CHPC Software Database

This is a database of the software supported at the CHPC. By clicking on the column headings, you will sort on that column. You can search on any term in the database and it will return all of the matches to that term in the database. Here are brief descriptions of the Columns:

  • Package: name of package
  • Version: the version(s) installed; versions surrounded by parentheses indicate the default version of the package.
  • Category: broad categorization of the package with four possible entries - Applications, Programming Tools, Libraries and Utilities
  • Cluster: cluster on which the software can be run - all, kingspeak, ash, ember
  • Tag: additional categorization which can be used to narrow searches, based on the functionality of the package
  • Info Link: link to the software's website
  • Module: Indicates whether the software is set up with Modules. More information about modules can be found here
  • Restriction: Package only available to users of group with license
  • Install Path: location of the package
  • Contact: CHPC staff person responsible for installation. If not listed, please contact issues@chpc.utah.edu
  • Expertise: Expertise level of Contact person; Installation only, novice user, intermediate user, experienced user
To navigate your way through this table: click on the table then use arrows to see further columns
Package Versions Category Cluster Tag Info Link Module Restriction Install Path Contact Expertise Level Note
Package Versions Category Cluster Tag Info Link Module Restriction Install Path Contact Expertise Level Note
7zip 9.13 Utilities All File compression /uufs/chpc.utah.edu/sys/pkg/7zip Martin Cuma Installation Only
abaqus 6.14-1, 6.14-2 Applications All Computer aided engineering, finite element /uufs/chpc.utah.edu/sys/installdir/abaqus Martin Cuma, Anita Orendt Installation Only, Installation Only
acml 2.7.0, 3.0.0, 4.0.0, 4.1.0, 4.4.0 Libraries All Math /uufs/chpc.utah.edu/sys/pkg/acml Wim Cardoen Intermediate User Not being updated, part of PGI compiler install, for best performance use Intel MKL instead
aladin 7.015b Applications All Astronomy /uufs/chpc.utah.edu/sys/pkg/aladin
allpaths-lg 52488 Applications all genomics /uufs/chpc.utah.edu/sys/installdir/allpaths-lg Anita Orendt Installation Only
amber amber14-GPU Applications ember chemistry, molecular dynamics, Computational chemistry, CUDA /uufs/ember.arches/sys/pkg/amber/amber14-cuda Wim Cardoen Installation Only
amber amber14 Applications All chemistry, molecular dynamics /uufs/chpc.utah.edu/sys/installdir/amber/amber14 Wim Cardoen, Anita Orendt Installation Only, Novice User
amber amber15 (amber14 with ambertools15) Applications All chemistry, molecular dynamics /uufs/chpc.utah.edu/sys/installdir/amber/amber15 Anita Orendt Novice User This is the build of amber14 with ambertools15
anaconda (python) 4.3.0 (Python 2.7.13, 3.6.0) Programming Tools All Python /uufs/chpc.utah.edu/sys/installdir/anaconda Wim Cardoen Installation Only
angsd 0.917, 0.916, 0.911 Applications all genomics, Genomic analysis /uufs/chpc.utah.edu/sys/installdir/angsd Anita Orendt Installation Only
ansys 12.1, 14.0, 14.5, 15.0, 16.1 17.1(D) Applications All engineering, fluid dynamics, computational fluid dynamics, Computer aided engineering, C, Finite difference /uufs/chpc.utah.edu/sys/installdir/ansys Martin Cuma, Anita Orendt Installation Only, Installation Only versions older than 15.0 are in /uufs/chpc.utah.edu/sys/pkg/ansys
Ansys Electronics Desktop 16.1, 17 /uufs/chpc.utah.edu/sys/installdir/ansysedt Martin Cuma Installation Only
apache-ant 1.9.7 Programming Tools All /uufs/chpc.utah.edu/sys/installdir/apache-ant Anita Orendt Installation Only
asciidoc 8.6.9 Utilities All Text editor /uufs/chpc.utah.edu/sys/installdir/asciidoc Wim Cardoen Installation Only
autoconf 2.69 Applications All Build tools /uufs/chpc.utah.edu/sys/installdir/autoconf Martin Cuma, Wim Cardoen Intermediate User, Intermediate User Built on CentOS6 due to it having older version.
autodock 4.2.5.1 Programming Tools All chemistry, Molecular Docking /uufs/chpc.utah.edu/sys/pkg/autodock Anita Orendt Novice User
avbin 7, 8.1 Utilities All Video Decoding /uufs/chpc.utah.edu/sys/pkg/avbin Martin Cuma Installation Only
AVL 2013.1 Applications All engineering, fluid dynamics, computational fluid dynamics /uufs/chpc.utah.edu/sys/pkg/AVL Anita Orendt Installation Only
Bazel 10/27/2016, 0.5.1
(D)
Applications All Build tools, Compilers, Compilers and Tools, C, Tools /uufs/chpc.utah.edu/sys/installdir/bazel/10272016/output Wim Cardoen Installation Only
bbcp 10.08.29.00.0, 12.08.17.00.0 Utilities All File transfer /uufs/chpc.utah.edu/sys/pkg/bbcp Martin Cuma Installation Only
bcftools 1.6 Applications all genomics /uufs/chpc.utah.edu/sys/installdir/bcftools Anita Orendt Installation Only
bcl2fastq2 2.17 Applications All genomics /uufs/chpc.utah.edu/sys/installdir/bcl2fastq2 Anita Orendt Installation Only
bedtools 2.24.0 Applications all Genetics, Genomic analysis /uufs/chpc.utah.edu/sys/installdir/bedtools Anita Orendt Installation Only 2.17.0 version installed in /uufs/chpc.utah.edu/sys/pkg
berkeley-nlp 1.1 Applications All Bioinformatics, Natural Language Processing /uufs/chpc.utah.edu/sys/pkg/berkeley-nlp
bernese BERN50 Applications All Astronomy, Global Navigation /uufs/chpc.utah.edu/sys/pkg/bernese Martin Cuma Installation Only
binutils 2.25 Programming Tools All Build tools /uufs/chpc.utah.edu/sys/installdir/binutils Martin Cuma Novice User Needed for AVX aware builds on CentOS6
bioperl 1.5.1, 1.6.1 Programming Tools all genomics /uufs/chpc.utah.edu/sys/pkg/bioperl/ Martin Cuma Installation Only
bismark v0.17.0, v0.12.2 Applications All genomics /uufs/chpc.utah.edu/sys/installdir/bismark Anita Orendt Installation Only Older version in /uufs/chpc.utah.edu/sys/pkg/bismark
blacs 1.1 Libraries All Math /uufs/chpc.utah.edu/sys/pkg/blacs Martin Cuma Intermediate User
blast 2.3.0+ Applications All Genomic sequencing, Genomic alignments /uufs/chpc.utah.edu/sys/installdir/blast Anita Orendt Installation Only Note -- have automatically updated ncbi databases in /uufs/chpc.utah.edu/32bit-sys/pkg/blastdb; module sets BLASTDB variable
blat 34 Applications All Genomic sequencing, Genomic alignments /uufs/chpc.utah.edu/sys/pkg/blat Anita Orendt Installation Only
boost 1.54.0, 1.58.0(i) (D), 1.59.0 (g) (D), 1.60.0 (Py 2.7.3) Libraries C++, C Wim Cardoen Intermediate User
boost 1.54.0 Libraries kingspeak C++ /uufs/kingspeak.peaks/sys/pkg/boost Wim Cardoen Intermediate User
boost 1.54.0 Libraries Ember C++ /uufs/ember.arches/sys/pkg/boost Wim Cardoen Intermediate User
boost 1.54.0 Libraries Ash C++ /uufs/ash.peaks/sys/pkg/boost Wim Cardoen Intermediate User
bowtie v1-0.12.5, v2-2.0.0-beta7 Applications All Genomic alignments /uufs/chpc.utah.edu/sys/pkg/bowtie Anita Orendt Installation Only
bsoft 1_8_6 Applications All Structural biology /uufs/chpc.utah.edu/sys/pkg/bsoft/ Anita Orendt Installation Only
bwa 0.7.10 Applications All genomics /uufs/chpc.utah.edu/sys/pkg/bwa Anita Orendt Installation Only
bzip2 1.0.6 Libraries All File compression /uufs/chpc.utah.edu/sys/installdir/bzip2/1.0.6 Wim Cardoen Installation Only
Cadence ~ 2015 Applications engineering /uufs/chpc.utah.edu/sys/installdir/cadence Martin Cuma Installation Only
cantera 2.2.0(D), 2.1 Applications All engineering, chemistry, Python /uufs/chpc.utah.edu/sys/installdir/python/2.7.10-4.9.2g Wim Cardoen Installation Only Version 2.2.0 was installed to be used with Python 2.7.10 (gcc 4.9.2). For new installations, please read the caveats.
