Software and Libraries

GPC Software

All the software listed on this page is accessed using a modules system.

To use particular software just load the module (the last column in the following table) as follows.

module load module_name_here

For a full list of available software packages that may be accesses with the modules system, use the command

module avail

For a list of the currently loaded modules in your shell, use the command

module list

For a description of a particular module, use the command

module help module_name_here

Software	Version	Comments	Command/Library	Module Name
Intel Compiler	11.1		icpc,icc,ifort, includes MKL library	intel
GCC Compiler	4.4.0		gcc,g++,gfortran	gcc
IntelMPI	3.2.2		mpicc,mpiCC,mpif77,mpif90	intelmpi
OpenMPI	1.3.3		mpicc,mpiCC,mpif77,mpif90	openmpi
MVAPICH2	1.4		mpicc,mpiCC,mpif77,mpif90	mvapich2
Emacs	23.1	New version of popular text editor	emacs	emacs
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
netCDF + udunits	4.0.1 + 2.1.8	Scientific data storage and retrieval	ncdump,ncgen,libnetcdf,libudunits2	netcdf
NCO	3.9.9	NCO utilities to manipulate netCDF files	ncap, ncap2, ncatted, etc.	nco
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
gsl	1.13	GNU Scientific Library	libgsl, libgslcblas	gsl
fftw	3.2.2	fftw fast Fourier transform library	libfftw3	fftw
GAMESS (US)	January 12, 2009 R3	General Atomic and Molecular Electronic Structure System	rungms	gamess
AMBER 10	Amber 10 + Amber Tools 1.3	Amber Molecular Dynamics Package	sander, sander.MPI	amber10
ncl/ncarg	5.1.1	NCARG graphics and ncl utilities	ncl	ncl
PETSc		Portable, Extensible Tolkit for Scientific Computation (PETSc)	libpetsc, etc..	petsc
extras		Full set of X11 libraries and others not installed on compute nodes	libXaw,...,libjpeg	extras
GDAL	1.7.1	Geospatial Data Abstraction Library	gdal_contour,gdal_rasterize,gdal_grid, libgdal	gdal
Matlab/IDL/Commercial software		Little to none. See the FAQ

TCS Software

The software listed below uses the same module system as described above for the GPC.

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	-lmpe	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	1.1.0	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