Modules: Difference between revisions
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If it is not available from your shell (it might be the case if you use zsh), ensure that <code>/etc/profile.d/lmod.sh</code> is sourced. | If it is not available from your shell (it might be the case if you use zsh), ensure that <code>/etc/profile.d/lmod.sh</code> is sourced. | ||
In addition, ''module'' must be executed in an actual shell to work: | In addition, ''module'' must be executed in an actual shell to work: a simple <code class="command">oarsub "module load gcc"</code> will fail, you must use either: | ||
<code>oarsub | {{Term|location=fnancy|cmd=<code class="command">oarsub</code> <code class="command">'bash -l -c "module load gcc; gcc --version"'</code>}} | ||
or alternatively: | |||
{{Term|location=fnancy|cmd=<code class="command">oarsub</code> <code class="command">". /etc/profile; module load gcc; gcc --version"</code>}} | |||
== Packages that require connection to license server == | == Packages that require connection to license server == | ||
Revision as of 16:20, 26 October 2021
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This page is actively maintained by the Grid'5000 team. If you encounter problems, please report them (see the Support page). Additionally, as it is a wiki page, you are free to make minor corrections yourself if needed. If you would like to suggest a more fundamental change, please contact the Grid'5000 team. | |
Grid'5000 provides a set of software (mainly scientific-related) using Environment modules, thanks to the module command line tool.
They are available from Grid5000 frontends or cluster's nodes (only on standard, big, and nfs environment if deployment is used).
The modules command
General usage
The module system is designed to load software and make it available by modifying environment (such as your PATH variable).
To get started, list available software using:
$ module avail --------------------------------------------- /grid5000/spack/share/spack/modules/linux-debian9-x86_64 --------------------------------------------- autoconf/2.69_gcc-6.4.0 gcc/8.3.0_gcc-6.4.0 magma/2.3.0_gcc-6.4.0 automake/1.16.1_gcc-6.4.0 gmp/6.1.2_gcc-6.4.0 memkind/1.7.0_gcc-6.4.0 boost/1.69.0_gcc-6.4.0 hwloc/1.11.11_gcc-6.4.0 miniconda2/4.5.11_gcc-6.4.0 cmake/3.13.4_gcc-6.4.0 hwloc/2.0.2_gcc-6.4.0 miniconda3/4.5.11_gcc-6.4.0 cuda/10.0.130_gcc-6.4.0(default) intel-mkl/2017.4.239_gcc-6.4.0 mpfr/4.0.1_gcc-6.4.0 cuda/7.5.18_gcc-6.4.0 intel-mkl/2018.1.163_gcc-6.4.0 netlib-lapack/3.8.0_gcc-6.4.0 cuda/8.0.61_gcc-6.4.0 intel-mkl/2019.1.144_gcc-6.4.0 netlib-xblas/1.0.248_gcc-6.4.0 cuda/9.0.176_gcc-6.4.0 intel-mpi/2019.1.144_gcc-6.4.0 numactl/2.0.12_gcc-6.4.0 cuda/9.1.85_gcc-6.4.0 intel-parallel-studio/cluster.2019.2_gcc-6.4.0 openblas/0.3.5_gcc-6.4.0 cuda/9.2.88_gcc-6.4.0 intel-tbb/2019.2_gcc-6.4.0 openmpi/3.1.3_gcc-6.4.0 cudnn/5.1_gcc-6.4.0 isl/0.19_gcc-6.4.0 openmpi/4.0.1_gcc-6.4.0 cudnn/6.0_gcc-6.4.0 jdk/11.0.2_9_gcc-6.4.0 papi/5.6.0_gcc-6.4.0 cudnn/7.3_gcc-6.4.0 libfabric/1.7.1_gcc-6.4.0 swig/3.0.12_gcc-6.4.0 gcc/6.4.0_gcc-6.4.0 libfabric/1.8.0_gcc-6.4.0 tar/1.31_gcc-6.4.0 gcc/6.5.0_gcc-6.4.0 likwid/4.3.2_gcc-6.4.0 gcc/7.4.0_gcc-6.4.0 llvm/7.0.1_gcc-6.4.0
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If you need additional software to be installed, feel free to contact Grid5000 support team and we can look into it. | |
To load something into your environment use the load command:
$ module load gcc $ gcc --version gcc (GCC) 8.3.0
By default, module loads the latest version available of a software (sorted by lexicographical order). You can also specify the version you need:
$ module load gcc/7.4.0_gcc-6.4.0 $ gcc --version gcc (GCC) 7.4.0
You can also find out more information about the package using whatis or show commands:
$ module whatis gcc $ module show gcc
If you want to unload one or all the currently loaded modules, you can use:
$ module unload gcc $ module purge
The full documentation of module command is available at: http://modules.sourceforge.net/
Using modules in jobs
The module command is not a real executable, but a shell function.
If it is not available from your shell (it might be the case if you use zsh), ensure that /etc/profile.d/lmod.sh is sourced.
In addition, module must be executed in an actual shell to work: a simple oarsub "module load gcc" will fail, you must use either:
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fnancy:
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oarsub 'bash -l -c "module load gcc; gcc --version"' |
or alternatively:
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fnancy:
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oarsub ". /etc/profile; module load gcc; gcc --version" |
Packages that require connection to license server
Some packages available with module are licensed and require a connection to a license server (e.g. the Intel tools). If your institution provides a license server for this software, you may forward the connection to that license server from the node where the software will be used.
For instance, to use Intel compilers from an Inria institute network (or when using Inria's VPN), you can use jetons.inria.fr license server by forwarding connections to ports 29030 and 34430 from your node using an SSH tunnel. Intel compilers must be configured to use localhost:29030 as the license server for connections to be forwarded in the tunnel. For instance, use the following commands:
# Assuming that your connecting from a network where jetons.inria.fr is available laptop: ssh -R 29030:jetons.inria.fr:29030 -R 34430:jetons.inria.fr:34430 <your_node>.g5k node: module load intel-parallel-studio node: export INTEL_LICENSE_FILE=29030@127.0.0.1 node: icc -v