carpy 2013-06-17 Applications All Python, Astronomy /uufs/chpc.utah.edu/sys/installdir/carpy/CarPy Wim Cardoen Installation Only
cbc 2.9.7 Library All Applied Math /uufs/chpc.utah.edu/sys/installdir/cbc/2.9.7 Wim Cardoen Installation Only
CCP4 6.4.0 Applications All Crystallography tools /uufs/chpc.utah.edu/sys/pkg/CCP4 Anita Orendt Installation Only
cctools 6.1.1 Applications All Batch Systems /uufs/chpc.utah.edu/sys/installdir/cctools/6.1.1/bin Wim Cardoen Installation Only Contains chirp, makeflow, parrot, sand, work_queue
cdo 1.8.2 Applications All Atmospheric Sciences /uufs/chpc.utah.edu/sys/installdir/cdo Martin Cuma Installation Only
cfitsio 3.24, 3.310, 3.35, 3.370(g)(D) Libraries all C, Fortran, File Reading/Writing, R /uufs/chpc.utah.edu/sys/installdir/cfitsio Wim Cardoen Installation Only
cgl 0.08 Applications All genomics, Genome Annotation /uufs/chpc.utah.edu/sys/pkg/cgl Anita Orendt Installation Only
charmm Applications All chemistry, molecular mechanics Anita Orendt Intermediate User
chimera 1.9, 1.10 Applications All chemistry, Molecular viewers /uufs/chpc.utah.edu/sys/installdir/chimera Anita Orendt Novice User
circos 0.69-5 Applications all visualization, genomics /uufs/chpc.utah.edu/sys/installdir/circos/0.69-5 Anita Orendt Installation Only
cleartk 1.4.1 Applications All Bioinformatics, Natural Language Processing, Machine learning /uufs/chpc.utah.edu/sys/installdir/cleartk
clhep 2.2.0.3 Libraries all Math /uufs/chpc.utah.edu/sys/pkg/clhep Wim Cardoen Installation Only
cluto 2.1.1 Applications All Bioinformatics, C, Clustering, Machine learning /uufs/chpc.utah.edu/sys/installdir/cluto
cmake 3.7.2
(D)
Programming Tools All Build tools /uufs/chpc.utah.edu/sys/installdir/cmake/3.7.2-c7/bin/cmake Wim Cardoen Intermediate User
cmaq 5 Applications All Atmospheric Sciences, Air quality modeling /uufs/chpc.utah.edu/sys/installdir/cmaq Wim Cardoen Installation Only
CMG 2012.105.G Applications All engineering, Computer aided engineering, C /uufs/chpc.utah.edu/sys/installdir/CMG Anita Orendt Installation Only
CodeBlocks 16.01 Programming Tools All C++, C, Fortran, IDE /uufs/chpc.utah.edu/sys/installdir/codeblocks/16.01/ Wim Cardoen Installation Only
comsol 3.2, 4.1, 4.3, 4.4 (D) Applications All Computer aided engineering /uufs/chpc.utah.edu/sys/pkg/comsol/ Martin Cuma Installation Only Version 4.4 (2014) the highest installed due to not renewing the license. User restrictions to be evaluated.
coot version-0.8-4968 Applications All chemistry, visualization, Crystallography tools, Molecular viewers /uufs/chpc.utah.edu/sys/pkg/coot/ Anita Orendt Installation Only
CSD 2016 Applications All chemistry, Crystallography tools /uufs/chpc.utah.edu/sys/installdir/csd Anita Orendt Experienced User updated yearly
ctakes 3.1.1 Applications All Bioinformatics, Natural Language Processing, UML /uufs/chpc.utah.edu/sys/installdir/ctakes
ctf 4.0.17 Applications All Structural biology, Electron microscopy analysis /uufs/chpc.utah.edu/sys/installdir/ctffind Anita Orendt Installation Only
Cudnn 8.0(D) Libraries All Machine learning /uufs/chpc.utah.edu/sys/installdir/cudnn/cuda-8.0 Wim Cardoen Installation Only
cufflinks 2.0.2, 2.1.2(D) Applications All genomics, Genomic sequencing /uufs/chpc.utah.edu/sys/installdir/cufflinks Wim Cardoen, Anita Orendt Installation Only, Installation Only
curl 7.35.1, 7.49.1, 7.54.1(D) Applications/Utilities All File transfer /uufs/chpc.utah.edu/sys/installdir/curl Wim Cardoen Installation Only
cwf 3.2.2, 3.3.0_54 (D) Libraries All Atmospheric Sciences /uufs/chpc.utah.edu/sys/pkg/cwf Wim Cardoen Installation Only
cyana 2.1 Applications All chemistry, NMR Structure, R /uufs/chpc.utah.edu/sys/installdir/cyana Anita Orendt Installation Only
cytoscape 3.2.1 Applications All visualization, Network Analysis /uufs/chpc.utah.edu/sys/installdir/cytoscape Wim Cardoen Installation Only
dakota 5.3 Applications kingspeak Math /uufs/kingspeak.peaks/sys/pkg/dakota Martin Cuma Installation Only Built to support Peridigm
DARS 2.12.005 Applications all computational fluid dynamics, Computer aided engineering /uufs/chpc.utah.edu/sys/installdir/dars Martin Cuma Installation Only
dcm4che 2.0.25 Applications All Healthcare /uufs/chpc.utah.edu/sys/pkg/dcm4che
ddt 4.2.2 Programming Tools All Profiling, Debugging http://www.allinea.com/products/ddt Martin Cuma Intermediate User Using CS license, which is relatively limited, thus, not advertising (may consider user restrictions).
degrib 1.90, 1.94 Applications All Atmospheric Sciences /uufs/chpc.utah.edu/sys/pkg/degrib Martin Cuma Installation Only Not updated much but possibly still used.
delft3d Applications All engineering /uufs/chpc.utah.edu/sys/installdir/delft3d/5275/bin Wim Cardoen Installation Only
DLPOLY 4.07 Applications All molecular dynamics /uufs/chpc.utah.edu/sys/srcdir/dlpoly Martin Cuma Installation Only
DNAnexus SDK 0.231.0 Programming Tools kingspeak, ember Bioinformatics /uufs/chpc.utah.edu/sys/installdir/dnanexus-sdk
DNAnexus Upload Agent 1.5.27 Applications/Utilities kingspeak, ember Bioinformatics /uufs/chpc.utah.edu/sys/installdir/dnanexus-ua
dock 3, 6.1, 6.4, 6.5 Applications All chemistry, Molecular Docking /uufs/chpc.utah.edu/sys/installdir/dock Anita Orendt Novice User
ds9 7.3.2 Applications All visualization, Astronomy /uufs/chpc.utah.edu/sys/installdir/ds9 Anita Orendt Installation Only
dssp 2.0.4, 2006 Applications All chemistry, Structural biology, C, Computational chemistry /uufs/chpc.utah.edu/sys/pkg/dssp Anita Orendt Installation Only
eautils 1.1.2-806 Applications All genomics, Genomic sequencing /uufs/chpc.utah.edu/sys/installdir/eautils Anita Orendt Installation Only
Eigen 2.0.17 Libraries ALL Math /uufs/chpc.utah.edu/sys/pkg/Eigen/2.0.17 Wim Cardoen Installation Only
eigensoft 6.0.1 Applications All Genetics, Genetic trait analysis /uufs/chpc.utah.edu/sys/installdir/eigensoft Anita Orendt Installation Only
EMAN2 2.12 Applications ALL Structural biology, Electron microscopy analysis /uufs/chpc.utah.edu/sys/installdir/eman2 Wim Cardoen, Anita Orendt Installation Only, Installation Only
esmf 6.3.0rp1 Applications ALL earth system modeling /uufs/chpc.utah.edu/sys/pkg/esmf/6.3.0rp1 Wim Cardoen Installation Only
exonerate 2.2.0 Applications All genomics, Genomic alignments /uufs/chpc.utah.edu/sys/pkg/exonerate Anita Orendt Installation Only
expat 2.1.0 Libraries All XML parser /uufs/chpc.utah.edu/sys/pkg/expat Martin Cuma Installation Only Newer version than stock RHEL6.
