Software and Libraries

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]

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 recommended to load frequently used modules in the file .bashrc in your home directory.

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) 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 'modulefind' 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]

Currently (Oct 5,2010), the following modules are deprecated on the GPC:

gcc/gcc-4.3.2          hdf5/184-v16-serial     intel/intel-v11.1.046               openmpi/1.3.3-intel-v11.0-ofed
hdf5/183-v16-openmpi   hdf5/184-v18-intelmpi   intelmpi/impi-3.2.1.009             openmpi/1.3.2-intel-v11.0-ofed.orig
hdf5/183-v18-openmpi   hdf5/184-v18-openmpi    intelmpi/impi-3.2.2.006             pgplot/5.2.2-gcc.old            
hdf5/184-v16-intelmpi  hdf5/184-v18-serial     intelmpi/impi-4.0.0.013             pgplot/5.2.2-intel.old
hdf5/184-v16-openmpi   intel/intel-v11.0.081   intelmpi/impi-4.0.0.025

On the TCS, currently (Oct 5,2010) the only deprecated module is:

ncl/5.1.1old

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

ARC/GPU Software

The CPUs in the GPU nodes of the ARC 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	includes MKL library	`icpc,icc,ifort`	`intel`
GCC Compiler	4.4.6, 4.6.1*, 4.7.0		`gcc,g++,gfortran`	`gcc`
Cuda	3.2, 4.0, 4.1*, 4.2	NVIDIA's extension to C for GPGPU programming	`nvcc`	`cuda`
PGI Compiler	12.5	supports OpenACC and CUDA Fortran	`pgcc,pgcpp,pgfortran`	`pgi`
IntelMPI	4.0.2	MPICH2 based MPI	`mpicc,mpiCC,mpif77,mpif90`	`intelmpi`
OpenMPI	1.4.4*, 1.5.4		`mpicc,mpiCC,mpif77,mpif90`	`openmpi`
UPC	2.12.2	Berkley Unified Parallel C Implementation	`upcc`	`upc`
Editors
Nano	2.2.4	Nano's another editor	`nano`	`nano`
Emacs	23.1.1	New version of popular text editor	`emacs`	`emacs`
XEmacs	21.4.22	XEmacs editor	`xemacs`	`xemacs`
Development tools
Autoconf	2.68		`autoconf, ...`	`autoconf`
Automake	1.11.2		`aclocal, automake`	`automake`
CMake	2.8.6	cross-platform, open-source build system	`cmake`	`cmake`
Scons	2.0	Software construction tool	`scons`	`scons`
Git	1.7.1	Revision control system	`git,gitk`	`git`
Intel tools	2011	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	3.1	Allinea's Distributed Debugging Tool	`ddt`	`ddt`
DDD	3.3.12	Data Display Debugger	`ddd`	`ddd`
GDB	7.3.1	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	2.0.1	sampling and MPI tracing	`openss, ...`	`openspeedshop`
Scalasca	1.2	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	3.6.1	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	Plotting utility	`gnuplot`	`gnuplot`
ParaView	3.12.0	Scientific visualization, server only	`pvserver,pvbatch,pvpython`	`paraview`
VMD	1.9	Visualization and analysis utility	`vmd`	`vmd`
NCL/NCARG	6.0.0	NCARG graphics and ncl utilities	`ncl`	`ncl`
ROOT	5.30.00	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`
Storage tools and libraries
NetCDF	4.1.3	Scientific data storage and retrieval	`ncdump,ncgen,libnetcdf`	`netcdf`
Ncview	2.1.1	Visualization for NetCDF files	`ncview`	`ncview`
NCO	4.0.8	NCO utilities to manipulate netCDF files	`ncap, ncap2, ncatted, etc.`	`nco`
CDO	1.5.1	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	GROMACS molecular mechanics, single precision, MPI	`grompp, mdrun`	`gromacs`
NAMD	2.8	NAMD - Scalable Molecular Dynammics	`namdmpiexec, namd2`	`namd`
NWChem	6.0	NWChem Quantum Chemistry	`nwchem`	`nwchem`
Quantum Espresso	4.3.2	Quantum Chemistry	`pw.x, ...`	`espresso`
BLAST	2.2.23+	Basic Local Alignment Search Tool	`blastn,blastp,blastx,psiblast,tblastn...`	`blast`
RAY	1.7 (small k-mer)	Parallel de novo genome assemblies	`Ray`	`ray`
CPMD	3.13.2	Carr-Parinello molecular dynamics, MPI	`cpmd.x`	`cpmd`
R	2.13.1	statistical computing	`R`	`R`
Octave	3.4.3	Matlab-like environment	`octave`	`octave`
Libraries
PETSc	3.1*	Portable, Extensible Toolkit for Scientific Computation (PETSc)	`libpetsc, etc..`	`petsc`
BOOST	1.47.0*	C++ Boost libraries	`libboost...`	`cxxlibraries/boost`
GotoBLAS	1.13	Optimized BLAS implementation	`libgoto2`	`gotoblas`
GSL	1.13*, 1.15	GNU Scientific Library	`libgsl, libgslcblas`	`gsl`
FFTW	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	2010	execute commands in parallel	`parallel`	`gnu-parallel`
Python	2.7.2	Python programming language	`python`	`python`
Ruby	1.9.1	Ruby programming language	`ruby`	`ruby`
Java	1.6.0	IBM's Java JRE ad SDK	`java`, `javac`	`java`
Other
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.

