Testcase without LLG

\n

You can run the following to simulate an air-filled X-band\ + \ rectangle waveguide:

\n

For MPI+OMP build

\n

make\ + \ -j 4 USE_LLG=FALSE
\nmpirun -n 4 ./main3d.gnu.TPROF.MTMPI.OMP.GPUCLOCK.ex\ + \ Examples/Waveguide/inputs_3d_empty_X_band

\n

For MPI+CUDA build

\n\ +

make -j 4 USE_LLG=FALSE USE_GPU=TRUE
\nmpirun -n 4 ./main3d.gnu.TPROF.MTMPI.CUDA.GPUCLOCK.ex\ + \ Examples/Waveguide/inputs_3d_empty_X_band

\n

Simple Testcase with LLG

\n

You can run the following to simulate an X-band magnetically\ + \ tunable filter:

\n

For MPI+OMP build

\n

make\ + \ -j 4 USE_LLG=TRUE
\nmpirun -n 8 ./main3d.gnu.TPROF.MTMPI.OMP.GPUCLOCK.ex\ + \ Examples/Waveguide/inputs_3d_LLG_filter

\n

For MPI+CUDA build

\n\ +

make -j 4 USE_LLG=TRUE USE_GPU=TRUE
\nmpirun -n 8 ./main3d.gnu.TPROF.MTMPI.CUDA.GPUCLOCK.ex\ + \ Examples/Waveguide/inputs_3d_LLG_filter

\n

Visualization and Data Analysis

\n

Refer to the following link for several\ + \ visualization tools that can be used for AMReX plotfiles.

\n

Visualization

\n

Data Analysis in Python using yt

\n

You can extract the data in numpy\ + \ array format using yt (you can refer to this for installation and usage of yt. After you have installed\ + \ yt, you can do something as follows, for example, to get variable 'Ex' (x-component\ + \ of electric field)

\n
import yt\nds = yt.load('./plt00001000/')\
+    \ # for data at time step 1000\nad0 = ds.covering_grid(level=0, left_edge=ds.domain_left_edge,\
+    \ dims=ds.domain_dimensions)\nE_array = ad0['Ex'].to_ndarray()\n
\n\ +

Publications

\n
    \n
  1. Z. Yao, R. Jambunathan, Y. Zeng and A. Nonaka, A\ + \ massively parallel time-domain coupled electrodynamics\u2013micromagnetics solver.\ + \ The International Journal of High Performance Computing Applications. 2022;36(2):167-181.\ + \ doi:10.1177/10943420211057906\nlink\n
  2. \n
  3. S. S. Sawant, Z. Yao, R. Jambunathan and\ + \ A. Nonaka, Characterization of transmission lines in microelectronic circuits\ + \ Using the ARTEMIS solver, IEEE Journal on Multiscale and Multiphysics Computational\ + \ Techniques, vol. 8, pp. 31-39, 2023, doi: 10.1109/JMMCT.2022.3228281\nlink\n\ +
  4. \n
  5. R. Jambunathan, Z. Yao, R. Lombardini, A. Rodriguez, and A. Nonaka,\ + \ Two-fluid physical modeling of superconducting resonators in the ARTEMIS framework,\ + \ Computer Physics Communications, 291, p.108836. doi:10.1016/j.cpc.2023.108836\n\ + link\n
  6. \n
\n" + stargazers_count: 10 + subscribers_count: 5 + topics: [] + updated_at: 1716409719.0 +Alpine-DAV/spack_configs: + data_format: 2 + description: spack envs + filenames: + - _experimental/envs/alpinedav/ubuntu_18_cuda_10.1_devel/spack.yaml + - _experimental/envs/alpinedav/ubuntu_18_devel/spack.yaml + full_name: Alpine-DAV/spack_configs latest_release: null - readme: '

ACCESS-OM3

+ readme: '

spack_configs

-

ACCESS-OM3 repository for spack configuration information

+

shared spack configs repo

' stargazers_count: 0 - subscribers_count: 5 + subscribers_count: 4 topics: [] - updated_at: 1712101237.0 -AMReX-Codes/pyamrex: + updated_at: 1639176281.0 +C2SM/spack-c2sm: data_format: 2 - description: GPU-Enabled, Zero-Copy AMReX Python Bindings including AI/ML + description: Repository for c2sm spack config and repo files filenames: - - docs/spack.yaml - full_name: AMReX-Codes/pyamrex - latest_release: '24.05' - readme: '

pyAMReX

The spack extension + of C2SM and MCH

-

Python3 - - Python3 API: Beta - - Documentation Status - - Discussions
- - Linux - - macOS - - Windows
- - License pyAMReX - - DOI (source)Documentation Status

-

The Python binding pyAMReX bridges the compute in AMReX block-structured codes - and data science: +

Spack is the package manager used by C2SM and MeteoSwiss to install and deploy + software on supercomputers, local machines and the cloud.

- it provides zero-copy application GPU data access for AI/ML, in situ analysis, - application coupling and enables rapid, massively parallel prototyping. +

Documentations

- pyAMReX enhances the Block-Structured - AMR Software Framework AMReX and its applications.

+

Infos about c2sm-supported software and machines

-

Users

+ - -

Install Dependencies

- -

macOS/Linux:

- -
spack env activate -d .
+    

With spack v0.18 we suggest local/individual spack instances and the use of + spack environments.

- # optional: +

A user clones the spack repo

- # spack add cuda +
git clone --depth 1 --recurse-submodules
+    --shallow-submodules -b v0.20.1.5 https://github.com/C2SM/spack-c2sm.git
- spack install
+

gets spack in the command line

-

(in new terminals, re-activate the environment with spack env activate - -d . again)

+
.
+    spack-c2sm/setup-env.sh
-

or macOS/Linux:

+

activates an environment

-
brew update
+    
spack env activate <path_to_env>
- brew install ccache cmake libomp mpi4py numpy open-mpi python
+

and starts exploring

-

Now, cmake --version should be at version 3.20.0 or newer.

+
spack info <package>
 
-    

Or go:

+ spack spec <spec>
-
python3 -m pip install -U pip
+    

and building

- python3 -m pip install -U build packaging setuptools wheel +
spack install <spec>
 
-    python3 -m pip install -U cmake
+ spack dev-build <spec>
-

If you wish to run unit tests, then please install pytest

+

a package.

-
python3 -m pip install -U pytest
+

Updating spack-c2sm is in the hands of the user.

-

Some of our tests depend on optional third-party modules (e.g., pandas, - cupy, numba, and/or pytorch). +

git pull
 
-    If these are not installed then their tests will be skipped.

+ git submodule update --recursive
-

Configure your compiler

+

After an update we advice to clean

-

For example, using the Clang compiler:

+
spack uninstall -a
 
-    
export
-    CC=$(which clang)
+    spack clean -a
 
-    export CXX=$(which
-    clang++)
+ rm -rf ~/.spack
-

If you also want to select a CUDA compiler:

+

and rebuild.

-
export
-    CUDACXX=$(which nvcc)
+    

Command cheat sheet

- export CUDAHOSTCXX=$(which - clang++)
+ -

Build

+ -

From the base of the pyAMReX source directory, execute:

+ -
#
-    optional controls (example):
+    
- #export AMREX_SPACEDIM=3 + - #export AMREX_MPI=ON + - #export AMREX_OMP=ON + - #export AMREX_GPU_BACKEND=CUDA + - #export AMREX_SRC=$PWD/../amrex + - #export CMAKE_BUILD_PARALLEL_LEVEL=8 + + - python3 -m pip install -U -r requirements.txt + - python3 -m pip install -v --force-reinstall --no-deps . + -

If you are iterating on builds, it will faster to rely on ccache - and to let CMake call the pip install logic:

+ -
cmake -S .
-    -B build -DAMReX_SPACEDIM="1;2;3"
+    
-

After successful installation, you can run the unit tests (assuming pytest - is +

- installed). If AMREX_MPI=ON, then please prepend the following commands - with mpiexec -np <NUM_PROCS>

+ -
#
-    Run all tests
+    
- python3 -m pytest tests/ + - python3 -m pytest tests/test_intvect.py + + - # Run a single test (useful during - debugging) + - python3 -m pytest tests/test_intvect.py::test_iv_conversions + - # Run all tests, do not capture "print" - output and be verbose + - python3 -m pytest -s -vvvv tests/ + -

Build Options

+
Command
Clonegit clone --depth 1 --recurse-submodules --shallow-submodules -b <branch/tag> + https://github.com/C2SM/spack-c2sm.git
Load - cmake --build build --target pip_install -j 8 + . spack-c2sm/setup-env.sh autodetects machine
or
. spack-c2sm/setup-env.sh + <machine> forces machine
or
. spack-c2sm/setup-env.sh + unknown uses blank config
spack compiler find autodetects compilers
spack external find --all + autodetects externally installed packages -

Test

+
Update + git pull
git submodule update --recursive - # Run tests from a single file +
Clean + spack uninstall -a uninstalls all packages
spack clean -a cleans all misc caches
rm -rf ~/.spack removes + user scope data
-

If you are using the pip-driven install, selected AMReX CMake options can be controlled with environment variables:

+

Spec syntax: <package>@<version>%<compiler>+<variant> ~<variant>^<sub-package> +<sub-package-variant><compiler flags>

@@ -653,11 +731,9 @@ AMReX-Codes/pyamrex: - - - + - + @@ -667,3190 +743,2505 @@ AMReX-Codes/pyamrex: - - - - + + spack find lists all installed packages.
spack find <spec> + lists all installed packages that match the spec. - - - + - + - + - + spack spec <spec> concretizes abstract spec (unspecfied variant + = any)
Spack is not required to use the default of an + unspecified variant. The default value is only a tiebreaker for the concretizer. - + - - - + - + - + - + + spack location --install-dir <spec> prints location of all + installs that satisfy the spec - - - - + + spack load <spec> loads run environment - - - + - + - - - + - + - + - +
Environment VariableDefault & ValuesDescriptionCommand
AMREX_OMPON/OFF + Find - Enable OpenMP
AMREX_GPU_BACKEND - - NONE/SYCL/CUDA/HIPInfoOn-node, accelerated GPU backendspack info <package>
AMREX_MPISpecON/OFF + - Enable MPI
AMREX_PRECISIONSINGLE/DOUBLE - - InstallPrecision of AMReX Real typespack install <spec>
AMREX_SPACEDIMLocate"1;2;3" - Dimension(s) of AMReX as a ;-separated list
AMREX_BUILD_SHARED_LIBSON/OFF + Load env - Build the core AMReX library as shared library
AMREX_SRCNoneActivate + envAbsolute path to AMReX source directory (preferred if set)spack env activate <env_name>
AMREX_REPOhttps://github.com/AMReX-Codes/amrex.gitDeactivate + envRepository URI to pull and build AMReX fromspack deactivate
AMREX_BRANCH
- development + ' + stargazers_count: 6 + subscribers_count: 18 + topics: [] + updated_at: 1716467715.0 +CHIP-SPV/chipStar-Spack: + data_format: 2 + description: Support for building chipStar and related libraries via Spack + filenames: + - Environments/LevelZero/spack.yaml + full_name: CHIP-SPV/chipStar-Spack + latest_release: null + readme: ' - Repository branch for AMREX_REPO +

Overview

- +

chipStar (formerly CHIP-SPV) - + is software that allows software written to use the - + Heterogeneous-compute + Interface for Portability - AMREX_INTERNAL + (HIP) - + interface and kernel language to target GPUs via the - ON/OFF + SPIR-V intermediate + language. - Needs a pre-installed AMReX library if set to OFF + chipStar can use either the Intel Level Zero runtime or an OpenCL - + runtime as a backend.

- +

This repository contains support for building chipStar and its - + dependencies via the Spack package - PYBIND11_INTERNAL + manager.

- +

Note: most development to date has been done with the Level Zero - ON/OFF + environment, and it is expected that substantial work is needed for - Needs a pre-installed pybind11 library if set to OFF + the environment targeting the OpenCL backend to work.

- +

Prerequisites

- + - +
$ spack install intel-oneapi-compilers@2023
 
-    
+    $ spack compiler add $(spack location
+    -i intel-oneapi-compilers@2023)/compiler/latest/linux
- PYAMREX_IPO +

Usage

- +
    - ON/OFF +
  1. Clone this repository to the target system.
  2. - Compile with interprocedural/link optimization (IPO/LTO) +
- +
$ git clone https://github.com/CHIP-SPV/CHIP-SPV-Spack
- +
    - PYINSTALLOPTIONS +
  1. Activate the environment you want to build. E.g., for the - None + environment that just builds chipStar with Level Zero backend:
  2. - Additional options for pip install, e.g., -v --user +
- +
$ cd
+    CHIP-SPV-Spack/Environments/LevelZero
 
-    
+    $ spack env activate .
- +
    - +
  1. Concretize the active environment. (In Spack terminology, -

    Furthermore, pyAMReX adds a few selected CMake build options:

    + "to concretize" means to let Spack examine the package specifications - + it has been asked to build, plus the available package repositories, - + resolve dependencies and check constraints, and decide exactly which - + packages it will build, in which order, and with which configuration.) - + - +
    $ spack concretize -f -U
    - +

    We suggest examining the output from running the spack concretize -

    + command to make sure that Spack''s concretizer has truly decided to - + use the configuration options and especially the compilers that you - + want it to use. Note that the environment and related configuration - + are purposefully not overly constrained to use the given compiler - + for every dependency package, so even though there are some packages - + built (or re-used from already-installed packages) using %gcc such - + as the system''s GCC installation.

    - +

    If Spack''s concretizer didn''t do what you want, you can re-concretize -

    + the environment and be more explicit about what you want using command-line - + configuration options (recommended) or by editing the environment''s - + is using. (Use spack config blame to see which configuration files + Spack is - + using.) For instance, if you have both clang@16.0.2 and clang@15.0.7 - + installed and registered as Spack compilers, and you want to build - + using clang@15.0.7, you may have to use a concretize command like + the - + following:

    - +

    As before, verify from the output of the spack concretize command + that it -

    + is using the compiler version you want, clang@15.0.7 in this example.

    - +
      -
    +
  2. Build the environment.
  3. - + - +

    Spack supports some options for controlling the build and installation, -

    + such as -j to limit the number of processes used for parallel builds, - + useful for being a good citizen on shared systems by not allowing Spack - + to use all available cores (its default). See the Spack documentation for - + more information.

    - +

    Assuming all goes well with the build and install, a spack find -

    + should show the packages that you just built.

    - +
      -
    +
  4. Use the installed software. There are several ways you might -
  5. + update your environment to use the software, including: - + +
  6. Activating the environment that you used to build the software
  7. - +
  8. If your Spack configuration is such that it can generate module files -
  9. + and module files have been generated for the software you built - + via this environment, module load chipstar - + - + - +

    Note that you may need to modify your environment to be able to run -

    + programs produced using chipStar and the H4I libraries built - + using this Spack repository. For instance, on some systems, - + one must load the intel_compute_runtime module before being - +

    TODO

    - + +
  10. Clean up and verify the OpenCL-based environment.
  11. - +
  12. Ensure the OpenCL-based environment can use any OpenCL implementation.
  13. - +
  14. Incorporate H4I HIP libraries like H4I-HipBLAS into an environments.
  15. - +
  16. Support using the software installed by the environment via -
  17. + module command. - + - + ' + stargazers_count: 0 + subscribers_count: 5 + topics: [] + updated_at: 1687550793.0 +CODARcode/z-checker-installer: + data_format: 2 + description: one-key installation to install gnuplot, sz, zfp, and z-checker, and + complete the configuration automatically for the testing. + filenames: + - libpressio-opt/spack.yaml + full_name: CODARcode/z-checker-installer + latest_release: 0.8.0 + readme: '

    Z-checker installer

    - +

    See COPYRIGHT in top-level directory.

    - + Other contributors: Robert Underwood, Hengzhi Chen

    - +

    3rd party libraries/tools

    - + +
  18. cmake (version: 3.13+)
  19. - +
  20. gcc (version: 7.3+)
  21. - +
  22. g++
  23. - +
  24. git
  25. - +
  26. curl
  27. - +
  28. texlive (e.g., execute ''sudo yum install texlive-*'' on linux)
  29. - +
  30. ghostscript(gsview) (z-checker-install.sh can install it automatically if + missing)
  31. - +
  32. gnuplot (z-checker-install.sh will install gnuplot automatically if missing)
  33. - +
  34. perl (used by only web-visualization support)
  35. - + - +

    Note: if you install only texlive (e.g., sudo yum install texlive), then you + also need to install latex packages ''comment.sty'', ''subfigure.sty'', ''nopageno.sty'' + and ''morefloats.sty'' by running ''sudo yum -y install "tex(${latexpkg})"'' (e.g., + sudo yum -y install "tex(comment.sty)")

    - +

    The following libraries - libpng, tif22pnm and sam2p are used to convert slice + image png files to eps. If plotSliceImag option is disabled (in zc.config), these + three libraries are not needed.

    - + +
  36. libpng (z-checker-install.sh will install tif22pnm automatically if missing; + in fact, libpng can be installed using system installation command such as ''yum + install libpng-devel'' on linux.)
  37. - +
  38. tif22pnm (z-checker-install.sh will install tif22pnm automatically if missing)
  39. -
    CMake OptionDefault & ValuesDescription
    AMReX_SPACEDIM + that must be built with %clang, there are others that may be - 3, use "1;2;3" for allDimension(s) of AMReX as a ;-separated list
    pyAMReX_CCACHE + spack.yaml file or other configuration options that your Spack installation - ON/OFFSearch and use CCache to speed up rebuilds
    pyAMReX_IPO +
    $ spack -c "packages:chipstar:require:''%clang@15.0.7''"
    +    concretize -f -U
    - ON/OFF
    Compile with interprocedural/link optimization (IPO/LTO)
    pyAMReX_INSTALL +
    $ spack install
    - ON/OFF
    Enable install targets for pyAMReX
    pyAMReX_amrex_srcNoneAbsolute path to AMReX source directory (preferred if set)
    pyAMReX_amrex_internal + - ON/OFFNeeds a pre-installed AMReX library if set to OFF +
  40. spack load chipstar
  41. -
    pyAMReX_amrex_repohttps://github.com/AMReX-Codes/amrex.gitRepository URI to pull and build AMReX from
    pyAMReX_amrex_branchdevelopmentRepository branch for pyAMReX_amrex_repo + able to run programs that use the Intel Level Zero runtime.

    -
    pyAMReX_pybind11_srcNoneAbsolute path to pybind11 source directory (preferred if set)
    pyAMReX_pybind11_internal +

    (C) 2017-2021 by Mathematics and Computer Science (MCS), Argonne National Laboratory.

    - ON/OFF
    Needs a pre-installed pybind11 library if set to OFF +

    Major authors: Sheng Di, Dingwen Tao, Hanqi Guo -

    pyAMReX_pybind11_repohttps://github.com/pybind/pybind11.gitRepository URI to pull and build pybind11 from
    pyAMReX_pybind11_branchv2.12.0Repository branch for pyAMReX_pybind11_repo +
  42. latexmk (z-checker-install.sh will install latexmk automatically if missing)
  43. -
    Python_EXECUTABLE(newest found)Path to Python executable
    +
  44. sam2p (z-checker-install.sh will install sam2p automatically if missing)
  45. -

    As one example, one can also build against a local AMReX copy. + - Assuming AMReX'' source is located in $HOME/src/amrex, then export - AMREX_SRC=$HOME/src/amrex.

    +

    For simplicity, + + the Fedora users need to run the following command for installation:

    + +
    sudo dnf install -y gcc gcc-c++
    +    git cmake zlib-devel libzstd-devel gfortran which xorg-x11-server-Xorg gnuplot
    +    libpng-devel findutils unzip latexmk texlive-*
    +
    +    <!-- required texlive package:
    +    "tex(comment.sty)"
    +    "tex(pifont.sty)"
    +    "tex(natbib.sty)"
    +    "tex(amsmath.sty)"
    +    "tex(morefloats.sty)"
    +    "tex(geometry.sty)"
    +    "tex(nopageno.sty)"
    +    "tex(subfigure.sty)"
    +    "tex(enumitem.sty)"
    +    "tex(morefloats.sty)"-->
     
    -    

    Or as a one-liner, assuming your AMReX source directory is located in ../amrex:

    + git clone http://github.com/CODARcode/z-checker-installer -
    AMREX_SRC=$PWD/../amrex
    -    python3 -m pip install -v --force-reinstall .
    + cd z-checker-installer -

    Note that you need to use absolute paths for external source trees, because - pip builds in a temporary directory.

    + ./z-checker-install.sh
    -

    Or build against an AMReX feature branch of a colleague. +

    the Ubuntu users need to run the following command for installation:

    - Assuming your colleague pushed AMReX to https://github.com/WeiqunZhang/amrex/ - in a branch new-feature then

    +
    sudo sudo apt-get install -y
    +    gcc g++ git cmake zlib-devel gfortran gnuplot libpng-devel xorg openbox findutils
    +    unzip latexmk texlive-full texlive-fonts-recommends --no-install-recommends
     
    -    
    unset
    -    AMREX_SRC  # preferred if set
    +    git clone http://github.com/CODARcode/z-checker-installer
     
    -    AMREX_REPO=https://github.com/WeiqunZhang/amrex.git AMREX_BRANCH=new-feature python3
    -    -m pip install -v --force-reinstall .
    + cd z-checker-installer -

    You can speed up the install further if you pre-install AMReX, e.g. with a - package manager. + ./z-checker-install.sh

    - Set AMREX_INTERNAL=OFF and add installation prefix of AMReX to the - environment variable CMAKE_PREFIX_PATH. +

    Testing/Installation + method

    - Please see the short CMake tutorial that we linked above - if this sounds new to you.

    +

    z-checker-install.sh will download latexmk, gnuplot, Z-checker, ZFP, and SZ + and install them one by one automatically, and then add the patches to let ZFP + and SZ fit for Z-checker.

    + +

    After installation, please download the two testing data sets, CESM-ATM and + MD-simulation (exaalt). The two data sets are available only for the purpose of + research of compression. Please ask for the data by contacting sdi1@anl.gov + if interested.

    + +

    LibpressioOPT is a library that is able to search for the appropriate error + bound setting based on user-sepcified metric values such as compression ratio + and PSNR. Z-checker itself has some simple built-in algorithms to do this work, + which may not be as accurate as LibpressioOPT. To this end, you also need to install + spack and use spack to install some preliminary libraries. For more details, please + read the z-checker-installer-instruction.pdf in the ./doc/ directory. If you don''t + need LibpressioOPT, you just need to run ''./z-checker-installer.sh'' to install + everything.

    + +

    Quick Start

    -

    Acknowledgements

    +

    Then, you are ready to conduct the compression checking. -

    This work was supported by the Laboratory Directed Research and Development - Program of Lawrence Berkeley National Laboratory under U.S. Department of Energy - Contract No. DE-AC02-05CH11231.

    + You can generate compression results with SZ and ZFP using the following simple + steps: -

    Copyright Notice

    + (Note: you have to run z-checker-install.sh to install the software before doing + the following tests)

    -

    pyAMReX Copyright (c) 2023, The Regents of the University of California, +

      + +
    1. - through Lawrence Berkeley National Laboratory, National Renewable Energy +

      Configure the error bound setting and comparison cases in errBounds.cfg.

      - Laboratory Alliance for Sustainable Energy, LLC and Lawrence Livermore +
    2. - National Security, LLC (subject to receipt of any required approvals from the - U.S. +
    3. - Dept. of Energy). All rights reserved.

      +

      Create a new test-case, by executing "createZCCase.sh [test-case-name]". You + need to replace [test-case-name] by a meaningful name. -

      If you have questions about your rights to use or distribute this software, + For example: - please contact Berkeley Lab''s Intellectual Property Office at + [user@localhost z-checker-installer] ./createZCCase.sh CESM-ATM-tylor-data

      - IPO@lbl.gov.

      +
    4. -

      Please see the full license agreement in LICENSE.
      +

    5. - Please see the notices in NOTICE.
      +

      Perform the checking by running the command "runZCCase.sh": runZCCase.sh [data_type] + [error-bound-mode] [test-case-name] [data dir] [extension] [dimensions....]. - The SPDX license identifier is BSD-3-Clause-LBNL.

      + Example: + + [user@localhost z-checker-installer] ./runZCCase.sh -f REL CESM-ATM-tylor-data + /home/shdi/CESM-testdata/1800x3600 dat 3600 1800

      + +
    6. + +
    + +

    Then, you can find the report generated in z-checker-installer/Z-checker/[test-case-name]/report.

    + +

    Step-by-step Checking

    + +

    Unlike the above one-command checking, the following steps present the generation + of compression results step by step.

    + +
      + +
    1. + +

      Go to zfp/utils/, and then execute "zfp-zc-ratedistortion.sh [data directory] + [dimension sizes....]". The compression results are stored in the compressionResults/ + directory. + + For example, suppose the directory of CESM-ATM data set is here: /home/shdi/CESM-testdata/1800x3600, + then the command is "zfp-zc-ratedistortion.sh /home/shdi/CESM-testdata/1800x3600 + 3600 1800". Note: the data files stored in the directory are also ending with + .dat and the dimension sizes are the same (1800x3600) in this test-case.

      + +
    2. + +
    3. + +

      Similarly, go to SZ/example/, and then generate compression results by SZ compressor + as follows: "sz-zc-ratedistortion.sh [data directory] [dimension sizes....]". + The compression results are stored in the compressionResults/ directory. + + As for the example CESM-ATM, the test command is "sz-zc-ratedistortion.sh /home/shdi/CESM-testdata/1800x3600 + 3600 1800".

      + +
    4. + +
    5. + +

      Then, go to Z-checker/examples/ directory, and run the command "./analyzeDataProperty.sh + [data directory] [dimension sizes....]" to generate the data properties based + on the data sets. This step has nothing to do with the compressors. The data analysis + results are stored in the dataProperties/ directory.

      + +
    6. + +
    7. + +

      Generate the figure files: run the command "./generateReport.sh" simply. The + results of comparing different compressors (such as sz and zfp in this test-case) + are stored in the directory called compareCompressors/.

      + +
    8. + +
    + +

    Create a new case

    + +

    "createZCCase.sh [test-case-name]" allows you to create a new test-case. This + command will create a new workspace directory in Z-checker, SZ, and zfp respectively. + The compression results will be put in those workspace directories to avoid bing + messed with other test-cases.

    + +

    For example, if you run the generateReport.sh in the directory ./Z-checker/examples, + it is actually one test case, where the compression results and data analysis + results will be put in the dataProperty/ and compressionResults/ under it. + + For another test case with another set of data or application, you can create + a new workspace directory by the script createZCCase.sh (which calls ./Z-checker/createNewCase.sh).

    + +

    z-checker-update.sh

    + +

    z-checker-update.sh can be used to update the repository (pull the new update + from the server), so that you don''t have to perform the update manually.

    + +

    web installation

    + +

    Web installation allows to install a web server on the local machine, such + that you can visualize the data through a local webpage and other people can view + the data/results via that page if public ip is provided. + + z-checker-web-install.sh

    + +

    Add a new compressor

    + +
      + +
    1. Make a monitoring program (e.g., called testfloat_CompDecomp.c) for your compressor. + An example can be found in SZ/example/testfloat_CompDecomp.c, which is used for + SZ compressor.)
    2. + +
    3. Modify the manageCompressor.cfg based on the workspaceDir on your computer + and directory containing the compiled executable monitoring program.
    4. + +
    5. Suppose the new compressor''s name is zz and the compression mode is called + ''best''; then, run the following command to add the new compressor: + + ./manageCompressor -a zz -m best -c manageCompressor.cfg
    6. + +
    7. Then, open errBounds.cfg to modify the error bounds for the new compressor; + and also modify the comparison cases as follows (the compressor name ''zz_b'' + was set in manageCompressor.cfg): + + comparisonCases="sz_f(1E-1),sz_d(1E-1),zfp(1E-1) sz_f(1E-2),sz_d(1E-2),zfp(1E-2)" + --> comparisonCases="sz_f(1E-1),sz_d(1E-1),zfp(1E-1),zz_b(1E-2) sz_f(1E-2),sz_d(1E-2),zfp(1E-2),zz_b(1E-2)"
    8. + +
    9. Finally, create a test case like this: ./createZCCase.sh case_name
    10. + +
    11. Perform the assessment by runZCCase.sh.
    12. + +
    + +

    Remove a compressor

    + +

    Remove sz_f (sz fast mode): + + $ manageCompressor -d sz -m fast -c manageCompressor-sz-f.cfg + + Remove sz_d (sz fast mode): + + $ manageCompressor -d sz -m deft -c manageCompressor-sz-d.cfg + + Remove zfp: + + $ manageCompressor -d zfp -c manageCompressor-zfp.cfg

    + +

    Generate Z-checker report + based on HDF5 files

    + +

    You can generate Z-checker report directly based on an HDF5 file. + + To this end, you need to install HDF5 library before hand, and then compile the + Z-checker/HDF5Reader as follows:

    + +

    You need to modify Makefile.linux2 by replacing "HDF5PATH = /home/sdi/Install/hdf5-1.10.1-install" + by your HDF5 installation path. + + Then: + + make -f Makefile.linux2

    + +

    You will find the executable ''testHDF5_CompDecomp'' generated on Z-checker/HDF5Reader/test/ + directory. + + You can use this command to read HDF5 file and generate analysis results.

