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5,001 changes: 2,501 additions & 2,500 deletions _data/packages-embeddings.csv

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Original file line number Diff line number Diff line change
@@ -0,0 +1,27 @@
# Copyright 2023 Lawrence Livermore National Security, LLC and other
# Benchpark Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: Apache-2.0

spack:
packages:
default-compiler:
#spack_spec: intel@2020b
spack_spec: gcc
compiler-gcc:
#spack_spec: gcc@12.2.0
spack_spec: gcc
compiler-intel:
#spack_spec: intel@2020b
spack_spec: intel
default-mpi:
#spack_spec: intel@2020b
spack_spec: openmpi@4.1.4
mpi-gcc:
spack_spec: openmpi@4.1.4
blas:
#spack_spec: openblas@0.3.5
spack_spec: blas
lapack:
#spack_spec: scalapack@2.0.2-openblas
spack_spec: lapack
20 changes: 9 additions & 11 deletions _stacks/NCAR/spack-derecho/spack.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -111,18 +111,8 @@ spack:
externals:
- spec: gcc@13.2.0 languages='c,c++,fortran'
prefix: /glade/u/apps/common/23.08/spack/opt/spack/gcc/13.2.0
extra_attributes:
compilers:
c: /glade/u/apps/common/23.08/spack/opt/spack/gcc/13.2.0/bin/gcc
cxx: /glade/u/apps/common/23.08/spack/opt/spack/gcc/13.2.0/bin/g++
fortran: /glade/u/apps/common/23.08/spack/opt/spack/gcc/13.2.0/bin/gfortran
- spec: gcc@7.5.0 languages='c,c++,fortran'
prefix: /usr
extra_attributes:
compilers:
c: /usr/bin/gcc-7
cxx: /usr/bin/g++-7
fortran: /usr/bin/gfortran-7
buildable: false
variants:
- +piclibs
Expand Down Expand Up @@ -991,6 +981,7 @@ spack:
baseenv:
root: /glade/u/apps/derecho/23.09/opt/view
select:
- ripgrep
- ncftp
- vim
- parallel
Expand Down Expand Up @@ -1054,7 +1045,10 @@ spack:
operating_system: sles15
target: x86_64
modules: []
environment: {}
environment:
set:
# Needed to use cargo for some reason (probably old openssl before certs=system)
CARGO_HTTP_CAINFO: /etc/ssl/ca-bundle.pem
extra_rpaths: []
- compiler:
spec: nvhpc@23.7
Expand Down Expand Up @@ -1298,6 +1292,7 @@ spack:
esmf:
autoload: none
exclude:
- ripgrep
- py-pandas@2.1.4
- py-tabulate
- qhull@2020.2
Expand Down Expand Up @@ -1540,6 +1535,8 @@ spack:
autoload: none
nccmp:
autoload: none
neovim:
template: ncar_neovim.lua
netcdf:
autoload: all
netcdf+mpi:
Expand Down Expand Up @@ -2102,3 +2099,4 @@ spack:
- esmf@8.6.1%oneapi@2024.0.2+mpi+pnetcdf ^cray-mpich@8.1.27%oneapi@2024.0.2
- esmf@8.6.1%cce@16.0.1+mpi+pnetcdf ^cray-mpich@8.1.27%cce@16.0.1
- neovim
- ripgrep
Original file line number Diff line number Diff line change
Expand Up @@ -9,45 +9,32 @@ spack:
definitions:
- packages-with-python:
# - amber@20 +openmp ^hdf@4.2.15 +external-xdr
- gromacs@2023 +double +lapack +plumed build_type=Release ^plumed@2.9.0
- gromacs@2022.5 +double +lapack +plumed build_type=Release ^plumed@2.8.2
- cp2k@2023.1 +plumed ^plumed@2.9.0
- lammps@20230615 +adios +asphere +atc +awpmd +bocs +body +brownian +cg-sdk +class2
+colloid +colvars +compress +coreshell +dielectric +diffraction +dipole +dpd-basic
+dpd-meso +dpd-react +dpd-smooth +drude +eff +extra-compute +extra-dump +extra-fix
+extra-molecule +extra-pair +fep +ffmpeg +granular +h5md +interlayer +jpeg +kim
+kokkos +kspace +latboltz +latte +machdyn +manifold +manybody +mc +meam +mesont
+mgpt +misc +ml-iap +ml-snap +mofff +molecule +molfile +mpiio +netcdf +openmp-package
+opt +orient +peri +phonon +plugin +plumed +png +poems +ptm +python +qeq +qtb
+reaction +reaxff +replica +rigid +shock +smtbq +sph +spin +srd +tally +uef
+voronoi +yaff build_type=Release ^kokkos@3.7.02+hwloc+memkind+numactl+openmp+tuning
build_type=Release ^plumed@2.9.0 ^adios2@2.9.0

