29.07.2022 Reupload of inadvertently deleted container (NO changes made to container, 2 links below changed slightly)
19.10.2021 update with new original container (version 2021.0.0). Now PETSc is also available.
13.10.2021 created
Download container built according to recipe below at https://cloud.sylabs.io/library/emefff/collection/code-aster-mpi-in-singularity-of-sm2021
or pull it with
singularity pull --arch amd64 library://emefff/collection/code-aster-mpi-in-singularity-of-sm2021:salome2021
Due to the naming conventions of cloud.sylabs.io please rename the downloaded container to 'salome_meca-lgpl-2021.0.0-0-20210601-scibian-9.sif'. Otherwise there is a conflict between the filename and the notes within the container.
In the following tutorial we will show how to build the MPI Version of Code Aster 15.4 within the Singularity Container of Salome-Meca 2021 (a big thank you goes out to Ing. Nicola, a fellow member of the Code_Aster Forum. All the important work was done by him. Thank you! Of course we owe Salome-Meca and Code_Aster to EDF's R&D-Team, www.code-aster.org)
The following steps of this little tutorial were tried and tested on Ubuntu 20.04 LTS (desktop and server version).
Install Singularity following the steps on https://singularity-tutorial.github.io/01-installation/:
Note: we assume that newer 3.x versions also work.
sudo apt-get update
sudo apt-get install -y build-essential libssl-dev uuid-dev libgpgme11 libgpgme-dev squashfs-tools libseccomp-dev wget pkg-config git cryptsetup debootstrap
wget https://dl.google.com/go/go1.13.linux-amd64.tar.gz
sudo tar --directory=/usr/local -xzvf go1.13.linux-amd64.tar.gz
export PATH=/usr/local/go/bin:$PATH
wget https://github.com/singularityware/singularity/releases/download/v3.5.3/singularity-3.5.3.tar.gz
tar -xzvf singularity-3.5.3.tar.gz
cd singularity
./mconfig
cd builddir
make
sudo make install
You may delete both tars now:
cd
rm go1.13.linux-amd64.tar.gz singularity-3.5.3.tar.gz
Download the Singularity Container of Salome-Meca 2021 from the Code_Aster Homepage www.code-aster.org: https://www.code-aster.org/FICHIERS/singularity/salome_meca-lgpl-2021.0.0-0-20210601-scibian-9.sif
and place it in your ~/
This file is about 5.5G in size.
Download the sources of Code_Aster 15.4 from https://sourceforge.net/p/codeaster/src/ci/15.4.0/tree/ via pressing the 'Download Snapshot' Button
Unzip and place this directory in /home/
Rename the directory to aster-src--> base directory of Code_Aster sources is now /home/aster-src
Copy above pkginfo.py in /home/aster-src/code_aster/ (only for cosmetical reasons, otherwise version number will be incorrect in SM)
Add an overlay to the Singularity container, so data can be written to it:
cd ~
dd if=/dev/zero of=overlay.img bs=1M count=1000 && mkfs.ext3 overlay.img
singularity sif add --datatype 4 --partfs 2 --parttype 4 --partarch 2 --groupid 1 salome_meca-lgpl-2021.0.0-0-20210601-scibian-9.sif overlay.img
The overlay.img is not needed anymore: rm overlay.img
Your container file salome_meca-lgpl-2021.0.0-0-20210601-scibian-9.sif should now be +1G larger (approx. 6.5G)
Open the container in a shell and bind /home to it:
sudo singularity run --bind /home:/home -w ~/salome_meca-lgpl-2021.0.0-0-20210601-scibian-9.sif shell
Now execute the following commands to build an install the MPI-Version of Code-Aster 15.4 within the container (denoted by Singularity> prefix):
Singularity> export TOOLS="/opt/salome_meca/Salome-V2021-s9/tools"
Singularity> export ASTER_ROOT="${TOOLS}/Code_aster_15_4_0_mpi"
Singularity> cd /home/aster-src
Singularity> ./waf_mpi configure --prefix=${ASTER_ROOT} --without-hg --install-tests --jobs=4
Singularity> ./waf_mpi build --jobs=4
Singularity> ./waf_mpi install
Singularity> echo "vers : stable_mpi:/opt/salome_meca/Salome-V2021-s9/tools/Code_aster_15_4_0_mpi/share/aster" >> ${TOOLS}/Code_aster_frontend-2021001/etc/codeaster/aster
The last command makes the MPI-version accessible within Salome-Meca. Now you should be able to launch Salome-Meca within the container, first exit the container shell with:
Singularity> exit
Launch the Singularity Container of SM 2021 according to the tutorial given on https://www.code-aster.org/V2/spip.php?article303:
singularity run --app install salome_meca-lgpl-2021.0.0-0-20210601-scibian-9.sif
It is best to run it on a machine with an Nvidia Graphics Card, the more RAM and CPU-cores, the better. Without Nvidia Graphics Cards software-rendering will be used (=slow 👎).
Now start Salome-Meca 2021 with: ./salome_meca-lgpl-2021.0.0-0-20210601-scibian-9
Salome Meca should launch. If you open 'Asterstudy' and click the 'History View' tab, you should be able to choose 'stable_mpi' in the 'version of code_aster' tab:
If everything was successful, the Code Aster sources may be deleted:
sudo rm -r /home/aster-src
To achieve a minimum in calculation time we've found the following parameters to be most suitable with the MPI-version on an otherwise unoccupied machine (no other task with notable CPU usage):
Number of MPI CPU = number_of_cores/2
Number of threads = 2
Please be aware, in systems with more than one CPU, these numbers may not be suitable.
In the sequential version (which you'll be likely not using anymore :-) ) the following parameters are most suitable:
Number of threads = number_of_cores/2
In any cases, especially on older CPUs, HyperThreading (Intel) or Simultaneous Multi-Threading (AMD) should be turned off. On a given CPU with an average number of cores (e.g. 8 or 10) a speed improvement of roughly 2-3 should be attainable in mechanical simulations with the MPI-version over the sequential version with OpenMP only. With older CPUs and if you are behind a strong firewall, you might also want to consider turning Spectre-Meltdown mitigations off to gain some more speed.
This container also works on headless machines. It should then choose software rendering automatically. If you log on via ssh, choose -X option on the client side. The GUI will be forwarded to your client.
Have fun,
emefff.