    + +

    After that, you can use ''installHDF5Reader.sh'' and ''runZCCase_hdf5.sh'' + to generate the .pdf report. + + More details can be found in testHDF5/README.txt

    + +

    Generate Z-checker report + based on ADIOS2 files

    + +

    Go to the directory ADIOS2Header, and then do the following steps:

    + +
      + +
    1. Modify the ADIOS2''s installation path in Makefile
    2. + +
    3. make
    4. + +
    5. execute ''testAdios2''
    6. + +
    + +

    Example: + + testAdios2 -i myVector_cpp.bp -n 2 -v bpFloats bpInts -o [target output directory]

    + +

    The generated binary data files will be put in the target output directory. + A meta file called ''varInfo.txt'' contains the extracted variables'' information + and it will be put in the target output directory as well. + + varInfo.txt and the binary files can be processed by runZCCase.sh

    ' - stargazers_count: 31 - subscribers_count: 16 - topics: - - amrex - - python - updated_at: 1716637941.0 -AMReX-Microelectronics/artemis: + stargazers_count: 5 + subscribers_count: 7 + topics: [] + updated_at: 1658448853.0 +CUP-ECS/beatnik: data_format: 2 - description: ARTEMIS (Adaptive mesh Refinement Time-domain ElectrodynaMIcs Solver) - couples the Maxwell's equations implementation in WarpX with classical equations - that describe quantum material behavior (such as, LLG equation for micromagnetics - and London equation for superconducting materials) for quantifying the performance - of next-generation microelectronics. + description: Initial Cabana/Cajita Low/High-order Z-model Interface Solver. Benchmark + for evaluating the performance of algorithms requiring global communication. Beatnik + is also a precursor to potential later a High Performance Parallel Interface solver. filenames: - - Docs/spack.yaml - full_name: AMReX-Microelectronics/artemis - latest_release: null - readme: "

    ARTEMIS

    \n

    ARTEMIS (Adaptive mesh Refinement Time-domain ElectrodynaMIcs\ - \ Solver) is a high-performance coupled electrodynamics\u2013micromagnetics solver\ - \ for full physical modeling of signals in microelectronic circuitry. The overall\ - \ strategy couples a finite-difference time-domain (FDTD) approach for Maxwell\u2019\ - s equations to a magnetization model described by the Landau\u2013Lifshitz\u2013\ - Gilbert (LLG) equation. The algorithm is implemented in the Exascale Computing\ - \ Project (ECP) software framework, AMReX, which provides effective scalability\ - \ on manycore and GPU-based supercomputing architectures. Furthermore, the code\ - \ leverages ongoing developments of the Exascale Application Code, WarpX, which\ - \ is primarily being developed for plasma wakefield accelerator modeling. Our\ - \ temporal coupling scheme provides second-order accuracy in space and time by\ - \ combining the integration steps for the magnetic field and magnetization into\ - \ an iterative sub-step that includes a trapezoidal temporal discretization for\ - \ the magnetization. The performance of the algorithm is demonstrated by the excellent\ - \ scaling results on NERSC multicore and GPU systems, with a significant (59\xD7\ - ) speedup on the GPU using a node-by-node comparison. The utility of our code\ - \ is validated by performing simulations of transmission lines, rectangle electromagnetic\ - \ waveguides, magnetically tunable filters, on-chip coplanar waveguides and resonators,\ - \ magnon-photon coupling circuits, and so on.

    \n

    Installation

    \n\ -

    Download AMReX Repository

    \n

    git\ - \ clone git@github.com:AMReX-Codes/amrex.git

    \n

    Download Artemis Repository

    \n

    git clone git@github.com:AMReX-Microelectronics/artemis.git

    \n\ -

    Build

    \n\ -

    Make sure that the AMReX and Artemis are cloned in the same location in their\ - \ filesystem. Navigate to the Exec folder of Artemis and execute\nmake -j\ - \ 4.
    \nYou can turn on and off the LLG equation by specifying USE_LLG\ - \ during compilation.
    \nThe following command compiles Artemis without LLG\n\ - make -j 4 USE_LLG=FALSE
    \nThe following command compiles Artemis\ - \ with LLG\nmake -j 4 USE_LLG=TRUE
    \nThe default value of USE_LLG\ - \ is TRUE.

    \n

    Running Artemis

    \n

    Example input scripts are\ - \ located in Examples directory.

    \n

    Simple Testcase without LLG

    \n

    You can run the following to simulate an air-filled X-band\ - \ rectangle waveguide:

    \n

    For MPI+OMP build

    \n

    make\ - \ -j 4 USE_LLG=FALSE
    \nmpirun -n 4 ./main3d.gnu.TPROF.MTMPI.OMP.GPUCLOCK.ex\ - \ Examples/Waveguide/inputs_3d_empty_X_band

    \n

    For MPI+CUDA build

    \n\ -

    make -j 4 USE_LLG=FALSE USE_GPU=TRUE
    \nmpirun -n 4 ./main3d.gnu.TPROF.MTMPI.CUDA.GPUCLOCK.ex\ - \ Examples/Waveguide/inputs_3d_empty_X_band

    \n

    Simple Testcase with LLG

    \n

    You can run the following to simulate an X-band magnetically\ - \ tunable filter:

    \n

    For MPI+OMP build

    \n

    make\ - \ -j 4 USE_LLG=TRUE
    \nmpirun -n 8 ./main3d.gnu.TPROF.MTMPI.OMP.GPUCLOCK.ex\ - \ Examples/Waveguide/inputs_3d_LLG_filter

    \n

    For MPI+CUDA build

    \n\ -

    make -j 4 USE_LLG=TRUE USE_GPU=TRUE
    \nmpirun -n 8 ./main3d.gnu.TPROF.MTMPI.CUDA.GPUCLOCK.ex\ - \ Examples/Waveguide/inputs_3d_LLG_filter

    \n

    Visualization and Data Analysis

    \n

    Refer to the following link for several\ - \ visualization tools that can be used for AMReX plotfiles.

    \n

    Visualization

    \n

    Data Analysis in Python using yt

    \n

    You can extract the data in numpy\ - \ array format using yt (you can refer to this for installation and usage of yt. After you have installed\ - \ yt, you can do something as follows, for example, to get variable 'Ex' (x-component\ - \ of electric field)

    \n
    import yt\nds = yt.load('./plt00001000/')\
    -    \ # for data at time step 1000\nad0 = ds.covering_grid(level=0, left_edge=ds.domain_left_edge,\
    -    \ dims=ds.domain_dimensions)\nE_array = ad0['Ex'].to_ndarray()\n
    \n\ -

    Publications

    \n
      \n
    1. Z. Yao, R. Jambunathan, Y. Zeng and A. Nonaka, A\ - \ massively parallel time-domain coupled electrodynamics\u2013micromagnetics solver.\ - \ The International Journal of High Performance Computing Applications. 2022;36(2):167-181.\ - \ doi:10.1177/10943420211057906\nlink\n
    2. \n
    3. S. S. Sawant, Z. Yao, R. Jambunathan and\ - \ A. Nonaka, Characterization of transmission lines in microelectronic circuits\ - \ Using the ARTEMIS solver, IEEE Journal on Multiscale and Multiphysics Computational\ - \ Techniques, vol. 8, pp. 31-39, 2023, doi: 10.1109/JMMCT.2022.3228281\nlink\n\ -
    4. \n
    5. R. Jambunathan, Z. Yao, R. Lombardini, A. Rodriguez, and A. Nonaka,\ - \ Two-fluid physical modeling of superconducting resonators in the ARTEMIS framework,\ - \ Computer Physics Communications, 291, p.108836. doi:10.1016/j.cpc.2023.108836\n\ - link\n
    6. \n
    \n" - stargazers_count: 10 - subscribers_count: 5 - topics: [] - updated_at: 1716409719.0 -Alpine-DAV/spack_configs: - data_format: 2 - description: spack envs - filenames: - - _experimental/envs/alpinedav/ubuntu_18_devel/spack.yaml - - _experimental/envs/alpinedav/ubuntu_18_cuda_10.1_devel/spack.yaml - full_name: Alpine-DAV/spack_configs - latest_release: null - readme: '

    spack_configs

    - -

    shared spack configs repo

    - - ' - stargazers_count: 0 - subscribers_count: 4 - topics: [] - updated_at: 1639176281.0 -C2SM/spack-c2sm: - data_format: 2 - description: Repository for c2sm spack config and repo files - filenames: - - upstreams/daint/icon-dsl/spack.yaml - full_name: C2SM/spack-c2sm - latest_release: v0.20.1.9 - readme: '

    The spack extension - of C2SM and MCH

    Beatnik - A Prototype + High Performance Parallel Interface Benchmark

    -

    Documentation Status

    +

    Description

    -

    Spack is the package manager used by C2SM and MeteoSwiss to install and deploy - software on supercomputers, local machines and the cloud.

    +

    Beatnik is a benchmark for global communication based on Pandya and Shkoller''s + 3D fluid interace "Z-Model" in the Cabana/Cajita mesh framework [1]. The goals -

    Documentations

    + of Beatnik are to:

    -

    Infos about c2sm-supported software and machines

    +
      -
    -
  46. +

    Beatnik uses a simple mesh-based representation of the surface manifold as + a Cabana grid 2D mesh in I/J space and a regular block 2D decomposition of this + manifold. The physical position of each element in the mesh is stored as a separate + vector in the nodes of the mesh. This design results in simple and efficient computation + and communication strategies for surface normals, artificial viscosity, and Fourier + transforms elements. However, it complicates methods where the data decomposition + and communication is based on the spatial location of manifold points, requiring + them to either maintain a separate spatial decomposition of the surface or to + continually construct a spatial decomposition. A surface mesh that decomposed + the mesh by spatial location would be an interesting alternative but would have + the opposite issue - communication for surface calculations would be more complex + but the (expensive) far force methods that rely on spatial decompositions (e.g. + distance sort and spatial tree methods like the fast multi-pole method) would + be less expensive.

    -

    spack-c2sm - v0.20.1.4

    +

    Building Beatnik

    -
  47. +

    Beatnik relies on multiple external packages to build, including:

    -
  48. + -
  49. +

    To ease building Beatnik, the configs/ directory includes Spack configuration + files for building in spack environments on multiple systems and test case run + scripts for a variety of systems. In addition, the latest version of Spack includes + a package description for directly building Beatnik. More information on building + Beatnik can be found in the README.md file in the configs/ directory.

    -
  50. +

    Running Beatnik

    -

    spack-c2sm - v0.18.1.12

    +

    By default, Beatnik solves a simple multi-mode rocket rig problem sized for + a single serial CPU core with approximately 4GB of memory. It also includes command + line options to change initial problem state, I/O frequency, and to weak-scale + scale up the initial problem to larger number of processes. It also includes problem-specific + command line parameters; setting these parameters accurately generally requires + expertise in fluid interface models. However, we provide several useful examples + drawn from the ZModel papers that recreate the results in those papers.

    -
  51. +

    General command line + parameters

    -
  52. + -

    spack-c2sm - v0.18.1.7

    +

    Problem-specific command + line parameters

    -
  53. + + -a [atwood] - Atwood''s constant for the difference in pressure + between the two fluids -

    General infos about spack

    +
  54. - -

    Workflow

    +

    Example 1: Periodic + Multi-mode Rocket Rig

    -

    With spack v0.18 we suggest local/individual spack instances and the use of - spack environments.

    +

    The simplest test case and the one to which the rocketrig example program defaults + is an initial interface distributed according to a cosine function. Simple usage + examples:

    -

    A user clones the spack repo

    +
      -
      git clone --depth 1 --recurse-submodules
      -    --shallow-submodules -b v0.20.1.5 https://github.com/C2SM/spack-c2sm.git
      +
    1. Serial execution: bin/rocketrig -x serial -

      gets spack in the command line

      +
    2. -
      .
      -    spack-c2sm/setup-env.sh
      +
    3. Cuda execution (on systems with GPUs) with a 512x512 mesh: bin/rocketrig + -x cuda -n 512 -

      activates an environment

      +
    4. -
      spack env activate <path_to_env>
      +
    5. Cuda execution with a 1024x1024 problem scaled up to be sixteen times as large + in terms of bounding box and number of total points with no I/O: bin/rocketrig + -x cuda -n 1024 -F 0 -w 16`
    6. -

      and starts exploring

      +
    -
    spack info <package>
    +    

    Example 2: Non-periodic + Single-mode Gaussian Rollup

    - spack spec <spec>
    +

    Another test case is a single-mode rollup test where the intitial interface + is set according to a hyperbolic secant function. This testcase recreates the + the Gaussian perturbation results in Panda and Shkoller''s paper from sections + 2.3 and 2.4. To run this testcase with a high-order model, use the following + command line parameters. Note that this works best with a GPU accelerator, as + the exact high-order far field force solver is very compute intensive and is generally + impractical for non-trivial mesh sizes without GPU acceleration: -

    and building

    + bin/rocketrig -x cuda -O high -n 64 -I sech2 -m 0.1 -p 9.0 -b free -a 0.15 + -M 2 -e 2

    -
    spack install <spec>
    +    

    Planned Development + Steps

    - spack dev-build <spec>
    +

    Beatnik is being implemented in multiple distinct steps, with associated planned + releases:

    -

    a package.

    +
+

Additionally, a symbolic link named impactx can be found in that + directory, which points to the last built ImpactX executable.

-
$ spack concretize -f -U
+

The command-line syntax for this executable is:

-

We suggest examining the output from running the spack concretize +

Usage:
+    impactx <inputs-file> [some.overwritten.option=value]...
 
-    command to make sure that Spack''s concretizer has truly decided to
 
-    use the configuration options and especially the compilers that you
+    Mandatory arguments (remove the <>):
 
-    want it to use.  Note that the environment and related configuration
+      inputs-file     the path to an input file; can be relative
+    to the current
 
-    are purposefully not overly constrained to use the given compiler
+                      working directory or absolute.
 
-    for every dependency package, so even though there are some packages
+                      Example: input_fodo.in
 
-    that must be built with %clang, there are others that may be
 
-    built (or re-used from already-installed packages) using %gcc such
+    Optional arguments (remove the []):
 
-    as the system''s GCC installation.

+ options this can overwrite any line in an inputs-file -

If Spack''s concretizer didn''t do what you want, you can re-concretize + Example: quad1.ds=0.5 sbend1.rc=1.5 - the environment and be more explicit about what you want using command-line - configuration options (recommended) or by editing the environment''s + Examples: - spack.yaml file or other configuration options that your Spack installation + In the current working directory, there is a file "input_fodo.in" + and the - is using. (Use spack config blame to see which configuration files - Spack is + "impactx" executable. - using.) For instance, if you have both clang@16.0.2 and clang@15.0.7 + The line to execute would look like this: - installed and registered as Spack compilers, and you want to build + ./impactx input_fodo.in - using clang@15.0.7, you may have to use a concretize command like - the - following:

+ In the current working directory, there is a file "input_fodo.in" + and the -
$ spack -c "packages:chipstar:require:''%clang@15.0.7''"
-    concretize -f -U
+ executable "impactx" is in a directory that is listed in + the "PATH" -

As before, verify from the output of the spack concretize command - that it + environment variable. - is using the compiler version you want, clang@15.0.7 in this example.

+ The line to execute would look like this: -
    + impactx input_fodo.in -
  1. Build the environment.
  2. -
+ In the current working directory, there is a file "input_fodo.in" + and the -
$ spack install
+ "impactx" executable. We want to voerwrite the segment length + of the beamline -

Spack supports some options for controlling the build and installation, + element "quad1" that is already defined in it. We also want + to change the - such as -j to limit the number of processes used for parallel builds, + radius of curvature of the bending magnet "sbend1" to a + different value than - useful for being a good citizen on shared systems by not allowing Spack + in the file "input_fodo.in". - to use all available cores (its default). See the Spack documentation for + The line to execute would look like this: - more information.

+ ./impactx input_fodo.in quad1.ds=0.5 sbend1.rc=1.5
-

Assuming all goes well with the build and install, a spack find +

Test

- should show the packages that you just built.

+

In order to run our tests, you need to have a few Python packages installed:

-
    +
    python3
    +    -m pip install --upgrade pip
     
    -    
  1. Use the installed software. There are several ways you might + python3 -m pip install --upgrade build packaging setuptools + wheel pytest - update your environment to use the software, including:
  2. + python3 -m pip install --upgrade -r tests/python/requirements.txt
    -
+

You can run all our tests with:

- - one must load the intel_compute_runtime module before being +

Acknowledgements

- able to run programs that use the Intel Level Zero runtime.

+

This work was supported by the Laboratory Directed Research and Development + Program of Lawrence Berkeley National Laboratory under U.S. Department of Energy + Contract No. DE-AC02-05CH11231.

-

TODO

+

ImpactX is supported by the CAMPA collaboration, a project of the U.S. Department + of Energy, Office of Science, Office of Advanced Scientific Computing Research + and Office of High Energy Physics, Scientific Discovery through Advanced Computing + (SciDAC) program.

- + The SPDX license identifier is BSD-3-Clause-LBNL.

' - stargazers_count: 0 - subscribers_count: 5 - topics: [] - updated_at: 1687550793.0 -COSIMA/spack-config: + stargazers_count: 24 + subscribers_count: 6 + topics: + - simulation + - beam-dynamics + - particle-in-cell + - gpu + - physics + - pic + - particle + - accelerator + - research + updated_at: 1716438419.0 +Exawind/exawind-builder: data_format: 2 - description: Spack configuration installed at /g/data/ik11/spack/ to provide ACCESS-OM3 - dependencies + description: Scripts to help building Exawind codes on various systems filenames: - - environments/cesm-0_2_0/spack.yaml - - environments/access-om3-0_x_0/spack.yaml - - environments/cesm-0_x_0/spack.yaml - full_name: COSIMA/spack-config - latest_release: access-om3-v0.2.0 - readme: "

COSIMA Spack\ - \ Configuration

\n\ -

This repository contains the spack configuration and the spack environments\ - \ used\nby COSIMA to deploy software on gadi.

\n\n\n\n

Installation instructions

\n

Clone this repository and its submodules to some appropriate\ - \ location (e.g.,\n/g/data/ik11/spack/0.21.2):

\n
$ git clone\
-    \ --recursive https://github.com/COSIMA/spack-config.git /g/data/ik11/spack/0.21.2
\n\ -

Next, create the python virtual environment:

\n
$ cd /g/data/ik11/spack/0.21.2\n\
-    $ ./bootstrap_venv.sh
\n

Finally, to\ - \ use this spack installation one just needs to activate the python\nenvironment:

\n\ -
$  . /g/data/ik11/spack/0.21.2/venv/bin/activate\n\
-    $ which spack\nspack ()\n\
-    { \n    : this is a shell function\
-    \ from: /g/data/ik11/spack/0.21.2/spack/share/spack/setup-env.sh;\n    : the real spack script is here: /g/data/ik11/spack/0.21.2/spack/bin/spack;\n\
-        _spack_shell_wrapper \"$@\";\n    return $?\n}
\n

Most\ - \ of the paths in the Spack configurations files in this repository are\nrelative\ - \ to the Spack location (e.g.,\n/g/data/ik11/spack/0.21.2/spack).\ - \ Unfortunately this is not the case for the\nglobal source's mirror defined in\ - \ config/system/mirror.yaml, so the URL in\nthis file needs to be\ - \ updated if usage of a mirror is planned (see next\nsection).

\n

At this\ - \ point it might be worth reviewing the compilers and packages defined in\nconfig/system/compilers.yaml\ - \ and config/system/packages.yaml and update them\nif necessary.

\n\ -

Installing software

\n

It is recommended that\ - \ all software be installed using spack\nenvironments. Currently the following\ - \ environments are provided (the names\nshould be self-explanatory):

\n
    \n\ -
  1. access-om3-0_1_0
  2. \n
  3. access-om3-0_2_0
  4. \n\ -
  5. access-om3-0_x_0
  6. \n
  7. cesm-0_1_0
  8. \n
  9. common_tools_and_libraries
  10. \n\ -
\n

Installation of a spack environment is usually quite straightforward,\ - \ but\nbecause this can be a CPU intensive operation and take quite some time,\ - \ it is\nbest to do this in parallel and to use an interactive job.

\n

Step-by-step instructions

\n
    \n\ -
  1. Activate spack environment
  2. \n
\n

First activate the spack environment

\n\ -
$ spack env activate <env>
\n\ -

where <env> by the actual name of the environment.

\n\ -
    \n
  1. Download the sources
  2. \n
\n

As the compute nodes\ - \ do not have internet access, one needs to download all the\nnecessary sources\ - \ from the login node. This is done using a spack mirror.

\n
$ spack mirror create\
-    \ -d sources -a
\n

Here sources is the name of\ - \ a mirror that has already been configured.

\n

Note that the spack environment\ - \ must have been concretized before creating the\nmirror, otherwise spack will\ - \ not know which files need downloading. To\nconcretize an environment, one uses\ - \ the following command:

\n
$ spack concretize
\n
    \n
  1. Submit interactive job
  2. \n
\n

This should not use more than\ - \ a single node. Also, make sure to add gdata/ik11\nand scratch/ik11\ - \ to the storage options.

\n
    \n
  1. Install software
  2. \n
\n\ -

Once the job has started, because it starts a completely new shell session,\ - \ one\nneeds to activate again both the python and the spack environments:

\n\ -
$ . /g/data/ik11/spack/0.21.2/venv/bin/activate\n\
-    $ spack env activate <env>
\n

Then one can simply do

\n\ -
$ spack install 
\n

In this case, although each individual\ - \ build will use some level of parallelism,\nspack will proceed through the installation\ - \ of the packages sequentially. To\nfully use parallelism one needs to tell spack\ - \ to create a Makefile and use this\nto install the software:

\n
$ spack env\
-    \ depfile -o Makefile\n$ make -j
\n\ -

In the end, all the packages should be available in some subdirectory of\n\ - /g/data/ik11/spack/0.21.2/opt/ and the corresponding environment\ - \ modules are\ninstalled under a subdirectory of /g/data/ik11/spack/0.21.2/modules.\ - \ The\nactual subdirectories depend on the selected environment.

\n

Updating to a new spack version

\n\ -

The way this repository is set up assumes that no update of spack will take\n\ - place within a given instance. This is to make sure all packages available\nwithin\ - \ a given instance are installed with the same version of spack and are\nfully\ - \ reproducible. This means that, in order to update spack, one needs to\ncreate\ - \ a new instance. Most of the process is therefore very similar to what is\ndescribed\ - \ in the Installation instructions\n\ - section, with a few modifications.

\n

Start by cloning this repository and\ - \ its submodules to some appropriate location\n(e.g., /g/data/ik11/spack/0.21.2):

\n\ -
$ git clone --recursive https://github.com/COSIMA/spack-config.git /g/data/ik11/spack/0.21.2
\n\ -

Next, create and checkout a new branch in the repository, using the spack\n\ - version as branch name:

\n
$ cd /g/data/ik11/spack/0.21.2\n\
-    $ git checkout -b 0.21.2
\n

This is\ - \ not mandatory, but it helps keeping all the different configurations and\nenvironments\ - \ clearly separated. It also allows to update instances that are\nusing different\ - \ versions of spack independently.

\n

Then we proceed with updating the spack\ - \ submodule:

\n
$\
-    \ cd spack\n$ git fetch --tags\n$ git checkout\
-    \ v0.21.2\n$ cd ..\n\
-    $ git commit spack -m \"Update spack to 0.21.2 tag.\"
\n\ -

Note that the git fetch step is only strictly necessary if you\ - \ want to use a\ntag from the spack repository (which is recommended).

\n

Finally,\ - \ just follow the remaining instructions in the Installation\ninstructions section to create the python virtual\nenvironment.

\n\ -

Design notes

\n

This section describes some of the design decisions and\ - \ their rationale.

\n

Package installation path

\n

In this repository, spack is configured to install the\ - \ packages to a path of the\nfollowing form:

\n

opt/{architecture}/{compiler.name}-{compiler.version}/{name}-{version}-{hash:7}

\n\ -

By adding the architecture, compiler name, and compiler version to the path,\n\ - installations of packages built with different compilers on different\narchitectures\ - \ are allowed to coexist without any clashes. The inclusion of part\nof the spack\ - \ hash also allows for the same version of a given package to be\ncompiled with\ - \ different options. Note that there is nothing specific to the\nspack environments,\ - \ as this is not necessary (two environments that require\nexactly the same package\ - \ built in exactly the same way will share the\ncorresponding installation).

\n\ -

Environment modules

\n

By default, the TCL environment\ - \ modules use the following naming scheme:

\n

`{name}/{version}-{compiler.name}-{compiler.version}-{hash:7}``

\n\ -

This ensures that there are no clashes, but unfortunately the inclusion of\ - \ the\nspack hash makes the use of the modules a bit cumbersome. To avoid the\ - \ use of\nthe hash, one can set the modules installation path and naming scheme\ - \ at the\nlevel of the spack environments. The existing environments include the\ - \ following\ndefinitions in their spack.yaml file:

\n
  modules:\n\
-    \    default:\n      roots:\n\
-    \        tcl: $spack/../modules/<env\
-    \ path>\n      tcl:\n        naming_scheme: '{name}/{version}'
\n

where <env path>\ - \ is a user-defined path for the environment in question. No\ncompiler information\ - \ is used, as our environments only use one compiler. We\nrecommend to follow\ - \ this scheme in all environments. Note that spack will\nautomatically append\ - \ the architecture to the root path. This allows to install\nthe same environment\ - \ on two different architectures without clashes.

\n

Python virtual environment

\n

Using a python virtual environment for the spack installation\ - \ has several\nadvantages. Besides the usual advantages of using such environments\ - \ (stability,\nportability and reproducibility), it allows to automatically perform\ - \ a few tasks\nwhen activating the environment, thus providing a more user-friendly\n\ - experience. These tasks include:

\n
    \n
  • Sourcing the spack/share/spack/setup-env.sh\ - \ file that takes care of setting\nup several environment variables and functions\ - \ necessary to use spack.
  • \n
  • Loading the appropriate Gadi python environment\ - \ module.
  • \n
  • Setting up some environment variables to customize the behavior\ - \ of spack.
  • \n
\n

Repository structure

\n\ -

This git repository contains the following directories:

\n
    \n
  • \nconfig:\ - \ the spack configuration files.
  • \n
  • \nenvironments: spack\ - \ environment definitions.
  • \n
  • \nrepos: several repositories\ - \ of spack package definitions.
  • \n
  • \nspack: the spack sources,\ - \ included as a git submodule.
  • \n
\n

The following directories will\ - \ be created by spack:

\n
    \n
  • \nmodules: environment modules\ - \ created by spack.
  • \n
  • \nsources: mirror for package sources.
  • \n\ -
  • \nopt: path where packages are installed.
  • \n
  • \nuser_cache\ - \ and var/cache: several caches used by spack.
  • \n
\n

Git branches

\n

Each branch in this git repository corresponds\ - \ to a spack version and is named\nafter that version (e.g. branch 0.21.2\ - \ corresponds to the v0.21.2 spack\nrelease). Note that there is\ - \ no main branch. Instead, the default branch is\nthe latest spack\ - \ version supported. This means that the default branch should be\nchanged whenever\ - \ support for a newer version of spack is added.

\n" - stargazers_count: 0 - subscribers_count: 7 - topics: [] - updated_at: 1692145219.0 -CUP-ECS/beatnik: - data_format: 2 - description: Initial Cabana/Cajita Low/High-order Z-model Interface Solver. Benchmark - for evaluating the performance of algorithms requiring global communication. Beatnik - is also a precursor to potential later a High Performance Parallel Interface solver. - filenames: - - configs/llnl/lassen/spack.yaml - full_name: CUP-ECS/beatnik - latest_release: v1.0.0 - readme: '

Beatnik - A Prototype - High Performance Parallel Interface Benchmark

- -

Description

- -

Beatnik is a benchmark for global communication based on Pandya and Shkoller''s - 3D fluid interace "Z-Model" in the Cabana/Cajita mesh framework [1]. The goals - - of Beatnik are to:

+ - etc/spack/nrel-eagle/spack.yaml + - etc/spack/spack/spack.yaml + full_name: Exawind/exawind-builder + latest_release: v0.1.0 + readme: '

ExaWind Code + Builder

-
    +

    Documentation

    -
  1. Provide an interesting and meaningful benchmark for numerical methods that - require global communication, for example for far-field force calculations. This - includes fast fourier transforms, distance sort cutoff-based methods, and (eventually) - fast multi-pole methods.
  2. +

    ExaWind Builder is a collection of bash scripts to configure and compile the -

  3. Understand the performance characteristics of different parallel decompositions - of the Z-Model based on both a 2D decomposition based on logical mesh location - location and a space-filling curve mesh decomposition.
  4. + codes used within the ExaWind project + on various -
  5. Provide a working prototype parallel implementation of the fluid interface - model that other codes can use to create multi-scale models and codes.
  6. + high-performance computing (HPC) systems. The builder provides the following

    -
+
    -

    Beatnik uses a simple mesh-based representation of the surface manifold as - a Cabana grid 2D mesh in I/J space and a regular block 2D decomposition of this - manifold. The physical position of each element in the mesh is stored as a separate - vector in the nodes of the mesh. This design results in simple and efficient computation - and communication strategies for surface normals, artificial viscosity, and Fourier - transforms elements. However, it complicates methods where the data decomposition - and communication is based on the spatial location of manifold points, requiring - them to either maintain a separate spatial decomposition of the surface or to - continually construct a spatial decomposition. A surface mesh that decomposed - the mesh by spatial location would be an interesting alternative but would have - the opposite issue - communication for surface calculations would be more complex - but the (expensive) far force methods that rely on spatial decompositions (e.g. - distance sort and spatial tree methods like the fast multi-pole method) would - be less expensive.

    +
  • -

    Building Beatnik

    +

    Platform configuration: Provides the minimal set of modules + that must be -

    Beatnik relies on multiple external packages to build, including:

    + loaded when compiling with different compilers and MPI libraries on different -
      + HPC systems.

      -
    • ECP CoPA''s Cabana/Grid particle and mesh framework [2]
    • + -
    • UT-Knoxville''s HeFFTe fast fourier transform library [3]
    • +
    • -
    • A high-performance GPU-aware MPI implementation such as OpenMPI, MPICH, or - MVAPICH
    • +

      Software configuration: Provides baseline CMake configuration + that can be -

    + used to configure the various options when building a project, e.g., -

    To ease building Beatnik, the configs/ directory includes Spack configuration - files for building in spack environments on multiple systems and test case run - scripts for a variety of systems. In addition, the latest version of Spack includes - a package description for directly building Beatnik. More information on building - Beatnik can be found in the README.md file in the configs/ directory.