Fasta fasta-36.3.6d Applications All Genomic sequencing /uufs/chpc.utah.edu/sys/pkg/Fasta Anita Orendt Installation Only
fastqc 0.11.4 Applications all genomics, Genomic sequencing /uufs/chpc.utah.edu/sys/installdir/fastqc Anita Orendt Installation Only
FastTree 1.2.9 Applications All Genomic alignments /uufs/chpc.utah.edu/sys/installdir/fasttree Anita Orendt Installation Only Installed openMP version, FastTreeMP
fastx_toolkit 0.0.13 Applications All genomics, Genomic sequencing /uufs/chpc.utah.edu/sys/installdir/fastx_toolkit Anita Orendt Installation Only
fbat 2.0.3 Applications All Genetics, Genetic trait analysis /uufs/chpc.utah.edu/sys/pkg/fbat Anita Orendt Installation Only
fdt 0.9.20 Utilities All File transfer /uufs/chpc.utah.edu/sys/pkg/fdt/0.9.20 Wim Cardoen Installation Only
ffmpeg 6/7/2013 Utilities All Video Decoding /uufs/chpc.utah.edu/sys/pkg/ffmpeg/2013-06-07_rhel6 Wim Cardoen Installation Only
fftw 3.3.4(D), 2.1.5 Libraries All Math /uufs/chpc.utah.edu/sys/pkg/fftw/, /uufs/chpc.utah.edu/sys/pkg/fftw Martin Cuma, Wim Cardoen Experienced User, Installation Only Separate builds for different compilers and some builds also for different MPIs (distributed FFTW version).
fftw 3.3.3, 2.1.5 Libraries kingspeak Math /uufs/kingspeak.arches/sys/pkg/fftw Martin Cuma, Wim Cardoen Experienced User, Experienced User
fftw 3.3.3, 2.1.5 Libraries Ember Math /uufs/ember.arches/sys/pkg/fftw Martin Cuma, Wim Cardoen Experienced User, Experienced User
fftw 3.3.3, 2.1.5 Libraries Ash Math /uufs/ash.peaks/sys/pkg/fftw Martin Cuma, Wim Cardoen Experienced User, Experienced User
findbugs 1.3.9 Programming Tools All Debugging Java programs debugger, very old version (current is 3.0.1).
FindEM 2 Applications All Electron microscopy analysis /uufs/chpc.utah.edu/sys/pkg/FindEM/ Anita Orendt Installation Only
fitsverify 4.17(D) Applications All Data tools /uufs/chpc.utah.edu/sys/installdir/fitsverify Wim Cardoen Installation Only
frealign 9.11 Applications All Electron microscopy analysis /uufs/chpc.utah.edu/sys/installdir/frealign Anita Orendt Installation Only
frealix 1.1 Applications All Electron microscopy analysis /uufs/chpc.utah.edu/sys/pkg/frealix Anita Orendt Installation Only
freebayes 1.0.2-16 Applications all genomics /uufs/chpc.utah.edu/sys/installdir/freebayes Anita Orendt Installation Only
freesurfer 5.0.0 Applications All visualization, brain imaging, Healthcare, Image Tool /uufs/chpc.utah.edu/sys/pkg/freesurfer
freetype 2.3.12, 2.4.11, 2.5.3(D) Libraries All C /uufs/chpc.utah.edu/sys/pkg/freetype/2.5.3 Wim Cardoen Installation Only
freud 0.6.1 Applications/Utilities All chemistry, molecular dynamics, C, Computational chemistry /uufs/chpc.utah.edu/sys/installdir/freud/04282017/ Wim Cardoen Installation Only MD Analysis package - To be used with /usr/bin/python
g2 0.72 Libraries All Graphics /uufs/chpc.utah.edu/sys/installdir/g2 Anita Orendt Installation Only
gate 6.0, 7.0 Applications All Natural Language Processing /uufs/chpc.utah.edu/sys/pkg/gate
gatk 3.7 Applications All Genomic analysis /uufs/chpc.utah.edu/sys/installdir/gatk Anita Orendt Installation Only
gaussian09 Applications All chemistry, quantum chemistry, Molecular viewers, Computational chemistry /uufs/chpc.utah.edu/sys/pkg/gaussian09 Anita Orendt Experienced User
Gaussian16 A.03 Applications All Computational chemistry /uufs/chpc.utah.edu/sys/installdir/gaussian16 Anita Orendt Experienced User includes GaussView6
gawk 4.1.3(D) Applications All File Reading/Writing, File conversion, R /uufs/chpc.utah.edu/sys/installdir/gawk/4.1.3/bin/ Wim Cardoen Intermediate User
gcc 4.4.7(D), 4.7.2, 4.8.4, 4.9.2, 5.4.0 Programming Tools Compilers, C, Fortran Wim Cardoen Experienced User
gcta 0.92.9 Applications All Genetic trait analysis /uufs/chpc.utah.edu/sys/pkg/gcta Anita Orendt Installation Only
gdal 1.9.2, 1.10.0, 2.0.1, 2.3.1(D) Library All Atmospheric Sciences /uufs/chpc.utah.edu/sys/installdir/gdal/2.1.3-c7 Wim Cardoen Installation Only
gdlib 2.1.1(D) Libraries All image processing /uufs/chpc.utah.edu/sys/pkg/gdlib/gd-2.1.1 Wim Cardoen Installation Only
geant4 4.10.01.p01(D) Applications All particle physics simulation /uufs/chpc.utah.edu/sys/installdir/geant4 Wim Cardoen Installation Only
gempak 5.11.1, 7.1.0, 7.3.0 (D) Applications All Atmospheric Sciences /uufs/chpc.utah.edu/sys/installdir/gempak Martin Cuma Installation Only
genesis-sim 2.3 Applications All Neuroscience /uufs/chpc.utah.edu/sys/pkg/genesis-sim Wim Cardoen Installation Only
genetorrent 3.8.5a Utilities All genomics, File transfer /uufs/chpc.utah.edu/sys/pkg/genetorrent Anita Orendt Installation Only
geomview 1.9.4 Applications All visualization /uufs/chpc.utah.edu/sys/pkg/geomview Anita Orendt Installation Only
geos 3.2.2, 3.3.8, 3.4.2, 3.5.0(D) Libraries All Math /uufs/chpc.utah.edu/sys/pkg/geos Wim Cardoen Installation Only
ghc 7.6.3(D) Programming Tools All Haskell /uufs/chpc.utah.edu/sys/pkg/ghc/7.6.3_rhel6 Wim Cardoen Installation Only
git 1.8.1.1, 1.8.3.4, 1.8.4.1(D), 2.10.0, 2.10.0-c7 Programming Tools ALL versioning /uufs/chpc.utah.edu/sys/installdir/git Wim Cardoen Intermediate User
globus 4.0.7 Utilities File transfer
glpk 4.35 Libraries All Math /uufs/chpc.utah.edu/sys/pkg/glpk/4.35 Wim Cardoen Installation Only
Gmap 2014-06-10, 2011-09-07 Applications All genomics, Genomic alignments /uufs/chpc.utah.edu/sys/pkg/Gmap Anita Orendt Installation Only
gmp 5.1.0, 6.0.0, 6.1.0 Libraries Toolkits Wim Cardoen Installation Only
gmt 5.1.2_r14049, 4.5.11 Applications All Graphing /uufs/chpc.utah.edu/sys/installdir/gmt Anita Orendt Installation Only Gmt5 is the new development version 4.5.11 version in /uufs/chpc.utah.edu/sys/installdir/gmt/4.5.11
gnuplot 4.4.3, 4.6.0, 5.0.3 (D) Applications All Graphing /uufs/chpc.utah.edu/sys/{pkg,installdir}/gnuplot Martin Cuma, Wim Cardoen Intermediate User, Installation Only
Google Test & Mock 05/25/2016 Applications All C++ /uufs/chpc.utah.edu/sys/installdir/googletest/05252016 Wim Cardoen Experienced User Env. variables GTEST_DIR, GTEST_LIB & GTEST_INC
grace 5.1.24 Applications All Graphing /uufs/chpc.utah.edu/sys/installdir/grace older versions in /uufs/chpc.utah.edu/sys/pkg/grace
grads 2.0.2.oga.2 Applications All visualization, earth system modeling /uufs/chpc.utah.edu/sys/installdir/grads Martin Cuma Installation Only
graphicsmagick 1.4 Applications All Graphics /uufs/chpc.utah.edu/sys/installdir/graphicsmagick/ Wim Cardoen Installation Only
grib 1.12.3 Libraries All I/O https://software.ecmwf.int/wiki/display/GRIB/Home Martin Cuma Installation Only
gromacs 5.0.4s, 5.0.4d(D) Applications All chemistry, molecular dynamics /uufs/chpc.utah.edu/sys/installdir/gromacs Wim Cardoen Installation Only A Slurm script/example can be found in the subdirectory scripts.
