Merge pull request #1032 from ExtremeFLOW/release/0.7

NEKO v0.7.0

Author: njansson

.gitattributes

@@ -2,4 +2,5 @@
 *.f90.in linguist-language=fortran
 *.F90.in linguist-language=fortran
 *.hip linguist-language=C++
+*.case linguist-language=json
 

.github/workflows/develop.yml

@@ -15,6 +15,13 @@ jobs:
       run: |
         sudo apt-get update && sudo apt-get install -y git openmpi-bin libopenmpi-dev autoconf automake autotools-dev libopenblas-dev make git m4 python3 doxygen fonts-freefont-ttf graphviz
         git clone https://github.com/ExtremeFLOW/doxygen-awesome-css doc/doxygen-awesome-css
+        git clone --depth 1 https://github.com/ExtremeFLOW/json-fortran/
+        cd json-fortran
+        mkdir build && cd build
+        cmake -DCMAKE_INSTALL_PREFIX=${HOME}/pkg/json-fortran -DUSE_GNU_INSTALL_CONVENTION=ON ..
+        make -j$(nproc) && make install && cd ../../
+        echo "PKG_CONFIG_PATH=${PKG_CONFIG_PATH}:${HOME}/pkg/json-fortran/lib/pkgconfig/" >> $GITHUB_ENV
+        echo "LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HOME}/pkg/json-fortran/lib/" >> $GITHUB_ENV
     - name: Doxygen
       run: |
         ./regen.sh
@@ -27,7 +34,9 @@ jobs:
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: ./doc/html/
-        enable_jekyll: false
         allow_empty_commit: false
-        force_orphan: true
+        force_orphan: false
         publish_branch: gh-pages
+        destination_dir: docs
+        keep_files: false
+        enable_jekyll: true

.github/workflows/documentation.yml

@@ -41,6 +41,8 @@ examples/*/*0.f0*
 contrib/average_field_in_space
 contrib/average_fields_in_time
 contrib/postprocess_fluid_stats
+*.chkp
+*.lst
 
 
 

.github/workflows/main.yml

@@ -12,15 +12,17 @@ git clone https://github.com/ExtremeFLOW/neko
 ```
 
 ## Building the project
-To build the project you will need: A Fortran compiler supporting the Fortran-08 standard, a working MPI installation and BLAS/lapack.
-We use automake to build the project. These instructions should work in general, but as the project is quickly developing, things might change.
+To build the project you will need: A Fortran compiler supporting the Fortran-08 standard, a working MPI installation, JSON-Fortran, and BLAS/lapack. Optional dependencies are gslib and ParMETIS. We use automake to build the project. These instructions should work in general, but as the project is quickly developing, things might change.
 
 ```bash
 cd neko
 ./regen.sh
 ./configure --prefix=/path/to/neko_install --with-pfunit=/path/to/pFUnit/installed/PFUNIT-VERSION
 make install
 ```
+
+More detailed installation instructions can be found in the documentation.
+
 ## Running examples
 After the project has been built
 
@@ -37,7 +39,7 @@ make check
 ```
 
 ## Documentation
-Documentation for Neko is available at https://extremeflow.github.io/neko/.
+Documentation for Neko is available at https://neko.cfd/docs.
 
