Software and Libraries

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Software Module System

All the software listed on this page is accessed using a modules system. This means that much of the software is not accessible by default but has to be loaded using the module command. The reason is that

  • it allows us to easily keep multiple versions of software for different users on the system;
  • it allows users to easily switch between versions.

The module system works similarly on the GPC and the TCS, although different modules are installed on these two systems.

Note that, generally, if you compile a program with a module loaded, you will have to run it with that same module loaded, to make dynamically linked libraries accessible.

Function Command Comments
List available software packages: 
$ module avail
  • If a module is not listed here, it is not supported.
  • The flag "(default)" is never part of the name.
Use particular software: 
 $ module load [module-name]
  • If possible, specify only the short name (the part before the "/").
  • When ambiguous, this loads the default one.
List available versions of a specific software package: 
$ module avail [short-module-name]
List currently loaded modules: 
$ module list
 For reproducability, it is a good idea to put this in your job scripts, so you know exactly what modules(+version) were used.
Get description of a particular module: 
$ module help [module-name]
Remove a module from your shell: 
$ module unload [module-name]
Remove all modules: 
$ module purge
Replace one loaded module with another: 
$ module switch [old-module-name] [new-module-name]
Find a module by name and check its dependencies: 
$ module find [part-of-module-name]
 This is a module extension by SciNet for the GPC
Find one way to resolve module dependencies: 
$ module advice [module-name]
 This is a module extension by SciNet for the GPC

Modules that load libraries, define environment variables pointing to the location of library files and include files for use Makefiles. These environment variables follow the naming convention 

SCINET_[short-module-name]_BASE
SCINET_[short-module-name]_LIB
SCINET_[short-module-name]_INC

for the base location of the module's files, the location of the libraries binaries and the header files, respectively.

So to compile and link the library, you will have to add -I${SCINET_[short-module-name]_INC} and -L${SCINET_[short-module-name]_LIB}, respectively, in addition to the usual -l[libname].

Errors in loaded modules can arise for a few reasons, for instance:

  • A module by that name may not exist.
  • Some modules require other modules to have been loaded; it this requirement is not met when you try to load that module, an error message will be printed explaining what module is needed.
  • Some modules cannot be loaded together: an error message will be printed explaining which modules conflict.

It is no longer recommended to load modules in the file .bashrc in your home directory, rather, load them explicitly on the command-line and in your job scripts.

Makefile example of using modules

For a single-file c++-code using boost's threading library, the Makefile could contain 

CPPFLAGS=-I${SCINET_BOOST_INC}
LDFLAGS=-L${SCINET_BOOST_LIB}
LDLIBS=-lboost_thread
all: boostthreadexample
boostthreadexample: boostthreadexample.o
boostthreadexample.o: boostthreadexample.cpp
clean:
  \rm -f boostthreadexample.o

On the command line, you'd type 

$ module load intel/15.0.2 openmpi/intel/1.6.4 cxxlibraries/boost/1.55.0-intel
$ make

(Note: openmpi is loaded here because the boost module includes the boost:mpi package, which is however not used in this example).

CMake example of using modules

Several versions of CMake are installed on the GPC: the default version is 2.6 (which may be too old in many cases), but there are more version available as modules Currently (Dec 2015), the most recent installed version is cmake/3.4.0 (type module avail cmake to see all available version.

Using cmake with the environment module eco-system requires a few tweaks. Because these tweaks are almost never discussed in the compilation instructions of package that use cmake, and are even hard to find in the CMake documentation itself, we explain these tweaks here.

For compiling the above example of a single-file c++ code using boost's threading library with CMake, one way is to have the CMakeLists.txt could contain 

include_directories($ENV{SCINET_BOOST_INC})
link_directories($ENV{SCINET_BOOST_LIB})
cmake_minimum_required(VERSION 2.6)
project(boostthreadexample)
add_executable(boostthreadexample boostthreadexample.cpp)
target_link_libraries(boostthreadexample boost_thread)

Make sure the include_directories and link_directories commands are given before the add_executable, or they may not take effect.

On the command line, you could then compile as follows: 

$ module load intel/15.0.2 openmpi/intel/1.6.4 cxxlibraries/boost/1.55.0-intel
$ cmake .
$ make

Although it is better to use a separate build directory. (Note: openmpi is loaded here because the boost module includes the boost:mpi package, which is however not used in this example).