    + enable/disable optional modules, automate specification of paths to various -

    Running Beatnik

    + libraries, configure release vs. debug builds.

    -

    By default, Beatnik solves a simple multi-mode rocket rig problem sized for - a single serial CPU core with approximately 4GB of memory. It also includes command - line options to change initial problem state, I/O frequency, and to weak-scale - scale up the initial problem to larger number of processes. It also includes problem-specific - command line parameters; setting these parameters accurately generally requires - expertise in fluid interface models. However, we provide several useful examples - drawn from the ZModel papers that recreate the results in those papers.

    +
  • -

    General command line - parameters

    +
  • -
      +

      Build script generation: Generates an executable end-user + script for a -

    • + combination of system, compiler, and project.

      - -x [cuda|threads|serial] - The node-level parallelism/accelerator - backend to use
    • +
    • - -F [write-frequency] - Interval between timesteps when I/O is written
    • +

      Exawind environment generation: Generates a source-able, platform-specific -

    • + script that allows the user to recreate the exact environment used to build - -O [solution order] - Order of solver to use (''high'', ''medium'', - or ''low''). ''low'' is the default.
    • + the codes during runtime.

      -
    • `-w [weak scaling factor] - Scale up the problem specification, including - the x/y bounding box, to be N times larger
    • +
    -

    Problem-specific command - line parameters

    +

    The build scripts are intended for developers who might want to compile the -

      + codes with different configuration options, build different branches during -
    • + their development cycle, or link to a different development version of a library - -n [i/j mesh dimension ] - Number of points on the interface manifold - in the I and J dimensions
    • + that is currently not available in the standard installation on the system. Please + see the -
    • `-t [timesteps] - number of timesteps to simulate
    • + documentation + for -
    • + details on how to use this to build ExaWind software.

      - -I [interface initialization] - Function to use for interface initial - condition. Currently only ''cos'' and ''sech2'' are supported.
    • +

      Installation and usage

      -
    • +

      Using exawind-builder + with pre-installed ExaWind environment

      - -m [magnitude] - The maximum magnitude of the initialization function.
    • +

      ExaWind Builder is already installed and setup on OLCF Summit, NREL -

    • + Eagle/Rhodes, and NERSC Cori systems. On these systems, you can proceed directly - -p [period] - The number of periods of the interface in the initial - bounding box
    • + to using build scripts from the central installation. Please consult user -
    • + manual to - -a [atwood] - Atwood''s constant for the difference in pressure between - the two fluids
    • + learn how to use the scripts.

      -
    • +

      Bootstrapping exawind-builder + with pre-configured system definitions

      - -g [gravity] - Gravitational acceleration in the -Z direction
    • +

      ExaWind builder has pre-built -

    • + configurations - -a [atwood] - Atwood''s constant for the difference in pressure - between the two fluids
    • + for several systems. On these systems you can use the bootstrap script + to -
    • + quickly get up and running. Please consult installation - -M [mu] - Mu, the artificial viscosity constant used in the Z-Model
    • + manual. The -
    • + relevant steps are shown below.

      - -e [epsilon] - Epsilon, the desingularization constant used in the - Z-Model expressed as a fraction of the distance between interface mesh points
    • +
      #
      +    Download bootstrap script
       
      -    
    + curl -fsSL -o bootstrap.sh https://raw.githubusercontent.com/exawind/exawind-builder/master/bootstrap.sh -

    Example 1: Periodic - Multi-mode Rocket Rig

    -

    The simplest test case and the one to which the rocketrig example program defaults - is an initial interface distributed according to a cosine function. Simple usage - examples:

    + # Make it executable -
      + chmod a+x bootstrap.sh -
    1. Serial execution: bin/rocketrig -x serial -
    2. + # Execute bootstrap and provide system/compiler + combination -
    3. Cuda execution (on systems with GPUs) with a 512x512 mesh: bin/rocketrig - -x cuda -n 512 + ./bootstrap.sh -s [SYSTEM] -c [COMPILER] -
    4. -
    5. Cuda execution with a 1024x1024 problem scaled up to be sixteen times as large - in terms of bounding box and number of total points with no I/O: bin/rocketrig - -x cuda -n 1024 -F 0 -w 16`
    6. + # Examples -
    + ./bootstrap.sh -s spack -c clang # + On MacOS with homebrew -

    Example 2: Non-periodic - Single-mode Gaussian Rollup

    + ./bootstrap.sh -s ornl-summit -c gcc $ Oakridge Summit system -

    Another test case is a single-mode rollup test where the intitial interface - is set according to a hyperbolic secant function. This testcase recreates the - the Gaussian perturbation results in Panda and Shkoller''s paper from sections - 2.3 and 2.4. To run this testcase with a high-order model, use the following - command line parameters. Note that this works best with a GPU accelerator, as - the exact high-order far field force solver is very compute intensive and is generally - impractical for non-trivial mesh sizes without GPU acceleration: + ./bootstrap.sh -s eagle -c gcc # + NREL Eagle - bin/rocketrig -x cuda -O high -n 64 -I sech2 -m 0.1 -p 9.0 -b free -a 0.15 - -M 2 -e 2

    + ./bootstrap.sh -s cori -c intel # + NERSC Cori -

    Planned Development - Steps

    + ./bootstrap.sh -s snl-ascicgpu -c gcc # + SNL GPU development machine -

    Beatnik is being implemented in multiple distinct steps, with associated planned - releases:

    +

    Creating new system + configuration

    - -

    Version 1.X Planned Features

    + ' + stargazers_count: 3 + subscribers_count: 5 + topics: + - cmake + - build + - exawind + - hpc + - exawind-builder + updated_at: 1643028069.0 +FZJ-INM1-BDA/siibra-python: + data_format: 2 + description: Software interfaces for interacting with brain atlases - Python client + filenames: + - .ebrains/spack/siibra-spack.yaml + full_name: FZJ-INM1-BDA/siibra-python + latest_release: null + stargazers_count: 45 + subscribers_count: 8 + topics: + - brain + - atlas + - neuroscience + - bigbrain + - bigbrainproject + - humanbrainproject + updated_at: 1715157395.0 +FairRootGroup/FairMQ: + data_format: 2 + description: C++ Message Queuing Library and Framework + filenames: + - spack.yaml + full_name: FairRootGroup/FairMQ + latest_release: v1.8.4 + readme: ' -
      +

      FairMQ

      -
    1. Rearchitecting of the z-model solve into explicitly-coupled surface mesh and - spatial mesh solvers
    2. +

      license -

    3. A spatial mesh cutoff-based approach for calculating far-field forces using - the Cabana particle framework. The goal of this work is to understand the accuracy/performance - tradeoffs in the Z-Model, particularly in the medium-order
    4. + DOI -
    5. Improved timestep, desingularization, and artificial viscosity parameter handling. - The goal of this is to provide good defaults when other input parameters are changed.
    6. + OpenSSF Best Practices -
    7. Additional interface initialization options, including Gaussian random and - file-based interface initialization (also useful for checkpointing)
    8. + fair-software.eu -
    9. Support for coupling with other applications through either I/O (e.g. ADIOS) - or Communication (e.g. Portage)
    10. + Spack package

      -
    11. Additional test case definitions
    12. +

      C++ Message Queuing Library and Framework

      -
    +

    Docs: Book

    -
  • +

    Find all FairMQ releases here.

    -
  • +

    Introduction

    -

    Potential later (e.g. >=2.0) features

    +

    FairMQ is designed to help implementing large-scale data processing workflows + needed in next-generation Particle Physics experiments. FairMQ is written in C++ + and aims to

    -
      +
        -
      • Direct fast multi-pole or P3M solver for scalable, high precision high-order - model solves.
      • +
      • provide an asynchronous message passing abstraction of different + data transport technologies,
      • -
      • Support for multiple interface manifolds in a single simulation.
      • +
      • provide a reasonably efficient data transport service (zero-copy, + high throughput),
      • -
    +
  • be data format agnostic, and
  • - +
  • provide basic building blocks that can be used to implement + higher level data processing workflows.
-

Acknowledgment, Contributors, - and Copyright Information

+

The core of FairMQ provides an abstract asynchronous message passing API with + scalability protocols -

Beatnik is primarily available as open source under a 3-Clause BSD License. - It is being developed at the University of New Mexico, Tennessee Tech University, - and the University of Alabama under funding the U.S. Department of Energy''s Predictive - Science Academic Alliance Partnership III (PSAAP-III) program. Contributors to - Beatnik development include:

+ inspired by ZeroMQ (e.g. PUSH/PULL, + PUB/SUB). -
    + FairMQ provides multiple implementations for its API (so-called "transports", -
  • Patrick G. Bridges (patrickb@unm.edu)
  • + e.g. zeromq and shmem (latest release of the ofi + transport in v1.4.56, removed since v1.5+)) to cover -
  • Thomas Hines (tmhines3@ua.edu)
  • + a variety of use cases -
  • Jered Dominguez-Trujillo (jereddt@unm.edu)
  • + (e.g. inter-thread, inter-process, inter-node communication) and machines (e.g. + Ethernet, Infiniband). -
  • Jacob McCullough (jmccullough12@unm.edu)
  • + In addition to this core functionality FairMQ provides a framework for creating + "devices" - actors which -
  • Jason Stewart (jastewart@unm.edu)
  • + are communicating through message passing. FairMQ does not only allow the user + to use different transport -
+ but also to mix them; i.e: A Device can communicate using different transport + on different channels at the -

The general structure of Beatnik and the rocketrig examples were taken from - the ExaMPM proxy application (https://github.com/ECP-copa/ExaMPM) - developed by the ECP Center for Particle Applications (CoPA), which was also available - under a 3-Clause BSD License when used for creating application structure.

+ same time. Device execution is modelled as a simple state machine that shapes + the integration points for -

References

+ the user task. Devices also incorporate a plugin system for runtime configuration + and control. -
    + Next to the provided devices + and -
  1. + plugins + the user can extend FairMQ -

    Gavin Pandya and Steve Shkoller. "3d Interface Models for Raleigh-Taylor Instability." - Published as arxiv.org preprint https://arxiv.org/abs/2201.04538, - 2022.

    + by developing his own plugins to integrate his devices with external configuration + and control services.

    -
  2. +

    FairMQ has been developed in the context of its mother project FairRoot + - -

  3. + a simulation, reconstruction and analysis framework.

    -

    https://github.com/ECP-copa/Cabana/

    +

    Installation from Source

    -
  4. +

    Recommended:

    -
  5. +
    git clone https://github.com/FairRootGroup/FairMQ
    +    fairmq_source
     
    -    

    Innovative Computing Laboratory. "heFFTe." URL: https://icl.utk.edu/fft/

    + cmake -S fairmq_source -B fairmq_build -GNinja -DCMAKE_BUILD_TYPE=Release -
  6. + cmake --build fairmq_build -
+ ctest --test-dir fairmq_build --output-on-failure --schedule-random -j<ncpus> - ' - stargazers_count: 4 - subscribers_count: 4 - topics: [] - updated_at: 1716587778.0 -CUP-ECS/cajitafluids: - data_format: 2 - description: A simple poisson finite difference fluid solver in Cabana/Kokkos for - testing MPI communication abstractions and their performance - filenames: - - configs/tutorial-uao-cuda/spack.yaml - full_name: CUP-ECS/cajitafluids - latest_release: null - readme: '

Poisson MPI Benchmark

+ cmake --install fairmq_build --prefix $(pwd)/fairmq_install -

This directory contains code for a relatively simple finite difference +

Please consult the manpages of your CMake version for more options.

- fluid advection solver for exploring communication issues on modern architectures +

If dependencies are not installed in standard system directories, you can hint + the installation location via - (particularly GPUs). The main goal is to look at different neighbor collective + -DCMAKE_PREFIX_PATH=... or per dependency via -D{DEPENDENCY}_ROOT=... + (*_ROOT variables can also be environment variables).

- and GPU communication approaches.

+

Usage

-

Computationally, the benchmark advects a material feature (that doesn''t otherwise - effect +

FairMQ ships as a CMake package, so in your CMakeLists.txt you + can discover it like this:

- fluid flow, e.g. by changing pressite) using the incompressible Euler fluid flow - equations. +
find_package(FairCMakeModules
+    1.0 REQUIRED)
 
-    Consider, for example, something like a dye being carried through a tank of water
-    or a
+    include(FairFindPackage2)
 
-    fragrance wafting across a room.

+ find_package2(FairMQ) -

The main elements of the benchmark are:

+ find_package2_implicit_dependencies()
-
    +

    The FairFindPackage2 module is part of the FairCMakeModules package.

    -
  • Solution of the pressure gradient at each timestep to maintain +

    If FairMQ is not installed in system directories, you can hint the installation:

    - incompressibility. The benchmark has two initial implementations: +
    list(PREPEND
    +    CMAKE_PREFIX_PATH /path/to/fairmq_install)
    - (1) Calling a matrix-free solver in HYPRE to solve the problem or (2) +

    Dependencies

    - running a local matrix-free preconditioned CG solver, in which different +
      - MPI approaches for the halo exchange are explored. +
    • Boost
    • -
    • Interpolation (either cubic splines or linear) for semi-Lagrangian +
    • CMake
    • - advection of the material being advected across timesteps. +
    • Doxygen
    • -
    • 3rd-order Runge Kutta for time integration
    • +
    • -
    + FairCMakeModules + (optionally bundled)
  • -

    Sources:

    +
  • FairLogger
  • -
      +
    • -
    • Fluid Simulation for Comptuer Graphics by Bridson
    • + GTest (optionally bundled) -
    • Incremental Fluids in Kokkos (git@github.com:pkestene/incremental-fluids-kokkos.git)
    • +
    • ZeroMQ
    - ' - stargazers_count: 0 - subscribers_count: 11 - topics: [] - updated_at: 1702247921.0 -E4S-Project/e4s: - data_format: 2 - description: E4S for Spack - filenames: - - environments/21.08/spack.yaml - - environments/23.08/oneapi-x86_64/spack.yaml - - environments/23.02/cuda-ppc64le/spack.yaml - - environments/23.08/cuda-aarch64/spack.yaml - - environments/24.05/ppc64-gcc-cuda-ubuntu20.04/spack.yaml - - environments/23.08/cuda-x86_64/spack.yaml - - environments/24.05/amd64-gcc-cpu-ubuntu22.04/spack.yaml - - environments/24.05/arm64-gcc-cpu-ubuntu22.04/spack.yaml - - environments/24.02/amd64-gcc-cpu-ubuntu20.04/spack.yaml - - environments/24.05/amd64-oneapi-ubuntu22.04/spack.yaml - - environments/23.02/cuda-x86_64/spack.yaml - - environments/22.08/oneapi.spack.yaml - - environments/22.05/rocm.spack.yaml - - environments/24.05/amd64-gcc-cuda-ubuntu22.04/spack.yaml - - environments/23.05/cuda-x86_64/spack.yaml - - environments/24.05/arm64-gcc-cuda-ubuntu22.04/spack.yaml - - environments/22.05/cuda-ppc64le.spack.yaml - - environments/24.02/arm64-gcc-cuda-ubuntu20.04/spack.yaml - - environments/22.05/cuda-x86_64.spack.yaml - full_name: E4S-Project/e4s - latest_release: v24.05 - readme: "

    \"E4S\"

    \n

    \"License\"\n\"Documentation\"\n\"GitHub\n\"GitHub

    \n

    E4S

    \n

    The Extreme-scale Scientific Software Stack (E4S) is a community effort to provide\ - \ open source\nsoftware packages for developing, deploying and running scientific\ - \ applications on high-performance\ncomputing (HPC) platforms. E4S provides from-source\ - \ builds and containers of a\nbroad collection of HPC software packages.

    \n

    E4S\ - \ is available to download in the following formats:

    \n
      \n
    • \n

      Containers:\ - \ Docker, Singularity, CharlieCloud, OVA

      \n
    • \n
    • \n

      Spack manifest (spack.yaml)\ - \ to install from source. These can be found in environments directory.

      \n
    • \n
    • \n

      AWS EC2 image with image name ami-0db9d49091db1c25f\ - \ in US-West-2 (Oregon)

      \n
    • \n
    • \n

      E4S Build Cache

      \n
    • \n
    \n

    Please see E4S Product Dictionary\ - \ for complete list of E4S products.

    \n
    Useful Links
    \n\ - \n

    Related\ - \ Projects

    \n\n

    License

    \n

    E4S is released as\ - \ MIT license for more details see LICENSE file

    \n

    Contact

    \n\n" - stargazers_count: 25 - subscribers_count: 10 - topics: [] - updated_at: 1716324686.0 -E4S-Project/e4s-alc: - data_format: 2 - description: "E4S \xE0 la carte is a tool that allows a user to customize a container\ - \ image by adding packages to it. These can be system packages and Spack packages. " - filenames: - - examples/ubuntu/light_spack.yaml - full_name: E4S-Project/e4s-alc - latest_release: v1.0.2 - readme: "

    E4S \xE0\ - \ la Carte

    \n

    Description

    \n\ -

    E4S \xE0 la Carte is a practical tool designed to facilitate the generation\ - \ of Dockerfiles and Singularity definition files infused with OS packages, Spack\ - \ packages, as well as custom commands. In the simplifying the process, this tool\ - \ targets the elimination of manual definition files scripting, enabling users\ - \ to concentrate on critical aspects such as application-specific resources and\ - \ configurations.

    \n

    Documentation

    \n

    \"Documentation

    \n

    Our documentation is located here: Documentation

    \n\ -

    Overview

    \n

    The e4s-alc tool is designed to facilitate\ - \ the process of crafting Dockerfiles and Singularity definition files. This tool\ - \ leverages .yaml files as input to generate images' definition files.

    \n\ -

    Installation

    \n

    Installing e4s-alc is simple.

    \n

    Clone\ - \ the project:

    \n
    git clone https://github.com/E4S-Project/e4s-alc.git\n\
    -    
    \n

    Run make:

    \n
    cd e4s-alc &&\
    -    \ make install\n
    \n

    Example

    \n

    Here is an example .yaml file. This input\ - \ file creates a Dockerfile using a Rhel8 base image. It installs gcc@11.2 and\ - \ installs kokkos using gcc@11.2. Notice how I've chosen to exclude parameters\ - \ to fit my build. This is one of the example .yaml files in the\ - \ examples directory.

    \n
    # rhel8-gcc11.2-kokkos.yaml\n\
    -    \n######## Base group ########\nbackend: podman\nregistry: registry.access.redhat.com\n\
    -    image: ubi8/ubi\n\n####### Spack group #######\nspack-version: latest\nspack-compiler:\
    -    \ gcc@11.2\nspack-packages:\n  - kokkos\n
    \n

    I build the Dockerfile\ - \ and image with:

    \n
    e4s-alc create -f rhel8-gcc11.2-kokkos.yaml\n\
    -    podman build .\n
    \n

    Then, run the image in interactive mode and\ - \ inspect the install:

    \n
    [root@c5ad0d45ba1d /]# module avail\n-----------------------------\
    -    \ /modulefiles/linux-rhel8-power9le -----------------------------------\ngcc/11.2.0\
    -    \  kokkos/4.0.01  \n[root@c5ad0d45ba1d /]# module load gcc\n[root@c5ad0d45ba1d\
    -    \ /]# module load kokkos\n
    \n

    Example YAML file with matrix feature

    \n

    Here is an example .yaml\ - \ file that creates multiple Dockerfiles using a single .yaml file.\ - \ Notice that for each registry-image-matrix item that we specify,\ - \ we build out a Dockerfile using each spack-compiler-matrix item.\ - \ This feature could be powerful for testing Spack packages across different operating\ - \ systems and compilers.

    \n
    backend: podman\nregistry-image-matrix:\n\
    -    \  - registry.access.redhat.com/ubi8/ubi\n  - ubuntu:20.04\n\n####### Spack group\
    -    \ #######\nspack: True\nspack-version: latest\n\nspack-compiler-matrix:\n  - gcc@8.5.0\
    -    \ \n  - gcc@11.2.0 \n  - gcc@12.0\n  - gcc@12.3.0\n\nspack-packages: \n  - kokkos\n\
    -    
    \n

    This .yaml file would create a directory named\ - \ dockerfiles that contains the following Dockerfiles:

    \n
    Dockerfile.rhel8.8-gcc@8.5.0\n\
    -    Dockerfile.rhel8.8-gcc@11.5.0\nDockerfile.rhel8.8-gcc@12.0\nDockerfile.rhel8.8-gcc@12.3.0\n\
    -    Dockerfile.ubuntu20.04-gcc@8.5.0\nDockerfile.ubuntu20.04-gcc@11.5.0\nDockerfile.ubuntu20.04-gcc@12.0\n\
    -    Dockerfile.ubuntu20.04-gcc@12.3.0\n
    \n" - stargazers_count: 5 - subscribers_count: 4 - topics: [] - updated_at: 1716571832.0 -ECP-CANDLE/Supervisor: - data_format: 2 - description: null - filenames: - - spack/spack.yaml - full_name: ECP-CANDLE/Supervisor - latest_release: null - stargazers_count: 7 - subscribers_count: 11 - topics: - - nci-doe-collaboration-capability - updated_at: 1716583724.0 -EnzymeAD/CMake-Template: - data_format: 2 - description: "\U0001F528 A template for using Enzyme with CMake" - filenames: - - spack.yaml - full_name: EnzymeAD/CMake-Template - latest_release: null - readme: "

    CMake-Template

    \n
    Usage
    \n
    Install dependencies
    \n\ -
      \n
    • cmake
    • \n
    • make
    • \n
    • llvm
    • \n
    • enzyme
    • \n
    \n

    Using\ - \ spack:

    \n
    spack env activate .\nspack install\n
    \n\ -

    Using homebrew:

    \n
    brew bundle install\n
    \n

    Configure and build

    \n

    Configure the CMake project using\ - \ the version of Enzyme installed on the system:

    \n
    mkdir build &&\
    -    \ cd build\ncmake ..\nmake\n
    \n

    Configure the CMake project using\ - \ a custom Enzyme version:

    \n
    mkdir build && cd build\ncmake\
    -    \ -DEnzyme_DIR=/path/to/Enzyme/enzyme/build \nmake\n
    \n" - stargazers_count: 0 - subscribers_count: 3 - topics: - - cmake - - enzyme-ad - - template - updated_at: 1687815556.0 -ExCALIBUR-NEPTUNE/NESO: - data_format: 2 - description: null - filenames: - - spack.yaml - full_name: ExCALIBUR-NEPTUNE/NESO - latest_release: v0.1.0 - readme: "

    NESO (Neptune\ - \ Exploratory SOftware)

    \n

    This is a work-in-progress respository\ - \ for exploring the implementation of\na series of tokamak exhaust relevant models\ - \ combining high order finite\nelements with particles, written in C++ and SYCL.

    \n\ -

    Dependencies

    \n
      \n
    • CMake
    • \n
    • Boost >= 1.74 (for tests)
    • \n\ -
    • SYCL implementation Hipsycl and fftw or OneAPI and MKL.
    • \n
    • Nektar++
    • \n\ -
    • NESO-Particles
    • \n
    \n

    Building with Spack

    \n\ -

    The easiest way to install NESO is using the\nSpack package manager, although\nthis can take a few hours\ - \ the first time you do it or if you change\ncompilers. This repository has been\ - \ set up so you can use a\nvariation of the Spack developer\nworkflow. Simply\nrun the following commands\ - \ at the top level of the repository:

    \n

    If you don't already have Spack\ - \ available on your computer, install it\naccording to the official documentation, or as follows:

    \n
    # Ensure all prerequisites are installed\napt update # For Ubuntu; other distros have their own\
    -    \ commands\napt install build-essential ca-certificates coreutils curl\
    -    \ environment-modules gfortran git gpg lsb-release python3 python3-distutils python3-venv\
    -    \ unzip zip\n\ngit clone -c feature.manyFiles=true -b v0.19.0 https://github.com/spack/spack.git\
    -    \ $HOME/.spack\necho\
    -    \ 'export SPACK_ROOT=$HOME/.spack' >> $HOME/.bashrc\necho 'source $SPACK_ROOT/share/spack/setup-env.sh' >> $HOME/.bashrc\nexport SPACK_ROOT=$HOME/.spack\nsource $SPACK_ROOT/share/spack/setup-env.sh
    \n

    Next,\ - \ install the Intel compilers if they are not already present on\nyour computer.

    \n\ -
    spack install intel-oneapi-compilers\n\
    -    spack load intel-oneapi-compilers\nspack compiler find\nspack unload intel-oneapi-compilers
    \n\ -

    Now, activate the NESO development environment and build it and its\ndependencies.\ - \ This must be done from the top level of this\nrepository.

    \n
    git\
    -    \ submodule update --init\n. activate\nspack install\n
    \n

    The activate\ - \ script sets some useful environment variables and runs\nspack activate\ - \ .... This activates an anonymous Spack\nenvironment\nbased on the settings in\ - \ the spack.yaml file. These\nconfigurations tell Spack\ - \ to install NESO and all of its\ndependencies. Rather than pulling fresh NESO\ - \ and Nektar++ source code\nfrom GitHub, it will use the copy of the code in your\ - \ current working\ndirectory and the Nektar++ submodule (respectively). You can\ - \ leave\nthis environment at any time by running deactivate.

    \n\ -

    spack install will build two copies of NESO: one with\nGCC/hipSYCL/FFTW3\ - \ and one with Intel's OneAPI/DPC++/MKL. These\npackages and their dependencies\ - \ will be installed in the usual Spack\nlocations. They will also be linked into\ - \ \"filesystem\nviews\"\nview/gcc-hipsycl and\ - \ view/oneapi-dpcpp. The NESO builds will be\ndone in directories\ - \ called something like spack-build-abc1234 (the\nhashes at the end\ - \ will differ). If you change your spack installation\nin some way (e.g., upgrading\ - \ the version of a dependency) then the\nhash will change and NESO and/or Nektar++\ - \ will be rebuilt. The\nactivation provides the convenience command cleanup\ - \ to delete these\nold builds.

    \n

    In order to tell which build is which,\ - \ symlinks builds/gcc-hipsycl\nand builds/oneapi-dpcpp\ - \ are provided. As Nektar++ is being built\nfrom the submodule, its build trees\ - \ are located at\nnektar/spack-build-abc1234 (the hashes at the end\ - \ will differ) and\ncan be accessed with symlinks nektar/builds/gcc\ - \ and\nnektar/builds/oneapi. Test binaries will be contained within\n\ - these build directories. The activation script launches a background\ntask which\ - \ regularly checks whether the hashes of your NESO and\nNektar++ builds has changed.\ - \ If they have, it will update the\nsymlinks. They will also be checked whenever\ - \ the environment is\nactivated or deactivated.

    \n

    It has been found that\ - \ the oneAPI and clang\ncompilers struggle to build NumPy and Boost due to very\ - \ large memory\nrequirements. As such, the oneAPI build of NESO compiles these\n\ - dependencies using another compiler (the Intel Classic compilers by default).\ - \ Feel free to\nexperiment with changing these or seeing if there is a way to\ - \ make the\nbuilds work with oneAPI.

    \n
    Developing
    \n

    As you develop the\ - \ code, there are a few options for how you\nrecompile. One is simply to run spack\ - \ install again. This will reuse\nthe existing build directory and reinstall\ - \ the results of the\nbuild. The build environment used is determined by the package\n\ - configuration for NESO (as specificed in the NESO package\nrepository and is\nthe same as if you were doing a traditional Spack\ - \ installation of a\nnamed version of NESO. This has the particular advantage\ - \ of building\nwith all toolchaings (i.e., GCC, OneAPI) at one time. It also works\n\ - well if you are developing NESO and Nektar++ simultaneously, as it\nwill rebuild\ - \ both. The main disadvantage of this approach is that\nSpack hides the output\ - \ of CMake during the build process and will only\nshow you any information on\ - \ the build if there is an error. This means\nyou will likely miss any compiler\ - \ warnings, unless you check the build\nlogs. There is also some overhead associated\ - \ with running Spack, which\nmakes the build a little slow.

    \n

    An alternative\ - \ approach is to prefix your usual build commands with\nspack build-env\ - \ neso%gcc or spack build-env neso%oneapi (depending\non which\ - \ compiler you want to use). This will cause the commands to be run in the\nsame\ - \ build environment as when installing that version of NESO. For example, you\n\ - could run

    \n
    spack build-env\
    -    \ neso%gcc cmake . -B build\nspack build-env neso%gcc\
    -    \ cmake --build build
    \n

    This would cause the build to occur in the\ - \ directory build. This\napproach works quite well. A slight downside\ - \ is the commands are\na bit cumbersome. It also won't build for both compilers\ - \ at once,\nalthough you might not want to do that anyway, early during the development\n\ - of a new feature.

    \n

    Finally, you could take advantage of the filesystem\ - \ views created\nwhen you installed the environment and which give you access\n\ - to all of the resources for the build that you need. For example, you\ncould run

    \n\ -
    cmake -DCMAKE_PREFIX_PATH=$(pwd)/gcc-hipsycl\
    -    \ . -B build\ncmake --build build
    \n

    CMake\ - \ will automatically be able to find all of the packages it needs\nin gcc-hipsycl.\ - \ The downside of this approach is that there is a\nrisk CMake will end up using\ - \ a different compiler or compiler version\nthan intended. This is especially\ - \ likely if not using a system\ncompiler. You should ensure you are aware of what\ - \ compilers you have\ninstalled and, if necessary, explicitly specify to CMake\ - \ which you\nwant to use.

    \n

    In general, it is recommended to use the spack\ - \ build-env ...\ncommand for compiling earlier in the development process\ - \ (if you\naren't simultaneously making changes to Nektar++), to ensure you see\n\ - any warnings and so you aren't spending extra times compiling things\ntwice. Once\ - \ you believe you have a working implementation with one\ncompiler (of if you\ - \ are working on NESO and Nektar++ simultaneously),\nyou can use spack install\ - \ to test the build against other\ncompilers. It is not recommended to\ - \ use the Spack views, as building\nthis way is less likely to be reproducible.

