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 additional information on installed packages

Additional software may have been installed since this page was updated. Log on to the system and run “module avail” to see the full list of installed software.

Installed software

• Bioinformatics and Biosciences
  • ABySS 2.0.2
  • Bcl2fastq 2.17.1.14
  • Beagle 2.1.2
  • Bedtools 2.25
  • BWA 0.7.13
  • Bowtie 1.1.2
  • Bowtie2 2.29
  • ctffind
  • Cufflinks 2.2.1
  • GATK 3.6.0
  • ghostz 1.1.0
  • Gubbins 2.1.0
  • Hmmer 3.0
  • megadock 4.0.2
  • motioncorr 2.1
  • MPIBlast 1.6.0
  • mutect
  • NCBI Blast 2.3.0+
  • phyluce 1.50
  • plink 1.07
  • Q 6
  • Relion 2.1
  • RSEM 1.3.0
  • Samtools 1.3
  • sentieon
  • shapeit 2.12
  • Tophat 2.1.1
  • vmd 1.9.2
• Chemistry and Materials Science
  • AmberTools 15update6
  • CP2K 4.1
  • CPMD 3.15.3 (requires individual user registration, contact helpdesk for access)
  • eman2
  • Fleur v26e
  • GAMESS
  • Gromacs 5.1.2, 2016 & 2018.2
  • LAMMPS 11Aug17
  • Mumax
  • Octopus
  • NAMD 2.11
  • NWChem 6.6
  • Octopus 6.0
  • Openbabel 2.4.1
  • Quantum Espresso 5.4.0
• Physics
  • MEEP
• Deep Learning
  • Caffe
  • Digits
  • TensorFlow
  • Theano
  • Torch
• Engineering
  • FDS 6
  • FDTD 8.19.1466
  • OpenFOAM 3.0+, 4.0 & 5.0
  • foam-extend
  • SU2 6.0.0
• Weather & Climate
  • Bicycle
  • WRF 3.8
  • NCL 6.3.0
• Containers
  • Singularity 3.4
• Scripting and Programming Languages
  • Julia 0.4.5
  • MATLAB Runtime Environment R2018b, R2018a, R2016a & R2015b (please note that this is just the runtime environment to execute pre-compiled MATLAB executables and not a full MATLAB installation)
  • Octave 4.0.3
  • Python: Anaconda
  • Python: Intel Python Distribution
  • Python 2.7.12 with following packages as reported by pip freeze
ase==3.11.0
backports-abc==0.5
backports.functools-lru-cache==1.5
backports.shutil-get-terminal-size==1.0.0
backports.ssl-match-hostname==3.5.0.1
beautifulsoup4==4.5.3
biopython==1.68
bleach==1.5.0
bx-python==0.7.3
catkin-pkg==0.4.1
certifi==2017.1.23
cffi==1.11.2
click==6.7
climate==0.4.6
configparser==3.5.0
cycler==0.10.0
Cython==0.24.1
dask==0.13.0
decorator==4.0.10
definitions==0.2.0
dill==0.2.5
docopt==0.6.2
docutils==0.14
downhill==0.4.0
drmaa==0.7.6
dsdtools==0.1.3
empy==3.3.2
entrypoints==0.2.2
enum34==1.1.6
Flask==0.12
Flask-SocketIO==2.8.2
Flask-WTF==0.14.2
funcsigs==1.0.2
functools32==3.2.3.post2
future==0.16.0
gevent==1.2.1
gevent-socketio==0.3.6
gevent-websocket==0.9.5
google==1.9.3
gpaw==1.1.0
graphviz==0.8.4
greenlet==0.4.12
gunicorn==19.6.0
h5py==2.6.0
html5lib==0.9999999
inspyred==1.0.1
ipykernel==4.5.2
ipython==5.1.0
ipython-genutils==0.1.0
ipywidgets==5.2.2
