Software installed on the cluster

This section gives a summary of the scientific software installed on the HPC cluster.

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)
• Gmol (ver.14.30.2)
• Orca (ver.4.2.1)
• Plumed (ver. 2.5.0)
• Schrodinger (2018-4, 2020-2)

Bioinformatics/genomics

• Bcftools (ver. 1.10.2)
• Bcl2fastq (ver. 1.8.4)
• Bedtools (ver. 2.29.2)
• Bowtie2 (ver. 2.4.1, 2.4.2)
• Bracken (ver. 2.5)
• DeepVariant (ver. 1.0.0)
• Diamond (ver. 2.0.3)
• Fastp (ver. 0.21.0)
• Fastqc (ver. 0.11.9)
• GATK4 (ver. 4.1.8.1)
• HTClib (ver. 1.11)
• Humann2 (ver. 2.81)
• Kraken2 (ver. 2.0.9-beta)
• Mafft (ver. 7.471)
• Metaphlan2 (ver. 2.6.0, 2.77)
• Metaphlan3 (ver. 3.02)
• Plink (ver. 1.90b6.21)
• STAR (vera2.7.5c)
• Samtools (ver. 1.9, 1.10)
• Strelka2 (ver. 2.9.10)
• Trapd
• Trimmomatic (ver. 0.39)
• VEP (ver. 101)
• Varscan (ver. 2.4.4)
• Vcgtools (ver. 0.1.17)

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, 3.0)
• OpenMPI (ver. 1.10.7, 3.1.1, 4.0.5)
• Conda/Anaconda (ver. 4.7.5)
• CUDA Toolkit (ver. 8.0, 9.2, 10.1, 10.2), cuDNN
• Python (ver. 2.7, 3.6)
• Intel Parallel Studio (ver. 2015)
• IntelMPI (ver. 4.0.3)
• Jaer 1.8.1

On request, additional software or other versions may be installed. Centos, EPEL, and OpenHPC repositories are used on the cluster. Tools available through the OpenHPC repository can be found in the following list: https://github.com/openhpc/ohpc/wiki/Component-List-v1.3.8.

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

Check the cluster directory /opt/exp_soft/user_info for the examples of software usage and job batch scripts.