Software

Manually installed scientific software is located in the /storage/software branch, where a separate folder exists for each application (mostly appname-version). This is accessible from all machines inside the clusters.

In case you wish to use software that is currently not present on the clusters and it is either difficult to install or would be useful to a larger number of people, feel free to contact support@hpc.ut.ee. Small binary files, “out-of-the-box” solutions that simply need unpacking to work, and other programs from trusted sources that are easy to install locally can simply be placed in the user’s home folder and run from there.

Some applications may require the user’s environment to be modified in order to be run. To make this process easier for the users, a package called modules has been installed on all of our clusters. It allows for dynamic modification of the user’s environment, such as setting up necessary environment variables for a specific application. (See example.)

Before trying to use anything under /storage/software, please take a look at module avail first. It might very well be that the software you want to use has already an environment module written for it.

Please do not use the following environment modules: intel_compiler, intelmpi. These are only neccessary to provide backwards compatibility for certain applications, and are otherwise completely replaced by the newer module intel_cluster_studio.

Some modules also load other modules that are required for their operations. In case you are unsure on what exact modules are currently loaded, you can always use module list.

Useful commands to know when using modules (NB! [module name] is case sensitive):

  • module avail – shows all available environment modules
  • module avail [(beginning of) module name]  – shows modules with names that begin with the desired pattern
  • module list – shows modules currently loaded into the environment
  • module load [module name] – loads the specified module into the environment
  • module rm [module name] – removes the specified module from the environment
  • module purge – removes all modules currently loaded into the environment
  • module – displays help

Available Software

  1. Intel Parallel Studio XE 2015

The following is a list of different scientific software available on the cluster.
This list is wont to be neither complete nor up-to-date, but can nevertheless be used to get a quick overview..

 Name  Version  Location  Modulefile
 Comsol  3.5  /storage/software/comsol35  –
 3.5a  /storage/software/comsol35a  –
 4.0  /storage/software/comsol40  –
 4.0a  /storage/software/comsol40a  –
 4.2  /storage/software/comsol42  –
 4.3a  /storage/software/comsol-4.3a  comsol-4.3a
 4.3b  /storage/software/comsol43b  –
 4.4  /storage/software/comsol-4.4  comsol-4.4
 5.0  /storage/software/comsol-5.0  –
 Gromacs
 4.5.2  /storage/software/gromacs-4.5.2  –
 4.5.4  /storage/software/gromacs-4.5.4  –
 4.5.7  /storage/software/gromacs-4.5.7  gromacs-4.5.7
 4.6.1  /storage/software/gromacs-4.6.1_intel
/storage/software/gromacs-4.6.1_vedur
 gromacs-4.6.1-intel
 R
 2.12.1  /storage/software/R-2.12.1  –
 2.13.1  /storage/software/R-2.13.1  –
 2.14.0  /storage/software/R-2.14.0  –
 2.15.0  /storage/software/R-2.15.0  R-2.15.0
 3.0.0  /storage/software/R-3.0.0  R-3.0.0
 3.0.2  /storage/software/R-3.0.2  R-3.0.2
 3.1.0  /storage/software/R-3.1.0  R-3.1.0
 3.1.1  /storage/software/R-3.1.1  R-3.1.1
 3.1.2  /storage/software/R-3.1.2  R-3.1.2
 3.2.0  /storage/software/R-3.2.0  R-3.2.0
 3.2.2  /storage/software/R-3.2.2  R-3.2.2
 3.3.0  /storage/software/R-3.3.0  R-3.3.0
 3.3.2  /storage/software/R-3.3.2  –