itsdangerous==0.24
Jinja2==2.9.5
joblib==0.10.3
jsonschema==2.5.1
jupyter==1.0.0
jupyter-client==4.4.0
jupyter-console==5.0.0
jupyter-core==4.2.1
Keras==1.2.1
kiwisolver==1.0.1
leveldb==0.194
llvmlite==0.20.0
lmdb==0.92
lxml==3.7.0
Mako==1.0.6
MarkupSafe==0.23
matlab-wrapper==0.9.7
matplotlib==2.2.3
mir-eval==0.4
mirnylib==0.0.0
mistune==0.7.3
mock==2.0.0
mpi4py==2.0.0
mpmath==0.19
nbconvert==5.1.1
nbformat==4.2.0
networkx==1.11
nltk==3.2.2
nose==1.3.7
nose-parameterized==0.5.0
notebook==4.3.2
numba==0.35.0
numexpr==2.6.2
numpy==1.11.2
olefile==0.44
openmm==0.2
pandas==0.18.1
pandocfilters==1.4.1
pathlib2==2.1.0
patsy==0.4.1
pbr==2.0.0
pexpect==4.2.1
pickleshare==0.7.4
PIL==1.1.7
Pillow==4.0.0
plac==0.9.6
ply==3.10
Pmw==2.0.1
POAP==0.1.24
prompt-toolkit==1.0.8
protobuf==3.2.0
ptyprocess==0.5.1
py-dempster-shafer==0.7
pyaml==17.10.0
pycparser==2.18
pyDOE==0.3.8
pydot-ng==1.0.0
PyFFTW3==0.2.1
Pygments==2.1.3
pyKriging==0.1.0
pyparsing==2.1.9
pysam==0.10.0
pySOT==0.1.25
PySoundFile==0.9.0.post1
python-dateutil==2.5.3
python-engineio==1.1.2
python-gflags==3.1.1
python-socketio==1.6.3
pytz==2016.6.1
PyYAML==3.12
pyzabbix==0.7.4
pyzmq==16.0.2
qtconsole==4.2.1
queuelib==1.4.2
requests==2.13.0
resampy==0.2.0
rosdep==0.11.8
rosdistro==0.6.6
rospkg==1.1.4
scikit-image==0.12.3
scikit-learn==0.17.1
scipy==1.1.0
seaborn==0.7.1
sets==0.3.2
simplegeneric==0.8.1
singledispatch==3.4.0.3
six==1.10.0
sklearn==0.0
stampy==0.2.0
statsmodels==0.6.1
subprocess32==3.2.7
sympy==1.0
terminado==0.6
testpath==0.3
theanets==0.7.3
Theano==0.8.2
toolz==0.8.2
tornado==4.4.2
tqdm==4.19.4
traitlets==4.3.1
UFL==2017.1.0.dev0
virtualenv==15.0.3
wcwidth==0.1.7
Werkzeug==0.11.15
widgetsnbextension==1.2.6
WTForms==2.1
xgboost==0.6a2
zmq==0.0.0
  • PyMOL
  • Python 3.5
  • R 3.3.1
• Developer Tools
  • ARM Allinea Forge 19.1.4
  • ARM Allinea Performance Reports 19.1.4
  • Autoconf 2.69
  • Autogen 5.18.7
  • Automake 1.15
  • Binutils 2.26
  • BLCR 0.8.5
  • Boost 1.60.0
  • CMAKE 3.5.0-rc3
  • CUDA 7.0, 7.5, 8.0, 9.2 and 10.1
  • Dejagnu 1.5.3
  • FFTW 3.3.4
  • GCC 4.4.7, 4.9.3 & 5.1.0
  • Go 1.13
  • GMP 6.1.0
  • gnuplot 5.0.3
  • HDF5 1.8.16
  • Intel Composer 2016.1.056, 2017.0.098, 2018.0.128, 2019.0.0.117
  • Intel MPI 5.1.2
  • ISL 0.14
  • Jasper 1.701.0
  • Java 1.8.0_91
  • Libtool 2.4.6
  • Lzip 1.18-rc2
  • MPC 1.0.3
  • MPFR 3.1.4
  • NAG Fortran Compiler
  • NAG Libraries
  • OpenMPI 1.10.4 and 3.0.1
  • GNU Parallel 20160222
  • PBS Professional 14.2.4
  • NetCDF 4.4.0
  • PETSc
  • QT 4.6.2-28.el6_5
  • Readline 6.3
  • Scotch 6.0.3
  • SZIP 2.1
  • TCL 8.5.7-6.el6
  • xmgrace 5.1.25
  • XZ 5.2.2
  • ZLIB 1.2.3-29.el6
• File transfer
  • Aspera client 3.5.4.102989