Software Installed on the Cluster
This section gives a summary of the scientific software installed on the HPC cluster.
Engeneering
ANSYS (2023-R2)
ANSYS Electronics Desktop(2023 [includes ansys HFSS])
Comsol Multiphysics (ver. 5.3a)
FreeFEM (ver. 4.10)
Gmsh (ver. 4.11)
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 (ver. 6.1)
Crystal explorer (ver. 21.3)
CSDS (ver.2022)
Gaussian (ver. g09_d01)
GROMACS (ver. 2018-2, 2021, 2022.3)
Gulp (ver.6.0, 6.1.2)
Jmol (ver.14.30.2)
Mopac (ver.2016)
NAMD (ver.2.14-multicore-cuda)
NWChem(ver. 7.0.2-conda)
ORCA (ver.4.2.1, 5.0.1)
Plumed (ver. 2.5.0, 2.7.2)
Pycharm(ver. 2020.2.3)
Pymol (ver. 2.3.0, 2.5.0)
Schrodinger (ver.2018-4, 2022-1, 2022-4, 2023-2)
VMD (ver.1.9.3 )
Bioinformatics/Genomics
Bcftools (ver. 1.10.2)
Bcl2fastq (ver. 1.8.4, 2.20.0)
Bedops (ver. 2.4.39)
Bedtools (ver. 2.29.2)
Bowtie2 (ver. 2.4.1, 2.4.2)
Bracken (ver. 2.5)
Chopper (ver. 0.3.0)
Cutadapt (ver. 3.5)
DeepVariant (ver. 1.0.0)
Diamond (ver. 2.0.3)
Dorado (ver. 0.1.1)
Drop (ver. 1.1.4)
Fastp (ver. 0.21.0)
Fastqc (ver. 0.11.9)
GATK4 (ver. 4.1.8.1)
HTseq (ver. 0.11.3)
HTSlib (ver. 1.11)
Humann2 (ver. 2.81)
Kraken2 (ver. 2.0.9-beta)
Lofreq (ver. 2.1.5)
Mafft (ver. 7.471)
Medaka (ver. 1.7.3)
Metaphlan2 (ver. 2.6.0, 2.7.7)
Metaphlan3 (ver. 3.0.2)
Metaphlan4 (ver. 4.0.6)
Nanofilt (ver. 2.8.0)
Plink (ver. 1.90b6.21)
Raven (ver. 1.8.1)
Saige (ver. 0.44.6.5)
Samtools (ver. 1.9, 1.10)
SRA Toolkit (ver. 3.0.1)
STAR (vera2.7.5c)
Strelka2 (ver. 2.9.10)
Trapd
Trimmomatic (ver. 0.39)
VEP (ver. 101)
Varscan (ver. 2.4.4)
Vcgtools (ver. 0.1.17)
Vep (ver. 101, 104.3, 108.2
Vsearch (ver. 2.15.0)
Other
Agisoft PhotoScan
Apptainer (ver. 1.1.6)
Blender (ver. 2.7)
Git (ver. 1.8.3.1. 2.41.0)
Hashcat
R (ver. 3.4.0, 3.5.3, 3.6.3,4.1.0)
Singularity (ver. 3.2.1, 3.4.1, 3.11.4)
Programming tools and compilers
Conda/Anaconda (ver. 4.7.5, 4.7.10, 4.13.0, 23.1.0)
CUDA Toolkit (ver. 8.0, 9.2, 10.1, 11.4), cuDNN
GNU Compiler Collection (ver. 4.8.5, 5.4.0,7.3.0, 8.3.0)
Intel Parallel Studio (ver. 2015)/ IntelMPI (ver. 4.0.3)
Jaer 1.8.1
OpenMPI (ver. 1.10.7, 3.1.1, 4.0.5, 4.1.1)
Mamba (1.4.4)
Perl (ver. 5)
Python (ver. 2.7, 3.6)
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: OpenHPC.
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.