gsl 1.15, 1.16, 2.1, 2.2.1 (D) Libraries All Math, C /uufs/chpc.utah.edu/sys/installdir/gsl Wim Cardoen Intermediate User
guidance 2.02,2.01 Applications All genomics, Genomic alignments /uufs/chpc.utah.edu/sys/installdir/guidance Anita Orendt Installation Only
hadoop 2.6.0(D) Libraries elephant Machine learning, Data Storage, Data Mining /uufs/chpc.utah.edu/sys/installdir/hadoop/elephant Wim Cardoen Intermediate User
Harminv 1.4 Applications All chemistry, Applied Math /uufs/chpc.utah.edu/sys/installdir/harminv/1.4-i16a Wim Cardoen Installation Only
Harp 1.0.beta (D) Applications ALL Astronomy /uufs/chpc.utah.edu/sys/installdir/harp/1.0-beta_mpich2-3.1.4_4.9.2g Wim Cardoen Installation Only
haskell-platform 2.0.0(D) Programming Tools All Haskell /uufs/chpc.utah.edu/sys/pkg/haskell-platform/2.0.0/ Wim Cardoen Installation Only
hdf4 4.2.9 Libraries All I/O /uufs/chpc.utah.edu/sys/pkg/hdf4 Martin Cuma Intermediate User
hdf5 1.8.14, 1.8.12 Libraries kingspeak I/O /uufs/kingspeak.arches/sys/pkg/hdf5 Martin Cuma Intermediate User
hdf5 1.8.14 (D), 1.8.12 Libraries Ember I/O /uufs/ember.arches/sys/pkg/hdf5 Martin Cuma Intermediate User
hdf5 1.8.14, 1.8.12 Libraries Ash I/O /uufs/ash.peaks/sys/pkg/hdf5 Martin Cuma, Wim Cardoen Intermediate User, Intermediate User
hdf5 1.8.14, 1.8.16, 1.8.17-c7 Library All I/O /uufs/chpc.utah.edu/sys/installdir/hdf5/1.8.16-2016i Martin Cuma, Wim Cardoen Intermediate User, Intermediate User Separate builds for GNU, Intel compilers and for MPICH
hdfeos 5.1.13, HDF-EOS2, HDF-EOS5 Libraries All I/O /uufs/chpc.utah.edu/sys/pkg/hdfeos Martin Cuma Installation Only
hdfview 2.5p3_64, 2.11.0 (D) Utilities All GUI /uufs/chpc.utah.edu/sys/pinstalldir/hdfview Martin Cuma Installation Only
healpix 3.11(D) Applications All visualization /uufs/chpc.utah.edu/sys/pkg/healpix/3.11/etc Wim Cardoen Installation Only
helyx-os 2.3.0 Applications All fluid dynamics, computational fluid dynamics, GUI /uufs/chpc.utah.edu/sys/installdir/helyx-os Anita Orendt Installation Only works with OpenFoam
hisat 0.1.6-beta Applications All genomics, Genomic alignments /uufs/chpc.utah.edu/sys/installdir/hisat Anita Orendt Installation Only
hisat2 2.0.4 Applications all genomics, Genomic alignments /uufs/chpc.utah.edu/sys/installdir/hisat2 Anita Orendt Installation Only
homer 5.4(D) Applications All Genomic analysis /uufs/chpc.utah.edu/sys/pkg/homer/bin Wim Cardoen Installation Only
HOOMD 2.1.3 (dp)(D), 2.1.3 (sp) Applications All chemistry, molecular dynamics, GPU, C, Computational chemistry /uufs/chpc.utah.edu/sys/installdir/hoomd/2.1.3g-dp-c7 Wim Cardoen Installation Only Updated: 03/08/2017
hpctoolkit 5.3.2 Programming Tools Kingspeak Toolkits, Profiling /uufs/kingspeak.peaks/sys/pkg/hpctoolkit Martin Cuma Intermediate User
hpctoolkit 5.3.2 Programming Tools Ember Toolkits, Profiling /uufs/ember.arches/sys/pkg/hpctoolkit Martin Cuma Intermediate User
hpctoolkit 5.3.2 Programming Tools Ash Toolkits, Profiling /uufs/ash.peaks/sys/pkg/hpctoolkit Martin Cuma Intermediate User
hpctoolkit-externals 5.3.2 Programming Tools Kingspeak Toolkits, Profiling /uufs/kingspeak.peaks/sys/pkg/hpctoolkit-externals Martin Cuma Intermediate User
hpctoolkit-externals 5.3.2 Programming Tools Ember Toolkits, Profiling /uufs/ember.arches/sys/pkg/hpctoolkit-externals Martin Cuma Intermediate User
hpctoolkit-externals 5.3.2 Programming Tools Ash Toolkits, Profiling /uufs/ash.peaks/sys/pkg/hpctoolkit-externals Martin Cuma Intermediate User
hpctraceviewer 5.3.2 Programming Tools Kingspeak Toolkits, Profiling /uufs/kingspeak.peaks/sys/pkg/hpctraceviewer Martin Cuma Intermediate User
hpctraceviewer 5.3.2 Programming Tools Ember Toolkits, Profiling /uufs/ember.arches/sys/pkg/hpctraceviewer Martin Cuma Intermediate User
hpctraceviewer 5.3.2 Programming Tools Ash Toolkits, Profiling /uufs/ash.peaks/sys/pkg/hpctraceviewer Martin Cuma Intermediate User
hpcviewer 5.3.2 Programming Tools Kingspeak Toolkits, Profiling /uufs/kingspeak.peaks/sys/pkg/hpcviewer Martin Cuma Intermediate User
hpcviewer 5.3.2 Programming Tools Ember Toolkits, Profiling /uufs/ember.arches/sys/pkg/hpcviewer Martin Cuma Intermediate User
hpcviewer 5.3.2 Programming Tools Ash Toolkits, Profiling /uufs/ash.peaks/sys/pkg/hpcviewer Martin Cuma Intermediate User
hsi 4.0.1.3 Utilities All File transfer /uufs/chpc.utah.edu/sys/pkg/hsi Martin Cuma Installation Only
htar 4.0.1.3 Utilities All File compression /uufs/chpc.utah.edu/sys/pkg/htar Martin Cuma Installation Only
httplog 2.1 Utilities File compression, File backup check, what is this for?
Humann2 Applications All genomics, metagenomics, microbial genomics installed with python2.7.3_rh6 Anita Orendt Installation Only module load python/2.7.3 will give you access to humann2 packages
hypre 2.9.0b, 2.10.1 (D) Libraries All Math /uufs/chpc.utah.edu/sys/installdir/hypre Martin Cuma Installation Only Built with Intel compilers
idba 1.1.1 Applications All Bioinformatics /uufs/chpc.utah.edu/sys/srcdir/idba
idl 8.1, 8.2, 8.2.3, 8.3, 8.4, 8.5.1 (D) Programming Tools All IDE /uufs/chpc.utah.edu/sys/pkg/idl Martin Cuma Installation Only
idv 5.2 Applications All visualization, Atmospheric Sciences, Radar processing, R /uufs/chpc.utah.edu/sys/installdir/idv Martin Cuma, Anita Orendt Installation Only, Installation Only
imagemagick 6.5.6-10, 6.9.0-4(D) Applications All image processing /uufs/chpc.utah.edu/sys/pkg/imagemagick Wim Cardoen Installation Only
infernal 1.1.1 Applications all Genomic sequencing /uufs/chpc.utah.edu/sys/installdir/infernal
inrich 1.1 Applications all Genomic analysis /uufs/chpc.utah.edu/sys/installdir/inrich Anita Orendt Installation Only
intel 2013, 2015, 2016(D), 2017 (D c7) Programming Tools All Compilers, C, Fortran /uufs/chpc.utah.edu/sys/installdir/intel Martin Cuma, Wim Cardoen Experienced User,
intelpy 2.7.12, 3.5.2 Programming Tools All Python /uufs/chpc.utah.edu/sys/installdir/intelpy/2017.0.035/ Wim Cardoen Experienced User
ioapi 3.1, 3.1 Libraries Atmospheric Sciences /uufs/chpc.utah.edu/sys/pkg/ioapi Martin Cuma Installation Only
isl 0.17, 0.12 Libraries Math, Applied Math Wim Cardoen Installation Only
jasper 1.900.1(D) Library ALL Toolkits, Graphics /uufs/chpc.utah.edu/sys/installdir/jasper Wim Cardoen Installation Only
jdk 1.8.0_25, 1.7.0_67(D) Programming Tools All Build tools, Compilers, C, Java /uufs/chpc.utah.edu/sys/installdir/jdk/ Wim Cardoen Experienced User
Julia 0.3.7, 0.4.0, 0.4.5, 0.5.0, 0.6.0 (D) Programming Tools All Compilers, Compilers and Tools, C, Tools /uufs/chpc.utah.edu/sys/installdir/julia/ Wim Cardoen Intermediate User
kallisto 0.42.2(D) Applications All Genomic sequencing /uufs/chpc.utah.edu/sys/installdir/kallisto Wim Cardoen Installation Only
king 1.4 Applications All genomics, Genomic analysis /uufs/chpc.utah.edu/sys/installdir/king Anita Orendt Installation Only
lammps 11Aug17(D) Applications All chemistry, molecular dynamics /uufs/chpc.utah.edu/sys/installdir/lammps/11Aug17 Wim Cardoen Intermediate User
LibElemental 08262015(D) Libraries ALL Math, Applied Math /uufs/chpc.utah.edu/sys/installdir/libelemental/08262015-4.9.2g Wim Cardoen Installation Only Requires GNU 4.9.2
LibFlame 08182015(D) Library All Math, Applied Math /uufs/chpc.utah.edu/sys/installdir/libflame/08182015-4.9.2g/ Wim Cardoen Installation Only
libxml2 2.9.1 Utilities all XML parser /uufs/chpc.utah.edu/sys/pkg/libxml2 Martin Cuma Installation Only Newer version than CentOS6
libyaml 0.1.5(D), 0.1.6 Library ALL C /uufs/chpc.utah.edu/sys/installdir/libyaml/0.1.5, /uufs/chpc.utah.edu/sys/i Wim Cardoen Installation Only The library has been compiled with gcc 4.9.2. I used it to compile PyYAML within Python 2.7.10
LLVM 3.7.0(D) Programming Tools All Compilers, C, Debugging /uufs/chpc.utah.edu/sys/installdir/llvm/3.7.0 Wim Cardoen Intermediate User
