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Millipede cluster user guide: Available software

Application software

The following applications have been installed on millipede and can be used afterloading the corresponding module.

  • A set of bioinformatics software (ABySS, bedtools, bowtie, bwa, cufflinx, fastqc, fastx, gmap-gsnap, samtools, tophat, trinity)
  • Gamess-US
  • Gromacs
  • Matlab
  • Meep
  • Nwchem
  • R
  • root
  • SPSS
  • Stata SE
  • And others ....

Some commercial software has been installed for a specific group or faculty and has not been listed here.

Please contact us if you need help with installlation of the software you use.

Compilers

If you have your own software or want to install software using source code you can make use of several compilers. Most software will support the GNU compilers suite.

The following compilers are available on the system:

  • GNU compilers. Standard compiler suite on Linux systems;
  • Intel compilers. High performance compiler developed by Intel;
  • Open64 compilers. Compiler suite recommended by AMD;
  • Pathscale compilers.

MPI libraries

For parallel programs several MPI libraries are available on the system:

  • LAM. LAM MPI implementation. Officially superseded by OpenMPI;
  • MPICH. MPI-1 implementation; MPICH2. Implementation of MPI-1 and MPI-2;
  • MVAPICH. MPI-1 implementation using the Infiniband interconnect;
  • MVAPICH2. MPI-1 and MPI-2 implementation using Infiniband interconnect;
  • OpenMPI. OpenMPI MPI implementation of MPI-1 and MPI-2, supports both Infiniband and the torque scheduler for starting processes.

Since the cluster is equipped with an Infiniband interconnect the MVAPICH2 and OpenMPI implementations are the two recommended ones to use. Note that there are versions specific to the different compilers installed.

The following command will load OpenMPI for the intel compiler into your environment:

$ module add openmpi/intel

Last modified:02 October 2015 10.23 p.m.