An alternative setup for working cmake is to keep the CMakeLists.txt simple and standard: 

cmake_minimum_required(VERSION 2.6)
project(boostthreadexample)
add_executable(boostthreadexample boostthreadexample.cpp)
target_link_libraries(boostthreadexample boost_thread)

And then to use the environment variables to get the paths 

$ module load intel/15.0.2 openmpi/intel/1.6.4 cxxlibraries/boost/1.55.0-intel
$ CMAKE_PREFIX=${SCINET_BOOST_BASE}
$ CMAKE_INCLUDE_PATH=${SCINET_BOOST_INC}
$ CMAKE_LIBRARY_PATH=${SCINET_BOOST_LIB}
$ CMAKE_PROGRAM_PATH=${SCINET_BOOST_BIN}
$ cmake .
$ make

Default and non-default modules

When you load a module with its 'short' name, you will get the default version, which is the most recent (usually), recommended version of that library or piece of software. In general, using the short module name is the way to go. However, you may have code that depends on the intricacies of a non-default version. For that reason, the most common older versions are also available as modules. You can find all available modules using the module avail command.

Naming convention

For modules that access applications, the full name of a module is as follows. 

  [short-module-name]/[version-number]

To have all modules conform to this convention, a number of modules' name change on Nov 3, 2010:

old name new name remarks
autoconf/autoconf-2.64      autoconf/2.64 short name unchanged
cuda/cuda-3.0 cuda/3.0 default's short name unchanged
cuda/cuda-3.1 cuda/3.1
debuggers/ddd-3.3.12 ddd/3.3.12
debuggers/gdb-7.1 gdb/7.1
editors/nano/2.2.4 nano/2.2.4
emacs/emacs-23.1 emacs/23.1.1 short name unchanged
gcc/gcc-4.4.0 gcc/4.4.0 short name unchanged
graphics/ncview ncview/1.93
graphics/graphics grace/5.1.22
gnuplot/4.2.6
svn/svn165 svn/1.6.5 short name unchanged
visualization/paraview paraview/3.8
amber10/amber10 amber/10.0.30
gamess/gamess gamess/May2209   default's short name unchanged

modulefind - Finding modules by name

The module avail command will only show you modules whose names start with the argument that you give it, and will alsi return modules that you cannot load due to conflicts with already loaded modules.

A little SciNet utility called modulefind (one word) or module find (two words) can do that. It will list all installed modules which contain the arguments, and will determine whether those modules have been loaded, could be loaded, cannot because of conflicts with already loaded modules, or have unresolved dependencies (i.e. for which other modules need to be loaded first). This is especially useful in cases like the "boost" libraries, whose module names are cxxlibraries/boost/1.47.0-gcc and cxxlibraries/boost/1.47.0-gcc, for the gcc and intel compiler, respectively. modulefind boost will find those, whereas module avail boost will not.

Note that just module find will list all top-level modules.

Making your own modules

How to make your own modules (e.g. for local installations or to access optional perl modules, ...), is possible and described on the Installing your own modules page.

Deprecated modules

Some older software modules for which newer versions exist, get deprecated, which means they do not get maintained. Since deprecated modules should only be needed in rare exceptional cases, they are not listed by the module avail command. However, if you have a piece of legacy code that really depends on a deprecated version of a library (and we urge you to check that it does not work with newer versions!), then you can load a deprecated version by 

module load use.deprecated [deprecated-module-name]

Before using any of these deprecated modules, make sure that there is not a regular module that satisfies your needs, likely by a very similar name.

Commercial software

Apart from the compilers on our systems and the ddt parallel debugger, we generally do not provide licensed application software, e.g., no Gaussian, IDL, Matlab, etc. See the FAQ.

Other software and libraries

If you want to use a piece of software or a library that is not on the list, you can in principle install it yourself in you /home directory. Note however that building libraries and software from source often uses a lot of files. To avoid running out of disk space, building software is therefore best done from the /scratch, from which you can copy/install only the libraries, header files and binaries to your /home directory.

If you suspect that a particular piece of software or a library would be of use to other users of SciNet as well, contact us, and we will consider adding it to the system.

