Software

All MCSR systems currently run SUSE Linux Enterprise Server (SLES) 12.

The two SGI systems, Sequoia and Catalpa, are very similar with regard to their software. However, Maple is a Cray system that uses the Bright Cluster Manager, and it is somewhat different from the other two.

All system use modules to easily allow users to bring various software packages into their environment. The command
module avail
will show all modules available on a system. To load a package, run
module load packagename

Most application-specific, locally-installed software can be found in /usr/local/apps. Some of this software is available via modules, some is not. See Running Jobs for information about using PBS.

Software installed on our systems include:

• Bioinformatics: Abyss, ALE, antiSMASH, anvi’o, Autometa, BAli-Phy, Bandage, BBMap, BEAST, Bedtools, BiG-SCAPE, BLAST, BlobTools, BRAT NextGen, Burrows-Wheeler Aligner, BUSCO, Canu, CD-HIT, CheckM, Circlator, ClonalFrameML, Concoct, D’accord, DeepBGC, EMBOSS, EMSAR, EukCC, EukDetect, ezTree, FastANI, FastSimBac, FastTree, FastQC, FGMP,  Filtlong, FMLRC, Gblocks, GeneMark-ES/ET/EP, Genome Analysis Toolkit (GATK), GMAP/GSNAP, HMMER, htseq, IDBA, IGVTools, InterProScan, IQTree, Kaiju, Krona Tools, MEGAHIT, MetaBGC, MetaPhlAn, Minimap2, MOCAT, MOPAC, MOTHUR, MultiQC, MUMmer, OpenThermo, Orthofinder, PacBio Tools, Pilon, PPanGGOLiN, PBSuite, phyloFlash, Picard, Picrust, pplacer, Prodigal, Prokka, QUAST, QIIME2, RAxML, REAPR, SamTools, Seq-Gen, Sickle, SimBac, SolidBin, SPAdes, SqueezeMeta, SRA Toolkit, SSU-ALIGN, STAR, Subread, Trimmomatic, UGENE, Unicycler
• Chemistry: ACES, Amber, CFOUR, GAMESS, Gaussian, Molden, Molpro, NWChem, Orca, Quantum Espresso, Siesta
• Frameworks/Libraries: CUDA, Intel MKL, LAPACK, MPI, OpenCL, OpenMP, ScaLAPACK
• Languages: C/C++, Fortran, Intel Compilers, Java, Julia, MATLAB*, Mathematica*, Python, R
• Machine Learning: TensorFlow
• Math/Statistics: MACEK, Mathematica*, R
• Molecular Dynamics: GROMACS, LAMMPS, NAMD
• Physics/Engineering: Abaqus, Materials Studio, MATLAB*
• Utility: AWS CLI

* – Only available to MCSR users at the University of Mississippi

Please send us an email if you would like software installed, modules created for existing software, or need help running software.