    \n\ -

    Manually Installing\ - \ Dependencies

    \n\ -

    CMake

    \n\ -

    Ensure a recent version of CMake is available.\nIf necessary, install with

    \n
    wget https://github.com/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1.tar.gz\n\
    -    tar xvf cmake-3.23.1.tar.gz\ncd cmake-3.23.1/\n./configure\nmake\n
    \n\ -

    Boost

    \n\ -

    The test suite requires the Boost library (version >= 1.74).\nIf this is not available on your system,\ - \ it can be built from source by doing

    \n
    wget https://boostorg.jfrog.io/artifactory/main/release/1.79.0/source/boost_1_79_0.tar.gz\n\
    -    tar xvf boost_1_79_0.tar.gz\ncd boost_1_79_0/\n./bootstrap.sh\n./b2\n
    \n\ -

    If the install is not automatically found by cmake, specify the path to the\n\ - install dir at configure time:

    \n
    cmake -DBoost_INCLUDE_DIR=/path/to/boost_1_79_0/\
    -    \ . -B build\n
    \n

    Nektar++

    \n

    To build with Nektar++, ensure that Nektar++ is installed\ - \ on your system.\nDetailed instructions can be found in the Nektar user guide,\nbut briefly,

    \n
    git clone https://gitlab.nektar.info/nektar/nektar\n\
    -    cd nektar\nmkdir build &&\
    -    \ cd build\ncmake .. \ncmake --build .\nmake install
    \n

    should install Nektar++.

    \n\ -

    To build NESO with Nektar++, set the Nektar++_DIR flag in cmake,\ - \ e.g.

    \n
    cmake -DNektar++_DIR=/path/to/nektar/build/dist/lib64/nektar++/cmake\
    -    \ . -B build\ncmake --build build\n
    \n

    where /path/to/nektar/build/dist/lib64/nektar++/cmake\ - \ is the folder containing\nthe Nektar++Config.cmake file.\nNote\ - \ that for this file to exist, you must do make install at the end\ - \ of the\nNektar++ build.

    \n

    NESO-Particles

    \n

    Install NESO-Particles\ - \ by following the installation instructions at https://github.com/ExCALIBUR-NEPTUNE/NESO-Particles. Additional configuration\ - \ options for NESO-Particles can be passed when NESO is configured through cmake.

    \n\ -

    NESO

    \n\ -

    Manually building\ - \ NESO

    \n

    To build the code\ - \ and the tests, do

    \n
    cmake . -B build\ncmake --build build\n
    \n\ -

    It may be necessary to tell CMake the location of dependencies:

    \n
      \n\ -
    • Boost by setting -DBoost_INCLUDE_DIR\n
    • \n
    • SYCL compiler\ - \ by setting -DCMAKE_CXX_COMPILER\n
    • \n
    • Nektar++ by setting\ - \ the location of Nektar++Config.cmake using -DNektar++_DIR\n\ -
    • \n
    \n

    For example:

    \n
    cmake -DCMAKE_CXX_COMPILER=dpcpp\
    -    \ -DBoost_INCLUDE_DIR=/root/code/boost_1_78_0 -DNektar++_DIR=/root/code/nektar/build/dist/lib64/nektar++/cmake\
    -    \ . -B build\ncmake --build build\n
    \n

    The executable NESO\ - \ is created in bin.

    \n

    Handling Submodules when Developing

    \n

    This repository contains some git\ - \ submodules, for code which is likely\nto undergo development tightly-coupled\ - \ with NESO (e.g., Nektar) or\nwhich it is convenient to distribute this way (NESO-spack).\ - \ When\nchecking out different branches, on which submodules are at different\n\ - commits, it can be easy to end up with working against different\nversions of\ - \ submodules than you think. This can cause headaches when\ntrying to reproduce\ - \ certain behaviour. Run git submodule update --recursive to ensure\ - \ everything is at the correct commit. You can\navoid this issue altogether by\ - \ using git checkout --recurse-submodules. You can also set this\ - \ as a default for your\ncopy of the repository by running git config --local\ - \ submodule.recurse true. Note, however, that these latter two options\n\ - can cause git to complain if trying to switch between two branches,\nonly one\ - \ of which contains a submodule.

    \n

    System-specific information

    \n

    Dirac (CSD3 @ Cambridge)

    \n\ -
    module unload intel/compilers/2017.4\nmodule unload intel/mkl/2017.4\n\
    -    module load gcc/11\nmodule load intel/oneapi/2022.1.0/compiler\nmodule load intel/oneapi/2022.1.0/mkl\n\
    -    module load intel/oneapi/2022.1.0/tbb\nexport  LD_LIBRARY_PATH=/usr/local/software/intel/oneapi/2022.1/compiler/latest/linux/lib:$LD_LIBRARY_PATH\n\
    -    
    \n

    Testing

    \n

    CMake also builds a suite unit tests (e.g. <build_dir>/test/unitTests)\n\ - and integration tests (<build_dir>/test/integrationTests).\ - \ The build\ndirectories are builds/gcc-hipsycl and builds/oneapi-dpcpp.

    \n\ -

    A subset of the tests may be run using appropriate flags:\ne.g. path/to/testExecutable\ - \ --gtest_filter=TestSuiteName.TestName.\nSee the googletest user guide\nfor more info, especially with regards\ - \ to running specific\ntests.

    \n

    Alternatively, you can call\n\ - CTest from\nwithin the build directory to execute your tests.

    \n

    Solvers

    \n

    Each solver has

    \n\ -
      \n
    • Source code: solvers/<solver_name>\n
    • \n
    • Integration\ - \ tests: test/integration/solvers/<solver_name>\n
    • \n
    • Examples:\ - \ examples/<solver_name>/<example_name>\n
    • \n
    \n\ -

    To run a solver example:

    \n
    ./scripts/run_eg.sh  [solver_name]\
    -    \ [example_name] <-n num_MPI> <-b build_dir>\n
    \n

    which\ - \ will look for the solver executable in the most recently modified spack-build-*\ - \ directory, unless one is supplied with -b. Output is generated\ - \ in example-runs/<solver_name>/<example_name>.

    \n\ -

    Address Sanitizers

    \n

    To debug for memory leaks,\ - \ compile with the options

    \n
    cmake . -B -DENABLE_SANITIZER_ADDRESS=on\
    -    \ -DENABLE_SANITIZER_LEAK=on\n
    \n
    Generating meshes
    \n\ -

    One pipeline for creating simple Nektar++ meshes is through Gmsh and NekMesh.\n\ - .geo -> .msh in Gmsh\n.msh -> .xml with NekMesh

    \n

    A .geo file can\ - \ be created using the Gmsh UI (each command adds a new line to the .geo file.\ - \ For simple meshes it may be easier to produce the .geo file in a text editor.\ - \ .geo files can also be loaded into the UI to edit.

    \n
    \n Expand\n\ - \ mesh.geo\n
    //Create construction points for the corners\
    -    \ of the mesh\n//Point(i)\
    -    \ = (x, y, z, scale)\nPoint(1) = {0, 0,\
    -    \ 0, 1.0};\nPoint(2) = {0, 1, 0, 1.0};\nPoint(3) = {1, 1,\
    -    \ 0, 1.0};\nPoint(4) = {1, 0, 0, 1.0};\n\n//Create\
    -    \ construction lines for the edges of the mesh\n//Line(i) = (Start_i, End_i) \nLine(1) = {1,\
    -    \ 2};\nLine(2) = {2, 3};\n\
    -    Line(3) = {3, 4};\nLine(4) = {4, 1};\n\n//Add physical\
    -    \ lines from the construction lines\nPhysical Line(5) = {1};\nPhysical Line(6) = {2};\nPhysical Line(7) = {3};\nPhysical Line(8) = {4};\n\
    -    \n//Close the lines with a curve\
    -    \ loop\nCurve Loop(1)\
    -    \ = {1,2,3,4};\n//Create a construction surface out of the curve loop\n\
    -    Plane Surface(1) = {1};\n//Create\
    -    \ a physical surface out of the construction surface\nPhysical Surface(1) = {1};\n\n//A transfinite\
    -    \ line means that 65 points are created along lines\n// 1 and 3, which will form the corners of 64 mesh\
    -    \ elements.\n//Progression\
    -    \ 1 means they are uniformly spaced\nTransfinite Line {1, 3} = 65 Using\
    -    \ Progression 1;\nTransfinite Line {2, 4} = 2\
    -    \ Using Progression 1;\n//Set the surface\nTransfinite Surface {1};\n\n//The default\
    -    \ is tris, this line is necessary to produce quads\nRecombine Surface \"*\";
    \n\ -
    \n

    Selecting 2D mesh in Gmsh and saving will produce a .msh file.\ - \ The mesh should be visible in the UI to check before saving. Alternatively\ - \ for simple meshes one can jump straight to this step by writing the .msh file\ - \ in a text editor.

    \n
    \n Expand\n mesh.msh\n\ -
    $MeshFormat\n4.1 0 8\n$EndMeshFormat\n$Entities\n4 4 1 0\n.\n.\n.\n\
    -    $EndEntities\n$Nodes\n9 130 1 130\n0 1 0 1\n.\n.\n.\n$EndNodes\n$Elements\n5 194\
    -    \ 1 194\n1 1 1 64\n.\n.\n.\n$EndElements\n
    \n
    \n

    Next call\ - \ NekMesh on the .msh file to convert it to .xml format

    \n
    ./NekMesh\
    -    \ path/to/src/mesh.msh path/to/dst/mesh.xml\n
    \n

    This will produce\ - \ a .xml file like the following:

    \n
    \n Expand\n\ - \ mesh.xml\n
    <NEKTAR>\n  <GEOMETRY DIM=\"2\" SPACE=\"2\"\
    -    >\n    <VERTEX COMPRESSED=\"B64Z-LittleEndian\" BITSIZE=\"64\">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</VERTEX>\n\
    -    \    <EDGE COMPRESSED=\"B64Z-LittleEndian\" BITSIZE=\"64\">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</EDGE>\n\
    -    \    <ELEMENT>\n      <Q COMPRESSED=\"B64Z-LittleEndian\" BITSIZE=\"\
    -    64\">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</Q>\n\
    -    \    </ELEMENT>\n    <COMPOSITE>\n      <C ID=\"1\"> Q[0-63]\
    -    \ </C>\n      <C ID=\"5\"> E[3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,75,78,81,84,87,90,93,96,99,102,105,108,111,114,117,120,123,126,129,132,135,138,141,144,147,150,153,156,159,162,165,168,171,174,177,180,183,186,189,192]\
    -    \ </C>\n      <C ID=\"6\"> E[191] </C>\n      <C ID=\"7\"\
    -    > E[190,187,184,181,178,175,172,169,166,163,160,157,154,151,148,145,142,139,136,133,130,127,124,121,118,115,112,109,106,103,100,97,94,91,88,85,82,79,76,73,70,67,64,61,58,55,52,49,46,43,40,37,34,31,28,25,22,19,16,13,10,7,4,1]\
    -    \ </C>\n      <C ID=\"8\"> E[0] </C>\n    </COMPOSITE>\n\
    -    \    <DOMAIN>\n<D ID=\"0\"> C[1] </D>\n    </DOMAIN>\n\
    -    \  </GEOMETRY>\n<Metadata>\n  <Provenance>\n    <GitBranch>refs/heads/master</GitBranch>\n\
    -    \    <GitSHA1>X</GitSHA1>\n    <Hostname>X</Hostname>\n\
    -    \    <NektarVersion>5.5.0</NektarVersion>\n    <Timestamp>T</Timestamp>\n\
    -    \  </Provenance>\n  <NekMeshCommandLine>path/to/src/mesh.msh path/to/dst/mesh.xml\
    -    \ </NekMeshCommandLine>\n</Metadata>\n  <EXPANSIONS>\n    <E\
    -    \ COMPOSITE=\"C[1]\" NUMMODES=\"4\" TYPE=\"MODIFIED\" FIELDS=\"u\"/>\n  </EXPANSIONS>\n\
    -    </NEKTAR>\n
    \n
    \n

    Note the edge composites run in\ - \ opposite directions. To align them to the same direction use the NekMesh module\ - \ peralign as follows:

    \n
    ./NekMesh -m peralign:surf1=5:surf2=7:dir=x\
    -    \ path/to/src/mesh.xml path/to/dst/mesh_aligned.xml\n
    \n

    Licence

    \n

    This is licenced under\ - \ MIT.

    \n

    In order to comply with the licences of dependencies, this software\ - \ is not to be released as a binary.

    \n" - stargazers_count: 4 - subscribers_count: 8 - topics: [] - updated_at: 1715782886.0 -Exawind/exawind-builder: - data_format: 2 - description: Scripts to help building Exawind codes on various systems - filenames: - - etc/spack/nrel-eagle/spack.yaml - - etc/spack/spack/spack.yaml - full_name: Exawind/exawind-builder - latest_release: v0.1.0 - readme: '

    ExaWind Code - Builder

    - -

    Documentation

    +

    Which dependencies are required depends on which components are built.

    -

    ExaWind Builder is a collection of bash scripts to configure and compile the +

    Supported platform is Linux. macOS is supported on a best-effort basis.

    - codes used within the ExaWind project - on various +

    CMake options

    - high-performance computing (HPC) systems. The builder provides the following

    +

    On command line:

    • -

      Platform configuration: Provides the minimal set of modules - that must be - - loaded when compiling with different compilers and MPI libraries on different + -DDISABLE_COLOR=ON disables coloured console output.

    • - HPC systems.

      +
    • -
    • + -DBUILD_TESTING=OFF disables building of tests.
    • -

      Software configuration: Provides baseline CMake configuration - that can be + -DBUILD_EXAMPLES=OFF disables building of examples.

    • - used to configure the various options when building a project, e.g., +
    • - enable/disable optional modules, automate specification of paths to various + -DBUILD_DOCS=ON enables building of API docs.
    • - libraries, configure release vs. debug builds.

      +
    • -
    • + -DFAIRMQ_CHANNEL_DEFAULT_AUTOBIND=OFF disable channel autoBind + by default -
    • +
    • You can hint non-system installations for dependent packages, see the #installation-from-source + section above
    • -

      Build script generation: Generates an executable end-user - script for a +

    - combination of system, compiler, and project.

    +

    After the find_package(FairMQ) call the following CMake variables + are defined:

    - + -
  • +
  • -

    Exawind environment generation: Generates a source-able, platform-specific +

    - script that allows the user to recreate the exact environment used to build + - the codes during runtime.

    + - + - + -

    The build scripts are intended for developers who might want to compile the +

    - codes with different configuration options, build different branches during + - their development cycle, or link to a different development version of a library + - that is currently not available in the standard installation on the system. Please - see the + - documentation - for + - details on how to use this to build ExaWind software.

    + -

    Installation and usage

    + -

    Using exawind-builder - with pre-installed ExaWind environment

    + -

    ExaWind Builder is already installed and setup on OLCF Summit, NREL +

    - Eagle/Rhodes, and NERSC Cori systems. On these systems, you can proceed directly + - to using build scripts from the central installation. Please consult user + - manual to + - learn how to use the scripts.

    + -

    Bootstrapping exawind-builder - with pre-configured system definitions

    + -

    ExaWind builder has pre-built +

    - configurations + - for several systems. On these systems you can use the bootstrap script - to + - quickly get up and running. Please consult installation + - manual. The + - relevant steps are shown below.

    + - curl -fsSL -o bootstrap.sh https://raw.githubusercontent.com/exawind/exawind-builder/master/bootstrap.sh + + - # Make it executable + - chmod a+x bootstrap.sh + - # Execute bootstrap and provide system/compiler - combination + - ./bootstrap.sh -s [SYSTEM] -c [COMPILER] + + - # Examples + - ./bootstrap.sh -s ornl-summit -c gcc $ Oakridge Summit system + - ./bootstrap.sh -s eagle -c gcc # - NREL Eagle + - ./bootstrap.sh -s cori -c intel # - NERSC Cori + - ./bootstrap.sh -s snl-ascicgpu -c gcc # - SNL GPU development machine + -

    Creating new system - configuration

    + -

    You can add new system definitions to exawind-builder for use on new systems +

    - that are not used by ExaWind team. Please see manual + - installation and + - adding - a new system + - sections in the user manual.

    + -

    Links

    + -
      +
    -
  • ExaWind
  • + -
  • ExaWind GitHub Organization
  • + -
  • A2e HFM
  • + - + - ' - stargazers_count: 3 - subscribers_count: 5 - topics: - - cmake - - build - - exawind - - hpc - - exawind-builder - updated_at: 1643028069.0 -FZJ-INM1-BDA/siibra-python: - data_format: 2 - description: Software interfaces for interacting with brain atlases - Python client - filenames: - - .ebrains/spack/siibra-spack.yaml - full_name: FZJ-INM1-BDA/siibra-python - latest_release: null - stargazers_count: 45 - subscribers_count: 8 - topics: - - brain - - atlas - - neuroscience - - bigbrain - - bigbrainproject - - humanbrainproject - updated_at: 1715157395.0 -FairRootGroup/FairMQ: - data_format: 2 - description: C++ Message Queuing Library and Framework - filenames: - - spack.yaml - full_name: FairRootGroup/FairMQ - latest_release: v1.8.4 - readme: ' + -

    FairMQ

    + -

    license +

    - DOI + - OpenSSF Best Practices + - fair-software.eu + - Spack package

    + -

    C++ Message Queuing Library and Framework

    + -

    Docs: Book

    + -

    Find all FairMQ releases here.

    + -

    Introduction

    + -

    FairMQ is designed to help implementing large-scale data processing workflows - needed in next-generation Particle Physics experiments. FairMQ is written in C++ - and aims to

    + -
      +
    -
  • provide an asynchronous message passing abstraction of different - data transport technologies,
  • + -
  • provide a reasonably efficient data transport service (zero-copy, - high throughput),
  • + -
  • be data format agnostic, and
  • + -
  • provide basic building blocks that can be used to implement - higher level data processing workflows.
  • + - + -

    The core of FairMQ provides an abstract asynchronous message passing API with - scalability protocols +

    VariableInfo
    ${FairMQ_PACKAGE_DEPENDENCIES}the list of public package dependencies
    ${FairMQ_<dep>_VERSION}the minimum <dep> version FairMQ requires
    ${FairMQ_<dep>_COMPONENTS}the list of <dep> components FairMQ depends on
    ${FairMQ_PACKAGE_COMPONENTS}the list of components FairMQ consists of
    ${FairMQ_#COMPONENT#_FOUND} -
    #
    -    Download bootstrap script
    +    TRUE if this component was built
    ${FairMQ_VERSION}the version in format MAJOR.MINOR.PATCH +
    ${FairMQ_GIT_VERSION}the version in the format returned by git describe --tags --dirty --match + "v*" - ./bootstrap.sh -s spack -c clang # - On MacOS with homebrew +
    ${FairMQ_PREFIX}the actual installation prefix
    ${FairMQ_BINDIR}the installation bin directory
    ${FairMQ_INCDIR}the installation include directory
    ${FairMQ_LIBDIR}the installation lib directory
    ${FairMQ_DATADIR}the installation data directory (../share/fairmq)
    ${FairMQ_CMAKEMODDIR}the installation directory of shipped CMake find modules
    ${FairMQ_BUILD_TYPE}the value of CMAKE_BUILD_TYPE at build-time
    ${FairMQ_CXX_FLAGS}the values of CMAKE_CXX_FLAGS and CMAKE_CXX_FLAGS_${CMAKE_BUILD_TYPE} + at build-time
    - inspired by ZeroMQ (e.g. PUSH/PULL, - PUB/SUB). +

    Documentation

    - FairMQ provides multiple implementations for its API (so-called "transports", +
      - e.g. zeromq and shmem (latest release of the ofi - transport in v1.4.56, removed since v1.5+)) to cover +
    1. - a variety of use cases + Device - (e.g. inter-thread, inter-process, inter-node communication) and machines (e.g. - Ethernet, Infiniband). - - In addition to this core functionality FairMQ provides a framework for creating - "devices" - actors which - - are communicating through message passing. FairMQ does not only allow the user - to use different transport - - but also to mix them; i.e: A Device can communicate using different transport - on different channels at the - - same time. Device execution is modelled as a simple state machine that shapes - the integration points for - - the user task. Devices also incorporate a plugin system for runtime configuration - and control. - - Next to the provided devices - and - - plugins - the user can extend FairMQ - - by developing his own plugins to integrate his devices with external configuration - and control services.

      - -

      FairMQ has been developed in the context of its mother project FairRoot - - - - a simulation, reconstruction and analysis framework.

      - -

      Installation from Source

      - -

      Recommended:

      - -
      git clone https://github.com/FairRootGroup/FairMQ
      -    fairmq_source
      -
      -    cmake -S fairmq_source -B fairmq_build -GNinja -DCMAKE_BUILD_TYPE=Release
      -
      -    cmake --build fairmq_build
      -
      -    ctest --test-dir fairmq_build --output-on-failure --schedule-random -j<ncpus>
      -
      -    cmake --install fairmq_build --prefix $(pwd)/fairmq_install
      - -

      Please consult the manpages of your CMake version for more options.

      - -

      If dependencies are not installed in standard system directories, you can hint - the installation location via - - -DCMAKE_PREFIX_PATH=... or per dependency via -D{DEPENDENCY}_ROOT=... - (*_ROOT variables can also be environment variables).

      - -

      Usage

      - -

      FairMQ ships as a CMake package, so in your CMakeLists.txt you - can discover it like this:

      - -
      find_package(FairCMakeModules
      -    1.0 REQUIRED)
      -
      -    include(FairFindPackage2)
      -
      -    find_package2(FairMQ)
      -
      -    find_package2_implicit_dependencies()
      - -

      The FairFindPackage2 module is part of the FairCMakeModules package.

      - -

      If FairMQ is not installed in system directories, you can hint the installation:

      +
        -
        list(PREPEND
        -    CMAKE_PREFIX_PATH /path/to/fairmq_install)
        +
      1. Topology
      2. -

        Dependencies

        +
      3. Communication Patterns
      4. -
      -
    2. Doxygen
    3. +
    4. - FairCMakeModules - (optionally bundled)
    5. + Transport Interface -
    6. FairLogger
    7. +
      1. - GTest (optionally bundled)
      2. - -
      3. ZeroMQ
      4. - -
- -

Which dependencies are required depends on which components are built.

+ Message -

Supported platform is Linux. macOS is supported on a best-effort basis.

+
    -

    CMake options

    +
  1. Ownership
  2. -

    On command line:

    +
-
    + -
  • +
  • Channel
  • - -DDISABLE_COLOR=ON disables coloured console output. +
  • Poller
  • -
  • + - -DBUILD_TESTING=OFF disables building of tests.
  • +
  • - -DBUILD_EXAMPLES=OFF disables building of examples.
  • + Configuration -
  • +
      - -DBUILD_DOCS=ON enables building of API docs. +
    1. Device Configuration
    2. - -DFAIRMQ_CHANNEL_DEFAULT_AUTOBIND=OFF disable channel autoBind - by default
    3. - -
    4. You can hint non-system installations for dependent packages, see the #installation-from-source - section above
    5. - -
- -

After the find_package(FairMQ) call the following CMake variables - are defined:

- - - - - - - - - - - - - - - - + Communication + Channels Configuration - +
    -
+
  • JSON Parser
  • - +
  • SuboptParser
  • - + - + - +
  • Introspection
  • - + - + - +
  • -
  • + Development - +
      -
    +
  • Testing
  • - +
  • -
  • + Static Analysis - +
      -
    +
  • CMake Integration
  • - +
  • Extra Compiler + Arguments
  • - + - + - + - +
  • -
  • + Logging - +
  • Log severity
  • - +
  • Log verbosity
  • - +
  • Color for console output
  • - +
  • File output
  • - + - + - +
  • Examples
  • - +
  • -
  • + Plugins - +
      -
    +
  • Usage
  • - +
  • Development
  • - +
  • -
  • + Provided Plugins - +
      -
    +
  • PMIx
  • - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    VariableInfo
    ${FairMQ_PACKAGE_DEPENDENCIES}the list of public package dependencies
    ${FairMQ_<dep>_VERSION}the minimum <dep> version FairMQ requires
    ${FairMQ_<dep>_COMPONENTS}the list of <dep> components FairMQ depends on
    ${FairMQ_PACKAGE_COMPONENTS}the list of components FairMQ consists of
    ${FairMQ_#COMPONENT#_FOUND} + - TRUE if this component was built
    ${FairMQ_VERSION}the version in format MAJOR.MINOR.PATCH +
      -
    ${FairMQ_GIT_VERSION}the version in the format returned by git describe --tags --dirty --match - "v*" +
  • Custom sinks
  • -
    ${FairMQ_PREFIX}the actual installation prefix
    ${FairMQ_BINDIR}the installation bin directory
    ${FairMQ_INCDIR}the installation include directory
    ${FairMQ_LIBDIR}the installation lib directory
    ${FairMQ_DATADIR}the installation data directory (../share/fairmq)
    ${FairMQ_CMAKEMODDIR}the installation directory of shipped CMake find modules
    ${FairMQ_BUILD_TYPE}the value of CMAKE_BUILD_TYPE at build-time
    ${FairMQ_CXX_FLAGS}the values of CMAKE_CXX_FLAGS and CMAKE_CXX_FLAGS_${CMAKE_BUILD_TYPE} - at build-time
    - -

    Documentation

    - -
      - -
    1. - - Device - -
        - -
      1. Topology
      2. - -
      3. Communication Patterns
      4. - -
      5. State Machine
      6. - -
      7. Multiple - devices in the same process
      8. - -
      - -
    2. - -
    3. - - Transport Interface - -
        - -
      1. - - Message - -
          - -
        1. Ownership
        2. - -
        - -
      2. - -
      3. Channel
      4. - -
      5. Poller
      6. - -
      - -
    4. - -
    5. - - Configuration - -
        - -
      1. Device Configuration
      2. - -
      3. - - Communication - Channels Configuration - -
          - -
        1. JSON Parser
        2. - -
        3. SuboptParser
        4. - -
        - -
      4. - -
      5. Introspection
      6. - -
      - -
    6. - -
    7. - - Development - -
        - -
      1. Testing
      2. - -
      3. - - Static Analysis - -
          - -
        1. CMake Integration
        2. - -
        3. Extra Compiler - Arguments
        4. - -
        - -
      4. - -
      - -
    8. - -
    9. - - Logging - -
        - -
      1. Log severity
      2. - -
      3. Log verbosity
      4. - -
      5. Color for console output
      6. - -
      7. File output
      8. - -
      9. Custom sinks
      10. - -
      - -
    10. - -
    11. Examples
    12. - -
    13. - - Plugins - -
        - -
      1. Usage
      2. - -
      3. Development
      4. - -
      5. - - Provided Plugins - -
          - -
        1. PMIx
        2. - -
        - -
      6. - -
      - -
    14. - -
    + ' stargazers_count: 82 @@ -3867,8 +3258,8 @@ FairRootGroup/FairSoft: description: Repository for installation routines of the external software required by FairRoot filenames: - - env/jun19/sim/spack.yaml - test/env/fairlogger/spack.yaml + - env/jun19/sim/spack.yaml - env/dev/sim_mt_headless/spack.yaml - env/apr21/sim_mt/spack.yaml full_name: FairRootGroup/FairSoft @@ -3940,72 +3331,301 @@ FairRootGroup/FairSoft: subscribers_count: 14 topics: [] updated_at: 1705588914.0 -GEOS-DEV/GEOS: +FluidNumerics/SELF: data_format: 2 - description: GEOS Simulation Framework + description: Spectral Element Library in Fortran filenames: - - scripts/spack_configs/toss_4_x86_64_ib/spack.yaml - - scripts/pygeosx_configs/toss_4_x86_64_ib/spack.yaml - full_name: GEOS-DEV/GEOS - latest_release: v1.0.1 - readme: '

    DOI - - codecov + - docker/deps/ubuntu2204/rocm/spack.yaml + full_name: FluidNumerics/SELF + latest_release: null + readme: '

    Spectral Element + Libraries in Fortran (SELF)

    - CI +

    Copyright 2020-2023 Fluid Numerics LLC

    - docscodecov

    -

    Welcome to the GEOS - project!

    -

    GEOS is a simulation framework for modeling coupled flow, transport, and geomechanics +

    SELF is licensed for use under a non-commercial use visible-source + license. Fluid Numerics is a small family-owned business and wants to make + SELF available to researchers for academic use. Under the license, you can use, + modify, and redistribute SELF so long as attribution is given to Fluid Numerics. + However, since we are interested in protecting our time-and-effort investment + in SELF, sale and commercial-use of SELF is prohibited under the license.

    - in the subsurface. The code provides advanced solvers for a number of target - applications, +

    If you are interested in commercial licensure and would like support from Fluid + Numerics, reach out to support@fluidnumerics.com

    - including

    +

    About

    + +

    SELF is an object-oriented Fortran library that support the implementation + of Spectral Element Methods for solving partial differential equations.

    + +

    The SELF API is designed based on the assumption that SEM developers and researchers + need to be able to implement derivatives in 1-D and divergence, gradient, and + curl in 2-D and 3-D on scalar, vector, and tensor functions using spectral collocation, + continuous galerkin, and discontinuous galerkin spectral element methods. Additionally, + as we enter the exascale era, we are currently faced with a zoo of compute hardware + that is available. Because of this, SELF routines provide support for GPU acceleration + through AMD''s HIP and support for multi-core, multi-node, and multi-GPU platforms + with MPI.

