Academic and Research Computing Systems


High Performance Computing Applications


HPC Applications
name desc versions website module cmd execute cmd path to s/w doc notes
Category : computational chemistry
gaussian03

gaussian09

Link 03

09

Link module load gaussian03

module load gaussian09

/afs/cad/sw.common/bin/{gaussian, gaussian03, guassian09} /afs/cad/linux/gaussian03/g03

/afs/cad/linux/gaussian09/g09

Link ---
Category : math & stats
matlab Link 2013a Link module load matlab /afs/cad/sw.common/matlab-2013a/bin/matlab /afs/cad/sw.common/matlab-2013a Link In submit script :
matlab -nojvm -nosplash < /path/to/matlab_script
R Link 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
3.0.1 (2013-05-16) -- "Good Sport"
Link module load R-2.15.1

module load +versions; module load R-3.0.1

/afs/cad/sw.common/bin/R /afs/cad/linux/R-<version> Link ---
RStudio Link 0.97 Link module load RStudio /afs/cad/sw.common/bin/rstudio /afs/cad/linux/Rstudio-0.97 Link ---
SAS Link 9.3 Link module load sas /afs/cad/sw.common/bin/sas /afs/cad/sw.common/sas-9.3/SASFoundation/9.3/bin/sas_en Link The program to run is named sas_en
SPSS Link 22 Link module load spss /afs/cad/sw.common/bin/spss /afs/cad/sw.common/spss/22/bin/stats Link The program to run is named stats
Category : molecular modeling
vmd Link 2.0.7 Link module load vmd vmd /afs/cad/linux/vmd-1.9.1 Link ---
Category : molecular dynamics
gromacs Link 4.5.5
4.6.3
Link module load gromacs-4.5

module load gromacs-4.6

/afs/cad/hpc/amd/opt/gromacs/4.5.5-gcc-4.4.4-openmpi/bin/*

/afs/cad/linux/gromacs-4.6.3_kong_openmpi-gnu4/bin/*

/afs/cad/hpc/amd/opt/gromacs/4.5.5-gcc-4.4.4-openmpi/bin

/afs/cad/linux/gromacs-4.6.3_kong_openmpi-gnu4/bin

Link ---
lammps Link 14.5 Link module load lammps /afs/cad/sw.common/bin/lammps /afs/cad/linux/lammps/src/lmp_openmpi Link ---
Category : sequencing
bowtie Link 0.12.9 Link module load bowtie 'bowtie --help' or 'bowtie-build --help' /afs/cad/linux/bowtie-0.12.9 Link ---
bowtie2 Link 2.0.5 Link module load bowtie2 'bowtie --help' or 'bowtie-build --help' /afs/cad/linux/bowtie2-2.0.5 Link ---
bwa Link 0.7.5a Link module load bwa bwa /afs/cad/linux/bwa-0.7.5a/bwa Link ---
cufflinks Link 2.0.2 Link module load cufflinks cufflinks /afs/cad/linux/cufflinks-2.0.2/cufflinks Link “module load cufflinks” also makes available : cuffcompare, cuffdiff, cuffmerge
samtools Link 0.1.18 Link module load samtools samtools /afs/cad/linux/samtools-0.1.18-2 Link ---
tophat Link 2.0.7 Link module load tophat tophat /afs/cad/linux/tophat-2.0.7 Link “module load tophat” also makes available : bam_merge, bam2fastx, bed_to_juncs, contig_to_chr_coords, fix_map_ordering, gtf_juncs, gtf_to_fasta, juncs_db, long_spanning_reads, map2gtf, prep_reads, sam_juncs, sra_to_solid, tophat_reports, tophat-fusion-post
name desc versions website module cmd execute cmd path to s/w doc notes