# - lammps@20210929.3 +adios +asphere +atc +awpmd +bocs +body +brownian +cg-sdk
# +class2 +colloid +colvars +compress +coreshell +dielectric +diffraction +dipole
# +dpd-basic +dpd-meso +dpd-react +dpd-smooth +drude +eff +extra-compute +extra-dump
# +extra-fix +extra-molecule +extra-pair +fep +ffmpeg +granular +h5md +interlayer
# +jpeg +kim +kokkos +kspace +latboltz +latte +machdyn +manifold +manybody +mc
# +meam +mesont +mgpt +misc +ml-iap +ml-snap +mofff +molecule +molfile +mpiio
# +netcdf +openmp-package +opt +orient +peri +phonon +plugin +plumed +png +poems
# +ptm +python +qeq +qtb +reaction +reaxff +replica +rigid +shock +smtbq +sph
# +spin +srd +tally +uef +voronoi +yaff build_type=Release ^kokkos@3.4.01+hwloc+memkind+numactl+openmp+tuning+rocm
# cxxstd=14 build_type=Release ^plumed@2.7.2 ^adios2@2.8.3
- gromacs@=2023 +double +lapack +plumed build_type=Release ^plumed@2.9.0
- gromacs@2022.5 +double +lapack +plumed build_type=Release ^plumed@2.8.2
- gromacs@=2023 ~double +lapack +plumed build_type=Release ^plumed@2.9.0
- gromacs@2022.5 ~double +lapack +plumed build_type=Release ^plumed@2.8.2
- cp2k@2023.2 +plumed ^plumed@2.9.0

- namd@2.14 interface=python fftw=3 +plumed ^charmpp@7.0.0 backend=ofi
- namd@2.15a2 interface=python fftw=3 ^charmpp@7.0.0 backend=ofi
- namd@2.15a2 +rocm amdgpu_target=gfx90a ^charmpp@7.0.0 backend=mpi ^ncurses@6.3+symlinks
- amdgromacs@2023 amdgpu_target=gfx90a +rocm
- namd@2.14 ~rocm interface=python fftw=3 +plumed ^charmpp@7.0.0 backend=ofi
- namd@2.15a2 ~rocm interface=python fftw=3 ^charmpp@7.0.0 backend=ofi
# - namd@2.15a2 +rocm amdgpu_target=gfx90a ^charmpp@7.0.0 backend=ofi ^ncurses@6.3+symlinks #broken - providing only through containers
# Failing: - openfoam-org@8 #Alexis still working on it
# Current alternative:
- openfoam@2206
- ncl@6.6.2 ^esmf ~mpi
- lammps:
# +latte and +cg-sdk is removed from the cpu build as well so we can use the same recipe for cpu and gpu lammps builds
# lammps: LAMMPS is incompatible with Kokkos 4.x until @20230802 so reverting to kokkos@3.7.02
- lammps@=20230802 ~rocm ^kokkos@3.7.02+hwloc+memkind+numactl+openmp+tuning~rocm build_type=Release
- lammps@=20230802.3 ~rocm ^kokkos@3.7.02+hwloc+memkind+numactl+openmp+tuning~rocm build_type=Release

- packages-with-oldpython:
- nwchem@7.2.0 +fftw3 +openmp ^python@3.9.15
- nwchem@7.2.0 +fftw3 +openmp ^python@3.9.15 ^netlib-scalapack@2.2.0

- packages:
- cpmd@4.3 +mpi +omp
- ansys-fluids@2022R1
- ansys-fluids@2023R1

#lapack and blas path not set, error in cmake file "SET(NATIVE_BLAS_LAPACK_SEARCH_PATHS /usr/lib /usr/lib64 /usr/local/lib /usr/local/lib64 )
# look into this file nektar/cmake/FindNativeBlasLapack.cmake
Expand All @@ -57,7 +44,7 @@ spack:

# weather utilities
- weather_utils:
# - cdo@2.1.0 #eccodes compilation issue on Joey
- cdo@2.2.2
- nco@5.1.6 ^pocl@4.0
- ncview@2.1.9

