Using pre-installed software¶
Software that is most used on clusters is often installed already on the CECI clusters: Fortran and C/C++ compilers, popular interpreters like Python or R, numerical libraries such as BLAS and LAPACK, and message passing libraries (e.g. OpenMPI). In addition, several versions are often installed.
They are available through the use of the module command:
module avail list available software (modules) module add|load [software] set up environment to use software module purge clears the environment module list list currently set up software module help get help
module available openmpi will list all available OpenMPI
modules. Assuming it returns something like
openmpi/1.4.5/intel-11.1.073 openmpi/1.4.5/pgi-11.2-1 openmpi/1.5.3/gcc-4.4.4 openmpi/1.5.3/intel-12.0.0.084
module load openmpi/1.5.3/intel-12.0.0.084 will enable the OpenMPI
version 1.5.3 compiled with the Intel compiler. After doing that, when you
mpirun without specifying the full path, you will be running that
specific version of OpenMPI. Note that introducing
module load openmpi
will load a default version.
Modules are organised around the notion of
A toolchain is a collection of compiler and libraries that are often used
together and known to interoperate perfectly. For instance, the
A toolchain version corresponds to a set of specific versions of the elements
of the toolchain. For instance the
foss/2016a toolchain corresponds to
GCC/4.9.3, OpenBLAS/0.2.15, OpenMPI/1.10.2, ScaLAPACK/2.0.2 and FFTW/3.3.4.
Beware that the module system is case sensitive and some versions might be named
Another catch with
module avail is that it outputs its results to
stderr, meaning that if you want to grep it, you’ll need to use
module avail |& grep softwarename
Note the ampersand after the pipe sign.
About some commercial software:
- Matlab: is not installed on the CÉCI clusters but free alternatives are available (e.g. Octave) and the Matlab Runtime (MCR) is installed on all the clusters. A training session is dedicated each year to the use of Matlab on the clusters.
- Gaussian is installed on most clusters, but its use is restricted and granted on a per case basis. You will need to contact both the system administrator of your university and that of the university hosting the cluster you want to use.