Knowledge Base

ACT software list

Overview of Installed Software

This page contains information about the software that is available on the academic computing cluster, the met-cluster and the NX nodes. The lists are not exhaustive as we restricted them to software that isn’t available by default in Centos 7 Linux and focus here on scientific software and programming tools.

 

Reading Academic Computing Cluster (RACC)

On the RACC software is both installed in default system paths from software package managers (rpms) and as environmental modules, which have to be loaded first.

Software installed from rpms

The default versions of these software packages are already in the path and the ‘module load’ command is not needed.

Package Description Commands
R Language for statistical computing and graphics,
https://www.r-project.org
R
rstudio GUI environment for R,
https://www.rstudio.com/
rstudio
octave Numerical programming suite compatible with Matlab,
https://www.gnu.org/software/octave/
octave
gcc GNU Compiler Collection,
https://www.gnu.org/software/gcc/
gcc, g++, gfortran
git Version control system,
https://git-scm.com
git
GSL GNU Scientific Library,
https://www.gnu.org/software/gsl/
boost Peer-reviewed portable C++ source libraries,
https://www.boost.org
lapack Linear Algebra Package,
http://www.netlib.org/lapack/
blas Basic Linear Algebra Subprograms,
http://www.netlib.org/blas/
gdal Geospatial Data Abstraction Library,
https://www.gdal.org
zlib A Massively Spiffy Yet Delicately Unobtrusive Compression Library,
https://zlib.net
grib-api ECMWF application program interface accessible for encoding and decoding data in grib format,
https://confluence.ecmwf.int/display/GRIB/Home
e.g. grib_ls, grib_info, grib_get
curl Command-line tool and library for transferring data,
https://curl.haxx.se
curl
fftw C subroutine library for computing the discrete Fourier transform (DFT),
http://www.fftw.org
udunits C library for units of physical quantities and a unit-definition and value-conversion utility,
https://www.unidata.ucar.edu/software/udunits/
udunits
expat A stream-oriented parser,
https://libexpat.github.io
proj A generic coordinate transformation software,
https://proj4.org
proj
ncl NCAR Command Language,
https://www.ncl.ucar.edu
ncl
nco netCDF Operators’
http://nco.sourceforge.net
e.g. ncks, ncecat, ncwa
ncview netCDF visual browser,
http://meteora.ucsd.edu/~pierce/ncview_home_page.html
ncview
cdo Climate Data Operators,
https://code.mpimet.mpg.de/projects/cdo
cdo
mplayer Movie Player,
http://www.mplayerhq.hu/design7/news.html
mplayer
cmake Tools to build, test and package software,
https://cmake.org
cmake
rsync File transfer utility,
https://rsync.samba.org
rsync
rclone A command line program to sync files and directories to and from cloud storage including OneDrive,
https://rclone.org
 rclone
firefox Web browser,
https://www.mozilla.org/en-GB/firefox/
firefox

 

Software available using environmental modules

If you’re not familiar with the ‘module’ commands, please see Accessing Software on the Cluster for information about using environmental modules.

Package Description Commands
ENVI (licensed for v. 5.5 and onward) Image analysis software
https://www.harrisgeospatial.com/Software-Technology/ENVI
envi
IDL Scientific programming language,
https://www.harrisgeospatial.com/Software-Technology/IDL
idl
Matlab Numerical computing software and programming language, see also: Running Matlab Scripts as Batch Jobs
https://uk.mathworks.com/products/matlab.html
matlab
Canopy python (2.7 and 3.5) Enthought python distribution and analysis environment for scientific and analytic computing, see also: Python on the Cluster
https://www.enthought.com/product/canopy/
python
Anaconda Python (2.7 and 3.5) Anaconda python distribution and analysis environment for scientific and analytic computing, see also: Python on the Cluster
https://www.anaconda.com
python
cuda NVIDIA parallel computing platform and programming model,
https://developer.nvidia.com/cuda-zone
nvcc
gcc GNU Compiler Collection,
https://www.gnu.org/software/gcc/
gcc, g++, gfortran
intel Intel Parallel Studio XE for Fortran,
https://software.intel.com/en-us/parallel-studio-xe
ifort
pgi PGI Fortran compiler and tools,
https://www.pgroup.com
e.g. pgf90, pgcc, pgunzip
solstudio Oracle Developer Studio compilers and tools,
https://www.oracle.com/technetwork/server-storage/developerstudio/overview/index.html
e.g. cc, CC, f90, f95
mpich High performance implementation of the Message Passing Interface (MPI) standard,
https://www.mpich.org
e.g. mpicc, mpifort, mpiexec
openmpi Open source implementation of the Message Passing Interface (MPI) standard,
https://www.open-mpi.org
e.g. mpicc, mpifort, mpiexec
nag NAG library, a collection of robust, documented, tested and maintained numerical algorithms,
https://www.nag.co.uk/content/nag-library 
NAG library on RACC
netCDF Libraries and tools that support the creation, access and sharing of array-oriented scientific data,
https://www.unidata.ucar.edu/software/netcdf/
e.g ncdump, ncgen, nccopy
hdf5 Technology suite for the management of extremely large and complex data collections,
https://support.hdfgroup.org/HDF5/
e.g h5dump, h5diff, h5ls

 

Met-Cluster

The met-cluster is now a legacy service. While it is still available, software on it can be accessed via the ‘module‘ command. Some of the software and packages that are listed for the RACC are also available for the met cluster, although these are older versions and are no longer maintained. For up to date software and libraries, please switch to the RACC as there are no more updates or additions planned to the met-cluster software.

 

NX nodes

The NX nodes use the NoMachine NX Enterprise software to provide a virtual linux desktop. The software is only installed in default system paths from software package managers (apt).

Package Description Commands
git Version control system,
https://git-scm.com
git
curl Command-line tool and library for transferring data,
https://curl.haxx.se
curl
ncview netCDF visual browser,
http://meteora.ucsd.edu/~pierce/ncview_home_page.html
ncview
rclone A command line program to sync files and directories to and from cloud storage including OneDrive, see also: Transferring files to OneDrive for Business via rclone
https://rclone.org
 rclone
rsync File transfer utility,
https://rsync.samba.org
rsync
firefox Web browser,
https://www.mozilla.org/en-GB/firefox/
firefox

Packages installed for Meteorology

Ubuntu  repositories:

cmake,ghostscript,gimp,git,gv,imagemagick,latexdiff,latex2rtf,libreoffice,lynx,pdftk,php,r-base,rcs,subversion,texlive-full,texmaker,w3m,vlc,xfig,xournal

Other repositories:

chrome

Packages installed for Computer Science

Ubuntu  repositories:

cmake-qt-gui,eclipse,git-gui,gedit,meld,nano,vim,gcc,clang,dnsutils,strace,doxygen

Other repositories:

atom,eclipse,visual_studio_code

Direct install from archive file

archi

News

RACC updates

We have changed the default partition to be the 'limited'. Users submitting jobs longer than 24h need to explicitly request another partition, e.g. 'cluster'. Jobs submitted with time limit exceeding the partition limit will be rejected.   Purchasing RACC nodes owned by projects can  be requested using the Self Service Portal form,  see /https://research.reading.ac.uk/act/knowledgebase/racc-paid-for-resources/....
Read More
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