Software lists

Gravity.Viz GPU Software

The CPUs in the GPU nodes of the Gravity cluster are of the same kind as those of the GPC, so all modules available on the GPC are available on the GPU nodes with a CentOS 6 image. This means that the different cuda variants that are available as modules, can be loaded on those GPC nodes as well, although they are of little use on that system.

GPC Software

Software Versions Comments Command/Library Module Name
Compilers
Intel Compiler 12.1.3*, 12.1.5, 13.1.1, 14.0.1, 15.0, 15.0.1, 15.0.2, 15.0.6, 16.0.3 includes MKL library, which includes BLAS, LAPACK, FFT, ... icpc,icc,ifort intel
GCC Compiler 4.4.6, 4.6.1*, 4.7.0, 4.7.2, 4.8.1, 4.9.0, 5.2.0 Version 5.2.0 supports coarrays gcc,g++,gfortran
caf,cafrun (gcc/5.2.0 only) 		gcc
Cuda 3.2, 4.0, 4.1*, 4.2, 5.0, 5.5, 6.0 NVIDIA's extension to C for GPGPU programming nvcc cuda
PGI Compiler 13.2 supports OpenACC and CUDA Fortran pgcc,pgcpp,pgfortran pgi
IntelMPI 4.0.2, 4.0.3, 4.1.2*, 5.0.1, 5.0.2 MPICH2 based MPI (intelmpi/5.* are in the 'experimental' modules) mpicc,mpiCC,mpif77,mpif90 intelmpi
OpenMPI 1.4.4*, 1.5.4, 1.6.4, 1.8.3 mpicc,mpiCC,mpif77,mpif90 openmpi
UPC 2.12.2 Berkley Unified Parallel C Implementation upcc upc
Haskell 7.4.2*, 6.12.3 Haskell compiler and Cabal package manager ghc,cabal haskell
Editors
Nano 2.2.4 Nano's another editor nano nano
Emacs 23.1.1, 24.4* New version of popular text editor emacs emacs
Vim 7.2.4*, 7.4.5 Vi editor. No module needs to be loaded for the default version vim vim
XEmacs 21.4.22 XEmacs editor xemacs xemacs
Midnight Commander 4.7.0*, 4.8.14 A visual file manager within the terminal with builtin editor and viewer mc, mcedit, mcview mc
Development tools
Autoconf 2.68 autoconf, ... autoconf
Automake 1.11.2 aclocal, automake automake
CMake 2.8.6, 2.8.8*, 3.1.0 cross-platform, open-source build system cmake cmake
Scons 2.0 Software construction tool scons scons
Git 1.7.1, 1.7.10*, 1.9.5 Revision control system git,gitk git
Git-annex 4.20130827, 5.20150219* Revision control system git,gitk git-annex
Intel tools 2013, 2015 Intel Code Analysis Tools Vtune Amplifier XE, Inspector XE inteltools
Mercurial 1.8.2 Version control system
(part of the python module!) 		hg python
Debug and performance tools
DDT 4.0, 4.1, 4.2.1* Allinea's Distributed Debugging Tool, + MAP MPI Profiler ddt, map ddt
DDD 3.3.12 Data Display Debugger ddd ddd
GDB 7.3.1*, 7.6 GNU debugger (the intel idbc debugger is available by default) gdb gdb
MPE2 2.4.5 Multi-Processing Environment with intel + OpenMPI mpecc, mpefc, jumpshot mpe
OpenSpeedShop 2.1 sampling and MPI tracing openss, ... openspeedshop
Scalasca 1.3.3, 1.4.3* SCalable performance Analysis of LArge SCale Applications (Compiled with OpenMPI) scalasca scalasca
IPM 0.983 Integrated Performance Monitors http://ipm-hpc.sourceforge.net/] ipm, ipm_parse, ploticus,... ipm
Valgrind 3.7,0*, 3.9.0 Memory checking utility valgrind,cachegrind valgrind
Padb 3.2 examine and debug parallel programs padb padb
Visualization tools
Grace 5.1.22 Plotting utility xmgrace grace
Gnuplot 4.2.6, 4.6.1* Plotting utility
Requires 'extras' module if used on compute nodes. 		gnuplot gnuplot
ParaView 3.12.0*, 3.14.1, 4.1.0 Scientific visualization, server only pvserver,pvbatch,pvpython paraview
VMD 1.8.6, 1.9* Visualization and analysis utility vmd vmd
