Supercomputer documentation is always a work in progress! Please email questions, corrections, or suggestions to the HPC support team at firstname.lastname@example.org as usual. Thanks!
For information on current problems and outages, see the News Blog page.
README FIRST All HPC users should be familiar with the information here.
New users should start with these pages. Old users who haven’t used the cluster in a while might take a look as well.
If you have a question, check the Frequently Asked Questions list.
Use the module list command to see what software modules have been loaded in your current login session. Use the module avail command to see what modules are available for you to use.
Use the Linux man command to get detailed help on most commands, packages, and libraries.
Look in the examples directory /share/cluster/examples/dlx on the cluster for sample job scripts and other information.
$ cd /share/cluster/examples/dlx $ ls amber fluent GPU MatStudio Molpro mpi OpenMP SatScan serial test
Red Hat Linux the operating system used on the cluster.
MOAB and SLURM
The batch job scheduler that decides which job should run next and the resource manager that allocates resources to it.
The Message Passing Interface protocol allows jobs spread across many nodes communicate.
Compilers and Development Software
Intel Compilers The Intel compilers will be the best choice for most applications.
Intel Library (IMKL)
Optimized versions of BLAS, LAPACK, BLACS and SCALAPACK are available through the Intel Math Kernel Library.
The GNU compilers are also available for those applications that need or require them.
Amber The Amber Molecular Dynamics package is a package of molecular simulation programs which includes source code and demos.
The Gaussian package is one of the most diverse quantum chemistry codes available, because of the wide range of properties it can compute.
NAMD is a parallel molecular dynamics code designed for high-performance computing. For any system with a parameterized force field, NAMD can be used to compute the evolution of forces on atoms over time.
A few example of the results computed here. [Under construction]
QCD vacuum structThree graphs produced by the QCD group, provided by Dr. Shao-Jing Dong.