Module files in clusters

Posted by Administrator on Thursday, 16 June 2016

What is an "Environment Module"?

Each module file contains the commands and files needed for configuring your shell in order to make them working in a user-friendly way. By the moment, not all modules are installed in all machines, so check before using a program.

How do I use a module?

For having a look on the available modules: module avail
If you want to know which modules you have loaded: module list
For loading a module: module load module_name
For unloading a module: module unload module_name

Examples

If you want to use any of the programs included in AMBER10 you may want know the available modules in the machine (in this example, SGI xecluster):

> module avail
 
----------- /usr/share/modules ---------------------
3.1.6                            modulefiles/gcc                  modulefiles/gromacs-4.0.4        modulefiles/mcce                 modulefiles/namd2                modulefiles/sge-mac
modulefiles/amber                modulefiles/gromacs              modulefiles/gromacs-4.0.7-plumed modulefiles/module-cvs           modulefiles/null                 modulefiles/sge-xec
modulefiles/amber-11             modulefiles/gromacs-3            modulefiles/gromacs-4.5.1        modulefiles/module-info          modulefiles/openmpi              modulefiles/use.own
modulefiles/amber-mpi            modulefiles/gromacs-3.3.3.1      modulefiles/gromacs-4.5.3        modulefiles/modules              modulefiles/openmpi-1.4.1        modulefiles/xplor
modulefiles/ambertools           modulefiles/gromacs-4            modulefiles/imp-1.0              modulefiles/mvapich2-intel       modulefiles/openmpi-intel
modulefiles/autodock-vina        modulefiles/gromacs-4-cvs        modulefiles/intel                modulefiles/namd-2.6-intel       modulefiles/perfcatcher
modulefiles/boost-1.45.0         modulefiles/gromacs-4.0          modulefiles/intel-11.1.073       modulefiles/namd-2.7             modulefiles/sge
modulefiles/dot                  modulefiles/gromacs-4.0.2        modulefiles/libgfortran2         modulefiles/namd-2.7b2           modulefiles/sge-ibm
 
---------- /usr/share/modules/modulefiles -----------
amber                boost-1.45.0         gromacs-3.3.3.1      gromacs-4.0.4        intel                module-info          namd-2.7b2           openmpi-intel        sge-xec
amber-11             dot                  gromacs-4            gromacs-4.0.7-plumed intel-11.1.073       modules              namd2                perfcatcher          use.own
amber-mpi            gcc                  gromacs-4-cvs        gromacs-4.5.1        libgfortran2         mvapich2-intel       null                 sge                  xplor
ambertools           gromacs              gromacs-4.0          gromacs-4.5.3        mcce                 namd-2.6-intel       openmpi              sge-ibm
autodock-vina        gromacs-3            gromacs-4.0.2        imp-1.0              module-cvs           namd-2.7             openmpi-1.4.1        sge-mac

After looking at the "amber" modules you will probably be interested in running the program pmemd (included in AMBER11). So, for having AMBER11 programs ready we do:

> module load amber-11

And now we can run it directly by doing:

> pmemd