VisIt 2.6.3, 2.6.3-parallel*, 2.10.0-bin, 2.10.0-bin_mesa Interactive, scalable, visualization, animation and analysis tool visit visit
NCL/NCARG 6.0.0 NCARG graphics and ncl utilities ncl ncl
ROOT 5.30.00, 5.30.03*, 5.34.03, 6.02.02 ROOT Analysis Framework from CERN root ROOT
ImageMagick 6.6.7 Image manipulation tools convert,animate,composite,... ImageMagick
PGPLOT 5.2.2 Graphics subroutine library libcpgplot,libpgplot,libtkpgplot pgplot
Splash 2.6.0 Visualization suite for SPH simulations asplash, dsplash, gsplash, nsplash, rsplash, srsplash, ssplash, tsplash, vsplash splash
Storage tools and libraries
NetCDF 4.1.3*, 4.2.1, 4.3.2 Scientific data storage and retrieval ncdump,ncgen,libnetcdf netcdf
Ncview 2.1.1, 2.1. Visualization for NetCDF files ncview ncview
NCO 4.0.8, 4.3.2 NCO utilities to manipulate netCDF files ncap, ncap2, ncatted, etc. nco
CDO 1.5.1, 1.5.4*, 1.6.1 Climate Data Operators cdo cdo
UDUNITS 2.1.11 unit conversion utilities libudunits2 udunits
HDF4 4.2.6 Scientific data storage and retrieval h4fc,hdiff,...,libdf,libsz hdf4
HDF5 1.8.7-v18* Scientific data storage and retrieval, parallel I/O h5ls, h5diff, ..., libhdf5 hdf5
EncFS 1.74 EncFS provides an encrypted filesystem in user-space, (works ONLY on gpc01..04) encfs encfs
Applications
AMBER 10 Amber 10 + Amber Tools 1.3 Amber Molecular Dynamics Package sander, sander.MPI amber
antlr 2.7.7 ANother Tool for Language Recognition antlr, antlr-config
libantlr, antlr.jar, antlr.py 		antlr
GAMESS (US) August 18, 2011 R1 General Atomic and Molecular Electronic Structure System rungms gamess
GROMACS 4.5.5, 4.5.7, 4.6.2, 4.6.3, 4.6.7, 5.0.4 GROMACS molecular dynamics, single precision, MPI grompp, mdrun, gmx, gmx_mpi gromacs
NAMD 2.8, 2.9* NAMD - Scalable Molecular Dynamics namdmpiexec, namd2 namd
NWChem 6.0 NWChem Quantum Chemistry nwchem nwchem
Quantum Espresso 4.3.2, 5.0.3 Quantum Chemistry pw.x, ... espresso
BLAST 2.2.23+ Basic Local Alignment Search Tool blastn,blastp,blastx,psiblast,tblastn... blast
RAY 2.1.0 (small k-mer), 2.2.0, 2.3.1 Parallel de novo genome assemblies Ray ray
[CP2K] 3.0 DFT molecular dynamics, MPI cp2k.psmp cp2k
CPMD 3.13.2 Carr-Parinello molecular dynamics, MPI cpmd.x cpmd
R 2.13.1, 2.14.1, 2.15.1*, 3.0.0, 3.0.1, 3.1.1 statistical computing R R
Octave 3.4.3*, 3.8.1 Matlab-like environment octave octave
OpenFOAM 2.1.0, 2.3.0 Open Source CFD Package *foam openfoam
Bedtools 2.21.0 Toolset for genome arithmetic bedtools ... bedtools
Samtools 0.1.19 Suite of programs for interacting with high-throughput sequencing data samtools
MrBayes 3.2.4 MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. mb mrbayes
Stacks 1.28 1.29* A software pipeline for building loci from short-read sequences. stacks
Libraries
PETSc 3.1*, 3.2, 3.3, 3.4.4 Portable, Extensible Toolkit for Scientific Computation (PETSc) libpetsc, etc.. petsc
BOOST 1.47.0, 1.54, 1.55 C++ Boost libraries libboost... cxxlibraries/boost
Rarray 1.0 C++ multidimensional array library rarray cxxlibraries/rarray
Armadillo 3.910.0 C++ armadillo libraries (implement Matlab-like syntax) armadillo armadillo
GotoBLAS 1.13 Optimized BLAS implementation libgoto2 gotoblas
OpenBLAS 1.13, 0.2.13* Open BLAS implementation including lapack, cblas and lapacke. Note that compilations with the Intel c/c++ compiler will need to link with -lifcore libopenblas openblas
GSL 1.13*, 1.15 GNU Scientific Library libgsl, libgslcblas gsl
FFTW 2.1.5, 3.3.0, 3.3.3* fast Fourier transform library