lmod 6.0.1(D) Utilities ALL Tools /uufs/chpc.utah.edu/sys/installdir/lmod/lmod Wim Cardoen Experienced User
lobSTR 4.0.6 Applications All genomics, Genomic sequencing /uufs/chpc.utah.edu/sys/installdir/lobstr Anita Orendt Installation Only
log4j 1.2.14 Programming Tools All Debugging /uufs/chpc.utah.edu/sys/installdir/log4j/ Wim Cardoen Installation Only
lrzip 0.552 Utilities All File compression /uufs/chpc.utah.edu/sys/pkg/lrzip/ Wim Cardoen Installation Only
lsdyna 8.1.0-smp, 8.0-smp Applications All engineering, finite element /uufs/chpc.utah.edu/sys/installdir/lsdyna Anita Orendt Installation Only
lua 5.1.4-2, 5.1.4.8, 5.1.5(D) Programming Tools ALL Lua /uufs/chpc.utah.edu/sys/pkg/lua/5.1.5/bin Wim Cardoen Installation Only
luarocks 2.1.2(D) Programming Tools ALL Scripting language, Compilers and Tools, Lua /uufs/chpc.utah.edu/sys/pkg/luatools/luarocks/2.1.2 Wim Cardoen Installation Only lua Rocks: lua package manager
lucene 1.4.1, 3.5.0 Applications All Indexing/Searching /uufs/chpc.utah.edu/32bit/pkg/lucene
lumerical 8.15.736, 8.16.1022 Applications All Finite difference, Maxwell equation solver /uufs/chpc.utah.edu/sys/installdir/lumerical Anita Orendt Installation Only
lvg 2010, 2014 Applications All Natural Language Processing /uufs/chpc.utah.edu/sys/pkg/lvg
maestro 2015-4 Applications All chemistry, Molecular viewers /uufs/chpc.utah.edu/sys/installdir/maestro Anita Orendt Novice User
Magma 2.0.1 Library Ember GPU, Math, Applied Math, CUDA /uufs/chpc.utah.edu/sys/installdir/magma/2.0.1i Wim Cardoen Installation Only See also:/uufs/chpc.utah.edu/sys/installdir/magma/2.0.1i/README.txt
mahout 0.5 Libraries All Machine learning /uufs/chpc.utah.edu/sys/pkg/mahout
Maker2 2.28 Applications All genomics, Genome Annotation /uufs/chpc.utah.edu/sys/pkg/Maker2 Anita Orendt Installation Only
marvin 6.1.2 Applications All Molecular viewers /uufs/chpc.utah.edu/sys/pkg/marvin Anita Orendt Installation Only requires a license, which is freely available to academic users
mathematica 10.4.1, 11.0.0, 11.0.1, 11.1.1 (D) Applications All Math, Applied Math /uufs/chpc.utah.edu/sys/installdir/mathematica/ Wim Cardoen Intermediate User
matlab R2011a, R2011b, R2012a, R2012b, R2013a, R2013b, R2014a, R2014b, R2015a, R2015b, R2016a, R2016b (D) Applications All engineering, Math, Graphing /uufs/chpc.utah.edu/sys/installdir/matlab Martin Cuma Experienced User
maven 3.0.4, 3.2.1, 3.2.5, 3.3.3 (D) Programming Tools ALL Toolkits /uufs/chpc.utah.edu/sys/installdir/maven/3.3.3 Wim Cardoen Intermediate User
MEEP 1.3 Applications All engineering, Finite difference, Maxwell equation solver /uufs/chpc.utah.edu/sys/installdir/meep/1.3-i16a-impi Wim Cardoen Installation Only
meme 4.11.2 Applications All genomics, Bioinformatics, genetic maps, Genetics, Genomic sequencing /uufs/chpc.utah.edu/sys/installdir/meme/4.11.2/bin Wim Cardoen Installation Only
mercurial 3.6(D) Programming Tools ALL versioning /uufs/chpc.utah.edu/sys/installdir/mercurial/3.6 Wim Cardoen Installation Only
merlin 1.1.2 Applications all Genetics /uufs/chpc.utah.edu/sys/installdir/merlin/1.1.2 Anita Orendt Installation Only
MET 4.1 Applications All Atmospheric Sciences /uufs/chpc.utah.edu/sys/pkg/MET Anita Orendt Installation Only
metamap linux_2014,linux_2013, linux_2012, linux_2011v2, linux_2011 Applications All Bioinformatics, Natural Language Processing /uufs/chpc.utah.edu/sys/pkg/metamap
metaphlan2 2.2.0 Applications All genomics, metagenomics, microbial genomics /uufs/chpc.utah.edu/sys/installdir/metaphlan2 Anita Orendt Installation Only
Metis 5.1.0 Library all Applied Math, finite element /uufs/chpc.utah.edu/sys/installdir/metis Wim Cardoen Installation Only Built with GNU and Intel compilers
midas 3.2.8 Applications/Utilities All Data Storage /uufs/chpc.utah.edu/sys/pkg/midas/Midas-3.2.8 Wim Cardoen Installation Only
minx 3.0<>(D) Applications All visualization /uufs/chpc.utah.edu/sys/pkg/minx/3.0 Wim Cardoen Installation Only
miranda 3.3a Applications All genomics /uufs/chpc.utah.edu/sys/installdir/miranda Anita Orendt Installation Only
mirdeep2 2.0.0.8 Applications All genomics /uufs/chpc.utah.edu/sys/installdir/mirdeep2 Anita Orendt Installation Only
mirth 1.8.2.4472.1351 Applications All Healthcare /uufs/chpc.utah.edu/sys/pkg/mirth
modeller 9.9 Applications All Protein modeling and analysis, homology modelling /uufs/chpc.utah.edu/sys/pkg/modeller Anita Orendt Installation Only
molden 4.4, 4.6, 4.7 Applications All Molecular viewers /uufs/chpc.utah.edu/sys/pkg/molden Anita Orendt Novice User
mopac 2012 Applications All chemistry, Computational chemistry, semiempirical quantum chemistry /uufs/chpc.utah.edu/sys/pkg/mopac Anita Orendt Novice User
mothur 1.35.1 Applications All genomics /uufs/chpc.utah.edu/sys/installdir/mothur Anita Orendt Installation Only installed version needed for qiime installation
motion-correct 1.0(D) Applications All /uufs/chpc.utah.edu/sys/pkg/motion-correct/ Martin Cuma Installation Only
MPB 1.5 Applications All Materials modeling /uufs/chpc.utah.edu/sys/installdir/mpb Wim Cardoen Installation Only There is a parallel & serial version. Each version has 2 executables: a.mpb :: without inversion-symmetry b.mpbi :: with inversion-symmetry Allows to use real fields (in Fourier space) instead of complex fields
mpc 1.0.1, 1.0.3 Libraries All Math, C /uufs/chpc.utah.edu/sys/pkg/mpc Wim Cardoen Installation Only Needed to build GNU compilers
mpfr 3.1.1, 3.1.2, 3.1.4 Libraries All Math, C /uufs/chpc.utah.edu/sys/pkg/mpfr Wim Cardoen Installation Only Needed to build GNU compilers
mpich2 3.1.1, 3.1.2, 3.1.4, 3.2(D) Libraries All Parallelization /uufs/chpc.utah.edu/sys/installdir/mpich Martin Cuma, Wim Cardoen Experienced User, Experienced User Different builds for supported compilers (GNU 4.4, 4.8, 4.9, Intel, PGI)
mplus 7.4 Applications all Analytics /uufs/chpc.utah.edu/sys/installdir/mplus Anita Orendt Installation Only
MRTSwath 10152014(D) Utilities All Atmospheric Sciences /uufs/chpc.utah.edu/sys/pkg/MRTSwath/ Wim Cardoen Installation Only
MultiNest 3.4(D) Applications All Math /uufs/chpc.utah.edu/sys/pkg/MultiNest/3.4 Wim Cardoen Installation Only
mvapich2 1.9, 2.0, 2.1, 2.2 (D) Libraries All Parallelization /uufs/chpc.utah.edu/sys/installdir/mvapich2 Martin Cuma Experienced User 3 builds for 3 compilers (GNU, Intel, PGI), Intel optimized for all clusters, GNU and PGI built with lowest common denominator hardware but should have minimal impact on performance
namd 2.10 Applications All molecular dynamics, Molecular viewers /uufs/chpc.utah.edu/sys/installdir/namd/ Martin Cuma Installation Only
nboview 1.1 Applications All electronic structure, Molecular viewers /uufs/chpc.utah.edu/sys/pkg/nboview Anita Orendt Installation Only
ncarg 5.1.1, 6.0.0, 6.1.0, 6.1.2 Utilities All Atmospheric Sciences /uufs/chpc.utah.edu/sys/pkg/ncarg
ncbrowse 1.67 Utilities All visualization, Graphing /uufs/chpc.utah.edu/sys/installdir/ncbrowse
ncdu 1.10(D) Utilities All Machine Metrics /uufs/chpc.utah.edu/sys/pkg/ncdu/1.10/ Wim Cardoen Installation Only
ncl 6.0.0, 6.1.0, 6.1.2 Programming Tools All Scripting language /uufs/chpc.utah.edu/sys/pkg/ncl/6.1.2_rhel6
nco 4.2.0, 4.4.4 Applications All Atmospheric Sciences /uufs/chpc.utah.edu/sys/pkg/nco Martin Cuma, Wim Cardoen Installation Only, Installation Only
ncview 1.93g, 2.1.2, 2.1.2 Applications All Atmospheric Sciences /uufs/chpc.utah.edu/sys/installdir/ncview/ Martin Cuma Installation Only
ndt 3.5.6(D) Utilities All Network performance /uufs/chpc.utah.edu/sys/pkg/ndt Wim Cardoen Installation Only
neon 0.25.5, 0.26.3, 0.28.4, 0.29.0, 0.30.0(D) Applications All HTTP and proxy server /uufs/chpc.utah.edu/sys/pkg/neon Wim Cardoen Installation Only
netcdf-c 4.3.2, 4.3.3.1, 4.4.1-c7 Libraries All I/O /uufs/chpc.utah.edu/sys/installdir/netcdf-c/ Martin Cuma, Wim Cardoen Installation Only, Installation Only GCC build should work with other compilers.