    + +

    Installation

    + +

    self can be installed using CMake on Linux platforms that have + the following packages already installed

      -
    • carbon sequestration,
    • +
    • CMake (3.21-3.27)
    • -
    • geothermal energy,
    • +
    • 2008 standard compliant Fortran Compiler
    • -
    • and similar systems.
    • +
    • ROCm 5.7.0 or greater
    • + +
    • CUDA 11 or greater (if building for Nvidia GPU)
    • + +
    • HDF5
    • + +
    • FEQParse
    -

    A key focus of the project is achieving scalable performance on current and - next-generation +

    Prerequisites

    - high performance computing systems. We do this through a portable programming - model and research into scalable algorithms.

    +

    All you need is a Fortran compiler that is compliant with the Fortran 2008 + standard and supports C interoperability. You can see which compilers are regularly + tested on the Github + actions page. Additionally, the table below lists the supported + compilers

    -

    You may want to browse our +

    CMake

    - publications +

    For a quick installation to ${HOME}/.local/self,

    - page for more details on the HPC, numerics, +
    mkdir build/
     
    -    and applied engineering components of this effort.

    + cd build/ -

    Documentation

    + cmake ../ -DCMAKE_INSTALL_PREFIX=${HOME}/.local/self + + make + + sudo make install + +
    + +

    If you''d like to run the provided tests to verify your installation, use ctest + to run the provided tests from within the build/ directory

    + +
    ctest .
    +
    +    
    + +

    The above steps install

    + +
    ${HOME}/.local/self/lib/libself-static.a
    +
    +    ${HOME}/.local/self/lib/libself.so
    +
    +    ${HOME}/.local/self/include/*.mod
    +
    +    ${HOME}/.local/self/example/
    +
    +    ${HOME}/.local/self/test
    +
    +    
    + +

    Supported Compilers, + Operating Systems, and software stacks

    + +

    The following combinations are tested on the main branch of self :

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    NameVersionPlatformBuild SystemStackArchitecture
    GNU Fortran13.2.0Ubuntu 22.04.2 LTScmakeopenmpi/5.0.0, feq-parse/2.0.3, hdf5/1.12.2x86_64 - gfx90a
    GNU Fortran13.2.0Ubuntu 22.04.2 LTScmakeopenmpi/5.0.0, feq-parse/2.0.3, hdf5/1.12.2x86_64 - gfx906
    + +

    "Supported" for us means that we test self regularly on the platforms + listed. Of course, we want to have self working on as many platforms + as possible; open + an issue if you encounter any problems installing or running self + on your own platform.

    + +

    Support

    + +

    Documentation

    + + + +

    If you''d like to contribute, see CONTRIBUTING.md + to get started.

    + +

    If you need help, open + an issue

    + + ' + stargazers_count: 45 + subscribers_count: 6 + topics: + - spectral-element-method + - gpu-acceleration + - gpu-computing + - hpc + - pde-solver + updated_at: 1716653145.0 +GEOS-DEV/GEOS: + data_format: 2 + description: GEOS Simulation Framework + filenames: + - scripts/pygeosx_configs/toss_4_x86_64_ib/spack.yaml + - scripts/spack_configs/toss_4_x86_64_ib/spack.yaml + full_name: GEOS-DEV/GEOS + latest_release: v1.0.1 + readme: '

    DOI + + codecov + + CI + + docs

    + +

    Welcome to the GEOS + project!

    + +

    GEOS is a simulation framework for modeling coupled flow, transport, and geomechanics + + in the subsurface. The code provides advanced solvers for a number of target + applications, + + including

    + +
      + +
    • carbon sequestration,
    • + +
    • geothermal energy,
    • + +
    • and similar systems.
    • + +
    + +

    A key focus of the project is achieving scalable performance on current and + next-generation + + high performance computing systems. We do this through a portable programming + model and research into scalable algorithms.

    + +

    You may want to browse our + + publications + + page for more details on the HPC, numerics, + + and applied engineering components of this effort.

    + +

    Documentation

    Our documentation is hosted here.

    @@ -4103,79 +3723,6 @@ GEOS-DEV/GEOS: - carbon-storage - llnl updated_at: 1715994007.0 -GoogleCloudPlatform/scientific-computing-examples: - data_format: 2 - description: Open Source examples using Google Cloud to solve various Scientific - and Technical Computing problems. - filenames: - - fluxfw-gcp/tf/examples/containers/spack.yaml - full_name: GoogleCloudPlatform/scientific-computing-examples - latest_release: null - readme: '

    Scientific Computing - with Google Cloud

    - -

    A repository of examples.

    - -

    These examples are currently organized by the various schedulers used to - - orchestrate the scientific workloads on the Google Cloud Platform (GCP).

    - -
    - -

    Flux

    - - - -

    Kubernetes

    - - - -

    Slurm

    - - - -

    Notebooks

    - -

    Various notebooks to demonstrate running Google Cloud from a notebook.

    - - - - ' - stargazers_count: 12 - subscribers_count: 19 - topics: [] - updated_at: 1715198738.0 HEPonHPC/hepnos_eventselection: data_format: 2 description: null @@ -4191,14 +3738,14 @@ JCSDA/spack-stack: data_format: 2 description: null filenames: - - configs/templates/skylab-dev/spack.yaml - - configs/templates/ufs-srw-public-v2/spack.yaml - configs/templates/jedi-mpas-nvidia-dev/spack.yaml - - configs/templates/gfs-v16.2/spack.yaml - - configs/templates/ufs-weather-model-static/spack.yaml - - configs/templates/ufs-weather-model/spack.yaml + - configs/templates/ufs-utils/spack.yaml - configs/templates/gsi-addon-dev/spack.yaml - - configs/templates/ufs-srw-dev/spack.yaml + - configs/templates/ufs-srw-public-v2/spack.yaml + - configs/templates/unified-dev/spack.yaml + - configs/templates/ufs-weather-model-static/spack.yaml + - configs/templates/skylab-dev/spack.yaml + - configs/templates/empty/spack.yaml full_name: JCSDA/spack-stack latest_release: 1.7.0 readme: '

    HPX/LCI Scripts

    Autonomous\ @@ -4600,6 +4146,7 @@ LLNL/Umpire: data_format: 2 description: An application-focused API for memory management on NUMA & GPU architectures filenames: + - .spack_env/llnl/spack.yaml - .spack_env/darwin/spack.yaml full_name: LLNL/Umpire latest_release: v2024.02.1 @@ -4765,17 +4312,75 @@ LLNL/Umpire: - radiuss - cpp updated_at: 1716462549.0 +LLNL/UnifyFS: + data_format: 2 + description: 'UnifyFS: A file system for burst buffers' + filenames: + - .spack-env/unifyfs-slurm-gcc12_1_1/spack.yaml + - .spack-env/unifyfs-lsf-gcc11_2_1/spack.yaml + - .spack-env/unifyfs-lsf-gcc8_3_1/spack.yaml + full_name: LLNL/UnifyFS + latest_release: v2.0 + readme: "\n\ +

    Node-local storage is becoming an indispensable hardware resource on\nlarge-scale\ + \ supercomputers to buffer the bursty I/O from scientific\napplications. However,\ + \ there is a lack of software support for node-local storage to\nbe used efficiently\ + \ by applications that use shared files.

    \n

    UnifyFS is an ephemeral, user-level\ + \ file system under active development.\nUnifyFS addresses a major usability factor\ + \ of current and future systems because it enables\napplications to gain performance\ + \ advantages from distributed storage devices on the system while being as easy\ + \ to use as a center-wide parallel file system.

    \n

    Documentation

    \n\ +

    UnifyFS documentation is at https://unifyfs.readthedocs.io.

    \n

    For instructions on how\ + \ to build and install UnifyFS,\nsee Build UnifyFS.

    \n
    Build Status

    \n\ +

    Status of UnifyFS development branch (dev):

    \n

    \"Build

    \n

    \"Read

    \n

    UnifyFS Citation

    \n\ +

    We recommend that you use this citation for UnifyFS:

    \n
      \n
    • Michael\ + \ Brim, Adam Moody, Seung-Hwan Lim, Ross Miller, Swen Boehm, Cameron Stanavige,\ + \ Kathryn Mohror, Sarp Oral, \u201CUnifyFS: A User-level Shared File System for\ + \ Unified Access to Distributed Local Storage,\u201D 37th IEEE International Parallel\ + \ & Distributed Processing Symposium (IPDPS 2023), St. Petersburg, FL, May\ + \ 2023.
    • \n
    \n

    Contribute and Develop

    \n\ +

    If you would like to help, please see our contributing guidelines.

    \n" + stargazers_count: 96 + subscribers_count: 19 + topics: + - system-software + - burst-buffers + - file-system + updated_at: 1715810413.0 LLNL/axom: data_format: 2 description: CS infrastructure components for HPC applications filenames: - - scripts/spack/configs/toss_4_x86_64_ib_cray/spack.yaml - - scripts/spack/configs/docker/ubuntu20/spack.yaml - scripts/spack/devtools_configs/toss_4_x86_64_ib/spack.yaml - scripts/spack/configs/toss_4_x86_64_ib/spack.yaml + - scripts/spack/configs/toss_4_x86_64_ib_cray/spack.yaml + - scripts/spack/configs/docker/ubuntu20/spack.yaml - scripts/spack/configs/linux_ubuntu_20/spack.yaml - - scripts/spack/configs/blueos_3_ppc64le_ib_p9/spack.yaml - - scripts/spack/configs/darwin/spack.yaml full_name: LLNL/axom latest_release: v0.9.0 readme: '

    HiOp - HPC\ @@ -5283,9 +4886,8 @@ LLNL/radiuss-spack-configs: data_format: 2 description: Shared spack configurations for RADIUSS projects filenames: - - toss_4_x86_64_ib_cray/spack.yaml - darwin/spack.yaml - - toss_3_x86_64_ib/spack.yaml + - toss_4_x86_64_ib_cray/spack.yaml full_name: LLNL/radiuss-spack-configs latest_release: null readme: '

    RADIUSS Spack @@ -5382,11 +4984,9 @@ LLNL/serac: data_format: 2 description: Serac is a high order nonlinear thermomechanical simulation code filenames: - - scripts/spack/configs/linux_ubuntu_22/spack.yaml - scripts/spack/devtools_configs/toss_4_x86_64_ib/spack.yaml - - scripts/spack/configs/docker/ubuntu20/spack.yaml - scripts/spack/configs/toss_4_x86_64_ib/spack.yaml - - scripts/spack/configs/docker/ubuntu22/spack.yaml + - scripts/spack/configs/linux_ubuntu_22/spack.yaml full_name: LLNL/serac latest_release: null readme: '

    SUNDIALS: SUite @@ -5789,8 +5389,8 @@ Lumi-supercomputer/lumi-spack-settings: data_format: 2 description: Spack configuration files for LUMI filenames: - - 22.08/0.19.0/spack.yaml - 22.08/0.18.1/spack.yaml + - 23.03/0.19.2/spack.yaml full_name: Lumi-supercomputer/lumi-spack-settings latest_release: null readme: '

    Spack configuration @@ -5920,129 +5520,13 @@ MeteoSwiss/meteodata-lab: topics: - numericalweatherpredictions updated_at: 1716560285.0 -MeteoSwiss/nwp-fdb-polytope-demo: - data_format: 2 - description: Example notebooks for Polytope and FDB data access and processing on - CSCS or remotely. - filenames: - - spack-env/spack.yaml - full_name: MeteoSwiss/nwp-fdb-polytope-demo - latest_release: null - readme: "\n\ -

    This repository contains all that is required to install and run various Jupyter\ - \ notebooks which demonstrate the simplified access to model data via FDB, the Polytope server and the Polytope\ - \ library (ECMWF), and then the subsequent post-processing via a data processing\ - \ framework meteodata-lab\ - \ (in development). The following use cases are covered by the notebooks:

    \n\ -
      \n
    • Retrieving a specified selection of GRIB fields into an xarray object\ - \ and processing with meteorological operators.
    • \n
    • Remotely retrieving\ - \ a very reduced subset of GRIB fields, eg just a few grid points, via the Polytope\ - \ algorithm, to create a timeseries over an extended period.
    • \n
    • Writing\ - \ GRIB fields data back to FDB having processed the model data at CSCS.
    • \n\ -
    \n

    The notebooks for the demo can be found in the directory notebooks.

    \n

    Jupyter Notebooks

    \n

    Notebooks\ - \ to run from CSCS (Balfrin/Eiger):

    \n
      \n
    • 1_Data_Retrieval_from_FDB_Preprocessing
    • \n\ -
    • 2_Precompute_and_Store_Echotop_to_FDB
    • \n
    \n

    Notebooks to run from\ - \ the LabVM:

    \n
      \n
    • 3_Retrieve_Echotop_and_Regrid
    • \n
    • 4_Location_and_TimeSeries_Access
    • \n\ -
    \n
    \n

    [!WARNING]\nNote that the FDB remote server is currently\ - \ deployed with minimal resources and is thus not expected to handle heavy load\ - \ at this time.\nIf you run the notebooks and experience timeouts or other issues,\ - \ please contact either christian.kanesan@meteoswiss.ch\ - \ or victoria.cherkas@meteoswiss.ch\ - \ who will try to help.

    \n
    \n

    Forecasts available in\ - \ FDB

    \n
    \n

    [!NOTE]\nThe remote FDB server references\ - \ an instance of FDB that normally contains only the two latest forecasts.\ - \ This means the FDB requests in the notebooks should usually use date = today\ - \ and time as either 0000, 0300, 0600, 0900 etc. given the forecasts are every\ - \ 3 hour). The data is usually available in the FDB a couple of hours after the\ - \ forecast start time. If the FDB returns no data, contact victoria.cherkas@meteoswiss.ch to enquire about which data is currently archived\ - \ in the FDB.

    \n
    \n

    Instructions

    \n

    To use the Jupyter\ - \ notebooks you have the following two options regarding the runtime dependencies\ - \ and the jupyter server:

    \n
      \n
    1. Jupyter server on the lab-vm or at CSCS\ - \ (Balfrin/Eiger) and runtime dependencies in a container
    2. \n
    3. Both the jupyter\ - \ server and the runtime dependencies in a container (LabVM only)
    4. \n
    \n\ -

    Jupyter server on\ - \ the Lab-VM or at CSCS (Balfrin/Eiger)

    \n\ -

    LabVM

    \n\ -

    With this approach you define a kernel definiton in your jupyter server with\ - \ a reference to the container.

    \n
    sudo apt install pipx\nexport REQUESTS_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt\n\
    -    pipx install jupyterlab\n\n./host/install_kernel.sh
    \n

    Connect to\ - \ the jupyter server

    \n
      \n
    • \nfrom VSCode:
      \n\ - Open the notebook and select the polytope-demo kernel in \"Select\ - \ Kernel\" -> \"Select another Kernel...\" -> \"Jupyter Kernel...\"
      \n\ -
    • \n
    • \nfrom your browser:\n
      pipx run jupyter lab --port 8080
      \nOpen the URL given in the\ - \ code and select the polytope-demo kernel.
    • \n
    \n

    CSCS (Balfrin/Eiger)

    \n

    Setup spack for the machine and build\ - \ FDB.

    \n
    spack env activate\
    -    \ -p spack-env\nspack install --no-checksum
    \n

    Setup the python environment.

    \n\ -
    conda env create -n demo\
    -    \ -f environment.yaml\nconda activate demo\ngit clone -b mars-levtype-echotop-2\
    -    \ https://github.com/cfkanesan/eccodes-cosmo-resources.git $CONDA_PREFIX/share/eccodes-cosmo-resources\npip install jupyterlab\n\
    -    python -m jupyter lab
    \n

    Use VSCode to forward the port that is binded\ - \ to the jupyter lab server to your local machine and open the link in the jupyter\ - \ lab server logs.\nCtrl-C once to show the link again.

    \n

    Jupyter server in a container (LabVM only)

    \n

    With this approach you have both\ - \ the Jupyter server and the runtime dependencies in a container.

    \n
    podman run \\\n  -e https_proxy=$https_proxy \\\n  -e REQUESTS_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt\
    -    \ \\\n  -e SSL_CERT_DIR=/etc/ssl/certs/ \\\n  --network=host \\\n  --rm \\\n \
    -    \ dockerhub.apps.cp.meteoswiss.ch/numericalweatherpredictions/polytope/demo/notebook:<TAG>
    \n\ -

    <TAG>:The current container tag can be retrieved from: https://nexus.meteoswiss.ch/nexus/service/rest/repository/browse/docker-all/v2/numericalweatherpredictions/polytope/demo/notebook/tags/

    \n\ -

    Afterwards connect to the external Jupyter server from the notebook with the\ - \ url from container log. Click \"Select Kernel\" -> \"Existing Jupyter Server...\"\ - \ and then paste the url form the container log.

    \n

    \"Exisiting

    \n
    \n

    [!NOTE]\n\ - With VSCode, you need to have the Jupyter VSCode extension (https://marketplace.visualstudio.com/items?itemName=ms-toolsai.jupyter)\ - \ insalled.

    \n
    \n" - stargazers_count: 0 - subscribers_count: 5 - topics: - - numericalweatherpredictions - updated_at: 1716037549.0 NCAR/ncar-spack: data_format: 2 description: NCAR supercomputer user software installed and maintained using Spack filenames: - - clusters/derecho/spack.yaml - clusters/casper/spack.yaml - - clusters/common/spack.yaml - clusters/test/spack.yaml + - clusters/common/spack.yaml full_name: NCAR/ncar-spack latest_release: null readme: "

    ncar-spack

    Spack Infrastructure

    timemory

    GSI Utility Tools

    -

    These are GSI utilities for various functions.

    +

    These are GSI utilities for various functions.

    + +

    For installation instruction see here

    + + ' + stargazers_count: 2 + subscribers_count: 8 + topics: [] + updated_at: 1715776622.0 +NOAA-EMC/NCEPLIBS-bufr: + data_format: 2 + description: The NCEPLIBS-bufr library contains routines and utilites for working + with the WMO BUFR format. + filenames: + - spack/spack.yaml + full_name: NOAA-EMC/NCEPLIBS-bufr + latest_release: v12.0.1 + readme: '

    Status

    + +

    NCEPLIBS-bufr library

    + +

    The NCEPLIBS-bufr library contains routines and utilites for working + + with the WMO + + BUFR + + format. It is part of the + + NCEPLIBS project.

    + +

    For full documentation of the library, see https://noaa-emc.github.io/NCEPLIBS-bufr/.

    + +

    NCEPLIBS-bufr is used by numerous other projects including:

    + + + +

    To submit bug reports, feature requests, or other code-related issues including + installation and usage questions, please create a GitHub + issue. For general NCEPLIBS inquiries, contact Edward + Hartnett (secondary point of contact Alex + Richert).

    + +

    Authors

    + +

    Jack Woollen, Jeff Ator, Dennis Keyser, Stacey Bender, Diane Stokes, Edward + Hartnett, + + Jeff Whitaker, Rahul Mahajan, Alex Richert, Ron McLaren, and Dom Heinzeller.

    + +

    Code manager: Jeff Ator

    + +

    How to Build and Install

    + +

    Download tarball from + + Releases and + + unpack.

    + +
    mkdir build && cd build
    +
    +    cmake -DCMAKE_INSTALL_PREFIX=path1 -DMASTER_TABLE_DIR=path2 ..
    +
    +    make -j4
    +
    +    ctest
    +
    +    make install
    +
    +    
    + +

    Both path1 and path2 may be full or relative pathnames + + on the system, up to a maximum of 90 characters each.

    + +

    Installation of the library and utilities will be under path1. + + Installation of the master BUFR tables will be under path2, or + + under path1 if -DMASTER_TABLE_DIR=path2 is omitted + + from the above cmake command.

    + +

    If Python interoperability is desired, -DENABLE_PYTHON=ON can + also + + be added to the above cmake command. However, version 3 of Python + + must be installed and available on the system.

    + +

    References

    + +

    Hartnett, E., Ator, J, Lei, H., Richert, A., Woollen, J., King, A., + + Hartnett, A., NCEPLIBS GRIB and BUFR Libraries: Maintaining and + + Modernizing NOAA''s Libraries for WMO Data + + Formats, + + American Geophysical Union (AGU) 2023. (See also + + poster).

    + +

    Disclaimer

    + +

    The United States Department of Commerce (DOC) GitHub project code is + + provided on an "as is" basis and the user assumes responsibility for + + its use. DOC has relinquished control of the information and no longer + + has responsibility to protect the integrity, confidentiality, or + + availability of the information. Any claims against the Department of + + Commerce stemming from the use of its GitHub project will be governed + + by all applicable Federal law. Any reference to specific commercial + + products, processes, or services by service mark, trademark, + + manufacturer, or otherwise, does not constitute or imply their + + endorsement, recommendation or favoring by the Department of + + Commerce. The Department of Commerce seal and logo, or the seal and + + logo of a DOC bureau, shall not be used in any manner to imply + + endorsement of any commercial product or activity by DOC or the United + + States Government.

    + + ' + stargazers_count: 38 + subscribers_count: 5 + topics: + - bufr + updated_at: 1716388567.0 +NOAA-EMC/UPP: + data_format: 2 + description: null + filenames: + - ci/spack.yaml + full_name: NOAA-EMC/UPP + latest_release: upp-srw-v2.2.0 + readme: '

    Unified Post + Processor (UPP)

    + +

    The Unified Post Processor (UPP) software package is a software + + package designed to generate useful products from raw model + + output.

    + +

    The UPP is currently used in operations with the Global Forecast + + System (GFS), GFS Ensemble Forecast System (GEFS), North American + + Mesoscale (NAM), Rapid Refresh (RAP), High-Resolution Rapid Refresh + + (HRRR), Short Range Ensemble Forecast (SREF), and Hurricane WRF (HWRF) + + applications. It is also used in the Unified Forecast System (UFS), + + including the Rapid Refresh Forecast System (RRFS), Hurricane Analysis and + + Forecast System (HAFS), and the Medium-Range Weather (MRW) and Short- + + Range Weather (SRW) Applications.

    + +

    The UPP provides the capability to compute a variety of diagnostic + + fields and interpolate to pressure levels or other vertical + + coordinates.

    + +

    UPP also incorporates the Joint Center for Satellite Data Assimilation + + (JCSDA) Community Radiative Transfer Model (CRTM) to compute model-derived brightness + temperature (TB) for various instruments and + + channels. This additional feature enables the generation of a number + + of simulated satellite products including GOES products.

    + +

    Output from the UPP is in National Weather Service (NWS) and World + + Meteorological Organization (WMO) GRIB2 format and can be used + + directly by visualization, plotting, or verification packages or for + + further downstream post-processing, e.g., statistical post-processing + + techniques.

    + +

    Examples of UPP products include:

    + +
      + +
    • T, Z, humidity, wind, cloud water, cloud ice, rain, and snow on pressure levels
    • + +
    • SLP, shelter level T, humidity, and wind fields
    • + +
    • Precipitation-related fields
    • + +
    • PBL-related fields
    • + +
    • Severe weather products (e.g. CAPE, Vorticity, Wind shear)
    • + +
    • Radiative/Surface fluxes
    • + +
    • Cloud related fields
    • + +
    • Aviation products
    • + +
    • Radar reflectivity products
    • + +
    • Satellite look-alike products
    • + +
    + +

    User Support

    + +

    Support for the UFS UPP is provided through GitHub + Discussions.

    + +

    Documentation

    + +

    User Guide for latest standalone public release: https://upp.readthedocs.io/en/latest/.

    + +

    Technical code-level documentation: https://noaa-emc.github.io/UPP/.

    + +

    Developer Information

    + +

    Please review the wiki

    + +

    Authors

    + +

    NCEP/EMC Developers

    + +

    Code Managers: Wen Meng, Huiya Chuang, Fernando Andrade-Maldonado

    + +

    Prerequisites

    + +

    The UPP requires certain NCEPLIBS packages to be installed via the + + spack-stack project. For instructions on installing these packages as a + + bundle via spack-stack, see: https://spack-stack.readthedocs.io/en/latest/. + + The UPP/modulefiles directory indicates which package versions are + + used and supported on Level 1 systems.

    + +

    Required NCEPLIBS packages:

    + + + +

    Also required to build NCEPpost executable (cmake option -

    For installation instruction see here

    + BUILD_POSTEXEC):

    - ' - stargazers_count: 2 - subscribers_count: 8 - topics: [] - updated_at: 1715776622.0 -NOAA-EMC/NCEPLIBS-bufr: - data_format: 2 - description: The NCEPLIBS-bufr library contains routines and utilites for working - with the WMO BUFR format. - filenames: - - spack/spack.yaml - full_name: NOAA-EMC/NCEPLIBS-bufr - latest_release: v12.0.1 - readme: '

    Status

    + - format. It is part of the +

    The NCEPLIBS-wrf_io - NCEPLIBS project.

    + library is required to build with NCEPpost with WRF-IO library (cmake -

    For full documentation of the library, see https://noaa-emc.github.io/NCEPLIBS-bufr/.

    + option BUILD_WITH_WRFIO).

    -

    NCEPLIBS-bufr is used by numerous other projects including:

    +

    The following third-party libraries are required:

    -
  • +

    Building

    - prepobs from the The NCEP Production Suite.
  • +

    Builds include:

    -
  • + -

    To submit bug reports, feature requests, or other code-related issues including - installation and usage questions, please create a GitHub - issue. For general NCEPLIBS inquiries, contact Edward - Hartnett (secondary point of contact Alex - Richert).

    +

    CMake is used to manage all builds of the UPP. -

    Authors

    -

    Jack Woollen, Jeff Ator, Dennis Keyser, Stacey Bender, Diane Stokes, Edward - Hartnett, +

    The United States Department of Commerce (DOC) GitHub project code is - Jeff Whitaker, Rahul Mahajan, Alex Richert, Ron McLaren, and Dom Heinzeller.

    + provided on an "as is" basis and the user assumes responsibility for -

    Code manager: Jeff Ator

    + its use. DOC has relinquished control of the information and no longer -

    How to Build and Install

    -

    Download tarball from +

    The UPP Terms of Use Notice is available at: https://github.com/NOAA-EMC/UPP/wiki/UPP-Terms-of-Use-Notice

    - Releases and + ' + stargazers_count: 31 + subscribers_count: 14 + topics: [] + updated_at: 1716562274.0 +NOAA-EMC/fv3atm: + data_format: 2 + description: null + filenames: + - ci/spack.yaml + full_name: NOAA-EMC/fv3atm + latest_release: null + readme: '

    fv3atm

    - unpack.

    +

    This repository contains a driver and key subcomponents of the -

    mkdir build && cd build
    +    atmospheric component of the NOAA''s Unified
    +    Forecast System
     
    -    cmake -DCMAKE_INSTALL_PREFIX=path1 -DMASTER_TABLE_DIR=path2 ..
    +    (UFS) weather model.

    - make -j4 +

    The subcomponents include:

    - ctest +
      - make install +
    • The Finite-Volume Cubed-Sphere (FV3) dynamical core, originally -
    + from the Geophysical Fluid + Dynamics -

    Both path1 and path2 may be full or relative pathnames + Laboratory.

  • - on the system, up to a maximum of 90 characters each.

    +
  • The Common Community Physics Package (CCPP) supported by the -

    Installation of the library and utilities will be under path1. + Developmental Testbed Center - Installation of the master BUFR tables will be under path2, or + (DTC), - under path1 if -DMASTER_TABLE_DIR=path2 is omitted + including: - from the above cmake command.

    +
      -

      If Python interoperability is desired, -DENABLE_PYTHON=ON can - also +

    • - be added to the above cmake command. However, version 3 of Python + CCPP Framework.
    • - must be installed and available on the system.

      +
    • CCPP Physics
    • -

      References

      +
    + +
  • + +
  • wrapper code to call UFS stochastic + + physics + +
  • + +
  • The io code handles netCDF I/O.
  • + +
  • The cpl coupler code connects the different components and allows + + them to communicate.
  • + + + +

    Prerequisites

    + +

    This package requires the following + + NCEPLIBS packages:

    + + + +

    If the INLINE_POST cmake variable is set, the upp library will be + + needed:

    + + + +

    This package also requires the following external packages:

    + + - Hartnett, A., NCEPLIBS GRIB and BUFR Libraries: Maintaining and + - Modernizing NOAA''s Libraries for WMO Data +

    To obtain fv3atm, clone the git repository, and update the submodules:

    - Formats, +
    git clone https://github.com/NOAA-EMC/fv3atm.git
     
    -    American Geophysical Union (AGU) 2023. (See also
    +    cd fv3atm
     
    -    poster).

    + git submodule update --init --recursive + +

    Disclaimer

    -

    The Unified Post Processor (UPP) software package is a software - - package designed to generate useful products from raw model +

    Contents

    - output.

    +
      -

      The UPP is currently used in operations with the Global Forecast +

    • What is HPC-ME
    • - System (GFS), GFS Ensemble Forecast System (GEFS), North American +
    • List of current compilers/MPI/OS
    • - Mesoscale (NAM), Rapid Refresh (RAP), High-Resolution Rapid Refresh +
    • List of current libraries
    • - (HRRR), Short Range Ensemble Forecast (SREF), and Hurricane WRF (HWRF) +
    • How to build
    • - applications. It is also used in the Unified Forecast System (UFS), +
    • How to use
    • - including the Rapid Refresh Forecast System (RRFS), Hurricane Analysis and +
    • GFDL example
    • - Forecast System (HAFS), and the Medium-Range Weather (MRW) and Short- +
    • Planned improvements
    • - Range Weather (SRW) Applications.

      +
    -

    The UPP provides the capability to compute a variety of diagnostic +

    What is HPC-ME

    + +

    HPC Portable Container - Model Environments is a set of Dockerfiles, Singularity + Definition files, and containers to provide portable model environments for scientific + applications that require the same set of libraries. The ultimate goal is to + have a community-based list of libraries that are needed for compiling, executing, + and post-processing earth science models. We all use many of the same underlying + libraries, and by working together we can agree upon a community-based approach + to making container usage as standardized as possible.