Expand All @@ -68,7 +55,7 @@ spack:
specs:
- matrix:
- [$packages-with-python]
- [^python@3.10.10 +optimizations+zlib~ssl]
- [^python@3.11.6 +optimizations+zlib~ssl]
- ['%gcc@12.2.0']
- [target=zen3]
- matrix:
Expand All @@ -86,5 +73,11 @@ spack:
- matrix:
- [$weather_utils]
- ['%gcc@12.2.0']
- [target=zen3]
- [target=zen3]
- matrix:
- [$lammps]
- [+adios +asphere +atc +awpmd +bocs +body +brownian +class2 +colloid +colvars +compress +coreshell +dielectric +diffraction +dipole +dpd-basic +dpd-meso +dpd-react +dpd-smooth +drude +eff +extra-compute +extra-dump +extra-fix +extra-molecule +extra-pair +fep +ffmpeg +granular +h5md +interlayer +jpeg +kim +kokkos +kspace +latboltz +machdyn +manifold +manybody +mc +meam +mesont +mgpt +misc +ml-iap +ml-snap +mofff +molecule +molfile +mpiio +netcdf +openmp-package +opt +orient +peri +phonon +plugin +plumed +png +poems +ptm +python +qeq +qtb +reaction +reaxff +replica +rigid +shock +smtbq +sph +spin +srd +tally +uef +voronoi +yaff build_type=Release ]
- [^plumed@2.9.0 ^adios2@2.9.2]
- ['%gcc@12.2.0']
- [target=zen3]
view: false
Original file line number Diff line number Diff line change
@@ -0,0 +1,97 @@
spack:
# They are currently buildable,
# because cray-libsci and cray-fftw are not in use (see packages.yaml)
packages:
'fftw-api:':
buildable: true
definitions:
- parallel:

# boost: might need several boosts with different stadards
# spack/0.19.0 offers only up to boost@1.80.0
- boost@1.83.0 +mpi +numpy +python cxxstd=14
- boost@1.83.0 +mpi +numpy +python cxxstd=98
- hpx@1.9.1 +async_mpi malloc=jemalloc max_cpu_count=128 networking=mpi
build_type=Release ^boost ^netlib-lapack@3.11.0

# rather silly kokkos has std=98,11, etc setting cxxstd. BUT all other packages
# use the flag cxxstd ... Update in recipes might fix this but for the moment, we fix
# this in our repo
# cxxstd=14 is not a variant in kokkos@3.7.02
- kokkos@4.1.00 +hwloc +memkind +numactl +openmp +tuning build_type=Release

# - kokkos@3.4.01 +hwloc +memkind +numactl +openmp +rocm +tuning cxxstd=14 build_type=Release
# for hpx must explicitly set openmp off
- kokkos@4.1.00 +hwloc +memkind +numactl +hpx +hpx_async_dispatch +tuning ~openmp
build_type=Release ^hpx@1.9.1 +async_mpi max_cpu_count=128 networking=mpi build_type=Release
# because of odd concretization of packages with python dependences defaulting to 3.9.9 and not the
# version specified in the packages.yaml, separate packages between those with python dep and those without
- numerical-with-python:

#- plasma@22.9.29 build_type=Release ^openblas #plasma conflicts with cce compiler

- slate@2023.11.05 +rocm amdgpu_target=gfx90a build_type=Release
- plumed@2.9.0

# some heavier numerical library builds
- opencv@4.8.0 build_type=Release

# - opencv@3.4.18 build_type=Release
- trilinos@15.0.0 +adios2 +openmp +python ~cuda ^adios2@2.9.2 build_type=Release
^hdf5@1.14.3 build_type=Release
- petsc-set:
- petsc@3.20.1
- numerical:

- netlib-lapack@3.11.0 build_type=Release
- netlib-scalapack@2.2.0
- blaspp@2023.08.25 ~cuda build_type=Release #^openblas # openblas fails with cce compiler
- eigen@3.4.0 build_type=Release # charris: build ok on Joey 2021-12-16
- fftw@2.1.5 +openmp precision=float,double # fftw 2 does not support long doubles
- fftw@3.3.10 +openmp precision=float,double,long_double
- gsl@2.7.1
- amd-with-python:

# AMD AOCL
- amdblis@3.0 threads=openmp
- amdblis@3.0

# variant below useful for at least one PaCER
- amdlibflame@3.0
- amdscalapack@3.0 build_type=Release
- aocl-sparse@3.0 build_type=Release
- amd:
- amdfftw@3.0 precision=float,double,long_double
specs:
- matrix:
- [$parallel]
- ['%cce@16.0.1']
- [^python@3.11.6]
- [target=zen3]
- matrix:
- [$petsc-set]
- ['%cce@16.0.1']
- [^python@3.11.6 ^fftw@3.3.10 ^netlib-lapack@3.11.0]
- [~complex] #+complex is throwing this error: unknown type name '__complex128'
- [+fftw ~trilinos +hwloc +openmp ~cuda]
- [target=zen3]
- matrix:
- [$numerical]
- ['%cce@16.0.1']
- [target=zen3]
- matrix:
- [$numerical-with-python]
- ['%cce@16.0.1']
- [^python@3.11.6 +optimizations+zlib]
- [target=zen3]
# for now don't build amd math libraries
#- matrix:
# - [$amd]
# - ['%gcc@12.2.0', '%cce@16.0.1', '%aocc@3.2.0']
# - [target=zen3]
#- matrix:
# - [$amd-with-python]
# - ['%gcc@12.2.0', '%cce@16.0.1', '%aocc@3.2.0']
# - [^python@3.11.6]
# - [target=zen3]
view: false
Original file line number Diff line number Diff line change
@@ -0,0 +1,39 @@
spack:
# fixing some versions to have only one version per package in this environment
# note: these preferred versions are now set in packages.yaml
definitions:
- packages:
- py-cython@3.0.4
- py-dask@2023.4.1 ^netlib-lapack@3.11.0
- py-h5netcdf@0.10.0 ^netlib-lapack@3.11.0
- py-h5py@3.8.0 ^netlib-lapack@3.11.0
- py-ipython@8.14.0
- py-matplotlib@3.8.1 +movies ^netlib-lapack@3.11.0
- py-mpi4py@3.1.5
# - py-netcdf4@1.5.8 ^netlib-lapack@3.11.0 #does not build due to error: incompatible pointer to integer conversion returning 'void *' from a function with result type 'int' [-Wint-conversion]
# - py-numba@0.57.0 ^netlib-lapack@3.11.0 #produces typedef redefinition with different types ('FILE' (aka 'struct _IO_FILE') vs 'struct __dirstream')




# py-numpy: using spack's recipe
- py-numpy@1.26.1 ^openblas threads=openmp build_system=cmake #^netlib-lapack@3.11.0
# - py-pandas@2.1.2 ^netlib-lapack@3.11.0 #fails to compile llvm/14.0.6, so py-llvmlite fails. py-numba is also a dependency
- py-plotly@5.14.1
# - py-scikit-learn@1.1.3 ^netlib-lapack@3.11.0 #does not build due to py-scipy@1.8.1 failure
# - py-scipy@1.8.1 ^netlib-lapack@3.11.0 #does not build due to error: assigning to '__m512' (vector of 16 'float' values) from incompatible type 'int'
# need these here, too, for the python collection
- utilities:
- py-pip@23.1.2
- py-setuptools@68.0.0
specs:
- matrix:
- [python@3.11.6 +optimizations+zlib]
- ['%cce@16.0.1']
- [target=zen3]
- matrix:
- [$packages, $utilities]
- [^python@3.11.6 +optimizations+zlib]
- ['%cce@16.0.1']
- [target=zen3]
view: false
Original file line number Diff line number Diff line change
Expand Up @@ -6,21 +6,21 @@
spack:
definitions:
- s3-python-set:
- awscli@1.27.84
- py-boto3@1.18.12
- awscli@1.29.41
- py-boto3@1.26.26
- s3-go-set:
- rclone@1.62.2
- rclone@1.63.1
# - miniocli@2023-06-28 #deprecated by pawsey
# add package specs to the `specs` list
specs:
- matrix:
- [$s3-python-set]
- [^python@3.10.10 +optimizations+zlib]
- ['%cce@15.0.1']
- [^python@3.11.6 +optimizations+zlib]
- ['%cce@16.0.1']
- [target=zen2, target=zen3]
- matrix:
- [$s3-go-set]
- ['%cce@15.0.1']
- ['%cce@16.0.1']
- [target=zen2, target=zen3]
view: false

Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
spack:
definitions:
- packages:

# aocc, rocm, gcc, llvm: provided by system installations
- perl@5.38.0
# this is a proposed change to eliminate openss and older go
#- openssl@3.0.7 ^perl@5.36.0
# do we really need openssl 3.0.7?
#- go@1.17.2 ^openssl@3.0.7
- go@1.21.3

# NotReadyYet:
# - julia@1.6.1 #Default recipe is very weak. Faulty. Lots of needed dependencies are missing.
- openjdk@17.0.8.1_1
- r@4.3.0
- ruby@3.1.0

# latest version of rust available may have issues but spack listed latest release is fine.
# CRISTIAN: commenting it out because the installation causes issues https://github.com/spack/spack/issues/44201
# - rust@1.70.0 ^python@3.11.6 +optimizations+zlib
- py-utilities:
- py-pip@23.1.2
- py-setuptools@68.0.0
specs:
- matrix:
- [$py-utilities]
- [^python@3.11.6 +optimizations+zlib]
- ['%gcc@12.2.0']
- [target=zen3]
- matrix:
- [$packages]
- ['%gcc@12.2.0']
- [target=zen3]
view: false
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