netcdf-cxx 4.2.1, 4.3.0-c7 Libraries All I/O /uufs/chpc.utah.edu/sys/installdir/netcdf-cxx Martin Cuma, Wim Cardoen Installation Only, Installation Only Separate builds for GNU and Intel.
netcdf-f 4.4.0, 4.4.4-c7 Libraries All I/O /uufs/chpc.utah.edu/sys/installdir/netcdf-f Martin Cuma, Wim Cardoen Installation Only, Installation Only Different builds for different compilers (GNU, Intel, PGI).
netcdf-perl 1.2.4 Libraries All I/O /uufs/chpc.utah.edu/sys/pkg/netcdf-perl Martin Cuma Installation Only Deprecated according to the URL.
neuroconstruct 1.3.6 Applications All Neuroscience /uufs/chpc.utah.edu/sys/pkg/neuroconstruct/1.3.6 Wim Cardoen Installation Only
neuron 7.2(D) Applications ALL Neuroscience /uufs/chpc.utah.edu/sys/pkg/neuron/7.2 Wim Cardoen Installation Only
nginx 1.7.8(D) Applications/Utilities All HTTP and proxy server /uufs/chpc.utah.edu/sys/pkg/nginx/1.7.8/sbin Wim Cardoen Installation Only
ngsTools 1.0.0 Applications All genomics, Genetics /uufs/chpc.utah.edu/sys/installdir/ngstools Anita Orendt Installation Only
novocraft 2.07.11 Applications All genomics, Genomic alignments /uufs/chpc.utah.edu/sys/pkg/novocraft Anita Orendt Installation Only
nwchem 6.1, 6.3 Applications A chemistry, Computational chemistry Anita Orendt Experienced User Working on 6.6 installation
octave 3.6.3, 3.6.4, 3.8.0(D) Programming Tools All Scripting language /uufs/chpc.utah.edu/sys/pkg/octave Wim Cardoen Installation Only
openbabel 2.3.2 Applications All chemistry, File conversion /uufs/chpc.utah.edu/sys/installdir/cdoopenbabel Anita Orendt Intermediate User
openblas 0.2.8, 0.2.7, 0.2.7_mt Libraries Kingspeak Math /uufs/kingspeak.peaks/sys/pkg/OpenBLAS Wim Cardoen Experienced User
openblas 0.2.8 Libraries Kingspeak Math /uufs/kingspeak.peaks/sys/pkg/OpenBLAS Wim Cardoen Experienced User
openblas 0.2.12, 0.2.13, 0.2.14 Libraries All Math /uufs/chpc.utah.edu/sys/installdir/openblas Wim Cardoen Experienced User
opencv 2.4.9(D) Applications Centos7 (VM) C, Machine learning, Computer vision /uufs/chpc.utah.edu/sys/installdir/opencv/2.4.9_c7/ Wim Cardoen Installation Only
OpenFoam 2.4.0,v1606+, 4.1 Applications All engineering, fluid dynamics, computational fluid dynamics /uufs/chpc.utah.edu/sys/installdir/openfoam Anita Orendt
openjpeg 1.5.2(D) Library All Graphics /uufs/chpc.utah.edu/sys/installdir/openjpeg Wim Cardoen Installation Only
openkim 1.2.1, 1.1.11, 1.0.1,1.7,1,1.7.2(D) Applications All chemistry /uufs/chpc.utah.edu/sys/installdir/openkim/1.7.2_intel2016 Wim Cardoen Installation Only
openmpi 1.6.5, 1.8.2, 1.10.0, 1.10.2 (D), 2.0.1 Programming Tools All MPI, Parallelization /uufs/chpc.utah.edu/sys/installdir/openmpi Martin Cuma, Wim Cardoen Experienced User, Experienced User 3 builds for supported compilers (GNU, Intel, PGI).
OpenMRS Demo-1.6.0 Applications All Healthcare /uufs/chpc.utah.edu/sys/pkg/OpenMRS
opennlp 1.5.3, 1.5.0, 1.4.3 Libraries All Natural Language Processing /uufs/chpc.utah.edu/sys/pkg/opennlp
packmol 14.225 Applications All molecular dynamics /uufs/chpc.utah.edu/sys/pkg/packmol Anita Orendt Installation Only
pandaseq 2.9 Applications All genomics, Genomic sequencing /uufs/chpc.utah.edu/sys/installdir/pandaseq Anita Orendt Installation Only
pandoc 1.11.1(D) Utilities All File conversion /uufs/chpc.utah.edu/sys/pkg/pandoc/1.11.1 Wim Cardoen Installation Only
panoply 4.0.3 Applications All Graphing /uufs/chpc.utah.edu/sys/pkg/panoply Martin Cuma Installation Only
papi 5.2.0 Programming Tools All Profiling /uufs/chpc.utah.edu/sys/pkg/papi/ Wim Cardoen Installation Only
parallel 20130722, 20150322(D) Utilities All Virtual Machine /uufs/chpc.utah.edu/sys/pkg/parallel Wim Cardoen Installation Only
paraview 5.3.0 Applications All visualization /uufs/chpc.utah.edu/sys/installdir/paraview/ParaView-5.3.0-Qt5-OpenGL2-MPI- Martin Cuma, Anita Orendt , Installation Only due to issues with OpenGL rendering, run as "paraview --mesa" to use Mesa based CPU rendering
parmetis 4.0.3 Library all Applied Math, finite element /uufs/chpc.utah.edu/sys/installdir/parmetis Martin Cuma Novice User Built with Intel compilers only
pcre 8.37 Applications/Utilities All perl /uufs/chpc.utah.edu/sys/installdir/pcre Wim Cardoen Installation Only PCRE: Perl Compatible Regular Expressions
pdb2pqr 1.9.0 Utilities all File conversion /uufs/chpc.utah.edu/sys/pkg/pdb2pqr Anita Orendt Installation Only
pear 0.9.6 Applications All genomics /uufs/chpc.utah.edu/sys/installdir/pear Anita Orendt Installation Only Paired-End reAd mergeR
peridigm Peridigm Applications kingspeak Physics /uufs/kingspeak.peaks/sys/pkg/peridigm Martin Cuma Installation Only 2014 build with Mellanox OFED, not tested on CentOS OFED.
perl 5.18.1, 5.10.0, 5.10.1 all Scripting language /uufs/chpc.utah.edu/sys/pkg/perl Martin Cuma Installation Only newer version than CentOS6
petsc 3.6.1 Libraries All Math /uufs/chpc.utah.edu/sys/installdir/petsc Martin Cuma Installation Only Multi-arch optimized with Intel compilers for Uintah build.
