Apptainer: pfft & p3dfft

fluiddyn · Jun 17, 2024 · 4c72438 · 4c72438
1 parent dcf97cf
commit 4c72438
Show file tree

Hide file tree

Showing 2 changed files with 37 additions and 3 deletions.
diff --git a/doc/apptainer/README.md b/doc/apptainer/README.md
@@ -15,7 +15,7 @@ apptainer build image-fluidsim.sif image-fluidsim.def
 
 ## Run the image to install Fluidsim from source
 
-From the host:
+From the host (a node of the cluster!):
 
 ```sh
 cd ~/apptainer
@@ -25,5 +25,16 @@ apptainer shell --no-home image-fluidsim.sif
 From the container:
 
 ```sh
-...
+python -m venv venv-fluidsim
+. venv-fluidsim/bin/activate
+HDF5_MPI="ON" pip install --no-binary=h5py h5py pytest pytest-mpi
+python -c 'import h5py; h5py.run_tests()'
+hg clone https://foss.heptapod.net/fluiddyn/fluidsim
+cd fluidsim/
+pip install ".[test,mpi,fft]"
+pytest --pyargs fluidsim
+pip install fluidfft-fftw fluidfft-fftwmpi fluidfft-mpi_with_fftw
+mpirun -np 2 pytest --pyargs fluidsim
+pip install fluidfft-p3dfft
+pip install fluidfft-pfft
 ```
diff --git a/doc/apptainer/image-fluidsim.def b/doc/apptainer/image-fluidsim.def
@@ -6,9 +6,16 @@ From: python:3.11
  apt-get -y install mercurial git less meld nano
 
  apt-get install -y --no-install-recommends \
- libfftw3-dev libfftw3-mpi-dev openmpi-bin libhdf5-openmpi-dev libopenblas-dev
+ libfftw3-dev libfftw3-mpi-dev openmpi-bin libhdf5-openmpi-dev libopenblas-dev \
+ gfortran
 
+ mkdir -p /root/.local/include
+ mkdir -p /root/.local/lib
  export PATH=/root/.local/bin:$PATH
+ export CPATH=/root/.local/include
+ export LIBRARY_PATH=/root/.local/lib
+ export LD_LIBRARY_PATH=/root/.local/lib
+
  python -m pip install pipx
 
  pipx install mercurial
@@ -19,12 +26,28 @@ From: python:3.11
 
  wget https://foss.heptapod.net/fluiddyn/fluidsim/-/raw/topic/default/apptainer/doc/apptainer/hgrc -O ~/hgrc
 
+ ln -s /usr/include/fftw* /root/.local/include
+ ln -s /usr/lib/x86_64-linux-gnu/libfftw3* /root/.local/lib
+
+ wget https://foss.heptapod.net/fluiddyn/fluidfft/raw/branch/default/doc/install/install_p3dfft.sh -O ./install_p3dfft.sh
+ chmod +x install_p3dfft.sh
+ export FCFLAGS="-w -fallow-argument-mismatch -O2"
+ export FFLAGS="-w -fallow-argument-mismatch -O2"
+ ./install_p3dfft.sh
+
+ wget https://foss.heptapod.net/fluiddyn/fluidfft/raw/branch/default/doc/install/install_pfft.sh -O ./install_pfft.sh
+ chmod +x install_pfft.sh
+ ./install_pfft.sh
+
 %startscript
  mkdir -p home
 
 %environment
  export LC_ALL=C
  export PATH=/root/.local/bin:$PATH
+ export CPATH=/root/.local/include
+ export LIBRARY_PATH=/root/.local/lib
+ export LD_LIBRARY_PATH=/root/.local/lib
  export HOME=$HOME/apptainer/home
  export HGRCPATH=/root/hgrc