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How to use the AMITEX_FFTP Apptainer image ?

Prerequisites

For more information on Apptainer containers, please look at this page or refer to this tutorial to have a quick look at Apptainer’s main commands.

Create a directory containing the amitex_fftp.sif image and the archive of the input files. Move into this directory and extract the archive as follows:

tar -xzf amitex-tutorial-inputs.tar.gz # Extracts the contents of the archive.

One-line command

For those in a hurry, here is how to launch an Amitex_FFTP computation:

apptainer exec amitex_fftp.sif mpirun -np <N> amitex_fftp <args>

Introduction

Amitex_FFTP is a massively parallel simulation code built around the MPI standard, allowing the computational workload to be distributed across multiple processes. There are two ways to run the containerized code in parallel:

  • MPI embedded in the container => guaranteed to work, but limited to a single machine (a single node)
  • Hybrid MPI using the host machine’s MPI => works across multiple nodes but may introduce compatibility issues.

Local simulation (embedded MPI)

apptainer exec amitex_fftp.sif mpirun amitex_fftp -nm concrete.vtk -m material.xml -c loading.xml -a algorithm.xml -s out

Note that the command first launches apptainer, which then executes mpirun amitex_fftp <args> inside the container.

Cluster simulation (hybrid MPI)

Example of a minimal launch script job.sh:

#!/bin/bash

#SBATCH --job-name=test_amitex
#SBATCH --output=slurm-%j.out
#SBATCH --error=slurm-%j.err
#SBATCH --ntasks=12
#SBATCH --time=00:05:00

srun apptainer run amitex_fftp.sif -nm concrete.vtk -m material.xml -c loading.xml -a algorithm.xml -s out

The computation can then be launched with the command:

sbatch job.sh

Launch without a scheduler

mpirun -np <N> apptainer run amitex_fftp.sif -nm concrete.vtk -m material.xml -c loading.xml -a algorithm.xml -s out

*The mpirun command must come from OpenMPI 4 for this to work.

For reference, apptainer run amitex_fftp.sif is a shortcut for apptainer exec amitex_fftp.sif amitex_fftp.

Visualizing the results

Generate strain curves with Gnuplot:

apptainer exec amitex_fftp.sif gnuplot < plot.gp

This creates concrete_stress_strain.svg, which can then be displayed with a standard image viewer.

To visualize .vtk files, Paraview must be used. We provide a Paraview container here. Once the Paraview container has been downloaded, the microstructure concrete.vtk can be visualized as follows:

apptainer run paraview.sif concrete.vtk
# Then in the graphical interface click "Apply" in the left Properties panel
# Then in the top menu bar select "MaterialId" in the drop-down menu instead of "Solid Color".
# Then in the top menu bar select "Surface" in the drop-down menu instead of "Outline".

(Advanced) User-defined material behavior law

UMAT Behaviors

It is possible to define custom material behavior laws using a UMAT-compatible procedure. We will look at an example of a user-defined material behavior law used with AMITEX_FFTP. You can retrieve the example provided in the container with:

apptainer exec amitex_fftp.sif cp -r /gnu/store/df6rv9zlllzrp8rrwxlc5ixf20kylmnf-amitex_fftp-8.17.14/cas_tests/comportements/polyxCC/comportement_umat .
chmod -R u+w comportement_umat

The provided example is already compiled, so you can start by cleaning the comportement_umat directory:

cd comportement_umat
apptainer exec ../amitex_fftp.sif make clean

You can now implement the desired behavior by modifying the files with your preferred text editor. Then, recompile the behavior law with:

apptainer exec ../amitex_fftp.sif make
cd ..

This creates comportement_umat/libUmatAmitex.so. Next, you need to modify material.xml to call this new behavior law by replacing, for example <Material numM="2" Lib="" Law="elasiso"> [...] </Material> with:

    <Material numM="2" Lib="comportement_umat/libUmatAmitex.so" Law="umatBCCHPP" >
                <Coeff Index="1" Type="Constant" Value="236.412E3"/>
                <Coeff Index="2" Type="Constant" Value="0.35"/>
                <Coeff Index="3" Type="Constant" Value="275.2E3"/>
                <Coeff Index="4" Type="Constant" Value="112.4E3"/>
                <Coeff Index="5" Type="Constant" Value="87.56E3"/>
                <Coeff Index="6" Type="Constant" Value="363."/>
                <Coeff Index="7" Type="Constant" Value="0."/>
                <Coeff Index="8" Type="Constant" Value="1000."/>
                <Coeff Index="9" Type="Constant" Value="10e-6"/>
                <Coeff Index="10" Type="Constant" Value="1e11"/>
                <Coeff Index="11" Type="Constant" Value="2.481e-7"/>
                <Coeff Index="12" Type="Constant" Value="100"/>
                <Coeff Index="13" Type="Constant" Value="3."/>
                <Coeff Index="14" Type="Constant" Value="2.e-6"/>
                <Coeff Index="15" Type="Constant" Value="0.84"/>
                <Coeff Index="16" Type="Constant" Value="1e5"/>
                <Coeff Index="17" Type="Constant" Value="1e5"/>
                <Coeff Index="18" Type="Constant" Value="1e-6"/>
                <Coeff Index="19" Type="Constant" Value="50"/>
                <Coeff Index="20" Type="Constant" Value="0"/>
                <Coeff Index="21" Type="Constant" Value="0.3"/>
                <Coeff Index="22" Type="Constant" Value="1."/>
                <Coeff Index="23" Type="Constant" Value="5.e-4"/>
                <Coeff Index="24" Type="Constant" Value="50"/>
                <Coeff Index="25" Type="Constant" Value="0."/>
                <Coeff Index="26" Type="Constant" Value="0."/>
                <Coeff Index="27" Type="Constant" Value="0."/>
                <IntVar Index="1" Type="Constant" Value="0."/>
                <IntVar Index="2" Type="Constant" Value="0."/>
                <IntVar Index="3" Type="Constant" Value="0."/>
                <IntVar Index="4" Type="Constant" Value="0."/>
                <IntVar Index="5" Type="Constant" Value="0."/>
                <IntVar Index="6" Type="Constant" Value="0."/>
                <IntVar Index="7" Type="Constant" Value="0."/>
                <IntVar Index="8" Type="Constant" Value="0."/>
                <IntVar Index="9" Type="Constant" Value="0."/>
                <IntVar Index="10" Type="Constant" Value="0."/>
                <IntVar Index="11" Type="Constant" Value="0."/>
                <IntVar Index="12" Type="Constant" Value="0."/>
                <IntVar Index="13" Type="Constant" Value="0."/>
                <IntVar Index="14" Type="Constant" Value="0."/>
                <IntVar Index="15" Type="Constant" Value="0."/>
                <IntVar Index="16" Type="Constant" Value="0."/>
                <IntVar Index="17" Type="Constant" Value="0."/>
                <IntVar Index="18" Type="Constant" Value="0."/>
                <IntVar Index="19" Type="Constant" Value="0."/>
                <IntVar Index="20" Type="Constant" Value="0."/>
                <IntVar Index="21" Type="Constant" Value="0."/>
                <IntVar Index="22" Type="Constant" Value="0."/>
                <IntVar Index="23" Type="Constant" Value="0."/>
                <IntVar Index="24" Type="Constant" Value="0."/>
                <IntVar Index="25" Type="Constant" Value="0."/>
                <IntVar Index="26" Type="Constant" Value="0."/>
                <IntVar Index="27" Type="Constant" Value="0."/>
                <IntVar Index="28" Type="Constant" Value="0."/>
                <IntVar Index="29" Type="Constant" Value="0."/>
                <IntVar Index="30" Type="Constant" Value="0."/>
                <IntVar Index="31" Type="Constant" Value="0."/>
                <IntVar Index="32" Type="Constant" Value="0."/>
                <IntVar Index="33" Type="Constant" Value="0."/>
                <IntVar Index="34" Type="Constant" Value="0."/>
                <IntVar Index="35" Type="Constant" Value="0."/>
                <IntVar Index="36" Type="Constant" Value="0."/>
                <IntVar Index="37" Type="Constant" Value="0."/>
                <IntVar Index="38" Type="Constant" Value="0."/>
                <IntVar Index="39" Type="Constant" Value="0."/>
                <IntVar Index="40" Type="Constant" Value="0."/>
                <IntVar Index="41" Type="Constant" Value="0."/>
                <IntVar Index="42" Type="Constant" Value="0."/>
                <IntVar Index="43" Type="Constant" Value="0."/>
                <IntVar Index="44" Type="Constant" Value="0."/>
                <IntVar Index="45" Type="Constant" Value="0."/>
                <IntVar Index="46" Type="Constant" Value="0."/>
                <IntVar Index="47" Type="Constant" Value="0."/>
                <IntVar Index="48" Type="Constant" Value="0."/>
                <IntVar Index="49" Type="Constant" Value="0."/>
    </Material>

You can now run the computation with the new behavior law, after removing <Loading Tag="2"> [...] </Loading> from loading.xml, which does not work in this example:

apptainer exec amitex_fftp.sif mpirun amitex_fftp -nm concrete.vtk -m material.xml -c loading.xml -a algorithm.xml -s out

MFRONT Behaviors

It is also possible to define custom material behavior laws using mfront. Here we present an example of a material behavior defined with mfront, then used with AMITEX_FFTP. The first step is to generate the dynamic library containing the UMAT function:

apptainer exec amitex_fftp.sif mfront --obuild --interface=umat Mazars.mfront

This creates src/libUmatBehaviour.so. You must then modify material.xml to call this new behavior law, replacing for example <Material numM="2" Lib="" Law="elasiso"> [...] </Material> by:

    <Material numM="2" Lib="src/libUmatBehaviour.so" Law="umatmazars" >
                    <Coeff Index="1" Type="Constant" Value="1.e+10"/>
                    <Coeff Index="2" Type="Constant" Value="0.2"/>
                    <Coeff Index="3" Type="Constant" Value="0."/>
                    <Coeff Index="4" Type="Constant" Value="0."/>
                    <Coeff Index="5" Type="Constant" Value="1.15"/>
                    <Coeff Index="6" Type="Constant" Value="0.8"/>
                    <Coeff Index="7" Type="Constant" Value="1391.3"/>
                    <Coeff Index="8" Type="Constant" Value="10000"/>
                    <Coeff Index="9" Type="Constant" Value="0.7"/>
                    <Coeff Index="10" Type="Constant" Value="9.375e-5"/>
                    <IntVar Index = "1" Type = "Constant" Value = "0." />
                    <IntVar Index = "2" Type = "Constant" Value = "0." />
                    <IntVar Index = "3" Type = "Constant" Value = "0." />
    </Material>

You can now run the computation with the new behavior law:

apptainer exec amitex_fftp.sif mpirun amitex_fftp -nm concrete.vtk -m material.xml -c loading.xml -a algorithm.xml -s out

Then visualize the results:

apptainer exec amitex_fftp.sif gnuplot < plot.gp

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