Software installed on the cluster

There are application and programming tools for different scientific fields installed on the cluster.

Open source application software: 

Engineering

  • ANSYS (2019-R1)
  • Comsol Multiphysics (ver. 5.3a)
  • MathWorks MATLAB (ver. R2018b)
  • Network-simulator NS-2 (ver. 2.34)
  • OpenFoam (ver. 2.4, 5.0)
  • Peridigm (ver. 1.5)
  • SalomeMeca (ver. 2015)
  • Scilab (ver. 5.4) 

Computational chemistry

  • CP2K (v6.1)
  • GROMACS (ver. 2018-2)
  • Schrodinger (2018-4)2020-2)  

Bioinformatics/genomics

  • bcl2fastq (ver. 1.8.4)
  • Bcftools (ver. 1.10.2)
  • Bowtie2 (ver. 2.4.1) 
  • Bracken (ver. 2.5) 
  • Kraken2 (ver. 2.0.9-beta) 
  • Samtools (ver. 1.9, 1.10) 
  • STAR (ver. 2.7.5c 

Other

  • Agisoft PhotoScan   
  • Blender (ver. 2.7)  
  • Hashcat 
  • R (ver. 3.4.0, 3.5.3, 3.6.3) 

Programming tools and compilers 

  • Perl (ver. 5) 
  • GNU Compiler Collection (ver. 4.8.5, 5.4.0,7.3.0, 8.3.0) 
  • OpenMPI (ver. 1.10.7, 3.1.1) 
  • Conda/Anaconda (ver. 4.7.5) 
  • CUDA Toolkit (ver. 8.0, 9.2, 10.1)  
  • Python (ver. 2.7, 3.6) 
  • Intel Parallel Studio (ver. 2015)/ IntelMPI (ver. 4.0.3) 
  • Jaer 1.8.1 

At the users request, additional application software or another other version may be installed. Centos, EPEL, and OpenHPC repositories are used on the cluster. They allow administrators to  install a range of pre-compiled applications quickly and easily. Tools included in the OpenHPC repository can be found in the following list: https://github.com/openhpc/ohpc/wiki/Component-List-v1.3.8. 

Users can install/compile the software themselves in their user area if the installation process does not require administrator (root) rights.

Check the cluster directory for examples of application usage and task scripts: /opt/exp_soft/user_info 

For some applications, user manuals are provided on the HPC Center’s web page: https://hpc.rtu.lv/hpc/hpc-software/?lang=en