Be careful in combining fftw3 and MKL: you need to link fftw3 first, with -L${SCINET_FFTW_LIB} -lfftw3, then link MKL

libfftw3 fftw
LAPACK Provided by the Intel MKL library See http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/ intel
RLog 1.4 RLog provides a flexible message logging facility for C++ programs and libraries. librlog cxxlibraries/rlog
Scripting/interpreted languages
GNU Parallel 2012-10-22, 20140622* execute commands in parallel parallel gnu-parallel
Python 2.7.2*, 2.7.3, , 2.7.5, 2.7.8 Python programming language. See Python page for details on installed packages. python python
Python 3.3.4 Python programming language. Modules included : numpy 1.8.1 , scipy 0.14.0 , matlotlib 1.3.1 , ipython 1.2.1 , cython 0.20.1 , h5py-2.3.0 , tables-3.1.1 , netCDF4-1.1.0 , astropy-0.3.2 , scikit_learn-0.15.0b1 python python
Ruby 1.9.1*, 1.9.3 Ruby programming language ruby ruby
Java 1.6.0, 1.7.1* IBM's Java JRE ad SDK java, javac java
Other
VNC 'Virtual Network Computing', an alterative for X forwarding. Only works on the devel nodes. See our VNC wiki page. vncstart, vncstop, vncstatus,... vnc
Xlibraries A collection of X graphics libraries and tools xterm, xpdf, ... Xlibraries
Extras A collection of standard linux and home-grown tools bc, screen, xxdiff, modulefind, ish, ... extras

* Several versions of this module are installed; listed is the default version.


P7 Software

Software Version Comments Command/Library Module Name
Compilers
IBM fortran compiler 14.1, 13.1 See P7 Linux Cluster xlf,xlf_r,xlf90,... xlf
IBM c/c++ compilers 12.1, 11.1 See P7 Linux Cluster xlc,xlC,xlc_r,xlC_r,... vacpp
Binutils 2.23.2 addr2line, ar, ld, ... binutils
IBM MPI library 5.2.2 IBM's Parallel Environment mpcc,mpCC,mpfort,mpiexec pe
GCC Compiler 4.6.1 , 4.8.1 GNU Compiler Collection gcc,g++,gfortran gcc
Java 7.0 IBM Java 1.7 implementation javac jdk
Debug/performancs tools
DDT 4.0, 4.1, 4.2.1* Allinea's Distributed Debugging Tool ddt ddt
Storage tools and libraries
HDF5 1.8.7 Scientific data storage and retrieval, parallel I/O libhdf5 hdf5
NetCDF 4.1.3 Scientific data storage and retrieval ncdump, ncgen, libnetcdf netcdf
parallel netCDF 1.2.0 Scientific data storage and retrieval using MPI-IO libpnetcdf.a parallel-netcdf
NCO 4.0.8 NCO utilities to manipulate netCDF files ncap2, ncatted, etc. nco
Libraries
GSL 1.13 GNU Scientific Library libgsl, libgslcblas gsl
Scripting/interpreted languages
Python 2.7.5 Python programming language. Modules included : numpy-1.8.0 , scipy-0.13.2 , matplotlib-1.3.1 , pyfits-3.2 , h5py-2.2.1 python python
Other
gnuplot 4.6.1 command-driven interactive function and data plotting program gnuplot gnuplot
antlr 2.7.7 ANother Tool for Language Recognition antlr, antlr-config
libantlr, antlr.jar, antlr.py 		antlr
udunits 2.1.11 unit conversion utilities libudunits2 udunits
extras Adds paths to a fuller set of applications and libraries to your user environment bindlaunch, ... extras

Manuals

Intel compilers and libraries (GPC)

IBM compilers and libraries (TCS/P7)

PGI compilers (Gravity/Viz)

Scheduler (Adaptive Computing/Cluster Resources)

DDT Debugger (Allinea)

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