    + +

    List of current compilers/MPI/OS

    - fields and interpolate to pressure levels or other vertical +

    For each container, there is a full version that contains the programming environment + and a smaller runtime environment that can be used to run compiled executables. + (The runtime container definition files will be added soon.) - coordinates.

    + #- gcc 8/mpich/ubuntu 20.04

    -

    UPP also incorporates the Joint Center for Satellite Data Assimilation +

      - (JCSDA) Community Radiative Transfer Model (CRTM) to compute model-derived brightness - temperature (TB) for various instruments and +
    • gcc 8/mpich/RHEL8
    • - channels. This additional feature enables the generation of a number +
    • - of simulated satellite products including GOES products.

      + intel oneAPI 2022.1/mpich(impi)/ubuntu + 18.04 -

      Output from the UPP is in National Weather Service (NWS) and World + #- intel oneAPI 2021.4/mpich(impi)/centos 8 - Meteorological Organization (WMO) GRIB2 format and can be used +

    • - directly by visualization, plotting, or verification packages or for +
    - further downstream post-processing, e.g., statistical post-processing +

    List of current libraries

    - techniques.

    +

    This is the current list of most of the libraries used in the HPC-ME containers + (We are trying to keep this up-to-date). -

    Examples of UPP products include:

    + The complete list should be found in the respective YAML file.

      -
    • T, Z, humidity, wind, cloud water, cloud ice, rain, and snow on pressure levels
    • - -
    • SLP, shelter level T, humidity, and wind fields
    • - -
    • Precipitation-related fields
    • - -
    • PBL-related fields
    • +
    • automake@1.16.3
    • -
    • Severe weather products (e.g. CAPE, Vorticity, Wind shear)
    • +
    • bacio@2.4.1
    • -
    • Radiative/Surface fluxes
    • +
    • berkeley-db@18.1.40
    • -
    • Cloud related fields
    • +
    • bison@3.7.6
    • -
    • Aviation products
    • +
    • bzip2@1.0.8
    • -
    • Radar reflectivity products
    • +
    • cmake@3.21.2
    • -
    • Satellite look-alike products
    • +
    • crtm@2.3.0
    • -
    +
  • curl@7.78.0
  • -

    User Support

    +
  • diffutils@3.7
  • -

    Support for the UFS UPP is provided through GitHub - Discussions.

    +
  • esmf@8.1.1
  • -

    Documentation

    +
  • expat@2.4.3
  • -

    User Guide for latest standalone public release: https://upp.readthedocs.io/en/latest/.

    +
  • g2@3.4.3
  • -

    Technical code-level documentation: https://noaa-emc.github.io/UPP/.

    +
  • g2tmpl@1.10.0
  • -

    Developer Information

    +
  • gdbm@1.19
  • -

    Please review the wiki

    +
  • gsl@2.7
  • -

    Authors

    +
  • hdf5@1.10.7
  • -

    NCEP/EMC Developers

    +
  • ip@3.3.3
  • -

    Code Managers: Wen Meng, Huiya Chuang, Fernando Andrade-Maldonado

    +
  • ip2@1.1.2
  • -

    Prerequisites

    +
  • jasper@2.0.32
  • -

    The UPP requires certain NCEPLIBS packages to be installed via the +

  • libbsd@0.11.3
  • - spack-stack project. For instructions on installing these packages as a +
  • libiconv@1.16
  • - bundle via spack-stack, see: https://spack-stack.readthedocs.io/en/latest/. +
  • libjpeg-turbo@2.1.0
  • - The UPP/modulefiles directory indicates which package versions are +
  • libmd@1.0.3
  • - used and supported on Level 1 systems.

    +
  • libpng@1.6.37
  • -

    Required NCEPLIBS packages:

    +
  • libsigsegv@2.13
  • - +
  • ncurses@6.2
  • -

    Also required to build NCEPpost executable (cmake option +

  • nemsio@2.5.2
  • - BUILD_POSTEXEC):

    +
  • netcdf-c@4.8.0
  • - +
  • perl@5.34.0
  • -

    The NCEPLIBS-wrf_io +

  • pkgconf@1.8.0
  • - library is required to build with NCEPpost with WRF-IO library (cmake +
  • readline@8.1
  • - option BUILD_WITH_WRFIO).

    +
  • sfcio@1.4.1
  • -

    The following third-party libraries are required:

    +
  • sigio@2.3.2
  • - -

    Building

    - -

    Builds include:

    +

    How to build

    -
      +

      We plan to make this step optional soon. In order to build + the Docker images, you will need access to a computer with root-like access, and + either docker or singularity installed. If you do not have root-like access to + a suitable machine, you can still run images that were already created (e.g. on + Docker hub), and we plan on hosting runnable Docker images along with the Dockerfiles + in this repository soon. If you have root-like access and docker, start by choosing + one of the currently supported model environments from the list above. Then build + the Docker container from the Dockerfile using docker build; for example, to build + the gcc8/mpich/ubuntu18 container:

      -
    • +
      docker build --file Dockerfile_gnu_ubuntu20.04 . --tag hpc-me.ubuntu.gnu
       
      -    

      Inline post (UPP library): Currently only supported for the GFS, RRFS, +

      - HAFS, and the UFS-MRW Application.

      +

      The build process takes approximately 2-3 hours, as the packages are downloaded + and compiled using Spack. After a successful build, you will see that the image + was built and tagged successfully:

      -
    • +
      Successfully built 90a878af77b4
       
      -    
    • + Successfully tagged hpc-me.rhel8.gnu:latest -

      Offline post (UPP executable): Supported for regional applications +

    • - including SRW, RRFS, HAFS, and standalone applications of UPP.

      +

      Then, you may run the container using docker or singularity on the same host. + To run the image on a different machine, pushing the image to Docker Hub is recommended. + Note that you will need a DockerHub account to do this (replace USER with your + Docker user ID in the examples below). For example:

      - +
      docker tag hpc-me.rhel8.gnu USER/hpc-me.rhel8.gnu
       
      -    
    + docker login -

    CMake is used to manage all builds of the UPP. + docker push USER/hpc-me.rhel8.gnu:latest - The script UPP/tests/compile_upp.sh can be used to automatically + - build UPP on fully supported platforms where HPC-stack is supported. +

    How to use

    - Details in this script can be used to build on new platforms.

    +

    We plan to make improvements on this process. Also, while we plan on making + Docker images available on the GitHub container registry, currently you must build + the images yourself. Please start with the Build instructions + to generate a Docker image with your desired OS/compiler HPC-ME environment. Then + you may run the container using docker or singularity; singularity is more likely + than docker to be available on HPC environments.

    -

    Disclaimer

    +

    The usage documentation consists of some general notes on serial/parallel usage, + files inside and outside the container, downloading the containers, and then specific + usage scenarios:

    -

    The United States Department of Commerce (DOC) GitHub project code is +

    - Commerce stemming from the use of its GitHub project will be governed +

    Serial and parallel + usage

    - by all applicable Federal law. Any reference to specific commercial +

    HPC-ME containers are intended for both serial and parallel applications. Serial + applications include compiling model executables, generating input grids, and + post-processing model output. Earth system, climate, and weather models require + parallelism to run efficiently, and use one of the Message Passage Interface (MPI) + implementations OpenMPI, Intel MPI, or mpich. GCC-based HPC-ME containers use + the mpich-based MPI library, which is widely available on most HPC sites, and + the Intel-based containers contain both mpich and Intel MPI.

    + +

    Notes on filesystems + and writing files

    - products, processes, or services by service mark, trademark, +

    We recommend not saving or modifying files within the environment container, + and instead create and modify files on your regular filesystem. To do this, you + will need to connect your filesystem to your container using bind mounts.

    - manufacturer, or otherwise, does not constitute or imply their +

    Downloading containers + and managing images on the filesystem

    - endorsement, recommendation or favoring by the Department of +

    Once you have pushed your images to DockerHub, you will need to download them + before using. In the examples below, replace USER with your Docker Hub ID. If + using docker,

    - Commerce. The Department of Commerce seal and logo, or the seal and +
    docker pull USER/hpc-me.rhel8.gnu:latest
     
    -    logo of a DOC bureau, shall not be used in any manner to imply
    +    
    - endorsement of any commercial product or activity by DOC or the United +

    If using singularity,

    - States Government.

    +
    singularity pull docker://USER/hpc-me.rhel8.gnu:latest
     
    -    

    UPP Terms of Use Notice

    +
    -

    The UPP Terms of Use Notice is available at: https://github.com/NOAA-EMC/UPP/wiki/UPP-Terms-of-Use-Notice

    +

    If using singularity, the image file (SIF format) is saved to the current working + directory

    - ' - stargazers_count: 31 - subscribers_count: 14 - topics: [] - updated_at: 1716562274.0 -NOAA-EMC/fv3atm: - data_format: 2 - description: null - filenames: - - ci/spack.yaml - full_name: NOAA-EMC/fv3atm - latest_release: null - readme: '

    fv3atm

    +
    > ls *.sif
     
    -    

    This repository contains a driver and key subcomponents of the + -rwxr-xr-x 532M Dec 10 16:09 hpc-me.rhel8.gnu_latest.sif* - atmospheric component of the NOAA''s Unified - Forecast System +

    - (UFS) weather model.

    +

    If using docker, the downloaded image is handled by the central docker service.

    -

    The subcomponents include:

    +

    Serial applications + using docker

    -
      +

      You may activate an interactive shell within the desired HPC-ME container using + docker. After running the container, the compilers and tools available within + the container will be accessible in your PATH; e.g.

      -
    • The Finite-Volume Cubed-Sphere (FV3) dynamical core, originally +
      > docker run -it hpc-me.rhel8.gnu:latest
       
      -    from the Geophysical Fluid
      -    Dynamics
       
      -    Laboratory.
    • + [root@0d2cf64e1175 /]# which nf-config -
    • The Common Community Physics Package (CCPP) supported by the + /opt/view/bin/nf-config - Developmental Testbed Center - (DTC), + [root@0d2cf64e1175 /]# nf-config --version - including: + netCDF-Fortran 4.5.3 -
        -
      • + [root@0d2cf64e1175 /]# nf-config --cflags - CCPP Framework.
      • + -I/opt/software/linux-rhel8-x86_64/gcc-8.4.1/netcdf-fortran-4.5.3-g5qfkdlp36unt2s4j4wyrc6heh2sa64n/include -
      • CCPP Physics
      • +
        -
      +

      Serial applications + using singularity

      -
    • +

      Singularity can run Docker images and is more likely to be available on HPC + environments. As with docker run, the HPC-ME tools and compilers are available + in the shell, somewhat similar to loading a set of Environment Modules prepared + by site administrators.

      -
    • wrapper code to call UFS stochastic +
      >singularity run hpc-me.rhel8.gnu_latest.sif
       
      -    physics
       
      -    
    • + Singularity> which nf-config -
    • The io code handles netCDF I/O.
    • + /opt/view/bin/nf-config -
    • The cpl coupler code connects the different components and allows - them to communicate.
    • + Singularity> nf-config --version -
    + netCDF-Fortran 4.5.3 -

    Prerequisites

    +
    -

    This package requires the following +

    Parallel applications + using singularity

    - NCEPLIBS packages:

    +

    HPC-ME containers can provide the runtime environment for MPI applications. + For instance, one could compile an MPI application using the instructions above + using one of the HPC-ME development containers; and then run the application using + the corresponding runtime HPC-ME container.

    -
      +

      Please note that we are continuing to improve the usability of HPC-ME containers + as well as provide more usage examples.

      -
    • NCEPLIBS-w3emc
    • +

      Usually, GFDL climate models are run on gaea by submitting a runscript to the + Slurm scheduler. The runscript loads needed runtime Environment Modules, prepares + input directories and files, and executes the MPI executable using srun. The HPC-ME + containers provide the necessary runtime environment, obviating the need for loading + Environment Modules. Currently, our approach for using the HPC-ME containers is + as follows:

      -
    • NCEPLIBS-bacio
    • +
        -
      1. NCEPLIBS-nemsio
      2. +
      3. Create a new container, starting with the desired HPC-ME runtime container
      4. -
      5. NCEPLIBS-sp
      6. +
      7. Add the MPI-compiled executable to the container filesystem
      8. -
    +
  • Set the MPI-compiled executable to as the container''s command (so that when + the container is run the MPI executable within the container runs)
  • -

    If the INLINE_POST cmake variable is set, the upp library will be +

  • Run the singularity container SIF file using srun within the runscript, replacing + the traditional MPI executable.
  • - needed:

    +
      -
    • Unified Post Processing Library
    • +
    • Replace "srun executable.x" with "srun singularity run container.SIF"
    • + +
    • Add --mpi=pmi2 to the srun call, which connects the system MPI to the container + MPI to the singularity run call
    • + +
    • Bind the working directory so that the container has access to the input files + and can write output files (singularity run -B=/path/to/workdir)
    -

    This package also requires the following external packages:

    +
      -
    -
  • netcdf-fortran Library
  • +

    We plan to provide more examples and usage scenarios, such as using the HPC-ME + containers as-is (i.e. not creating a new container as described above)

    -
  • ESMF
  • +

    GFDL example

    -
  • GFDL''s Flexible Modeling System
  • +

    An example of using an HPC-ME container with the GFDL FRE workflow can be found + here

    - +

    Planned improvements

    -

    Obtaining fv3atm

    +

    HPC-ME is a work in progress under active development, so please check back + or follow the repository for more updates.

    -

    To obtain fv3atm, clone the git repository, and update the submodules:

    +

    Build cache

    -
    git clone https://github.com/NOAA-EMC/fv3atm.git
    +    

    We are working to create a build cache for the libraries listed so that building + the containers is quick and easy.

    - cd fv3atm +

    Github container registry

    - git submodule update --init --recursive +

    We are working to add CI capability to this repository, so that the containers + will be automatically built and stored in the github container registry. This + will make building unnecessary for most cases, though users may build the containers + themselves if they wish (e.g. for custom modifications).

    -
    +

    More usage examples + and documentation, especially for MPI applications

    -

    Disclaimer

    We are still learning how to best use the HPC-ME containers with MPI appliations, + so please check back.

    + +
    -

    The United States Department of Commerce (DOC) GitHub project code is +

    The United States Department of Commerce (DOC) GitHub project code is provided - provided on an "as is" basis and the user assumes responsibility for + on an ''as is'' basis and the user assumes responsibility for its use. DOC has - its use. DOC has relinquished control of the information and no longer + relinquished control of the information and no longer has responsibility to - has responsibility to protect the integrity, confidentiality, or + protect the integrity, confidentiality, or availability of the information. Any - availability of the information. Any claims against the Department of + claims against the Department of Commerce stemming from the use of its GitHub - Commerce stemming from the use of its GitHub project will be governed + project will be governed by all applicable Federal law. Any reference to - by all applicable Federal law. Any reference to specific commercial + specific commercial products, processes, or services by service mark, - products, processes, or services by service mark, trademark, + trademark, manufacturer, or otherwise, does not constitute or imply their - manufacturer, or otherwise, does not constitute or imply their + endorsement, recommendation or favoring by the Department of Commerce. The - endorsement, recommendation or favoring by the Department of + Department of Commerce seal and logo, or the seal and logo of a DOC bureau, - Commerce. The Department of Commerce seal and logo, or the seal and + shall not be used in any manner to imply endorsement of any commercial product - logo of a DOC bureau, shall not be used in any manner to imply + or activity by DOC or the United States Government.

    - endorsement of any commercial product or activity by DOC or the United +

    This project code is made available through GitHub but is managed by NOAA-GFDL - States Government.

    + at https://gitlab.gfdl.noaa.gov.

    ' - stargazers_count: 28 - subscribers_count: 24 - topics: - - numerical-weather-prediction - - nwp - - weather - updated_at: 1716320581.0 + stargazers_count: 3 + subscribers_count: 7 + topics: [] + updated_at: 1714755517.0 ORNL/ReSolve: data_format: 2 description: Library of GPU-resident linear solvers filenames: - buildsystem/spack/ascent/spack.yaml - - buildsystem/spack/incline/spack.yaml - buildsystem/spack/crusher/spack.yaml + - buildsystem/spack/incline/spack.yaml full_name: ORNL/ReSolve latest_release: null readme: "

    ReSolve

    Pawsey Spack @@ -8425,15 +8447,14 @@ RMeli/my-spack: data_format: 2 description: Spack environments filenames: - - envs/alps/dlaf/oneapi-mt/spack.yaml - - envs/local/dlaf/mkl-mt-mpich-cuda-scalapack-pika/spack.yaml - - envs/alps/cp2k/cpu/openblas/spack.yaml - - envs/local/cp2k-dlaf/dlafort-scalapack/spack.yaml + - envs/local/dlaf/mkl-mt-mpich/spack.yaml - envs/local/cp2k-dlaf/mkl-mt-mpich/spack.yaml + - envs/alps/cp2k/cpu/openblas/spack.yaml - envs/alps/sirius/cuda/spack.yaml - envs/local/cp2k/openblas-cuda/spack.yaml - - envs/local/cp2k-dlaf/mkl-mt-mpich-cuda/spack.yaml - - envs/local/dlaf/mkl-mt-mpich/spack.yaml + - envs/local/cp2k-dlaf/dlafort-scalapack/spack.yaml + - envs/alps/dlaf/oneapi-mt/spack.yaml + - envs/local/dlaf/mkl-mt-mpich-cuda-scalapack-pika/spack.yaml full_name: RMeli/my-spack latest_release: null readme: ' - -

    centos7 spack configuration and scripts

    - -

    contents

    - -

    compilers.yaml - compiler list - - config.yaml - global config - - install.sh - package installation commands - - modules.yaml - hierarchical layout for lua modules - - packages.yaml - system installed packages - - README.md - this file - - setupSpack.sh - env needed for executing spack commands

    - - ' - stargazers_count: 1 - subscribers_count: 6 - topics: [] - updated_at: 1696768501.0 -SCOREC/dcs-spack-config: - data_format: 2 - description: Spack config for CCI DCS (AiMOS) system - filenames: - - rhel8NvhpcWdmapp/spack.yaml - - spack.yaml - full_name: SCOREC/dcs-spack-config - latest_release: null - readme: '

    dcs-spack-config

    - -

    CCI DCS (AiMOS) spack configuration and scripts for building the XGC depdencies - - with the IBM XL compilers and Spectrum-MPI.

    - -

    contents

    - -

    compilers.yaml - compiler list

    - -

    config.yaml - global config

    - -

    install.sh - package installation commands

    - -

    modules.yaml - hierarchical layout for lua modules

    - -

    packages.yaml - system installed packages

    - -

    README.md - this file

    - -

    setupSpack.sh - env needed for executing spack commands

    - -

    spack.yaml - list of packages to install

    - -

    setup

    - -
    git clone git@github.com:spack/spack.git spack
    -
    -    cd !$
    -
    -    git checkout v0.13.3
    -
    -    # add the simmetrix-simmodsuite package from the develop branch
    -
    -    git cherry-pick 5ddf5e2
    -
    -    # create the environment
    -
    -    spack env create v0133
    -
    -    spack env activate v0133
    -
    -    # copy the yaml files into the v0133
    -
    -    cp /path/to/the/dir/with/the/yaml/files/* var/spack/environments/v0133/.
    -
    -    # copy the compiler yaml file into the spack etc dir
    -
    -    cp /path/to/the/dir/with/the/yaml/files/compilers.yaml etc/spack/.
    -
    -    
    - -

    install cmake

    - -

    The bootstrap step of the cmake install fails with the XL compilers. I - - installed it manually outside of the environment with spack and gcc4.8.5

    - -
    spack install cmake%gcc@4.8.5_rhel7
    -
    -    
    - -

    Then added the path to packages.yaml.

    - -

    resuming work in an - environment

    - -
    source /gpfs/u/software/dcs-spack-src/dcs-spack-config/setupSpack.sh
    -
    -    spack env activate v0133
    -
    -    
    - - ' - stargazers_count: 0 - subscribers_count: 5 - topics: [] - updated_at: 1633029356.0 -SCOREC/pcms: - data_format: 2 - description: null - filenames: - - spack/spack.yaml - full_name: SCOREC/pcms - latest_release: null - readme: '

    PCMS: Parallel - Coupler For Multimodel Simulations

    - -

    Adios2-based xgc_coupler for XGC and GENE

    - -

    Dependencies

    - - - -

    Build Instructions

    - -

    Build with modules

    - -

    SCOREC Rhel7 environment

    - -
    module unuse /opt/scorec/spack/lmod/linux-rhel7-x86_64/Core
    -
    -    module use /opt/scorec/spack/v0154_2/lmod/linux-rhel7-x86_64/Core
    -
    -    module load \
    -
    -    gcc/10.1.0 \
    -
    -    mpich \
    -
    -    cmake/3.20.0 \
    -
    -    fftw \
    -
    -    gdb
    -
    -    
    - -

    Build, install, and test

    - -
    git clone git@github.com:SCOREC/wdmapp_testcases.git #test data
    -
    -    git clone git@github.com:SCOREC/wdmapp_coupling.git
    -
    -
    -    cmake -S wdmapp_coupling -B buildWdmCpl \
    -
    -    -Dredev_ROOT=/path/to/redev/install \
    -
    -    -DOmega_h_ROOT=/path/to/omegah/install \
    -
    -    -DCMAKE_INSTALL_PREFIX=$PWD/buildWdmCpl/install \
    -
    -    -DPCMS_TEST_DATA_DIR=$PWD/wdmapp_testcases \
    -
    -    -DCatch2_ROOT=/path/to/catch2/install
    -
    -
    -    cmake --build buildWdmCpl --target install
    -
    -
    -    ctest --test-dir buildWdmCpl --output-on-failure
    -
    -    
    - -

    Spack based build

    - -
      + readme: '

      centos7-spack-config

      -
    1. +

      centos7 spack configuration and scripts

      -

      Install spack

      +

      contents

      -
      $ mkdir
      -    /lore/$USER/spack
      +    

      compilers.yaml - compiler list - $ cd /lore/$USER/spack + config.yaml - global config - $ git clone -c feature.manyFiles=true -b releases/v0.20 https://github.com/spack/spack.git + install.sh - package installation commands - $ . spack/share/spack/setup-env.sh

      + modules.yaml - hierarchical layout for lua modules -

      We can also add the spack setup line into the ~/.bashrc with `echo - ". spack/share/spack/setup-env.sh" >> ~/.bashrc". This will load the spack - setup script every time we start our terminal session.

      + packages.yaml - system installed packages -
    2. + README.md - this file -
    3. + setupSpack.sh - env needed for executing spack commands

      -

      Get PCMS spack repo + ' + stargazers_count: 1 + subscribers_count: 6 + topics: [] + updated_at: 1696768501.0 +SCOREC/dcs-spack-config: + data_format: 2 + description: Spack config for CCI DCS (AiMOS) system + filenames: + - rhel8NvhpcWdmapp/spack.yaml + full_name: SCOREC/dcs-spack-config + latest_release: null + readme: '

      dcs-spack-config

      - The following commands will add the pcms recipe files to spack. They are not currently - installed inthe upstream spack repository.

      +

      CCI DCS (AiMOS) spack configuration and scripts for building the XGC depdencies -

      $ git
      -    clone https://github.com/jacobmerson/pcms-spack.git
      +    with the IBM XL compilers and Spectrum-MPI.

      - $ spack repo add pcms-spack/pcms
      +

      contents

      -
    4. +

      compilers.yaml - compiler list

      -
    5. +

      config.yaml - global config

      -

      Add Spack binary mirror +

      install.sh - package installation commands

      - Addding the binary mirrors will avoid some compilation by downloading prebuilt - binaries when available.

      +

      modules.yaml - hierarchical layout for lua modules

      -
      $ spack
      -    mirror add v0.20.1 https://binaries.spack.io/v0.20.1
      +    

      packages.yaml - system installed packages

      - $ spack buildcache keys --install --trust
      +

      README.md - this file

      -
    6. +

      setupSpack.sh - env needed for executing spack commands

      -
    7. +

      spack.yaml - list of packages to install

      -

      Install PCMS repo

      +

      setup

      -
      $ mkdir
      -    /lore/$USER/pcms-coupler
      +    
      git clone git@github.com:spack/spack.git spack
       
      -    $ cd /lore/$USER/pcms-coupler
      +    cd !$
       
      -    $ git clone -b pcms-spack https://github.com/jacobmerson/pcms
      +    git checkout v0.13.3
       
      -    $ cd pcms/spack
      +    # add the simmetrix-simmodsuite package from the develop branch
       
      -    $ spack env create -d env spack.yaml
      +    git cherry-pick 5ddf5e2
       
      -    $ cd env
      +    # create the environment
       
      -    $ spack env activate .
      +    spack env create v0133
       
      -    $ spack install
      + spack env activate v0133 -
    8. + # copy the yaml files into the v0133 -
    + cp /path/to/the/dir/with/the/yaml/files/* var/spack/environments/v0133/. -

    At this point hopefully, spack will now install all of the relavant dependencies - and a baseline build of PCMS. The default environment has PCMS in develop mode. - To modify and recompile PCMS you can modify the code and rerun spack install.

    + # copy the compiler yaml file into the spack etc dir -

    BUILD TODO

    + cp /path/to/the/dir/with/the/yaml/files/compilers.yaml etc/spack/. -
      + -
    • create a spack environment that''s part of this project that can build the - whole stack. +

      install cmake

      - most of the pieces are in place for this, but it will require createing a package - for redev +

      The bootstrap step of the cmake install fails with the XL compilers. I - and of the SCOREC version of Omega_h + installed it manually outside of the environment with spack and gcc4.8.5

      - +
      source /gpfs/u/software/dcs-spack-src/dcs-spack-config/setupSpack.sh
       
      -    
    • + spack env activate v0133 -
    + ' - stargazers_count: 2 - subscribers_count: 19 + stargazers_count: 0 + subscribers_count: 5 topics: [] - updated_at: 1681842553.0 + updated_at: 1633029356.0 SCOREC/rhel7-spack-config: data_format: 2 description: rhel7 spack configuration and scripts filenames: - - v0.15.4/spack.yaml + - v0.20.1/v2/spack.yaml - v0.20.1/v1/spack.yaml full_name: SCOREC/rhel7-spack-config latest_release: null @@ -9134,20 +8946,19 @@ UO-OACISS/e4s: data_format: 2 description: E4S Spack environments and container recipes filenames: - - docker-recipes/runner/ubuntu22.04-amd64-oneapi-2024.1.0/spack.yaml - - docker-recipes/runner/ubuntu22.04-amd64-oneapi-2024.0.1/spack.yaml - - docker-recipes/runner/ubuntu24.04-arm64-gcc-13.2/spack.yaml - - spack-sdk-environments/visualization_analysis_reduction/spack.yaml + - docker-recipes/runner/_archived/ubuntu20.04-amd64-clang-16/spack.yaml + - docker-recipes/archived/special/superlu-sc/spack.yaml - docker-recipes/runner/_archived/ubuntu20.04-x86_64-gcc-11.2/spack.yaml - - docker-recipes/archived/minimal/ubuntu22.04-ppc64le/spack.yaml - - docker-recipes/minimal/ubuntu20.04-ppc64le/spack.yaml + - docker-recipes/runner/alinux2023-arm64-gcc-11.4/spack.yaml + - spack-sdk-environments/e4s_ecosystem/spack.yaml - docker-recipes/runner/_archived/ubuntu20.04-x86_64-gcc-11.4-spack/spack.yaml - - docker-recipes/archived/special/superlu-sc/spack.yaml - - docker-recipes/runner/_archived/ubuntu20.04-amd64-clang-16/spack.yaml + - docker-recipes/runner/ubuntu22.04-amd64-oneapi-2024.1.0/spack.yaml - docker-recipes/archived/rhel7-runner-x86_64/spack.yaml - - docker-recipes/runner/alinux2023-arm64-gcc-11.4/spack.yaml - - docker-recipes/runner/ubuntu24.04-amd64-gcc-13.2/spack.yaml - docker-recipes/runner/_archived/rhel8-ppc64le/spack.yaml + - docker-recipes/runner/ubuntu24.04-amd64-gcc-13.2/spack.yaml + - docker-recipes/archived/minimal/ubuntu22.04-ppc64le/spack.yaml + - docker-recipes/runner/ubuntu24.04-arm64-gcc-13.2/spack.yaml + - docker-recipes/runner/ubuntu22.04-amd64-oneapi-2024.0.1/spack.yaml full_name: UO-OACISS/e4s latest_release: null readme: '

    This is a collection of configurations for building ECP SDK @@ -9378,22 +9189,12 @@ alexpacheco/spackenv: subscribers_count: 2 topics: [] updated_at: 1657632897.0 -aminaramoon/config: - data_format: 2 - description: null - filenames: - - packages/spack.yaml - full_name: aminaramoon/config - latest_release: null - stargazers_count: 0 - subscribers_count: 2 - topics: [] - updated_at: 1673135222.0 aparnasasidharan2017/H5Apps: data_format: 2 description: null filenames: - openpmd/.github/ci/spack-envs/clang14_py311_nompi_h5_ad1_ad2/spack.yaml + - openpmd/spack.yaml full_name: aparnasasidharan2017/H5Apps latest_release: null stargazers_count: 0 @@ -9404,8 +9205,8 @@ boutproject/BOUT-configs: data_format: 2 description: Configuration scripts for BOUT++ filenames: - - lassen/spack_env/bout/spack.yaml - lassen/spack_env/bout_petsc_with_hypre/spack.yaml + - lassen/spack_env/bout/spack.yaml full_name: boutproject/BOUT-configs latest_release: null readme: "

    Configuration\ @@ -9566,38 +9367,6 @@ celeritas-project/celeritas: - detector-simulation - particle-transport updated_at: 1716467409.0 -chipbuster/ljkdfhsgblkdsjhfglksdjfhg: - data_format: 2 - description: null - filenames: - - spack.yaml - full_name: chipbuster/ljkdfhsgblkdsjhfglksdjfhg - latest_release: null - readme: "

    CMake-Template

    \n
    Usage

    \n
    Install dependencies

    \n\ -
      \n
    • cmake
    • \n
    • make
    • \n
    • llvm
    • \n
    • enzyme
    • \n
    \n

    Using\ - \ spack:

    \n
    spack env activate .\nspack install\n
    \n\ -

    Using homebrew:

    \n
    brew bundle install\n
    \n

    Configure and build

    \n

    Configure the CMake project using\ - \ the version of Enzyme installed on the system:

    \n
    mkdir build &&\
    -    \ cd build\ncmake ..\nmake\n
    \n

    Configure the CMake project using\ - \ a custom Enzyme version:

    \n
    mkdir build && cd build\ncmake\
    -    \ -DEnzyme_DIR=/path/to/Enzyme/enzyme/build \nmake\n
    \n" - stargazers_count: 0 - subscribers_count: 1 - topics: [] - updated_at: 1698092884.0 d-SEAMS/seams-core: data_format: 2 description: The d-SEAMS C++ core engine @@ -9952,9 +9721,8 @@ eflows4hpc/workflow-registry: data_format: 2 description: Registry to store workflow descriptions filenames: - - ipgp/backtrackBB/spack.yaml - - minimal_workflow/wordcount/spack.yaml - kaust/exageostat/spack.yaml + - minimal_workflow/wordcount/spack.yaml full_name: eflows4hpc/workflow-registry latest_release: 2nd_stack_release readme: "

    Workflow\ @@ -10021,7 +9789,7 @@ eth-cscs/spack-batteries-included: data_format: 2 description: Installing spack without system dependencies filenames: - - build/1_ccache/spack.yaml + - build/2_compiler/spack.yaml - build/3_more_tools/spack.yaml full_name: eth-cscs/spack-batteries-included latest_release: develop @@ -10147,6 +9915,18 @@ eth-cscs/spack-batteries-included: - squashfs - libfuse updated_at: 1713141858.0 +eth-cscs/spack-stack: + data_format: 2 + description: fast spack builds on slow filesystem + filenames: + - packages/nvhpc/spack.yaml + - recipe/nvhpc.spack.yaml + full_name: eth-cscs/spack-stack + latest_release: null + stargazers_count: 2 + subscribers_count: 4 + topics: [] + updated_at: 1684144105.0 eugeneswalker/exawind-containers: data_format: 2 description: null @@ -10310,8 +10090,8 @@ eugeneswalker/llvm-containers: data_format: 2 description: null filenames: - - x86_64/spack.yaml - ppc64le/spack.yaml + - x86_64/spack.yaml full_name: eugeneswalker/llvm-containers latest_release: null stargazers_count: 1 @@ -10322,8 +10102,8 @@ eugeneswalker/noaa: data_format: 2 description: null filenames: - - gnu/spack.yaml - oneapi/failures/spack.yaml + - gnu/spack.yaml full_name: eugeneswalker/noaa latest_release: null stargazers_count: 0 @@ -10341,21 +10121,224 @@ fnalacceleratormodeling/synergia2-containers: id="user-content-synergia2-containers" class="anchor" aria-label="Permalink: synergia2-containers" href="#synergia2-containers">

    -

    This repository contains docker recipes for building containers that contain - all dependencies for synergia2. These recipes are generated using spack environments via spack containerize, with some minor modifications. - GithubActions is used to build these containers for x86_64_v2 ISA - and these containers can be pulled from the github container registry. For instructions - on how to pull a particular image, visit the page associated with it here.