pgi 15.1, 15.7 (D) All Compilers, C /uufs/chpc.utah.edu/sys/installdir/pgi Martin Cuma Experienced User
phase 2.1.1 Applications All genetic maps /uufs/chpc.utah.edu/sys/pkg/phase Anita Orendt Installation Only
phast 1.3(D) Applications All genomics, Genomic analysis, Genomic modeling /uufs/chpc.utah.edu/sys/pkg/phast Wim Cardoen Installation Only
phenix 1.9-1692 Applications All Crystallography tools /uufs/chpc.utah.edu/sys/pkg/phenix Anita Orendt Installation Only
picard 1.55, 1.122. 2.1.1(D) Applications All genomics, Genomic sequencing /uufs/chpc.utah.edu/sys/installdir/picard Wim Cardoen, Anita Orendt Installation Only, Installation Only usage: java -jar $PICARD -h
pigz 2.1.6 Utilities All File compression /uufs/chpc.utah.edu/sys/pkg/pigz Martin Cuma Installation Only
plink 1.09, 1.07 Applications All genomics, Genomic analysis /uufs/chpc.utah.edu/sys/pkg/plink Anita Orendt Installation Only
prank 170427 Applications all genomics, Genomic alignments /uufs/chpc.utah.edu/sys/installdir/prank Anita Orendt Installation Only
prest 4.09 Applications All genomics, Genomic analysis /uufs/chpc.utah.edu/sys/installdir/prest Anita Orendt Installation Only
proj 4.6.1, 4.7.0, 4.9.0(D) Libraries All Applied Math /uufs/chpc.utah.edu/sys/pkg/proj Wim Cardoen Installation Only
pssac2 11042014(D) Applications all geophysical modeling /uufs/chpc.utah.edu/sys/installdir/pssac2 Wim Cardoen Installation Only earth sciences
PyMOL 1.6.0, 1.7.0 Applications All visualization, Molecular viewers /uufs/chpc.utah.edu/sys/pkg/PyMOL Anita Orendt Installation Only
python 2.7.11, 3.5.2 (D), 3.6.3 Programming Tools All Scripting language /uufs/chpc.utah.edu/sys/installdir/python Wim Cardoen Experienced User
q3c 1.4.15, 1.4.19, 1.4.23(D) Utilities All Database /uufs/chpc.utah.edu/sys/pkg/q3c Wim Cardoen Installation Only
qiime 1.9.1 Applications All genomics, metagenomics, microbial genomics installed with python2.7.3_rh6 Anita Orendt Installation Only module load python/2.7.3 will give you access to qiime packages
qiv 2.3.1 Utilities Image viewer /uufs/chpc.utah.edu/sys/pkg/qiv Martin Cuma Installation Only
QRNA 2.0.3c Applications All genomics, Genomic sequencing /uufs/chpc.utah.edu/sys/pkg/QRNA Anita Orendt Installation Only
Qt 4.6.0, 4.8.2, 4.8.4, 4.8.6, 5.4.1(D) Programming Tools All GUI /uufs/chpc.utah.edu/sys/installdir/qt, /uufs/chpc.utah.edu/sys/pkg/Qt Wim Cardoen Installation Only
Quantum Espresso (QE) 5.3.0, 5.0.3, 5.0.2, 4.3.1 Applications All chemistry, materials, C, Computational chemistry /uufs/chpc.utah.edu/sys/installdir/qe Anita Orendt Intermediate User
R 3.3.1, 3.3.2(D), 3.4.1 Programming Tools All IDE /uufs/chpc.utah.edu/sys/installdir/R Martin Cuma, Wim Cardoen Novice User, Intermediate User Optimized versions built with Intel compiler and multi-threading.
radx 20140113(D) Libraries All C /uufs/chpc.utah.edu/sys/pkg/radx Wim Cardoen Installation Only
rclone 1.17,1.21. 1.22, 1.24 Utilities All File transfer /uufs/chpc.utah.edu/sys/installdir/rclone
RDPTools 2016-06-09 Applications All Genomic analysis /uufs/chpc.utah.edu/sys/installdir/rdptools Anita Orendt Installation Only
rdp_classifier 2.2 Applications All genomics, metagenomics /uufs/chpc.utah.edu/sys/installdir/rdp_classifier Anita Orendt Installation Only installed for use with qiime
rdseed 4.7, 5.3.1 Applications/Utilities all File conversion /uufs/chpc.utah.edu/sys/pkg/rdseed Anita Orendt Installation Only
relion 2.0.4 ,2-beta, 1.4, 1.3, 1.2, 1.1 Applications All Electron microscopy analysis /uufs/chpc.utah.edu/sys/installdir/relion Anita Orendt Installation Only older versions in pkg branch; 2.0.4, 2-beta has gpu
RepeatMasker 4.0.3 Applications all Genomic sequencing /uufs/chpc.utah.edu/sys/pkg/RepeatMasker Anita Orendt Installation Only
rnahybrid 2.1.2 Applications All genomics /uufs/chpc.utah.edu/sys/installdir/rnahybrid Anita Orendt Installation Only
root 6.03.03, 6.03.04 (D) Applications All Data tools /uufs/chpc.utah.edu/sys/installdir/root/6.03.04_4.9.2g/bin Wim Cardoen Installation Only
Rosetta 3.5, 2016.13 Applications All Protein modeling and analysis /uufs/chpc.utah.edu/sys/installdir/rosetta Anita Orendt Installation Only
rsem (RNA-Seq by Expectation-Maximixation) 1.3.0 Applications All genomics /uufs/chpc.utah.edu/sys/installdir/rsem/1.3.0/bin Anita Orendt Installation Only
RSL 1.49 Library All Atmospheric Sciences, Radar processing /uufs/chpc.utah.edu/sys/installdir/rsl/1.49 Wim Cardoen Installation Only
RStudio 0.99.903 , 1.0.153(D) Programming Tools All R /uufs/chpc.utah.edu/sys/installdir/rstudio Wim Cardoen Intermediate User
rzip64 3 Utilities all File compression /uufs/chpc.utah.edu/sys/pkg/rzip64/ Martin Cuma Installation Only
SAC 101.5c, 101.6a (D) Applications All /uufs/chpc.utah.edu/sys/pkg/SAC Martin Cuma Installation Only seismic processing, version from 2012
samstat 1.08 Applications all genomics, Genomic sequencing http://samstat.sourceforge.net/ Anita Orendt Installation Only
samtools 1.5,1.2 (D), 1.1, 0.1.11, 0.1.18 Applications all genomics, Genomic alignments /uufs/chpc.utah.edu/sys/installdir/samtools Anita Orendt Installation Only older versions in /uufs/chpc.utah.edu/sys/pkg/samtools
sas 9.4, 9.2_phase2 Applications all Analytics /uufs/chpc.utah.edu/sys/pkg/sas Anita Orendt Installation Only
scala 2.10.5, 2.11.5(D) Programming Tools All Scala /uufs/chpc.utah.edu/sys/installdir/scala Wim Cardoen Installation Only
scalapack 2.0.2 Libraries All Math, Applied Math /uufs/chpc.utah.edu/sys/installdir/scalapack/ Wim Cardoen Novice User
seqprep 1.1 Applications All genomics /uufs/chpc.utah.edu/sys/installdir/seqprep Anita Orendt Installation Only installed for use with qiime
shapefile 1.3.0 Library All C /uufs/chpc.utah.edu/sys/builddir/shapefile Martin Cuma Installation Only
sickle 1.33 Applications all genomics, Genomic sequencing /uufs/chpc.utah.edu/sys/installdir/sickle Anita Orendt Installation Only
slony 2.2.1 Utilities All Database /uufs/chpc.utah.edu/sys/pkg/slony Martin Cuma Installation Only
slurm 14.11.4, 14.03.8, 14.03.7 Utilities All Resource Management /uufs/chpc.utah.edu/sys/installdir/slurm Martin Cuma Intermediate User
smoke 3.1 Applications All Atmospheric Sciences, Air quality modeling /uufs/chpc.utah.edu/sys/pkg/smoke/3.1 Wim Cardoen Installation Only
SNAP 2013-02-16 Applications All genomics /uufs/chpc.utah.edu/sys/pkg/SNAP Anita Orendt Installation Only
snappy 1.1.2 Utilities All File compression /uufs/chpc.utah.edu/sys/installdir/snappy Wim Cardoen Installation Only
SOAPdenovo2 2.04-r240 Applications All genomics, Genomic alignments /uufs/chpc.utah.edu/sys/installdir/soapdenovo2 Anita Orendt Installation Only
sod 3.2.6 Applications/Utilities all geophysical modeling /uufs/chpc.utah.edu/sys/installdir/sod Martin Cuma Installation Only
solo 3-20140711 Applications ALL Atmospheric Sciences /uufs/chpc.utah.edu/sys/pkg/solo/3-20140711 Wim Cardoen Installation Only
sortmerna 2.0 Applications All genomics /uufs/chpc.utah.edu/sys/installdir/sortmerna Anita Orendt Installation Only
Spades 3.7.0 Applications All genomics, metagenomics /uufs/chpc.utah.edu/sys/installdir/spades Anita Orendt Installation Only Runs with python 2.x; tested against /usr/bin/python (2.6) and python/2.7.3
