General software and libraries (Hexagon)
From HPC documentation portal
This documentation page is outdated, will be updated soon.
Full up to date list is available at NOTUR
Application software by discipline:
Bio-informatics
| Software | Version | Module | Resources | Notes |
|---|---|---|---|---|
| NAMD | 2.8b1 | namd | Homepage | Recommended env variables (loaded with module): export MPICH_PTL_SEND_CREDITS=-1 export MPICH_MAX_SHORT_MSG_SIZE=8000 export MPICH_PTL_UNEX_EVENTS=100000 export MPICH_UNEX_BUFFER_SIZE=100M aprun -n $PBS_NNODES -cc cpu namd2 Use Support for support. |
| MEME | 4.4.0 | meme | Homepage | NOTE: linking was forced on this installation. Please compare output with previous (non-forced) runs for correctness.
Use Support for support. |
Chemistry
| Software | Version | Module | Resources | Notes |
|---|---|---|---|---|
| ADF | NA | NA | NA | Not supported on Hexagon |
| Daulton | User installation | NA | NA | Use Support for support |
| Gamess | NA | NA | NA | Not supported on Hexagon |
| Gaussian | NA | NA | NA | Not supported on Hexagon |
| Molpro | NA | NA | NA | Not supported on Hexagon |
| NWChem | 5.1.1 | nwchem-cnl | The module sets necessary variables | |
| VASP | User installation | NA | NA | Use Support for support |
Fluid dynamics
| Software | Version | Module | Resources | Notes |
|---|---|---|---|---|
| OpenFOAM | 1.5, 1.6, 1.7.1 | openfoam | Homepage | Limited amount of solvers are available due to static linking |
Geosciences
| Software | Version | Module | Resources | Notes |
|---|---|---|---|---|
| BOM | User installation | NA | Bergen Ocean Model | Use Support for support |
| EnKF | User installation | NA | Use Support for support | |
| HYCOM | User installation | NA | Homepage | Use Support for support |
| MYCOM | User installation | NA | MICOM group homepage Parallel MICOM page | Use Support for support |
| NCL | 5.1.1, 5.2 | ncl_ncarg | Default version is aprun compatible. If you are missing some features, you can use ncl_ncarg/##-login version | |
| NCO | 3.9.6, 4.0.0 | nco-cnl | ||
| ROMS | User installation | NA | Homepage | Use Support for support |
| UDUNITS2 | 2.1.7 | udunits-cnl | ||
| WPS | 3.0.1, 3.1, 3.1.1, 3.2, 3.2.1, 3.3 | WPS-cnl | WPS site | NOTE: some results can be different (it depends on the input files) if WRF module is loaded. In this case please ensure that WRF module is not loaded |
| WRF | 2.2.1, 3.0.1.1, 3.1, 3.1.1, 3.2, 3.2.1, 3.3 | WRF-cnl | WRF site | If you are using spectral nudging you will need to use 8000MB of memory per core. Otherwise despite of message that spectral nudging was enabled the output netcdf file will not be properly produced (see case #21869) |
| WRF (special version) | 3.1.1, 3.2 | WRFquiet-cnl | This version of WRF is not producing rsl* files during execution, but send all output to STDOUT&STDERR. You can use this module to avoid producing big amount of rsl files.
Remember! aprun wrf.exe > /dev/null | |
| WRFDA | 3.1.1, 3.2 | WRFDA | ||
| WRFNL | 3.2 | WRFNL | ||
| WRFPLUS | 3.2 | WRFPLUS | ||
| WRFchem | 3.0.1.1, 3.1, 3.1.1, 3.2, 3.2.1, 3.3 | WRFchem-cnl | WRFchem site | |
| WRFpolar-cnl | 3.1.1 | WRFpolar-cnl |
Performance libraries
| Software | Version | Module | Resources | Notes |
|---|---|---|---|---|
| BLAS LAPACK ScaLAPACK BLACS IRT SuperLU sparse solver routines CRAFFT |
System | xt-libsci | CrayXT Programming Environment User Guide | BLAS and LAPACK include routines from the 64-bit libGoto library from the University of Texas (GotoBLAS). |
| PETSc: MUMPS SuperLU ParMETIS HYPRE |
System | petsc | CrayXT Programming Environment User Guide | |
| ACML | System | acml | CrayXT Programming Environment User Guide | |
| FFTW | System | fftw | CrayXT Programming Environment User Guide | |
| Fast_mv | System | libfast | CrayXT Programming Environment User Guide |
Scientific data libraries
| Software | Version | Module | Resources | Notes |
|---|---|---|---|---|
| NetCDF 3 | System | netCDF | ||
| NetCDF 4 | System | netcdf | CrayXT Programming Environment User Guide | |
| NetCDF 4 parallel | System | netcdf-hdf5parallel | ||
| HDF5 | System | hdf5 | CrayXT Programming Environment User Guide | Will be loaded automatically with the module netcdf |
| HDF5 parallel | System | hdf5-parallel | Will be loaded automatically with the module netcdf-hdf5parallel |
General
| Software | Version | Module | Resources | Notes |
|---|---|---|---|---|
| Matlab | 2007b, 2008b, 2009a | matlab | Can not be run on compute nodes, therefore must be used only to preview some data, but not massive calculations | |
| Gnuplot | 4.2.5 | gnuplot-login | ||
| GSL | 1.11 | gsl-cnl | ||
| Perl | 5.8.8 | perl-cnl | ||
| Python | 2.6.2, 2.6.5 | python-cnl | Version 2.6.2 is statically linked and contains only essential Python modules, numpy, netCDF4, Cython, mpi4py Version 2.6.5 is dynamically linked, contains mostly all Python modules, NumPy, netCDF4, SciPy, Matplotlib, lxml, pyYaml | |
| Paraview | 3.6.1 | paraview-cnl, paraview-login | Statically compiled, supports only pvbatch, with MPI enabled | |
| R | 2.15.0, 3.0.2 | R | To run R in batch (on compute nodes) adjust your job script as follows: #PBS -l mppwidth=1,mppnppn=1,mppmem=32000mb # # fix for temporary filesystem export TMP=/work/$USER/ export TMPDIR=$TMP # aprun -B R --no-save <./myscript.R | |
| Trilinos | System | trilinos | http://trilinos.sandia.gov/index.html |