    +

    This repository contains docker recipes for building containers that contain + all dependencies for synergia2. These recipes are generated using spack environments via spack containerize, with some minor modifications. + GithubActions is used to build these containers for x86_64_v2 ISA + and these containers can be pulled from the github container registry. For instructions + on how to pull a particular image, visit the page associated with it here.

    + +

    These containers are used as test environments for testing synergia2 via GithubActions.

    + + ' + stargazers_count: 2 + subscribers_count: 1 + topics: [] + updated_at: 1715182572.0 +goma/goma: + data_format: 2 + description: A Full-Newton Finite Element Program for Free and Moving Boundary Problems + with Coupled Fluid/Solid Momentum, Energy, Mass, and Chemical Species Transport + filenames: + - spack.yaml + full_name: goma/goma + latest_release: v7.6.1 + readme: '

    Goma

    + +

    A Full-Newton Finite Element Program for Free and Moving Boundary Problems + with Coupled Fluid/Solid Momentum, Energy, Mass, and Chemical Species Transport

    + +

    For more information see the Goma + website

    + +

    Documentation

    + +

    Most of the documentation can be found at https://www.gomafem.com/documentation.html

    + +

    License

    + +

    See LICENSE file. + + and are noted at the top of the cmake file.

    + +

    Third party library + licenses

    + +

    CMake modules

    + +

    Some cmake modules under cmake/ were modified from the Eigen library + + and are noted at the top of the cmake file.

    + +

    See licenses at https://gitlab.com/libeigen/eigen

    + +

    FindMETIS.cmake

    + +
      + +
    • @copyright (c) 2009-2014 The University of Tennessee and The University
    • + +
    • + +
                           of Tennessee Research Foundation.
      +
      +    
      + +
    • + +
    • + +
                           All rights reserved.
      +
      +    
      + +
    • + +
    • @copyright (c) 2012-2014 Inria. All rights reserved.
    • + +
    • @copyright (c) 2012-2014 Bordeaux INP, CNRS (LaBRI UMR 5800), Inria, Univ. + Bordeaux. All rights reserved.
    • + +
    + +

    FindUMFPACK.cmake

    + +

    nanoflann is included + under the BSD license, please see nanoflann.hpp + +

    + + + +

    Major Changes

    + +

    See CHANGES.md

    + +

    Build Instructions

    + +

    See BUILD.md

    + +

    Spack package

    + +

    The Spack package manager https://spack.io + can be used to install + + Goma and all of Goma''s third party libraries

    + +

    Currently available on the develop branch of spack.

    + +

    Example for a bash-like shell:

    + +
    git clone https://github.com/spack/spack.git
    +
    +    . spack/share/spack/setup-env.sh
    +
    +    spack install goma
    +
    +    
    + +

    For more information on build options see:

    + +
    spack info goma
    +
    +    
    + +

    For more information on using spack see the spack documentation.

    + +

    Third party libraries

    + +
      + +
    • Metis 5.1.0 (Optional)
    • + +
    • SEACAS 2022-01-27 (Required: Exodus and Aprepro)
    • + +
    • BLAS/LAPACK (Configured through Trilinos)
    • + +
    • Trilinos matrix solvers 13.0.1 and up (Required: AztecOO, Amesos, Epetra, + TPL LAPACK; Optional: Stratimikos [with Teko, Ifpack, Belos, Tpetra])
    • + +
    • PETSc matrix solvers (KSP, PC)
    • + +
    • MUMPS 5.4.0 (through Trilinos or PETSc only)
    • + +
    • Superlu_dist 7.2.0 (through Trilinos or PETSc only, Trilinos requires parmetis + build)
    • + +
    • UMFPACK, SuiteSparse 5.10.1 (Optional)
    • + +
    • ARPACK/arpack-ng 3.8.0 (Optional)
    • + +
    • sparse 1.4b (Optional)
    • + +
    • Catch2 (Optional testing)
    • + +
    + +

    Run the tutorial

    + +

    To get started with Goma, use the following:

    + + ' - stargazers_count: 2 - subscribers_count: 1 - topics: [] - updated_at: 1715182572.0 + stargazers_count: 107 + subscribers_count: 26 + topics: + - finite-elements + - finite-element-analysis + - simulation + - parallel + - multiphysics + - fem + - snl-applications + updated_at: 1715913905.0 haampie/sirius-appimage: data_format: 2 description: SIRIUS AppImage (using just the bare minimum) @@ -10738,8 +10721,8 @@ jedwards4b/spackenvironments: data_format: 2 description: my spack environments for software builds filenames: - - esmfserialbld/spack.yaml - esmfbld/spack.yaml + - esmfserialbld/spack.yaml full_name: jedwards4b/spackenvironments latest_release: null stargazers_count: 0 @@ -10786,10 +10769,10 @@ jrood-nrel/spack-configs: data_format: 2 description: Spack configuration files and scripts for use on machines at NREL filenames: - - envs/exawind/spack.yaml - - configs/rhodes/utilities/spack.yaml - - configs/eagle/compilers/spack.yaml - configs/eagle/software/spack.yaml + - configs/eagle/compilers/spack.yaml + - configs/rhodes/utilities/spack.yaml + - envs/exawind/spack.yaml full_name: jrood-nrel/spack-configs latest_release: null readme: '

    Spack configuration @@ -11024,122 +11007,407 @@ key4hep/key4hep-spack: every stack on cvmfs.

    -

    Repository Contents

    +

    Repository Contents

    + +

    Apart from the recipes for key4hep packages in the folder packages, + the + + repository contains a collection of environments used to build the stack in + + environments and some scripts used for publishing on cvmfs and other + utilities + + in scripts. The builds run in Gitlab CI runners and the workflows + can be found + + in the file .gitlab-ci.yml in the gitlab + + repository.

    + +

    Additionally, the file .latest-commit contains the latest commit + of Spack used + + for the recent builds, which is updated from time to time to keep up with the + + develop branch of Spack. In addition, the file .cherry-pick contains + some + + fixes needed to build the stack. These can also be found in the file + + .cherry-pick that is shipped with every stack on cvmfs.

    + +

    Central Installations

    + +

    Installations of the software stack can be found under /cvmfs/sw.hsf.org + (for + + CentOS 7) and /cvmfs/sw-nightlies.hsf.org (for CentOS 7, AlmaLinux + 9 and + + Ubuntu) see:

    + +

    https://key4hep.github.io/key4hep-doc/setup-and-getting-started/README.html

    + +

    Requirements

    + +

    To compile the key4hep stack some system packages are required; without these, + + the spack concretization or compilation can fail. The packages needed are an + + OpenGL implementation that can be installed:

    + +
    yum install -y mesa-libGL mesa-libGL-devel
    +    mesa-libGLU mesa-libGLU-devel      #
    +    Centos 7
    +
    +    apt install -y libgl1-mesa-glx libgl1-mesa-dev libglu1-mesa libglu1-mesa-dev  # Ubuntu
    +
    +    dnf install -y mesa-libGL mesa-libGL-devel mesa-libGLU mesa-libGLU-devel      # AlmaLinux 9
    + +

    The environments that make use of these libraries or headers expect them to + be + + found under /usr, which is the typical location when they are installed + + system-wide (for example in /usr/include or /usr/lib).

    + +

    Alternatively, one can install + + HEP_OSlibs, + which will + + install the previous and more libraries.

    + +

    In addition, for Ubuntu and Alma 9 the compilers are picked up from the system, + + so, for example, building in an image without gcc or glibc + won''t work. These + + commands should install most of the compilers and the development tools:

    + +
    apt install -y build-essential
    +    gfortran                            #
    +    Ubuntu
    +
    +    dnf groupinstall -y "Development
    +    Tools" &&
    +    dnf install -y gfortran # AlmaLinux
    +    9
    + +

    Dockerfiles with the images that are used to build the key4hep stack can be + + found in https://github.com/key4hep/key4hep-images.

    + + ' + stargazers_count: 8 + subscribers_count: 10 + topics: [] + updated_at: 1716282017.0 +kokkos/kokkos-resilience: + data_format: 2 + description: Resilience Extensions for Kokkos + filenames: + - ci/spack.yaml + full_name: kokkos/kokkos-resilience + latest_release: null + readme: '

    Kokkos Resilience

    + +

    Kokkos Resilience is an experimental extension to Kokkos + for providing convenient resilience + + and checkpointing to scientific applications.

    + +

    Building

    + +

    Kokkos Resilience is built using CMake + version 3.17 or later. It has been tested on + + compilers such as GCC 11.2.0 and LLVM/Clang 11.0.0. It should work on any C++14 + supporting compiler, but your mileage + + may vary.

    + +

    Dependencies

    + +

    Kokkos

    + +

    First and foremost, Kokkos Resilience requires an install of Kokkos. + This can be compiled or a version bundled with + + other software (such as Trilinos) or as a package on a machine.

    + +

    Note: Kokkos Resilience currently requires the develop + branch of Kokkos for compile-time view hooking capabilities.

    + +

    Boost

    + +

    Kokkos-resilience uses Boost for a replacement for some C++17 features such + as the filesystem library, std::optional, and std::variant. + + This dependency will likely be removed in the future when Kokkos requires C++17.

    + +

    VeloC

    + +

    Additionally, Kokkos Resilience uses the Veloc + library for efficient asynchronous + + checkpointing. If you desire automatic checkpointing to be available this library + (and additionally MPI) must be installed.

    + +

    We are maintaining a special spack package for VeloC since the main one is + not up-to-date. It can be found + + here + and can be installed via:

    + +
    git clone git@gitlab-ex.sandia.gov:kokkos-resilience/kr-spack.git
    +
    +    spack repo add kr-spack
    +
    +    spack install veloc@barebone
    + +

    It is recommended to install the "barebone" variant/branch of VeloC since it + has reduced dependencies.

    + +

    CMake Invocation

    + +

    It is recommended to use the CMake presets to configure the project. More information + on presets can be found here. Note that CMake 3.19 or higher is required to use presets, + and to inherit from presets bundled with Kokkos Resilience, you + + need at least CMake 3.21.

    + +

    Kokkos Resilience includes a set of presets in CMakePresets.json. + These can be inherited from and represent common aaplication configurations.

    + +

    CMake paths

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    PathDescription
    Kokkos_ROOTPath to the root of the Kokkos install
    VeloC_ROOTPath to the root of VeloC if it is enabled (see below)
    HDF5_ROOTPath to the root of HDF5 if HDF5 is enabled (see below)
    + +

    Supported CMake Options

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -

    Apart from the recipes for key4hep packages in the folder packages, - the +

    - repository contains a collection of environments used to build the stack in + - environments and some scripts used for publishing on cvmfs and other - utilities + - in scripts. The builds run in Gitlab CI runners and the workflows - can be found + - in the file .gitlab-ci.yml in the gitlab + - repository.

    + -

    Additionally, the file .latest-commit contains the latest commit - of Spack used +

    - for the recent builds, which is updated from time to time to keep up with the + - develop branch of Spack. In addition, the file .cherry-pick contains - some + - fixes needed to build the stack. These can also be found in the file + - .cherry-pick that is shipped with every stack on cvmfs.

    + -

    Central Installations

    + -

    Installations of the software stack can be found under /cvmfs/sw.hsf.org - (for +

    - CentOS 7) and /cvmfs/sw-nightlies.hsf.org (for CentOS 7, AlmaLinux - 9 and + - Ubuntu) see:

    + -

    https://key4hep.github.io/key4hep-doc/setup-and-getting-started/README.html

    + -

    Requirements

    + -

    To compile the key4hep stack some system packages are required; without these, +

    - the spack concretization or compilation can fail. The packages needed are an + - OpenGL implementation that can be installed:

    + -
    yum install -y mesa-libGL mesa-libGL-devel
    -    mesa-libGLU mesa-libGLU-devel      #
    -    Centos 7
    +    
    - apt install -y libgl1-mesa-glx libgl1-mesa-dev libglu1-mesa libglu1-mesa-dev # Ubuntu + - dnf install -y mesa-libGL mesa-libGL-devel mesa-libGLU mesa-libGLU-devel # AlmaLinux 9 + -

    The environments that make use of these libraries or headers expect them to - be +

    - found under /usr, which is the typical location when they are installed +
    VariableDefaultDescription
    KR_ENABLE_VELOCONEnables the VeloC backend
    KR_VELOC_BAREBONEOFFEnable VeloC barebone mode
    KR_ENABLE_TRACINGOFFEnable performance tracing of resilience functions
    KR_ENABLE_STDIOOFFUse stdio for manual checkpoint
    KR_ENABLE_HDF5OFFAdd HDF5 support for manual checkpoint
    KR_ENABLE_HDF5_PARALLELOFFUse parallel version of HDF5 for manual checkpoint
    KR_ENABLE_TESTSONEnable tests in the build
    KR_ENABLE_EXAMPLESONEnable examples in the build
    - system-wide (for example in /usr/include or /usr/lib).

    +

    Usage

    -

    Alternatively, one can install +

    Kokkos Resilience is designed to work with CMake projects, so using + CMake is typically much easier. In your own - HEP_OSlibs, - which will + project, call:

    - install the previous and more libraries.

    +
    find_package(resilience)
     
    -    

    In addition, for Ubuntu and Alma 9 the compilers are picked up from the system, + target_link_libraries(target PRIVATE + Kokkos::resilience)

    - so, for example, building in an image without gcc or glibc - won''t work. These +

    Ensure that the build or install directory of Kokkos Resilience is + in CMAKE_PREFIX_PATH, or the variable - commands should install most of the compilers and the development tools:

    + resilience_ROOT points to the build/install directory, or the variable + resilience_DIR points to the location of -
    apt install -y build-essential
    -    gfortran                            #
    -    Ubuntu
    +    the Kokkos Resilience resilienceConfig.cmake file. This
    +    file is located in the root build directory of Kokkos
     
    -    dnf groupinstall -y "Development
    -    Tools" &&
    -    dnf install -y gfortran # AlmaLinux
    -    9
    + Resilience or the path <install directory>/share/resilience/cmake. + See the -

    Dockerfiles with the images that are used to build the key4hep stack can be + CMake + documentation for more details on how packages - found in https://github.com/key4hep/key4hep-images.

    + are found.

    ' - stargazers_count: 8 - subscribers_count: 10 + stargazers_count: 4 + subscribers_count: 14 topics: [] - updated_at: 1716282017.0 + updated_at: 1716240118.0 lanl/CELLAR: data_format: 2 description: The CELL Adaptive mesh Refinement (CELLAR) application provides cell-based adaptive mesh refinement data structures and execution for parallel computing architectures. filenames: - - spack/snow/spack.yaml - spack/ci/spack.yaml + - spack/agaspar/spack.yaml + - spack/snow/spack.yaml full_name: lanl/CELLAR latest_release: null readme: '

    CELLAR - EAP @@ -11818,6 +12086,7 @@ laristra/ristra_spackages: data_format: 2 description: 'A mirror of Ristra''s internal gitlab repository. ' filenames: + - env/x86_64/flecsalemm-deps/spack.yaml - env/broadwell/flecsalemm-deps/spack.yaml full_name: laristra/ristra_spackages latest_release: null @@ -12265,13 +12534,13 @@ lcompilers/lpython: - compiler - high-performance - python - updated_at: 1716644476.0 + updated_at: 1716736756.0 lezzidan/spack: data_format: 2 description: Spack clone filenames: - - share/spack/gitlab/cloud_pipelines/stacks/radiuss-aws-aarch64/spack.yaml - share/spack/gitlab/cloud_pipelines/stacks/aws-isc/spack.yaml + - share/spack/gitlab/cloud_pipelines/stacks/radiuss-aws-aarch64/spack.yaml full_name: lezzidan/spack latest_release: null readme: "\n

    \"project

    \n

    LFortran is a modern open-source (BSD\ + \ licensed) interactive Fortran compiler\nbuilt on top of LLVM. It can execute\ + \ user's code interactively to allow\nexploratory work (much like Python, MATLAB\ + \ or Julia) as well as compile to\nbinaries with the goal to run user's code on\ + \ modern architectures such as\nmulti-core CPUs and GPUs.

    \n

    Website: https://lfortran.org/

    \n\ +

    Try online: https://dev.lfortran.org/

    \n\ +

    Documentation

    \n

    All documentation, installation instructions, motivation,\ + \ design, ... is\navailable at:

    \n

    https://docs.lfortran.org/

    \n

    Which is generated using\ + \ the files in the doc directory.

    \n

    Development

    \n\ +

    We welcome all contributions.\nThe main development repository is at GitHub:

    \n\ +

    https://github.com/lfortran/lfortran

    \n\ +

    Please send Pull Requests (PRs) and open issues there.

    \n

    See the CONTRIBUTING document for more information.

    \n

    Main\ + \ mailinglist:

    \n

    https://groups.io/g/lfortran

    \n

    You can also chat with us on Zulip (\"project).

    \n

    Note: We moved to the above GitHub\ + \ repository from GitLab on July 18, 2022.

    \n

    Donations

    \n

    You\ + \ can support LFortran's development by donating to NumFOCUS or Open\nCollective\ + \ as well as GitHub Sponsors:

    \n\n

    All donations will be used strictly to fund LFortran development, by\ + \ supporting\ntasks such as paying developers to implement features, sprints,\ + \ improved\ndocumentation, fixing bugs, etc.

    \n

    The donations to LFortran\ + \ are managed by the NumFOCUS foundation. NumFOCUS is a\n501(c)3 non-profit foundation,\ + \ so if you are subject to US Tax law, your\ncontributions will be tax-deductible.

    \n\ +

    If you want to discuss another way to fund or help with the development, feel\n\ + free to contact Ond\u0159ej \u010Cert\xEDk (ondrej@certik.us).

    \n

    Star History

    \n

    \"Star

    \n" + stargazers_count: 881 + subscribers_count: 24 + topics: + - fortran + - interactive + - compiler + - library + - repl + - jupyter + - jupyter-notebook + - jupyter-kernels + - fortran-compiler + updated_at: 1716728314.0 mdorier/test-ssg-cori: data_format: 2 description: null @@ -12492,15 +12836,10 @@ mochi-hpc-experiments/platform-configurations: description: This repository provides a set of configuration files and example scripts for running Mochi experiments on various platforms. filenames: - - ANL/Sunspot/spack.yaml - - ORNL/Frontier/spack.yaml + - ORNL/Summit/spack.yaml - ANL/JLSE/spack.yaml - - ANL/Aurora/spack.yaml - ANL/ThetaGPU/spack.yaml - - ORNL/Summit/spack.yaml - - ORNL/Crusher/spack.yaml - ANL/Polaris/spack.yaml - - NERSC/Cori/spack.yaml full_name: mochi-hpc-experiments/platform-configurations latest_release: null readme: '

    Platform configurations @@ -13107,7 +13446,6 @@ mochi-hpc/mochi-margo: data_format: 2 description: Argobots bindings for the Mercury RPC library filenames: - - spack.yaml - tests/spack.yaml full_name: mochi-hpc/mochi-margo latest_release: v0.16.0 @@ -13256,185 +13594,6 @@ mochi-hpc/mochi-raft: subscribers_count: 6 topics: [] updated_at: 1692622489.0 -mochi-hpc/mochi-sdskv: - data_format: 2 - description: simple margo-projected keyval service - filenames: - - spack.yaml - full_name: mochi-hpc/mochi-sdskv - latest_release: v0.1.14 - readme: "

    SDSKV (SDS\ - \ Key/Val)

    \n

    Installation

    \n\ -

    SDSKV can easily be installed using Spack:

    \n

    spack install sdskeyval

    \n\ -

    This will install SDSKV (and any required dependencies).\nAvailable backends\ - \ will be Map (in-memory C++ std::map, useful for testing)\nand BwTree\ - \ (deprecated). To enable the BerkeleyDB and LevelDB backends,\nass +bdb\ - \ and +leveldb respectively. For example:

    \n

    spack install\ - \ sdskeyval+bdb+leveldb

    \n

    Note that if you are using a system boost\ - \ path in spack (in your\npackages.yaml) rather than letting spack build boost,\ - \ then you must\ninstall libboost-system-dev and libboost-filesystem-dev packages\ - \ on\nyour system.

    \n

    Architecture

    \n

    List most mochi services, SDSKV relies\ - \ on a client/provider architecture.\nA provider, identified by its address\ - \ and multiplex id, manages one or more\ndatabases, referenced externally\ - \ by their database id.

    \n

    Starting a daemon

    \n

    SDSKV\ - \ ships with a default daemon program that can setup providers and\ndatabases.\ - \ This daemon can be started as follows:

    \n

    sdskv-server-daemon [OPTIONS]\ - \ <listen_addr> <db name 1>[:map|:bwt|:bdb|:ldb] <db name 2>[:map|:bwt|:bdb|:ldb]\ - \ ...

    \n

    For example:

    \n

    sdskv-server-daemon tcp://localhost:1234\ - \ foo:bdb bar

    \n

    listen_addr is the address at which to listen; database\ - \ names should be provided in the form\nname:type where type\ - \ is map (std::map), bwt (BwTree), bdb (Berkeley DB),\ - \ or ldb (LevelDB).

    \n

    For database that are persistent like BerkeleyDB\ - \ or LevelDB, the name should be a path to the\nfile where the database will be\ - \ put (this file should not exist).

    \n

    The following additional options are\ - \ accepted:

    \n
      \n
    • \n-f provides the name of the file in\ - \ which to write the address of the daemon.
    • \n
    • \n-m provides\ - \ the mode (providers or databases).
    • \n
    \n

    The providers mode indicates\ - \ that, if multiple SDSKV databases are used (as above),\nthese databases should\ - \ be managed by multiple providers, accessible through\ndifferent multiplex ids\ - \ 1, 2, ... N where N is the number of databases\nto manage. The targets mode\ - \ indicates that a single provider should be used to\nmanage all the databases.\ - \ This provider will be accessible at multiplex id 1.

    \n

    Client API

    \n

    The\ - \ client API is available in sdskv-client.h.\nThe codes in the test\ - \ folder illustrate how to use it.

    \n

    Provider API

    \n

    The server-side API\ - \ is available in sdskv-server.h.\nThe code of the daemon (src/sdskv-server-daemon.c)\ - \ can be used as an example.

    \n

    Custom key comparison function

    \n

    It is possible to specify a custom function for comparing/sorting\ - \ keys\nwhen creating a provider. A comparison function must have the following\ - \ prototype:

    \n

    int (*)(const void* key1, size_t keysize1, const void*\ - \ key2, size_t keysize2)

    \n

    Its return value must be < 0 if key1\ - \ < key2, 0 if key1 = key2, > 0 if key1 > key2.\nIt must define a total\ - \ order of the key space.

    \n

    C++ API

    \n

    An object-oriented C++ API is available in sdskv-client.hpp\ - \ and sdskv-server.hpp.\nOn the client side this API provides the\ - \ client, provider_handle, and database\ - \ objects.\nExamples of usage of these objects can be found in the test/sdskv-cxx-test.cc.\n\ - On the server side, this API provides a provider object.

    \n

    Benchmark

    \n

    SDSKV can be compiled with --enable-benchmark\ - \ (or +benchmark in Spack). In this case,\nSDSKV requires the JsonCPP\ - \ and MPI dependencies (when compiling manually, use CXX=mpicxx in\n\ - your configure step, for example), and it will build and install the sdskv-benchmark\ - \ program.

    \n

    This program is an MPI program that reads a JSON file describing\ - \ a series of access patterns.\nRank 0 of this MPI program acts as an SDSKV server.\ - \ Other ranks act as clients, all executing\nthis access pattern.

    \n

    The\ - \ following is an example of a JSON file.

    \n
    {\n\t\"protocol\" : \"tcp\",\n\t\"seed\" : 0,\n\t\"server\" : {\n\t\t\"use-progress-thread\"\
    -     : false,\n\t\t\"rpc-thread-count\"\
    -     : 0,\n\t\t\"database\"\
    -     : {\n\t\t\t\"type\" : \"map\",\n\
    -    \t\t\t\"name\" : \"benchmark-db\",\n\t\t\t\
    -    \"path\" : \"/dev/shm\"\n\t\t}\n\t},\n\t\"benchmarks\" : [\n\t{\n\t\t\"type\" : \"put\",\n\t\t\"repetitions\"\
    -     : 10,\n\t\t\"num-entries\"\
    -     : 30,\n\t\t\"key-sizes\"\
    -     : [ 8, 32 ],\n\
    -    \t\t\"val-sizes\" : [ 24,\
    -    \ 48 ],\n\t\t\"erase-on-teardown\"\
    -     : true\n\t},\n\t{\n\t\t\"type\" : \"get\",\n\t\t\"repetitions\"\
    -     : 10,\n\t\t\"num-entries\"\
    -     : 30,\n\t\t\"key-sizes\"\
    -     : 64,\n\t\t\"val-sizes\"\
    -     : 128,\n\t\t\"erase-on-teardown\"\
    -     : true\n\t}\n\t]\n}
    \n

    The JSON\ - \ file starts with the protocol to use, and a seed for the random-number generator\ - \ (RNG).\nThe actual seed used on each rank will actually be a function of this\ - \ global seed and the rank of\nthe client. The RNG will be reset with this seed\ - \ after each benchmark.

    \n

    The server field sets up the provider\ - \ and the database. Database types can be map, ldb,\ - \ or bdb.\nThen follows the benchmarks entry, which\ - \ is a list of benchmarks to execute. Each benchmark is composed\nof three steps.\ - \ A setup phase, an execution phase, and a teardown\ - \ phase. The setup phase may for\nexample store a bunch of keys in the database\ - \ that the execution phase will read by (in the case of a\nget benchmark,\ - \ for example). The teardown phase will usually remove all the keys that were\ - \ written\nduring the benchmark, if \"erase-on-teardown\" is set to true.

    \n\ -

    Each benchmark entry has a type (which may be put,\ - \ put-multi, get, get-multi, length,\n\ - length-multi, erase, and erase-multi),\ - \ and a number of repetitions. The benchmark will be\nexecuted as many times as\ - \ requested (without resetting the RNG in between repetitions). Taking the\nexample\ - \ of the put benchmark above, each repetition will put 30 key/value\ - \ pairs into the database.\nThe key size will be chosen randomly in a uniform\ - \ manner in the interval [8, 32 [ (32 excluded).\nThe value size\ - \ will be chosen randomly in a uniform manner in [24, 48 [ (48 excluded).\ - \ Note that\nyou may also set a specific size instead of a range.