specex 10132015(D) Applications All Astronomy, Physics /uufs/chpc.utah.edu/sys/installdir/specex/10132015 Wim Cardoen Installation Only
sphinx 2.0.4 Utilities Wim Cardoen Installation Only
spider 21.02 Applications all image processing /uufs/chpc.utah.edu/sys/pkg/spider Anita Orendt Installation Only
sqlite3 3.8.0.2, 3.7.13, 3.6.22 Utilities All Database /uufs/chpc.utah.edu/sys/pkg/sqlite3 Martin Cuma Installation Only
sra-toolkit 2.5.2 Applications All genomics, Data tools /uufs/chpc.utah.edu/sys/installdir/sra-toolkit Anita Orendt Installation Only
stanford-nlp 3.3.1, 1.3.4 Applications All Bioinformatics, Natural Language Processing /uufs/chpc.utah.edu/sys/pkg/stanford-nlp
STAR 2.5 Applications all genomics, Genomic alignments /uufs/chpc.utah.edu/sys/installdir/star Anita Orendt Installation Only
star-ccm+ 5.04.006, 7.04.006, 8.06.007, 9.04.009, 9.06.011, 10.02.010, 11.02.009, 11.04.10 (D) Applications All engineering, Computer aided engineering, C /uufs/chpc.utah.edu/sys/pkg/star-ccm+ Martin Cuma Installation Only Two separate installations for each version, one for single precision and other for double precision
starcd 3.26, 4.16, 4.06, 4.02 Applications All engineering, Computer aided engineering, C /uufs/chpc.utah.edu/sys/pkg/starcd Martin Cuma Installation Only Not updated for ca. 5 years, superceeded by Star-CCM+
SU2 4.0 Applications computational fluid dynamics /uufs/chpc.utah.edu/sys/installdir/su2 Martin Cuma Installation Only
suitesparse 4.4.3, 4.4.5(D) Libraries ALL Math /uufs/chpc.utah.edu/sys/installdir/suitesparse Wim Cardoen Installation Only
sundials 2.6.2 (D), 2.6.1 Library All Math, Applied Math /uufs/chpc.utah.edu/sys/installdir/sundials/2.6.2-2.7.10py Wim Cardoen Installation Only 2.6.2 has been compiled with gcc/4.9.2
svn 1.8.3 Programming Tools all versioning /uufs/chpc.utah.edu/sys/pkg/svn Wim Cardoen Installation Only newer version than stock CentOS6
swish 2.4.7 Utilities ALL XML parser /uufs/chpc.utah.edu/sys/pkg/swish/2.4.7 Wim Cardoen Installation Only
szip 2.1(D) Utilities All File compression /uufs/chpc.utah.edu/sys/pkg/szip Martin Cuma Installation Only Support library for HDF5
tassel 5.0 Applications all genomics, Genomic analysis, Genetic trait analysis /uufs/chpc.utah.edu/sys/installdir/tassel Anita Orendt Installation Only
tcltk 8.4.20(D), 8.5.12, 8.5.9 Programming Tools All Scripting language /uufs/chpc.utah.edu/sys/pkg/tcltk Wim Cardoen Installation Only
texinfo 6.0 Applications All Utility /uufs/chpc.utah.edu/sys/installdir/texinfo Wim Cardoen Installation Only
texlive 2014 Applications All /uufs/chpc.utah.edu/sys/pkg/texlive Wim Cardoen Intermediate User
tinker 8.2.1 Applications all molecular dynamics, molecular mechanics, Computational chemistry /uufs/chpc.utah.edu/sys/installdir/tinker/8.2.1 Anita Orendt Installation Only
tophat 2.0.4(D) Applications ALL Bioinformatics, Genomic analysis /uufs/chpc.utah.edu/sys/pkg/tophat Wim Cardoen Installation Only
totalview 8.14.0, 8.15.0, 2016.01, 2016.05 (D) Programming Tools All Debugging /uufs/chpc.utah.edu/sys/installdir/totalview Martin Cuma Experienced User
trilinos 11.12.1 Applications Math /uufs/chpc.utah.edu/sys/installdir/trilinos Anita Orendt Installation Only
trimmomatic 0.33 Applications All genomics /uufs/chpc.utah.edu/sys/installdir/trimmomatic Anita Orendt Installation Only
trim_galore 0.3.3 Applications All genomics, Genomic analysis /uufs/chpc.utah.edu/sys/pkg/trim_galore Anita Orendt Installation Only wrapper for cutadapt and fastqc
trinity 2.2.0 Applications All genomics /uufs/chpc.utah.edu/sys/installdir/trinity Anita Orendt Installation Only Note there are earlier version in /uufs/chpc.utah.edusys/pkg/trinity
udunits 2.2.19, 2.2.25 (D) Applications All Atmospheric Sciences /uufs/chpc.utah.edu/sys/installdir/udunits Martin Cuma Installation Only
uima apache-uima-as-2.6.0 Applications All /uufs/chpc.utah.edu/sys/installdir/uima older versions in pkg
umls Applications Healthcare
unphased 3.1.5 Applications All Genetics, Genetic trait analysis /uufs/chpc.utah.edu/sys/pkg/unphased Anita Orendt Installation Only
Unrar 5.3.11 Applications/Utilities All File compression /uufs/chpc.utah.edu/sys/installdir/unrar/5.3.11/bin Wim Cardoen Installation Only
usearch 6.1.544 Applications All genomics, Genomic analysis /uufs/chpc.utah.edu/sys/installdir/usearch Anita Orendt Installation Only
useq 7.9.3 Applications All genomics, Genomic sequencing /uufs/chpc.utah.edu/sys/pkg/useq There are newer versions available
usf (Uppsala Software Factory) Applications all Structural biology, Crystallography tools /uufs/chpc.utah.edu/sys/installdir/usf/bin64 Anita Orendt Installation Only Note this is an old package and about half of the 35 tools in the package did not work. Those were remove from the installation. See contents in /uufs/chpc.utah.edu/sys/installdir/usf/bin64 for the ones that run.
vaast 2.1.6, 2.1.3 Applications All genomics, Genomic analysis /uufs/chpc.utah.edu/sys/installdir/vaast Anita Orendt Installation Only
vapor 1.5.2, 2.0.2, 2.2.4, 2.5.0 Applications ALL visualization, Atmospheric Sciences /uufs/chpc.utah.edu/sys/pkg/vapor Martin Cuma Installation Only
vat 2.0.1 Applications All genomics, Genomic analysis /uufs/chpc.utah.edu/sys/pkg/vat Anita Orendt Installation Only
vcftools 0.1.11, 0.1.7, 0.1.14-20 (D) Applications All genomics, Genomic analysis /uufs/chpc.utah.edu/sys/installdir/vcftools Anita Orendt Installation Only
VisIt 2.10.0, 2.10.1, 2.10.2, 2.10.3 (D) Applications All visualization /uufs/chpc.utah.edu/sys/installdir/VisIt Martin Cuma Novice User
VisualSFM 0.5.26 Applications All visualization /uufs/chpc.utah.edu/sys/installdir/visualfsm Anita Orendt Installation Only
vmd 1.9.2 Applications All chemistry, visualization /uufs/chpc.utah.edu/sys/installdir/vmd Anita Orendt Intermediate User earlier versions in pkg branch
voronoi 0.4.5, 0.4.6(D) Library All Math, C, Applied Math, Delaunay triangulation /uufs/chpc.utah.edu/sys/installdir/voronoi Wim Cardoen Installation Only
weblogo 2.8.2 Applications All genomics /uufs/chpc.utah.edu/sys/pkg/weblogo Anita Orendt Installation Only
weka 3.6.12 Applications All Machine learning /uufs/chpc.utah.edu/sys/installdir/weka Martin Cuma Novice User
wgrib 1.8.0 Applications All Atmospheric Sciences /uufs/chpc.utah.edu/sys/pkg/wgrib Martin Cuma Installation Only
wgrib2 2.0.2 Applications All Atmospheric Sciences /uufs/chpc.utah.edu/sys/installdir/wgrib2 Martin Cuma Installation Only
wien2k 14.2 Applications All chemistry, C, Computational chemistry /uufs/chpc.utah.edu/sys/installdir/wien2k Anita Orendt Installation Only
wxWidgets 2.9.4 Libraries All C /uufs/chpc.utah.edu/sys/pkg/wxWidgets/ Wim Cardoen Installation Only
xerces c-3.1.1(D) Utilities All XML parser /uufs/chpc.utah.edu/sys/pkg/xerces Wim Cardoen Installation Only
xz (lzma) 5.2.2 Applications All File compression /uufs/chpc.utah.edu/sys/installdir/xz/5.2.2 Wim Cardoen Installation Only The library is called liblzma; the executable is called xz/lzma
zeromq 4.0.5, 4.1.3(D) Library All /uufs/chpc.utah.edu/sys/installdir/zeromq Wim Cardoen Installation Only
zlib 1.2.7 Library All Compilers, Compilers and Tools, C, Tools /uufs/chpc.utah.edu/sys/installdir/zlib Wim Cardoen Installation Only