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.

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
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]_{LIB,INC,BASE}

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.

Deprecated modules

Some older software for which newer versions exist, get deprecated. In contrast to the non-default modules, the deprecated modules are not found by the module avail command. 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, the following modules are deprecated:

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

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.

GPC Software

Software	Version	Comments	Command/Library	Module Name
Intel Compiler	11.1,update 6*	includes MKL library	`icpc,icc,ifort`	`intel`
GCC Compiler	4.4.0		`gcc,g++,gfortran`	`gcc`
IntelMPI	3.2.2*		`mpicc,mpiCC,mpif77,mpif90`	`intelmpi`
OpenMPI	1.4.1*		`mpicc,mpiCC,mpif77,mpif90`	`openmpi`
Emacs	23.1	New version of popular text editor	`emacs`	`emacs`
xemacs	21.4.22	xemacs editor	`xemacs`	`xemacs`
Git	1.6.3	Revision control system	`git,gitk`	`git`
Valgrind	3.4.1	Memory checking utility	`valgrind,cachegrind`	`valgrind`
grace	5.22.1	Plotting utility	`xmgrace`	`graphics`
Gnuplot	4.2.6	Plotting utility	`gnuplot`	`graphics`
VMD	1.8.6	Visualization and analysis utility	`vmd`	`vmd`
ferret	6.4	Plotting utility	`ferret`	`ferret`
ncl/ncarg	5.1.1	NCARG graphics and ncl utilities	`ncl`	`ncl`
ROOT	5.26.00	ROOT Analysis Framework from CERN	`root`	`ROOT`
ParaView	3.8.0	Scientific visualization, server only	`pvserver,pvbatch,pvpython`	`visualization`
NetCDF	4.0.1*	Scientific data storage and retrieval	`ncdump,ncgen,libnetcdf`	`netcdf`
parallel netCDF	1.1.1	Scientific data storage and retrieval using MPI-IO	`libpnetcdf.a`	`parallel-netcdf`
ncview	1.93g	Visualization for NetCDF files	`ncview`	`graphics/ncview`
NCO	3.9.9	NCO utilities to manipulate netCDF files	`ncap, ncap2, ncatted, etc.`	`nco`
udunits	2.1.11	unit conversion utilities	`libudunits2`	`udunits`
HDF4	4.2r4*	Scientific data storage and retrieval	`h4fc,hdiff,...,libdf,libsz`	`hdf4`
HDF5	1.8.4-v18*	Scientific data storage and retrieval, parallel I/O	`h5ls, h5diff, ..., libhdf5`	`hdf5`
GAMESS (US)	January 12, 2009 R3	General Atomic and Molecular Electronic Structure System	`rungms`	`gamess`
BLAST	2.2.23+	Basic Local Alignment Search Tool	`blastn,blastp,blastx,psiblast,tblastn...`	`blast`
AMBER 10	Amber 10 + Amber Tools 1.3	Amber Molecular Dynamics Package	`sander, sander.MPI`	`amber10`
GDAL	1.7.1	Geospatial Data Abstraction Library	`gdal_contour,gdal_rasterize,gdal_grid, libgdal`	`gdal`
PETSc	3.0.0*	Portable, Extensible Toolkit for Scientific Computation (PETSc)	`libpetsc, etc..`	`petsc`
MEEP	1.1.1*	MIT Electromagnetic Equation Propagation	`meep, meep-mpi`	`meep/1.1.1-serial meep/1.1.1-intelmpi meep/1.1.1-openmpi`
Matlab/IDL/Gaussian/Commercial software		Little to none. See the FAQ
gsl	1.13	GNU Scientific Library	`libgsl, libgslcblas`	`gsl`
guile + ctl	1.8.7 + 3.1	guile + libctl scheme interpreter	`libguile, libctl`	`guile`
fftw	3.2.2*	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`
extras		Full set of X11 libraries and others not installed on compute nodes	`bc, dmidecode, gv, iostat, lsof, tkdiff, zip, libXaw,...,libjpeg`	`extras`

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

TCS Software

Software	Version	Comments	Command/Library	Module Name
antlr	2.7.7	ANother Tool for Language Recognition	`antlr, antlr-config libantlr, antlr.jar, antlr.py`	`antlr`
gsl	1.13	GNU Scientific Library	`libgsl, libgslcblas`	`gsl`
HDF4	4.2.5	Scientific data storage and retrieval	`h4fc, hdiff, ..., libdf, libsz`	`hdf4`
mpe 2	1.0.6	Performance Visualization for Parallel Programs	`libmpe`	`mpe`
NetCDF + ncview	4.0.1*	Scientific data storage and retrieval	`ncdump, ncgen, libnetcdf, ncview`	`netcdf`
NCL	5.1.1	NCAR Command Language	`ncl, libncl, ...`	`ncl`
NCO	3.9.6*	NCO utilities to manipulate netCDF files	`ncap, ncap2, ncatted,` etc.	`nco`
parallel netCDF	1.1.1*	Scientific data storage and retrieval using MPI-IO	`libpnetcdf.a`	`parallel-netcdf`
scalasca	1.2	SCalable performance Analysis of LArge SCale Applications	`scalasca, ...`	`scalasca`
upc	1.2	Unified Parallel C	`xlupc`	`upc`
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`