The SCC uses Software Environment Modules to make a lot of additional software packages available. These software packages should be favored to local installed software because they are optimized for performance and available options and will not change with updates. Also you can try several versions including the latest available. Of course the local installed software can be used too (availability depends on openSUSE version) and the known commands (like /software/bin/mathematica) still work.
Environment modules allow for setting the environment to use additional software packages and easily switch between multiple versions. These modules work on any computer in the cluster. A few packages can be automatically loaded on startup by using module load default-modules. Using module commands in a terminal only affects the environment within that terminal. Another login or a job submitted will remain unaffected by these commands. To make your configuration permanent on all nodes, the commands can be placed in $HOME/.bashrc. If the module command is not available on your computer please type . /etc/profile.d/modules.sh before using it.
| Command | Function | Example |
|---|---|---|
| module av <category> | shows all available packages | module av gsl |
| module li | shows all loaded packages | |
| module purge | remove all loaded packages | |
| module load [pkg] | loads package [pkg] and all dependencies | module load mkl |
| module rm [pkg] | removes package [pkg] and all dependencies | module rm mkl |
| module swap [pkg1] [pkg2] | switch from package [pkg1] to package [pkg2] | module swap gsl gsl/1.14 |
| module whatis [pkg] | short info about package [pkg] | module whatis mkl |
| module help [pkg] | long info about package [pkg] | module help mkl |
| module show [pkg] | show settings of package [pkg] | module show mkl |
| Category | Description | Contents |
|---|---|---|
| cluster | Cluster software | mpich2, openmpi, ... |
| compiler | Compiler | GNU, Intel, Oracle, Pathscale, ... |
| devel | Development packages | cmake, eclipse, python, ... |
| lib | standard libraries | boost, hdf5, cuda, ... |
| numlib | numerical libraries | gsl, mkl, fftw, ... |
| math | mathematical packages | Matlab, Mathematica, octave, ... |
| phys | physics packages | abinit, cpmd, lammps, octopus, ... |
| chem | chemistry packages | gaussian, gromacs, nwchem, ... |
| bio | biology packages | bcftools, bowtie, mothur, ... |
| sys | system packages | glib, gtk+, qt, ... |
| vis | visualisation packages | gnuplot, povray, vmd, ... |
$ module avail
...
intel/12.1
...
$ module whatis intel/12.1
intel/12.1 : Intel(R) compiler suite (icc, icpc, ifort), debugger (idb), IPP and TBB ver 12.1.1.256
$ module load intel/12.1
$ module list
intel/12.1
$ which icc
/software/packages/intel-2011sp1u1/composer_xe_2011_sp1.7.256/bin/intel64/icc
Remark: using module load intel will always load the default version (marked with (default)).
If you need further software packages or other versions or find a bug anywhere, just let us know.