Software
HPC Software packages on W&M/VIMS clusters
The Research Computing staff installs a number of scientific/computational packages on our HPC clusters. All software is either in a users default path or access via an environtment module. Since the hardware/software refresh in summer 2024 the following packages should be available on all clusters (both main-campus and VIMS). Please send email to [[w|hpc-help@wm.edu]] for any requests to add more standard packages to the cluster.
Common software packages installed on main-campus and VIMS clusters
| Name | Description | Notes |
|---|---|---|
| g++/gcc/gfortran | GNU compiler suite | default version 11.4.1 |
| emacs / nano / vi | Command line text editors | |
| svn | Subversion repo control | |
| git | Git repo control | |
| gdb | GNU g++/gcc/gfortran debugger | |
| ImageMagick | Image manipulation tool | |
| gnuplot | Plotting program | |
| xmgrace | Plotting program | |
| mysql | Databases | |
| cmake | Software configuration and compilation | |
| bc | Command-line calculator | use the '-l' option for floating-point math |
| tmux | Terminal multiplexer | |
| screen | Terminal multiplexer | |
| singularity | Container orchestration | |
| perl | Scripting language | |
| strace | User space stack trace utility | |
| ncdu | Ncurses disk usage calculator |
Many software packages are also installed as environtment modules. For instance, when running module avail on the bora cluster, you will see:
------------------------------------------------- /usr/share/Modules/modulefiles -------------------------------------------------
dot module-git module-info modules null use.own
------------------------------------------------- /usr/local/Modules/modulefiles -------------------------------------------------
cuda/12.3 netcdf-c/gcc-11.4.1/4.9.2_openmpi openmpi-ib/gcc-11.4.1/4.1.6 solps/3.0.8
hdf5/gcc-11.4.1/1.14.3_openmpi netcdf-c/intel-2024.0/4.9.2_intelmpi openmpi-ib/intel-2024.0/4.1.6
hdf5/intel-2024.0/1.14.3_intelmpi netcdf-c/intel-2024.0/4.9.2_openmpi proj/gcc-11.4.1/5.2.0
hdf5/intel-2024.0/1.14.3_openmpi netcdf-fortran/gcc-11.4.1/4.6.1_openmpi python/gcc-11.4.1/3.11.9
legacy-tools/gcc-8.5.0 netcdf-fortran/intel-2024.0/4.6.1_intelmpi r/gcc-11.4.1/4.4.0
legacy-tools/gcc-9.5.0 netcdf-fortran/intel-2024.0/4.6.1_openmpi singularity-ce/4.1.0
ncl/gcc-11.4.1/6.6.2_openmpi openblas/gcc-11.4.1/0.3.27 slurm/23.11.9
--------------------------------------------------- /sciclone/apps/modulefiles ---------------------------------------------------
anaconda3/2023.09 hyperworks/24 intel/compiler-2022.2.1 intel/mpi-2021.7.1 julia/1.9.4 matlab/R2024a
comsol/6.2 intel/2019 intel/compiler-2024.0 intel/mpi-2021.11 matlab/R2020b
gaussian/g16 intel/2019-mpi intel/mkl-2024.0 intel/tbb-2021.7.1 matlab/R2023a
All of the modules listed above can be added to your environment with a module load command. See environtment modules for more information.
