List of Softwares

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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 Download Script
ANSYS	14.5	/opt/ANSYS/ansys_inc/v145
STAR-CCM+	9.06	/opt/CD-adapco/STAR-CCM+9.06.009/star/bin/starccm+ Download Script
STAR-CCM+	10.04	/opt/CD-adapco/STAR-CCM+10.04.009/star/bin/starccm+ Download Script
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 Download Script
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