{"id":212,"date":"2016-04-01T10:54:16","date_gmt":"2016-04-01T10:54:16","guid":{"rendered":"https:\/\/help.nscc.sg\/?page_id=212"},"modified":"2023-05-12T17:09:34","modified_gmt":"2023-05-12T09:09:34","slug":"software-list","status":"publish","type":"page","link":"https:\/\/help-2626.nscc.sg\/software-list\/","title":{"rendered":"Software List"},"content":{"rendered":"<h1>NSCC Software List<\/h1>\n<h3><strong>ASPIRE 2A:<\/strong><\/h3>\n<p><em>Last updated 12 May 2023<\/em><\/p>\n<p>Please refer to the <a href=\"https:\/\/help.nscc.sg\/wp-content\/uploads\/NSCC-ASPIRE-2A-Software-List.pdf\">NSCC ASPIRE 2A Software List<\/a>.<\/p>\n<h3><strong>ASPIRE 1:<\/strong><\/h3>\n<p><em>Last updated 06 October 2020<\/em><\/p>\n<p><a href=\"\/software-help\">Software help page with additional information on installed packages<\/a><\/p>\n<p>Additional software may have been installed since this page was updated. Log on to the system and run &#8220;module avail&#8221; to see the full list of installed software.<\/p>\n<h3>Installed software<\/h3>\n<ul>\n<li>Bioinformatics and Biosciences\n<ul>\n<li>ABySS 2.0.2<\/li>\n<li><a href=\"\/software-help#bcl2fastq\">Bcl2fastq 2.17.1.14<\/a><\/li>\n<li>Beagle 2.1.2<\/li>\n<li><a href=\"\/software-help#bedtools\">Bedtools 2.25<\/a><\/li>\n<li><a href=\"\/software-help#bwa\">BWA 0.7.13<\/a><\/li>\n<li><a href=\"\/software-help#bowtie\">Bowtie 1.1.2<\/a><\/li>\n<li><a href=\"\/software-help#bowtie\">Bowtie2 2.29<\/a><\/li>\n<li>ctffind<\/li>\n<li><a href=\"\/software-help#cufflinks\">Cufflinks 2.2.1<\/a><\/li>\n<li><a href=\"https:\/\/www.broadinstitute.org\/gatk\/download\/\">GATK 3.6.0<\/a><\/li>\n<li>ghostz 1.1.0<\/li>\n<li>Gubbins 2.1.0<\/li>\n<li><a href=\"\/software-help#hmmer\">Hmmer 3.0<\/a><\/li>\n<li>megadock 4.0.2<\/li>\n<li>motioncorr 2.1<\/li>\n<li><a href=\"\/software-help#mpiblast\">MPIBlast 1.6.0<\/a><\/li>\n<li><a href=\"https:\/\/www.broadinstitute.org\/cancer\/cga\/mutect\">mutect<\/a><\/li>\n<li><a href=\"\/software-help#ncbi-blast\">NCBI Blast 2.3.0+<\/a><\/li>\n<li>phyluce 1.50<\/li>\n<li>plink 1.07<\/li>\n<li>Q 6<\/li>\n<li>Relion 2.1<\/li>\n<li>RSEM 1.3.0<\/li>\n<li><a href=\"\/software-help#samtools\">Samtools 1.3<\/a><\/li>\n<li>sentieon<\/li>\n<li>shapeit 2.12<\/li>\n<li><a href=\"\/software-help#tophat\">Tophat 2.1.1<\/a><\/li>\n<li>vmd 1.9.2<\/li>\n<\/ul>\n<\/li>\n<li>Chemistry and Materials Science\n<ul>\n<li><a href=\"\/software-help#ambertools\">AmberTools 15update6<\/a><\/li>\n<li>CP2K 4.1<\/li>\n<li><a href=\"\/software-help#cpmd\">CPMD 3.15.3<\/a> (requires individual user registration, contact helpdesk for access)<\/li>\n<li>eman2<\/li>\n<li>Fleur v26e<\/li>\n<li>GAMESS<\/li>\n<li><a href=\"\/software-help#gromacs\">Gromacs 5.1.2, 