Software¶
When you connect to the IQ HPC Platform, your environment contains only minimal software. You can add more from a vast selection of available software. Pre-installed and optimised for HPC, these packages are the same ones that are available on the national clusters, which guarantees that your jobs can run reproducibly on all clusters.
Adding software to your environment is mostly done with the module command.
If you are not familiar with its usage, read using modules first. Briefly, you
can list loaded modules with module list, search for modules with module
spider, and add them to your environment with module load. For instance:
[alice@ip09 ~]$ module list
Currently Loaded Modules:
1) CCconfig 6) ucx/1.14.1 11) flexiblas/3.3.1
2) gentoo/2023 (S) 7) libfabric/1.18.0 12) imkl/2023.2.0 (math)
3) gcccore/.12.3 (H) 8) pmix/4.2.4 13) StdEnv/2023 (S)
4) gcc/12.3 (t) 9) ucc/1.2.0 14) mii/1.1.2
5) hwloc/2.9.1 10) openmpi/4.1.5 (m) 15) slurm-completion/23.02.7
Where:
S: Module is Sticky, requires --force to unload or purge
m: MPI implementations / Implémentations MPI
math: Mathematical libraries / Bibliothèques mathématiques
t: Tools for development / Outils de développement
H: Hidden Module
[alice@ip09 ~]$ module spider gromacs
--------------------------------------------------------------------------------------
gromacs:
--------------------------------------------------------------------------------------
Description:
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the
Newtonian equations of motion for systems with hundreds to millions of
particles.
Versions:
gromacs/2016.6
gromacs/2020.4
gromacs/2020.6
gromacs/2021.2
gromacs/2021.4
gromacs/2021.6
gromacs/2022.2
gromacs/2022.3
gromacs/2023
gromacs/2023.2
gromacs/2023.3
gromacs/2023.5
gromacs/2024.1
gromacs/2024.4
Other possible modules matches:
gromacs-colvars gromacs-cp2k gromacs-ls gromacs-plumed gromacs-ramd
gromacs-swaxs
--------------------------------------------------------------------------------------
To find other possible module matches execute:
$ module -r spider '.*gromacs.*'
--------------------------------------------------------------------------------------
For detailed information about a specific "gromacs" package (including how to load
the modules) use the module's full name. Note that names that have a trailing (E)
are extensions provided by other modules. For example:
$ module spider gromacs/2024.4
--------------------------------------------------------------------------------------
[alice@ip09 ~]$ module spider gromacs/2024.4
--------------------------------------------------------------------------------------
gromacs: gromacs/2024.4
--------------------------------------------------------------------------------------
Description:
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the
Newtonian equations of motion for systems with hundreds to millions of
particles.
Properties:
Chemistry libraries/apps / Logiciels de chimie
You will need to load all module(s) on any one of the lines below before the
"gromacs/2024.4" module is available to load.
StdEnv/2023 gcc/12.3 openmpi/4.1.5
StdEnv/2023 gcc/12.3 openmpi/4.1.5 cuda/12.2
Help:
Description
===========
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the
Newtonian equations of motion for systems with hundreds to millions of
particles.
More information
================
- Homepage: http://www.gromacs.org
[alice@ip09 ~]$ module load StdEnv/2023 gcc/12.3 openmpi/4.1.5
[alice@ip09 ~]$ module load gromacs/2024.4
[alice@ip09 ~]$ module list
Currently Loaded Modules:
1) CCconfig 10) hwloc/2.9.1
2) gentoo/2023 (S) 11) ucx/1.14.1
3) imkl/2023.2.0 (math) 12) libfabric/1.18.0
4) StdEnv/2023 (S) 13) pmix/4.2.4
5) mii/1.1.2 14) ucc/1.2.0
6) slurm-completion/23.02.7 15) openmpi/4.1.5 (m)
7) gcc/12.3 (t) 16) fftw/3.3.10 (math)
8) flexiblas/3.3.1 17) gromacs/2024.4 (chem)
9) gcccore/.12.3 (H)
Where:
S: Module is Sticky, requires --force to unload or purge
m: MPI implementations / Implémentations MPI
math: Mathematical libraries / Bibliothèques mathématiques
t: Tools for development / Outils de développement
chem: Chemistry libraries/apps / Logiciels de chimie
H: Hidden Module
Software environment version¶
The Alliance team in charge of software periodically releases new versions of
the environment, such as StdEnv/2023 or StdEnv/2020. On the IQ HPC
Platform, StdEnv/2023 is the environment initially loaded when you connect.
The other environments are available and can be loaded. For instance:
[alice@ip09 ~]$ module load StdEnv/2020
Inactive Modules:
1) slurm-completion
Due to MODULEPATH changes, the following have been reloaded:
1) mii/1.1.2
The following have been reloaded with a version change:
1) StdEnv/2023 => StdEnv/2020 5) libfabric/1.18.0 => libfabric/1.10.1
2) gcccore/.12.3 => gcccore/.9.3.0 6) openmpi/4.1.5 => openmpi/4.0.3
3) gentoo/2023 => gentoo/2020 7) ucx/1.14.1 => ucx/1.8.0
4) imkl/2023.2.0 => imkl/2020.1.217
Optimisation target¶
Alliance software available on the IQ HPC Platform is optimised for x86
processors that support the AVX2 instruction set. It was not compiled to use
more recent instruction sets such as AVX512. This is the best choice to support
both the Intel and AMD CPUs on the compute nodes while ensuring good
performance. If you compile your code with GCC, the corresponding optimisation
option is -march=core-avx2. With Intel compilers, use -xCORE-AVX2.
We do not recommend to use a different architecture (e.g. module load
arch/avx512) or to compile your code with a different option (e.g.
-march=native or -xHost) since that can lead to compatibility issues.
BLAS/LAPACK libraries¶
The Alliance software offers several implementations of the BLAS and LAPACK libraries for linear algebra. Intel MKL is used by default on the IQ HPC Platform and most Alliance clusters.
Software guides¶
The following pages detail the use of specific software packages. Some are also available on the national clusters, in which case the focus is on the specificities of using that software on the IQ HPC Platform.