 To generate the documentation, you need to have both doxygen and dot (part of the Graphviz package) installed (they will be picked up by configure). Once installed, you should be able to generate the documentation with
 ```bash
@@ -49,9 +51,10 @@ make html
 * Karp, M., Podobas, A., Kenter, T., Jansson, N., Plessl, C., Schlatter, P. and Markidis, S., 2022. *A high-fidelity flow solver for unstructured meshes on field-programmable gate arrays: Design, evaluation, and future challenges*. In proc. HPCAsia 2022.
 * Karp, M., Jansson, N., Podobas, A., Schlatter, P., and Markidis, S., 2022. *Reducing Communication in the Conjugate Gradient Method: A Case Study on High-Order Finite Elements*. In proc. PASC 2022.
 * Karp, M., Massaro, D., Jansson, N., Hart, A., Wahlgren, J., Schlatter, P., and Markidis, S., 2022. *Large-Scale Direct Numerical Simulations of Turbulence Using GPUs and Modern Fortran*. arXiv preprint arXiv:2207:07098.
+* Jansson, N., Karp, M., Perez, A., Mukha, T., Ju, Y., Liu, J., Páll, S., Laure, E., Weinkauf, T., Schumacher, J., Schlatter, P., Markidis, S., 2023. *Exploring the Ultimate Regime of Turbulent Rayleigh–Bénard Convection Through Unprecedented Spectral-Element Simulations*. SC '23: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis.
 
 ## Acknowledgments
 The development of Neko was supported by the European Commission Horizon 2020 project grant *EPiGRAM-HS: Exascale Programming Models for Heterogeneous Systems* (grant reference 801039), the Swedish Research Council project grant *Efficient Algorithms for Exascale Computational Fluid Dynamics* (grant reference 2019-04723) and the SeRC Exascale Simulation Software Initiative (SESSI). The Neko logo was designed by Robert Hansen Jagrelius.
 
 
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+[<img src="https://raw.githubusercontent.com/zulip/zulip/143baa42432cde9f288bd202336ef2b11172f6e4/static/images/logo/zulip-icon-128x128.png" width="32"/>](https://zulip.com) Sponsored by Zulip, an open-source modern team chat app designed to keep both live and asynchronous conversations organized.

.gitignore

@@ -32,7 +32,7 @@ program axbench
   call nmsh_file%read(msh)  
 
   call space_init(Xh, GLL, lx, lx, lx)
-  call field_init(w, msh, Xh, "w")
+  call w%init(msh, Xh, "w")
 
   allocate(g(6, Xh%lx, Xh%ly, Xh%lz, msh%nelv))
   call setup_g(g, Xh%wx, Xh%lx, Xh%ly, Xh%lz, msh%nelv)
@@ -58,8 +58,8 @@ program axbench
 
   deallocate(u,ur,us,ut,wk)
   call space_free(Xh)
-  call field_free(w)
-  call mesh_free(msh)
+  call w%free()
+  call msh%free()
 
   call neko_finalize
 

README.md

@@ -34,12 +34,12 @@ program gsbench
 
   nmsh_file = file_t(fname)
   call nmsh_file%read(msh)
-  call mesh_generate_conn(msh)
+  call msh%generate_conn()
 
-  call space_init(Xh, GLL, lx, lx, lx)
+  call Xh%init(GLL, lx, lx, lx)
 
   dm = dofmap_t(msh, Xh)
-  call gs_init(gs_h, dm)
+  call gs_h%init(dm)
 
   n = Xh%lx * Xh%ly * Xh%lz * msh%nelv
 
@@ -50,7 +50,7 @@ program gsbench
 
   ! warmup
   do i = 1, niter
-    call gs_op(gs_h, u, n, GS_OP_ADD)
+    call gs_h%op(u, n, GS_OP_ADD)
     call device_sync()
   end do
 
@@ -60,7 +60,7 @@ program gsbench
 
   do i = 1, niter
      t(i) = MPI_Wtime()
-     call gs_op(gs_h, u, n, GS_OP_ADD)
+     call gs_h%op(u, n, GS_OP_ADD)
      call device_sync()
      t(i) = MPI_Wtime() - t(i)
   end do
@@ -82,8 +82,8 @@ program gsbench
   stop
 
   deallocate(u)
-  call space_free(Xh)
-  call mesh_free(msh)
+  call Xh%free()
+  call msh%free()
 
   call neko_finalize
 

bench/ax/driver.f90

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Extract time and enstrophy from neko output on stdin
+# Extract time and enstrophy from neko output from argument $1
 
 echo "# Time Enstrophy"
-grep -a Enstrophy | cut -d" " -f3,8
+awk '/enst:/ {print($3, $NF)}' $1

bench/gs/driver.f90

@@ -1,19 +1,47 @@
-&NEKO_CASE
-mesh_file= '32768.nmsh'
-fluid_scheme='pnpn'
-lx = 8
-source_term = 'noforce'
-initial_condition = 'user'
-/
-&NEKO_PARAMETERS
-dt = 1d-3
-T_end = 20
-nsamples = 2
-rho = 1
-Re = 1600
-abstol_vel = 1d-9
-abstol_prs = 1d-9
-pc_vel = 'jacobi'
-pc_prs = 'hsmg'
-proj_prs_dim = 20
-/
+{
+  "version": 1.0,
+  "case":
+  {
+  "mesh_file": "32768.nmsh",
+  "output_boundary": false,
+  "output_checkpoints": false,
+  "output_at_end": false,
+  "end_time": 20.0,
+  "timestep": 1e-3,
+  "numerics": {
+    "time_order": 3,
+    "polynomial_order": 7,
+    "dealias": true
+  },
+  "fluid": {
+    "scheme": "pnpn",
+    "Re": 1600,
+    "initial_condition": {
+      "type": "user"
+    },
+    "velocity_solver": {
+      "type": "cg",
+      "preconditioner": "jacobi",
+      "projection_space_size": 0,
+      "absolute_tolerance": 1e-9,
+      "max_iterations": 800
+    },
+    "pressure_solver": {
+      "type": "gmres",
+      "preconditioner": "hsmg",
+      "projection_space_size": 20,
+      "absolute_tolerance": 1e-9,
+      "max_iterations": 800
+    },
+    "output_control": "simulationtime",
+    "output_value": 10 
+  },
+ "simulation_components": 
+  [
+    {
+      "type": "vorticity",
+      "compute_control": "tsteps",
+      "compute_value": 50}
+  ]
+  }
+}