2016 &amp; 2018.2<\/a><\/li>\n<li>LAMMPS 11Aug17<\/li>\n<li>Mumax<\/li>\n<li>Octopus<\/li>\n<li>NAMD 2.11<\/li>\n<li><a href=\"\/software-help#nwchem\">NWChem 6.6<\/a><\/li>\n<li>Octopus 6.0<\/li>\n<li>Openbabel 2.4.1<\/li>\n<li><a href=\"\/software-help#quantum-espresso\">Quantum Espresso 5.4.0<\/a><\/li>\n<\/ul>\n<\/li>\n<li>Physics\n<ul>\n<li><a href=\"\/software-help#meep\">MEEP<\/a><\/li>\n<\/ul>\n<\/li>\n<li>Deep Learning\n<ul>\n<li>Caffe<\/li>\n<li>Digits<\/li>\n<li>TensorFlow<\/li>\n<li>Theano<\/li>\n<li>Torch<\/li>\n<\/ul>\n<\/li>\n<li>Engineering\n<ul>\n<li>FDS 6<\/li>\n<li>FDTD 8.19.1466<\/li>\n<li><a href=\"\/software-help#openfoam\">OpenFOAM 3.0+, 4.0 &amp; 5.0<\/a><\/li>\n<li>foam-extend<\/li>\n<li>SU2 6.0.0<\/li>\n<\/ul>\n<\/li>\n<li>Weather &amp; Climate\n<ul>\n<li>Bicycle<\/li>\n<li><a href=\"\/software-help#wrf\">WRF 3.8<\/a><\/li>\n<li><a href=\"\/software-help#ncl\">NCL 6.3.0<\/a><\/li>\n<\/ul>\n<\/li>\n<li>Containers\n<ul>\n<li>Singularity 3.4<\/li>\n<\/ul>\n<\/li>\n<li>Scripting and Programming Languages\n<ul>\n<li><a href=\"\/software-help#julia\">Julia 0.4.5<\/a><\/li>\n<li>MATLAB Runtime Environment R2018b, R2018a, R2016a &amp; R2015b (please note that this is just the runtime environment to execute pre-compiled MATLAB executables and not a full MATLAB installation)<\/li>\n<li>Octave 4.0.3<\/li>\n<li>Python: Anaconda<\/li>\n<li>Python: Intel Python Distribution<\/li>\n<li><a href=\"\/software-help#python\">Python 2.7.12<\/a> with following packages as reported by <code>pip freeze<br \/>\nase==3.11.0<br \/>\nbackports-abc==0.5<br \/>\nbackports.functools-lru-cache==1.5<br \/>\nbackports.shutil-get-terminal-size==1.0.0<br \/>\nbackports.ssl-match-hostname==3.5.0.1<br \/>\nbeautifulsoup4==4.5.3<br \/>\nbiopython==1.68<br \/>\nbleach==1.5.0<br \/>\nbx-python==0.7.3<br \/>\ncatkin-pkg==0.4.1<br \/>\ncertifi==2017.1.23<br \/>\ncffi==1.11.2<br \/>\nclick==6.7<br \/>\nclimate==0.4.6<br \/>\nconfigparser==3.5.0<br \/>\ncycler==0.10.0<br \/>\nCython==0.24.1<br \/>\ndask==0.13.0<br \/>\ndecorator==4.0.10<br \/>\ndefinitions==0.2.0<br \/>\ndill==0.2.5<br \/>\ndocopt==0.6.2<br \/>\ndocutils==0.14<br \/>\ndownhill==0.4.0<br \/>\ndrmaa==0.7.6<br \/>\ndsdtools==0.1.3<br \/>\nempy==3.3.2<br \/>\nentrypoints==0.2.2<br \/>\nenum34==1.1.6<br \/>\nFlask==0.12<br \/>\nFlask-SocketIO==2.8.2<br \/>\nFlask-WTF==0.14.2<br \/>\nfuncsigs==1.0.2<br \/>\nfunctools32==3.2.3.post2<br \/>\nfuture==0.16.0<br \/>\ngevent==1.2.1<br \/>\ngevent-socketio==0.3.6<br \/>\ngevent-websocket==0.9.5<br \/>\ngoogle==1.9.3<br \/>\ngpaw==1.1.0<br \/>\ngraphviz==0.8.4<br \/>\ngreenlet==0.4.12<br \/>\ngunicorn==19.6.0<br \/>\nh5py==2.6.0<br \/>\nhtml5lib==0.9999999<br \/>\ninspyred==1.0.1<br \/>\nipykernel==4.5.2<br \/>\nipython==5.1.0<br \/>\nipython-genutils==0.1.0<br \/>\nipywidgets==5.2.2<br \/>\nitsdangerous==0.24<br \/>\nJinja2==2.9.5<br \/>\njoblib==0.10.3<br \/>\njsonschema==2.5.1<br \/>\njupyter==1.0.0<br \/>\njupyter-client==4.4.0<br \/>\njupyter-console==5.0.0<br \/>\njupyter-core==4.2.1<br \/>\nKeras==1.2.1<br \/>\nkiwisolver==1.0.1<br \/>\nleveldb==0.194<br \/>\nllvmlite==0.20.0<br \/>\nlmdb==0.92<br \/>\nlxml==3.7.0<br \/>\nMako==1.0.6<br \/>\nMarkupSafe==0.23<br \/>\nmatlab-wrapper==0.9.7<br \/>\nmatplotlib==2.2.3<br \/>\nmir-eval==0.4<br \/>\nmirnylib==0.0.0<br \/>\nmistune==0.7.3<br \/>\nmock==2.0.0<br \/>\nmpi4py==2.0.0<br \/>\nmpmath==0.19<br \/>\nnbconvert==5.1.1<br \/>\nnbformat==4.2.0<br \/>\nnetworkx==1.11<br \/>\nnltk==3.2.2<br \/>\nnose==1.3.7<br \/>\nnose-parameterized==0.5.0<br \/>\nnotebook==4.3.2<br \/>\nnumba==0.35.0<br \/>\nnumexpr==2.6.2<br \/>\nnumpy==1.11.2<br \/>\nolefile==0.44<br \/>\nopenmm==0.2<br \/>\npandas==0.18.1<br \/>\npandocfilters==1.4.1<br \/>\npathlib2==2.1.0<br \/>\npatsy==0.4.1<br \/>\npbr==2.0.0<br \/>\npexpect==4.2.1<br \/>\npickleshare==0.7.4<br \/>\nPIL==1.1.7<br \/>\nPillow==4.0.0<br \/>\nplac==0.9.6<br \/>\nply==3.10<br \/>\nPmw==2.0.1<br \/>\nPOAP==0.1.24<br \/>\nprompt-toolkit==1.0.8<br \/>\nprotobuf==3.2.0<br \/>\nptyprocess==0.5.1<br \/>\npy-dempster-shafer==0.7<br \/>\npyaml==17.10.0<br \/>\npycparser==2.18<br \/>\npyDOE==0.3.8<br \/>\npydot-ng==1.0.0<br \/>\nPyFFTW3==0.2.1<br \/>\nPygments==2.1.3<br \/>\npyKriging==0.1.0<br \/>\npyparsing==2.1.9<br \/>\npysam==0.10.0<br \/>\npySOT==0.1.25<br \/>\nPySoundFile==0.9.0.post1<br \/>\npython-dateutil==2.5.3<br \/>\npython-engineio==1.1.2<br \/>\npython-gflags==3.1.1<br \/>\npython-socketio==1.6.3<br \/>\npytz==2016.6.1<br \/>\nPyYAML==3.12<br \/>\npyzabbix==0.7.4<br \/>\npyzmq==16.0.2<br \/>\nqtconsole==4.2.1<br \/>\nqueuelib==1.4.2<br \/>\nrequests==2.13.0<br \/>\nresampy==0.2.0<br \/>\nrosdep==0.11.8<br \/>\nrosdistro==0.6.6<br \/>\nrospkg==1.1.4<br \/>\nscikit-image==0.12.3<br \/>\nscikit-learn==0.17.1<br \/>\nscipy==1.1.0<br \/>\nseaborn==0.7.1<br \/>\nsets==0.3.2<br \/>\nsimplegeneric==0.8.1<br \/>\nsingledispatch==3.4.0.3<br \/>\nsix==1.10.0<br \/>\nsklearn==0.0<br \/>\nstampy==0.2.0<br \/>\nstatsmodels==0.6.1<br \/>\nsubprocess32==3.2.7<br \/>\nsympy==1.0<br \/>\nterminado==0.6<br \/>\ntestpath==0.3<br \/>\ntheanets==0.7.3<br \/>\nTheano==0.8.2<br \/>\ntoolz==0.8.2<br \/>\ntornado==4.4.2<br \/>\ntqdm==4.19.4<br \/>\ntraitlets==4.3.1<br \/>\nUFL==2017.1.0.dev0<br \/>\nvirtualenv==15.0.3<br \/>\nwcwidth==0.1.7<br \/>\nWerkzeug==0.11.15<br \/>\nwidgetsnbextension==1.2.6<br \/>\nWTForms==2.1<br \/>\nxgboost==0.6a2<br \/>\nzmq==0.0.0<\/code><\/li>\n<li>PyMOL<\/li>\n<li><a