    \n

    An MPI\ - \ barrier between clients is executed in between each benchmark and in between\ - \ the setup,\nexecution, and teardown phases, so that the execution phase is always\ - \ executed at the same time\non all the clients. Once all the repetitions are\ - \ done for a given benchmark entry, the program\nwill report statistics on the\ - \ timings: average time, variance, standard deviation, mininum, maximum,\nmedian,\ - \ first and third quartiles. Note that these times are for a repetition, not for\ - \ single operations\nwithin a repetition. To get the timing of each individual\ - \ operation, it is then necessary to divide\nthe times by the number of key/value\ - \ pairs involved in the benchmark.

    \n" - stargazers_count: 0 - subscribers_count: 6 - topics: [] - updated_at: 1635867720.0 -mochi-hpc/mochi-yokan: - data_format: 2 - description: Remote Key/Value storage service for Mochi - filenames: - - spack.yaml - full_name: mochi-hpc/mochi-yokan - latest_release: v0.4.2 - readme: '

    Yokan - Mochi''s - Key/Value (and more) storage service

    - -

    - - codecov

    - -

    Please see documentation here.

    - - ' - stargazers_count: 1 - subscribers_count: 1 - topics: [] - updated_at: 1709780289.0 mochi-hpc/py-mochi-bake: data_format: 2 description: Python wrapper for BAKE @@ -13447,251 +13606,6 @@ mochi-hpc/py-mochi-bake: subscribers_count: 5 topics: [] updated_at: 1633975348.0 -mochi-hpc/py-mochi-margo: - data_format: 2 - description: Python wrapper for Margo. Can be used to prototype Margo services in - Python. - filenames: - - spack.yaml - full_name: mochi-hpc/py-mochi-margo - latest_release: v0.5.2 - readme: "

    Py-Margo

    \n

    Py-Margo provides a Python wrapper on top of Margo.\nIt enables\ - \ one to develop Margo-based service in Python.

    \n

    Dependencies

    \n\ -
      \n
    • margo (and its dependencies)
    • \n
    • python
    • \n
    • pybind11
    • \n\ -
    • py-pkgconfig
    • \n
    \n

    Installing

    \n

    The easiest way to install Py-Margo\ - \ is to use spack.\nFollow\ - \ the instructions here\nto add the sds namespace and its packages (instal\ - \ spack first, if needed).\nThen type:

    \n
    spack install py-margo\n\
    -    
    \n

    Once installed, you need the py-margo package (and its dependencies)\ - \ to\nbe loaded to use it.

    \n

    Examples

    \n

    Basic example

    \n

    The following is an example\ - \ of provider programmed in Python.\nLet's put is in a file server.py.\n\ - The provider listens to an address on a given multiple id (here 42).\nWhenever\ - \ it receives an RPC, it prints \"Hello from\" and the name sent\nby the client,\ - \ then sends the \"Hi \"+name+\"!\" string back to the client,\nand finally terminates.

    \n\ -
    import\
    -    \ sys\nfrom pymargo.core import Engine, Provider\n\
    -    \nclass HelloProvider(Provider):\n\n\tdef __init__(self, engine, provider_id):\n\t\tsuper(engine, provider_id)\n\t\tself.register(\"say_hello\", \"hello\")\n\n\tdef hello(self, handle,\
    -    \ name):\n\t\tprint(\"Hello from \"+name)\n\t\tprint(\"RPC id is \"+str(handle.get_id()))\n\t\t\
    -    handle.respond(\"Hi \"+name+\"!\")\n\
    -    \t\tself.get_engine().finalize()\n\ndef WhenFinalize():\n\tprint(\"Finalize was called\")\n\nengine\
    -    \ = Engine('tcp')\nprovider_id = 42\nprint(\"Server running at address \" +\
    -    \ str(engine.addr()) + \"\
    -    \ with provider_id \" + str(provider_id))\n\nengine.on_finalize(WhenFinalize)\n\
    -    provider = HelloProvider(engine, provider_id)\n\nengine.wait_for_finalize()
    \n

    The following code is the corresponding\ - \ client code (client.py).

    \n
    import sys\nimport pymargo\nfrom pymargo.core import Engine\n\
    -    \ndef call_rpc_on(engine, rpc_id, addr_str, provider_id, name):\n\taddr = engine.lookup(addr_str)\n\thandle = engine.create_handle(addr, rpc_id)\n\treturn handle.forward(provider_id,\
    -    \ name)\n\nwith Engine('tcp', mode=pymargo.client) as engine:\n\trpc_id = engine.register(\"say_hello\")\n\tret = call_rpc_on(engine, rpc_id, sys.argv[1],\
    -    \ int(sys.argv[2]), str(sys.argv[3]))\n\tprint(str(ret))
    \n

    First, run the\ - \ server on a new terminal:

    \n
    python server.py\n
    \n\ -

    This will output something like

    \n
    Server running at address ofi+sockets://10.0.2.15:39151\
    -    \ with provider_id=42\n
    \n

    Then run the client on a new terminal:

    \n\ -
    python client.py ofi+sockets://10.0.2.15:39151 42 Matthieu\n
    \n\ -

    Sending/receiving\ - \ Python objects

    \n\ -

    The example above shows the basic principles of Py-Margo.\nPy-Margo's RPC always\ - \ use a string as input and respond with a string.\nYet this is sufficient to\ - \ cover any use-cases you may have: Python\nindeed comes with a serialization\ - \ package, pickle, that can take\ncare of converting almost any Python\ - \ object from/to a string.

    \n

    Let us assume we have a file named mymaths.py\ - \ which contains the\nfollowing definition of a point in 3D.

    \n
    class Point():\n\tdef __init__(self,x,y,z):\n\t\t\
    -    self.x = x\n\t\tself.y = y\n\t\tself.z\
    -    \ = z\n\tdef __str__(self):\n\
    -    \t\treturn 'Point ('+str(self.x)+','+str(self.y)+','+str(self.z)+')'
    \n

    Then here is a server that can compute a cross product\ - \ on two points sent by\na client.

    \n
    from pymargo.core import Engine\nfrom pymargo.core import Provider\nfrom mymaths import Point\n\
    -    import pickle\n\nclass VectorMathProvider(Provider):\n\n\tdef __init__(self, engine, provider_id):\n\t\tsuper().__init__(engine, provider_id)\n\t\tself.register(\"cross_product\", \"cross_product\")\n\n\t\
    -    def cross_product(self, handle, args):\n\t\tpoints = pickle.loads(args)\n\t\tprint(\"Received: \"+str(points))\n\t\tx\
    -    \ = points[0].y*points[1].z - points[0].z*points[1].y\n\t\ty = points[0].z*points[1].x\
    -    \ - points[0].x*points[1].z\n\t\tz =\
    -    \ points[0].x*points[1].y - points[0].y*points[1].x\n\
    -    \t\tres = Point(x,y,z)\n\t\thandle.respond(pickle.dumps(res))\n\t\tself.get_engine().finalize()\n\
    -    \nengine = Engine('tcp')\nprovider_id = 42\n\
    -    print(\"Server running at address\
    -    \ \"+str(mid.addr())+\"with provider_id=\"+str(provider_id))\n\
    -    \nprovider = VectorMathProvider(engine, provider_id)\n\nengine.wait_for_finalize()
    \n

    And here is a client.

    \n\ -
    import\
    -    \ sys\nimport pymargo\nimport pickle\nfrom mymaths\
    -    \ import Point\nfrom pymargo.core import Engine\n\
    -    \ndef call_rpc_on(engine, rpc_id, addr_str, provider_id, p1, p2):\n\taddr = engine.lookup(addr_str)\n\thandle = engine.create_handle(addr, rpc_id, provider_id)\n\targs = pickle.dumps([p1,p2])\n\tres = handle.forward(args)\n\treturn pickle.loads(res)\n\nwith\
    -    \ Engine('tcp', mode=pymargo.client) as\
    -    \ engine:\n\trpc_id\
    -    \ = mid.register(\"cross_product\")\n\tp1 = Point(1,2,3)\n\tp2 = Point(4,5,6)\n\tret = call_rpc_on(mid, rpc_id, sys.argv[1],\
    -    \ int(sys.argv[2]), p1,\
    -    \ p2)\n\tprint(str(ret))
    \n" - stargazers_count: 2 - subscribers_count: 5 - topics: [] - updated_at: 1675190754.0 mochi-hpc/py-mochi-s4m: data_format: 2 description: Python library using Mochi to broadcast data @@ -13777,7 +13691,6 @@ mpbelhorn/olcf-spack: description: Spack fork used on OLCF resources filenames: - share/spack/gitlab/cloud_pipelines/stacks/e4s/spack.yaml - - share/spack/gitlab/cloud_pipelines/stacks/radiuss/spack.yaml full_name: mpbelhorn/olcf-spack latest_release: null readme: " + +

    Testing batch capabilities of OpenShift

    + +

    Simple NFS Storage

    + +

    Just create a simple NFS server for shared storage this uses the upstream: + https://github.com/kubernetes-sigs/nfs-ganesha-server-and-external-provisioner/tree/nfs-server-provisioner-1.8.0

    + +
    $ oc apply -k simple-nfs/
    +
    +    
    + +

    Todo

    + +
      + +
    • AWS FSx Lustre support in demo
    • + +
    • Move users to external ldap maybe with https://github.com/glauth/glauth + +
    • + +
    • Implement UID/GID enforcement per namespace
    • + +
    • More advanced view of how jobs are scheduled and placed on the cluster
    • + +
    • Add and schedule workloads to specialized hardware like GPU or IB
    • + +
    + + ' + stargazers_count: 5 + subscribers_count: 3 + topics: [] + updated_at: 1699820410.0 noaa-oar-arl/nexus-spack-buildcache: data_format: 2 description: null @@ -14203,10 +14167,9 @@ olcf/spack-environments: data_format: 2 description: Spack Environments Templates for OLCF resources filenames: - - linux-rhel8-zen3/baseline/spack.yaml - linux-sles15-zen2/spock/spack.yaml - - linux-rhel8-ppc64le/summit/spack.yaml - linux-centos7-broadwell/or-slurm/spack.yaml + - linux-rhel8-ppc64le/summit/spack.yaml full_name: olcf/spack-environments latest_release: null readme: '

    OLCF Spack Environments Templates

    @@ -14247,8 +14210,8 @@ openPMD/openPMD-api: description: ':floppy_disk: C++ & Python API for Scientific I/O' filenames: - .github/ci/spack-envs/clang14_py311_nompi_h5_ad2/spack.yaml - - .github/ci/spack-envs/clangtidy_nopy_ompi_h5_ad2/spack.yaml - spack.yaml + - .github/ci/spack-envs/clangtidy_nopy_ompi_h5_ad2/spack.yaml full_name: openPMD/openPMD-api latest_release: 0.15.2 readme: "

    C++ &\ @@ -14810,12 +14773,14 @@ pnnl/ExaGO: description: High-performance power grid optimization for stochastic, security-constrained, and multi-period ACOPF problems. filenames: - - buildsystem/container/spack.yaml - - buildsystem/spack/summit/spack.yaml - - buildsystem/spack/newell/spack.yaml - - buildsystem/spack/deception/spack.yaml + - buildsystem/spack/ascent/spack.yaml - performance_analysis/spack.yaml + - buildsystem/spack/deception/spack.yaml + - buildsystem/spack/incline/spack.yaml + - buildsystem/spack/newell/spack.yaml - buildsystem/spack/crusher/spack.yaml + - buildsystem/spack/summit/spack.yaml + - buildsystem/container/spack.yaml full_name: pnnl/ExaGO latest_release: v1.6.0 readme: "

    \nExascale\ @@ -15699,17 +15664,6 @@ sandialabs/optimism: - snl-science-libs - scr-2709 updated_at: 1715712190.0 -simonpintarelli/acclapack-tests: - data_format: 2 - description: null - filenames: - - spack-envs/rocm/spack.yaml - full_name: simonpintarelli/acclapack-tests - latest_release: null - stargazers_count: 0 - subscribers_count: 1 - topics: [] - updated_at: 1667393188.0 simonpintarelli/nlcglib: data_format: 2 description: Nonlinear CG methods for wave-function optimization in DFT @@ -15910,35 +15864,33 @@ spack/spack-configs: data_format: 2 description: Share Spack configuration files with other HPC sites filenames: - - NERSC/cori/e4s-21.02/prod/spack.yaml - - OLCF/frontier/spack.yaml - - NREL/configs/eagle/compilers/spack.yaml - - BOISESTATE/borah/environments/b4s/_spack.yaml - - ANL/JLSE/Arcticus/E4S-21.05/spack.yaml - - NERSC/perlmutter/e4s-23.05/gcc/spack.yaml - - ANL/JLSE/Arcticus/E4S-21.11/spack.yaml - - NERSC/perlmutter/spack-v0.22/prod/gcc/spack.yaml - - NERSC/perlmutter/e4s-22.05/nvhpc/spack.yaml - - NERSC/perlmutter/e4s-22.05/prod/cce/spack.yaml - - NERSC/perlmutter/e4s-22.11/cuda/spack.yaml + - ANL/JLSE/Arcticus/E4S-22.05/spack.yaml + - NERSC/perlmutter/e4s-23.08/gcc/spack.yaml - UOREGON/E4S-21.05-Facility-Examples/Frank-Jupiter/spack.yaml + - NERSC/perlmutter/e4s-23.05/nvhpc/spack.yaml + - NERSC/perlmutter/e4s-23.05/cce/spack.yaml + - NERSC/perlmutter/e4s-23.05/cuda/spack.yaml + - NERSC/perlmutter/e4s-22.11/gcc/spack.yaml + - ANL/JLSE/Arcticus/E4S-22.08/spack.yaml + - NERSC/perlmutter/e4s-22.05/nvhpc/spack.yaml - NERSC/perlmutter/spack-v0.22/cuda/spack.yaml - - BOISESTATE/borah/applications/gromacs/_spack.yaml + - OLCF/frontier/spack.yaml - NREL/configs/eagle/software/spack.yaml - - NERSC/perlmutter/e4s-23.05/cce/spack.yaml - - NREL/configs/eagle/utilities/spack.yaml - - NERSC/perlmutter/e4s-22.05/prod/gcc/spack.yaml - NREL/configs/rhodes/utilities/spack.yaml - - NERSC/perlmutter/e4s-23.05/prod/nvhpc/spack.yaml - - ANL/JLSE/Arcticus/E4S-22.05/spack.yaml - - ANL/JLSE/Arcticus/E4S-22.08/spack.yaml - - NERSC/perlmutter/e4s-23.05/cuda/spack.yaml - - NERSC/perlmutter/e4s-23.05/nvhpc/spack.yaml - - NERSC/perlmutter/e4s-23.08/gcc/spack.yaml + - NERSC/perlmutter/e4s-22.05/prod/gcc/spack.yaml + - OLCF/summit/spack.yaml + - NREL/configs/eagle/utilities/spack.yaml - NREL/configs/rhodes/compilers/spack.yaml + - NERSC/perlmutter/e4s-23.05/gcc/spack.yaml + - ANL/JLSE/Arcticus/E4S-21.11/spack.yaml - NERSC/perlmutter/e4s-23.08/prod/gcc/spack.yaml - - NERSC/perlmutter/e4s-22.11/gcc/spack.yaml - - OLCF/summit/spack.yaml + - ANL/JLSE/Arcticus/E4S-21.05/spack.yaml + - BOISESTATE/borah/environments/b4s/_spack.yaml + - NERSC/perlmutter/spack-v0.22/prod/gcc/spack.yaml + - NERSC/perlmutter/e4s-22.05/prod/cce/spack.yaml + - NERSC/perlmutter/e4s-23.05/prod/nvhpc/spack.yaml + - NREL/configs/eagle/compilers/spack.yaml + - NERSC/perlmutter/e4s-22.11/cuda/spack.yaml full_name: spack/spack-configs latest_release: null readme: '

    Spack Configs

    \"SST\"

    \n

    Structural Simulation Toolkit (SST) Spack Packages

    \n

    Copyright (c) 2009-2023, National Technology and\ + \ Engineering Solutions of Sandia, LLC (NTESS)

    \n\ +

    Basic Usage

    \n

    Make sure you have downloaded Spack and added it to your path.\nThe easiest way to do this is often (depending\ + \ on your SHELL):

    \n
    > source spack/share/spack/setup-env.sh\n\
    +    
    \n

    To get the most up-to-date version of the SST Spack packages,\ + \ after downloading the sst-spack GitHub repository, you simply need to run

    \n\ +
    > spack repo add sst-spack/sst\n
    \n

    To validate that\ + \ Spack now sees the repo with the SST packages, run:

    \n
    > spack\
    +    \ repo list\n
    \n

    This should now list your newly downloaded Spack\ + \ repo.\nYou can display information about how to install the individual packages\ + \ with, e.g.:

    \n
    > spack info sst-core\n
    \n

    This\ + \ will print all the information about variants and dependencies of the package.\n\ + For detailed instructions on how to use Spack, see the Owner's Manual.

    \n

    A basic installation of a package\ + \ is done as:

    \n
    > spack install sst-core +pdes-mpi\n
    \n\ +

    which tells Spack to install the core with PDES support using MPI.\nFor downstream\ + \ packages like sst-elements, sst-core and all dependencies will be automatically\ + \ installed.\nWe can visualize this with either spack spec or spack\ + \ graph, e.g.

    \n
    > spack spec sst-elements +pin +hybridsim\n\
    +    Input spec\n--------------------------------\nsst-elements+hybridsim+pin\n\nConcretized\n\
    +    --------------------------------\nsst-elements@master%gcc@7.4.0~dramsim2~goblin~hbm+hybridsim~nvdimmsim+pin~ramulator\
    +    \ arch=linux-centos7-haswell\n    ^autoconf@2.69%gcc@7.4.0 arch=linux-centos7-haswell\n\
    +    \    ^automake@1.16.1%gcc@7.4.0 arch=linux-centos7-haswell\n    ^dramsim2@2.2%gcc@7.4.0\
    +    \ arch=linux-centos7-haswell\n    ^hybridsim@2.0%gcc@7.4.0 patches=e266e00e3777feb1d9b3691f6a5a88d1d99c5aa0e0811fcf5461d55e0ac4a7bd\
    +    \ arch=linux-centos7-haswell\n        ^nvdimmsim@2.0%gcc@7.4.0 arch=linux-centos7-haswell\n\
    +    \    ^intel-pin@2.14%gcc@7.4.0 arch=linux-centos7-haswell\n    ^libtool@2.4.6%gcc@7.4.0\
    +    \ arch=linux-centos7-haswell\n    ^python@2.7%gcc@7.4.0+bz2+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix~tkinter~ucs4~uuid+zlib\
    +    \ arch=linux-centos7-haswell\n    ^sst-core@master%gcc@7.4.0~hdf5+pdes-mpi~zlib~zoltan\
    +    \ arch=linux-centos7-haswell\n        ^openmpi@3.1.5%gcc@7.4.0~cuda+cxx_exceptions\
    +    \ fabrics=none ~java~legacylaunchers~memchecker~pmi schedulers=none ~sqlite3~thread_multiple+vt\
    +    \ arch=linux-centos7-haswell\n
    \n

    This shows what will be installed\ + \ along with the specification of all the dependencies.\nIf any of the dependencies\ + \ are missing, Spack will download and install them.\nNote here that the default\ + \ compiler for this Spack is GCC 7.4.\nIf we wish to use a different compiler,\ + \ we can specify it as, e.g:

    \n
    > spack install sst-elements +pin\
    +    \ +hybridsim %clang@9.1.0\n
    \n

    To make sure your desired compiler\ + \ is known to Spack, you can check:

    \n
    > spack compiler list\n\
    +    ==> Available compilers\n-- clang centos7-x86_64 -----------------------------------------\n\
    +    clang@7.0.0\n\n-- gcc centos7-x86_64 -------------------------------------------\n\
    +    gcc@7.4.0  gcc@4.8.5\n
    \n

    All compilers in the path are usually\ + \ located by running spack compiler find and automatically added.

    \n\ +

    Testing and Developing\ + \ with Spack

    \n\ +

    Spack has historically been much more suited to deployment of mature\ + \ packages than active testing or developing.\nHowever, recent features have improved\ + \ support for development.\nFuture releases are likely to make this even easier\ + \ and incorporate Git integration.

    \n

    Testing

    \n

    A common pattern in testing\ + \ is validating a successful build of feature branches.\nSpack provides the dev-build\ + \ feature for building and installing from a custom source folder.\nFor example:

    \n\ +
    > git clone git@github.com:sstsimulator/sst-core.git -b devel src\n\
    +    > spack dev-build -d src sst-core@devel +pdes-mpi\n
    \n

    is equivalent\ + \ to just running

    \n
    > spack install sst-core@devel +pdes-mpi\n\
    +    
    \n

    For validating a complete build of the \"core\" packages (sst-core,\ + \ sst-elements, sst-macro) with any combination of branches, one can simply run:

    \n\ +
    > git clone git@github.com:sstsimulator/sst-core.git -b feature-core\
    +    \ sst-core-src\n> git clone git@github.com:sstsimulator/sst-macro.git -b devel\
    +    \ sst-macro-src\n> git clone git@github.com:sstsimulator/sst-elements.git -b\
    +    \ feature-elems sst-elements-src\n> spack dev-build -d sst-core-src sst-core@devel\
    +    \ core-variants... %compiler\n> spack dev-build -d sst-macro-src sst-macro@devel\
    +    \ macro-variants... ^sst-core@devel core-variants... %compiler\n> spack dev-build\
    +    \ -d sst-elements-src sst-elements@devel elem-variants... ^sst-core@devel core-variants...\
    +    \ %compiler\n
    \n

    Here %compiler is a spec like gcc@7.4.0.\n\ + core-variants... is the desired sst-core spec like +pdes-mpi\ + \ +zoltan.\nNote the the ^ syntax used here to ensure that\ + \ sst-elements and sst-macro depend on a precise variant of sst-core.\nFor example:

    \n\ +
    > spack dev-build -d sst-macro-src sst-macro@devel +otf2 +core ^sst-core+pdes-mpi+zoltan\n\
    +    
    \n

    Because we are doing feature branch testing, we use @devel\ + \ to build the branches as-if they were the devel branch.

    \n

    Developing

    \n

    The above commands will do a full build and install of\ + \ the packages.\nIf doing development, you may wish to merely set up a build environment.\n\ + This allows you to modify the source and re-build.\nIn this case, you can stop\ + \ after configuring:

    \n
    > spack dev-build -d sst-core-src -u configure\
    +    \ sst-core@devel +otf2 +core ^sst-core+pdes-mpi+zoltan\n
    \n

    This\ + \ sets up a development environment for you in sst-core-src, which\ + \ you can use (Bash example shown):

    \n
    > cd sst-core-src\n>\
    +    \ source spack-build-env.txt\n> cd spack-build\n> make\n
    \n\ +

    Before sourcing the Spack development environment, you may wish to save your\ + \ current environment:

    \n
    > declare -px > myenv.sh\n
    \n\ +

    When done with Spack, you can then restore your original environment:

    \n\ +
    source myenv.sh\n
    \n
    Configuring Default Spack Packages

    \n

    Spack assumes nothing is available\ + \ on your system, including even basic utilities like Perl and M4.\nThis leads\ + \ to Spack \"bootstrapping\" for each new install (and each compiler!) many, many\ + \ packages.\nIt is recommended to set up a packages.yaml file in\ + \ a $HOME/.spack folder that identifies your default local packages.\n\ + Below is an example file with the most important packages for efficient SST development:

    \n\ +
    packages:\n zlib:\n  paths:\n    zlib: /usr\n  buildable: False\n libtool:\n\
    +    \  paths:\n   libtool@2.4.6: /opt/local\n  buildable: False\n cmake:\n  paths:\n\
    +    \   cmake@3.15: /opt/local\n  buildable: False\n pkg-config:\n  paths:\n   pkg-config:\
    +    \ /opt/local\n m4:\n  paths:\n    m4: /usr\n  buildable: False\n numactl:\n  paths:\n\
    +    \   numactl@2.0.12: /opt/local\n   buildable: False\n hwloc:\n  paths:\n   hwloc@2.0.2:\
    +    \ /usr\n   hwloc@1.11: /opt/local\n   buildable: False\n python:\n  paths:\n \
    +    \  python@2.7: /usr\n   python@3.6: /opt/local\n  variants: +shared\n  buildable:\
    +    \ False\n
    \n

    The paths would need to be updated for your system.\n\ + If you never want Spack to re-build a library (which is often the case\ + \ for C libraries like hwloc),\nyou need the buildable: False entry.\n\ + In most cases a single version suffices, but you may need multiple versions to\ + \ resolve conflicts (as was the caes here for Python and hwloc).\nIn other cases,\ + \ you may need to identify the Spack variants supported by your local installation.\n\ + In this case, we had to inform Spack that our Python has shared libraries.\nWith\ + \ the packages.yaml, our Spack dependency graph for spack graph\ + \ sst-core +pdes-mpi is:

    \n
    o  sst-core\n|\\\n| o  openmpi\n\
    +    | |\\\n| | |\\\n| o | |  zlib\n|  / /\no | |  python\n / /\n o |  numactl\n  /\n\
    +    \  o  hwloc\n
    \n

    In this case, the only dependency Spack will build\ + \ is openmpi (recommended due to the compiler dependence).\nWithout\ + \ the packages.yaml, a huge dependency graph would be built:

    \n\ +
    o  sst-core\n|\\\no |  python\n|\\ \\\n| |\\ \\\n| | |\\ \\\n| | |\
    +    \ |\\ \\\n| | | | |\\ \\\n| | | | | |\\ \\\n| | | | | | |\\ \\\n| | | | | | |\
    +    \ |\\ \\\n| | | | | | | | |\\ \\\n| | | | | | | | | |\\ \\\n| | | | | | | | |\
    +    \ | |\\ \\\n| | o | | | | | | | | | |  sqlite\n| |/| | | | | | | | | | |\n|/|\
    +    \ | | | | | | | | | | |\n| | |/ / / / / / / / / /\n| | | | o | | | | | | |  openssl\n\
    +    | |_|_|/| | | | | | | |\n|/| | | | | | | | | | |\n| | | | | | | | | | | o  openmpi\n\
    +    | |_|_|_|_|_|_|_|_|_|/|\n|/| | | | | | | | | | |\n| | | | | | | | | | | |\\\n\
    +    | | | | | | | | | | | | o  hwloc\n| | | | |_|_|_|_|_|_|_|/|\n| | | |/| | | | |\
    +    \ | | |/|\n| | | | | | | | | | | | |\\\n| | | | | | | o | | | | | |  gettext\n\
    +    | | |_|_|_|_|/| | | | | | |\n| |/| | | | |/| | | | | | |\n| | | | | |/| | | |\
    +    \ | | | |\n| | | | | | | |\\ \\ \\ \\ \\ \\ \\\n| | | | | | | | |\\ \\ \\ \\ \\\
    +    \ \\ \\\n| | | | | | | | | |_|_|_|_|/ /\n| | | | | | | | |/| | | | | |\n| | |\
    +    \ | | | | | | | |/ / / /\n| | | | | | | | | |/| | | |\n| | | | | | | | o | | |\
    +    \ | |  libxml2\n| |_|_|_|_|_|_|/| | | | | |\n|/| |_|_|_|_|_|/| | | | | |\n| |/|\
    +    \ | |_|_|_|/| | | | | |\n| | | |/| | | | | | | | | |\no | | | | | | | | | | |\
    +    \ | |  zlib\n / / / / / / / / / / / / /\n o | | | | | | | | | | | |  xz\n  / /\
    +    \ / / / / / / / / / /\n  | | | | | | | | | | | o  libpciaccess\n  | | |_|_|_|_|_|_|_|_|/|\n\
    +    \  | |/| | | | | | | | | |\n  | | | | | | | | | | | |\\\n  | | | | | | | | | |\
    +    \ | o |  util-macros\n  | | | | | | | | | | |  /\n  | | | | | o | | | | | |  tar\n\
    +    \  | | | | | |/ / / / / /\n  | | | | | | | | | o |  numactl\n  | | | | | | | |\
    +    \ | |\\|\n  | | | | | | | | | |\\ \\\n  | | | | | | | | | | |\\ \\\n  | | | |\
    +    \ | | | | | | o | |  automake\n  | | | |_|_|_|_|_|_|/| | |\n  | | |/| | | | |\
    +    \ | | | | |\n  | | | | | | | | | | |/ /\n  | | | | | | | | | | o |  autoconf\n\
    +    \  | | | |_|_|_|_|_|_|/| |\n  | | |/| | | | | | |/ /\n  | | o | | | | | | | |\
    +    \  perl\n  | | | |_|_|_|/ / / /\n  | | |/| | | | | | |\n  | | o | | | | | | |\
    +    \  gdbm\n  | |/ / / / / / / /\n  |/| | | | | | | |\n  o | | | | | | | |  readline\n\
    +    \  | |/ / / / / / /\n  |/| | | | | | |\n  o | | | | | | |  ncurses\n  |/ / / /\
    +    \ / / /\n  o | | | | | |  pkgconf\n   / / / / / /\n   | | | | | o  libtool\n \
    +    \  | | | | |/\n   | | | | o  m4\n   | | | | o  libsigsegv\n   | | | |\n   | |\
    +    \ o |  bzip2\n   | | o |  diffutils\n   | |/ /\n   | o |  libiconv\n   |  /\n\
    +    \   o |  libffi\n    /\n    o  expat\n    o  libbsd\n
    \n" + stargazers_count: 0 + subscribers_count: 14 + topics: [] + updated_at: 1701377450.0 sxs-collaboration/spectre: data_format: 2 description: SpECTRE is a code for multi-scale, multi-physics problems in astrophysics @@ -16314,8 +16441,8 @@ tachidok/scicellxx: description: SciCell++ is an object-oriented framework for the simulation of biological and physical phenomena modelled as continuous or discrete processes. filenames: - - docs/source/initial_steps/installation/spack.yaml - tools/development/docker_and_spack/01_build_docker_DEVEL_spack_INSTALLED/spack.yaml + - docs/source/initial_steps/installation/spack.yaml full_name: tachidok/scicellxx latest_release: null readme: "

    SciCell++

    Spack @ UC Davis