TCS Software

Software	Version	Comments	Command/Library	Module Name
Compilers
IBM compilers	10.1(c/c++) 12.1(fortran)	See TCS Quickstart	`xlc,xlC,xlf,xlc_r,xlC_r,xlf_r`	standard available
IBM MPI library		See TCS Quickstart	`mpcc,mpCC,mpxlf,mpcc_r,mpCC_r,mpxlf_r`	standard available
UPC	1.2	Unified Parallel C	`xlupc`	`upc`
IBM fortran compiler	13.1	newer version	`xlf,xlf_r`	xlf/13.1
IBM c/c++ compilers	11.1	new versions	`xlc,xlC,xlc_r,xlC_r`	vacpp
Debug/performancs tools
MPE2	1.0.6	Performance Visualization for Parallel Programs	`libmpe`	`mpe`
Scalasca	1.2	SCalable performance Analysis of LArge SCale Applications	`scalasca, ...`	`scalasca`
Storage tools and libraries
HDF4	4.2.5	Scientific data storage and retrieval	`h4fc, hdiff, ..., libdf, libsz`	`hdf4`
HDF5		Scientific data storage and retrieval, parallel I/O Part of the extras module on the tcs: compile with `-I${SCINET_EXTRAS_INC}` link with `-L${SCINET_EXTRAS_LIB}`	`libhdf5`	`extras`
NetCDF + ncview	4.0.1*	Scientific data storage and retrieval	`ncdump, ncgen, libnetcdf, ncview`	`netcdf`
parallel netCDF	1.1.1*	Scientific data storage and retrieval using MPI-IO	`libpnetcdf.a`	`parallel-netcdf`
NCO	3.9.6*	NCO utilities to manipulate netCDF files	`ncap, ncap2, ncatted,` etc.	`nco`
Libraries
FFTW	3.2.2	Fast Fourier transform library Part of the extras module on the tcs: compile with `-I${SCINET_EXTRAS_INC}` link with `-L${SCINET_EXTRAS_LIB}`	`libfftw, libfftw_mpi,libfftw3`	`extras`
GSL	1.13	GNU Scientific Library	`libgsl, libgslcblas`	`gsl`
extras		Adds paths to a fuller set of libraries to your user environment compile with `-I${SCINET_EXTRAS_INC}` link with `-L${SCINET_EXTRAS_LIB}`	`libfftw, libfftw_mpi, libfftw3, libhdf5, liblapack, ...`	`extras`
Other
antlr	2.7.7	ANother Tool for Language Recognition	`antlr, antlr-config libantlr, antlr.jar, antlr.py`	`antlr`
NCL	5.1.1	NCAR Command Language	`ncl, libncl, ...`	`ncl`