href=\"\/software-help#python\">Python 3.5<\/a><\/li>\n<li><a href=\"\/software-help#r\">R 3.3.1<\/a><\/li>\n<\/ul>\n<\/li>\n<li>Developer Tools\n<ul>\n<li><a href=\"\/software-help#allinea\">ARM Allinea Forge 19.1.4<\/a><\/li>\n<li><a href=\"\/software-help#allinea\">ARM Allinea Performance Reports 19.1.4<\/a><\/li>\n<li>Autoconf 2.69<\/li>\n<li>Autogen 5.18.7<\/li>\n<li>Automake 1.15<\/li>\n<li>Binutils 2.26<\/li>\n<li>BLCR 0.8.5<\/li>\n<li>Boost 1.60.0<\/li>\n<li>CMAKE 3.5.0-rc3<\/li>\n<li>CUDA 7.0, 7.5, 8.0, 9.2 and 10.1<\/li>\n<li>Dejagnu 1.5.3<\/li>\n<li>FFTW 3.3.4<\/li>\n<li>GCC 4.4.7, 4.9.3 &amp; 5.1.0<\/li>\n<li>Go 1.13<\/li>\n<li>GMP 6.1.0<\/li>\n<li><a href=\"\/software-help#gnuplot\">gnuplot 5.0.3<\/a><\/li>\n<li>HDF5 1.8.16<\/li>\n<li>Intel Composer 2016.1.056, 2017.0.098, 2018.0.128, 2019.0.0.117<\/li>\n<li>Intel MPI 5.1.2<\/li>\n<li>ISL 0.14<\/li>\n<li>Jasper 1.701.0<\/li>\n<li>Java 1.8.0_91<\/li>\n<li>Libtool 2.4.6<\/li>\n<li>Lzip 1.18-rc2<\/li>\n<li>MPC 1.0.3<\/li>\n<li>MPFR 3.1.4<\/li>\n<li><a href=\"\/software-help#nag\">NAG Fortran Compiler<\/a><\/li>\n<li><a href=\"\/software-help#nag\">NAG Libraries<\/a><\/li>\n<li>OpenMPI 1.10.4 and 3.0.1<\/li>\n<li>GNU Parallel 20160222<\/li>\n<li>PBS Professional 14.2.4<\/li>\n<li>NetCDF 4.4.0<\/li>\n<li>PETSc<\/li>\n<li>QT 4.6.2-28.el6_5<\/li>\n<li>Readline 6.3<\/li>\n<li>Scotch 6.0.3<\/li>\n<li>SZIP 2.1<\/li>\n<li>TCL 8.5.7-6.el6<\/li>\n<li>xmgrace 5.1.25<\/li>\n<li>XZ 5.2.2<\/li>\n<li>ZLIB 1.2.3-29.el6<\/li>\n<\/ul>\n<\/li>\n<li>File transfer\n<ul>\n<li><a href=\"\/software-help#aspera\">Aspera client 3.5.4.102989<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>NSCC Software List ASPIRE 2A: Last updated 12 May 2023 Please refer to the NSCC ASPIRE 2A Software List. ASPIRE 1: Last updated 06 October 2020 Software help page with\u2026 <a href=\"https:\/\/help-2626.nscc.sg\/software-list\/\" class=\"read-more-link\">read more &rarr;<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"_links":{"self":[{"href":"https:\/\/help-2626.nscc.sg\/wp-json\/wp\/v2\/pages\/212"}],"collection":[{"href":"https:\/\/help-2626.nscc.sg\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/help-2626.nscc.sg\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/help-2626.nscc.sg\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/help-2626.nscc.sg\/wp-json\/wp\/v2\/comments?post=212"}],"version-history":[{"count":58,"href":"https:\/\/help-2626.nscc.sg\/wp-json\/wp\/v2\/pages\/212\/revisions"}],"predecessor-version":[{"id":4161,"href":"https:\/\/help-2626.nscc.sg\/wp-json\/wp\/v2\/pages\/212\/revisions\/4161"}],"wp:attachment":[{"href":"https:\/\/help-2626.nscc.sg\/wp-json\/wp\/v2\/media?parent=212"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}