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 | 183-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 | |
| 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 |
libfftw, libfftw_mpi, libfftw3, libhdf5, liblapack, ... | extras |