Software Available Through MCSR
MCSR offers support for numerous software systems.
All MCSR systems use software modules. Run module avail to browse available packages and module load packagename to load one.
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
* MATLAB and Mathematica are listed by MCSR as available only to MCSR users at the University of Mississippi.
BBMap
MCSR systems: All systems
Maple: module load bbmap; Sequoia/Catalpa: add /usr/local/apps/bbmap to PATH and load javaBEAST
MCSR systems: Maple; Sequoia/Catalpa
Maple: module load beast; Sequoia/Catalpa: version 2.3.0 without moduleBUSCO
MCSR systems: Maple
module load python; source activate busco (4.0.6); older 3.x via busco modulephyloFlash
MCSR systems: Maple
export PHYLOFLASH_DBHOME=/ddn/home2/appl/138; module load python/3; source activate phyloflashGaussian
MCSR documentation mentions Gaussian 09 on Sequoia and Gaussian 16 (Revision C.01) on Maple. Multi-core jobs are limited to a single node.
Gaussian 09 is installed on Sequoia; Gaussian 16 Revision C.01 is installed on Maple. Jobs may use multiple cores on one node, but cannot span multiple nodes. The Maple installation does not support its GPUs.
Example jobs
Sequoia/Catalpa: /usr/local/apps/example_jobs/g09_sequoia_example. Maple: /usr/local/apps/example_jobs/g16_maple_example. Sequoia/Catalpa also provide the g09sub job-submission helper.
Interactive setup on Sequoia / Catalpa
export g09root=/usr/local/apps/source $g09root/g09/bsd/g09.profileInteractive setup on Maple
export g16root=/usr/local/apps/gaussian/g16-c01-avx. $g16root/g16/bsd/g16.profileMolpro
Available on all systems. The MCSR page lists Molpro 2019.02 on Maple.
module load molproMolpro is available on all MCSR systems, with example jobs provided. On Maple, version 2019.02 (Patch Level 3) is available.
module load molproNWChem
Available on all systems; MCSR lists version 7.0.0 on Maple.
module load nwchemNWChem is available on all systems. Maple has version 7.0.0, accessible through the nwchem module.
module load nwchemTo install the default NWChem configuration in your home directory:
cp /usr/local/apps/nwchem/7.0.0/data/default.nwchemrc ~/.nwchemrcIntel MKL
Intel Math Kernel Library (MKL), with optimized numerical libraries.
module load intel/mklMCSR provides Intel C (icc), C++ (icpc), and Fortran (ifort) compilers. Some programs may require adjustments to compile with Intel rather than GNU compilers.
Maple
module load intel/compilerIntel Math Kernel Library (MKL) includes optimized routines such as BLAS, LAPACK, and FFTW.
module load intel/mklSequoia / Catalpa
module load intelIntel Compilers
C, C++ and Fortran compilers. The MCSR page gives separate commands for Maple and Sequoia/Catalpa.
Maple: module load intel/compilerSequoia/Catalpa: module load intelMCSR provides Intel C (icc), C++ (icpc), and Fortran (ifort) compilers. Some programs may require adjustments to compile with Intel rather than GNU compilers.
Maple
module load intel/compilerIntel Math Kernel Library (MKL) includes optimized routines such as BLAS, LAPACK, and FFTW.
module load intel/mklSequoia / Catalpa
module load intelPython
Anaconda Python is available on MCSR systems.
module load pythonThe operating-system Python is available by default for basic scripts. For Anaconda Python, IPython, and packages such as NumPy, SciPy, matplotlib, and pandas, load the Python module.
module load pythonCreating and using a Conda environment
conda create --name name_of_environmentsource activate name_of_environmentconda install package_namesR
R modules are available for statistics and data analysis.
module load RR is available on most systems. The R module provides the most recent version available on a system.
module load RUse a scheduled or interactive PBS session to run R on the compute systems. Additional packages can be installed in your home directory.
Install a package from within R
install.packages("package_name")If a previously installed package is missing, check the system and R version; packages may need to be reinstalled for a newer R version.
R
R modules are available for statistics and data analysis.
module load RR is available on most systems. The R module provides the most recent version available on a system.
module load RUse a scheduled or interactive PBS session to run R on the compute systems. Additional packages can be installed in your home directory.
Install a package from within R
install.packages("package_name")If a previously installed package is missing, check the system and R version; packages may need to be reinstalled for a newer R version.
GROMACS
The MCSR documentation lists an MPI-enabled GROMACS 2020 installation on Maple.
An MPI-enabled installation of GROMACS 2020 is available on Maple. MCSR notes that its example job is incomplete. Other systems have older GROMACS installations.
AWS CLI
Amazon Web Services command-line interface on Maple.
module load awscliThe Amazon Web Services command-line tool is available on Maple.
module load awscli