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Below are the list of software that are installed in the cluster.

All the software are installed under /opt file-system of the cluster.

We are using CentOS-6.7 64-bit as the Operating System in the cluster.

Compilers
Software Version Binary Path
Cuda 6.5 /root/cuda-drivers in GPU nodes /usr/local/cuda/bin/nvcc/

 

Parallel Scientifc Libraries
Software Version Binary Path
Magma 1.6.0 -
Paralution 1.0 /opt/paralution/1.0/paralution-1.0.0/build/bin

 

High Fidelity Multi-Physics Computational Engineering Softwares
Commercial
Software Version Binary Path
Gaussian Version 09
Revision E.01
/opt/Gaussian09/G09/tar/g09/g09
ANSYS 14.5 /opt/ANSYS/ansys_inc/v145

STAR-CCM+

9.06 /opt/CD-adapco/STAR-CCM+9.06.009/star/bin/starccm+
10.04 /opt/CD-adapco/STAR-CCM+10.04.009/star/bin/starccm+
Open Source
Software Version Binary Path
Charmm 39 /opt/charmm/em64t_M; Download sample_charmm_script.txt (will provide soon)
Quantum Espresso 5.4.0 /opt/QuantumEspresso/pkgs/espresso-5.4.0/bin/pw.x
NAMD 2.10 /opt/NAMD/NAMD_2.10b2_Linux-x86_64/namd2
OpenFOAM 2.2.2 /opt/openfoam1/OpenFOAM-2.2.2/bin
Palabos 1.4r1 -

DEAL.II

8.3.0 /opt/Deal2-8.3_14Aug2015/dealii-8.3.0/bin/mesh_converter
Sailfish   -
SU2 3.2.2  
MACS   /opt/umas_sw/macs/MACS-1.3.7.1/bin/macs
Samtools 1.3 /opt/umas_sw/samtools/samtools-1.3/samtools
bedtools 2.25.0 /opt/umas_sw/bedtools/bedtools2/bin/bedtools
cufflinks 2.2.1 /opt/umas_sw/cufflink/cufflinks-2.2.1.Linux_x86_64/cufflinks
seqmonk 0.33 /opt/umas_sw/seqmonk/seqmonk/SeqMonk/seqmonk
bedgraph   /opt/umas_sw/bedgraph/bedGraphToBigWig
R 3.3.0 /opt/umas_sw/R-software/R/bin/R
fastqc 0.11.5 /opt/umas_sw/fastqc/FastQC/fastqc
Bismark 0.16.1 /opt/umas_sw/bismark/bismark_v0.16.1
FatsX 0.0.13 /opt/umas_sw/fastx/bin
Bowtie 2.2.9 /opt/umas_sw/bowtie/bowtie2-2.2.9
Meme 4.11.2 /opt/umas_sw/meme/meme_4.11.2/src
Homer 4.8.3 /opt/umas_sw/homer/bi
BWA 0.7.15 /opt/umas_sw/bwa-0.7.15/bwa-0.7.15/bwa

 



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