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Ascend, Owens, Pitzer
NetCDF (Network Common Data Form) is an interface for array-oriented data access and a library that provides an implementation of the interface. The netcdf library also defines a machine-independent format for representing scientific data. Together, the interface, library, and format support the creation, access, and sharing of scientific data.
Owens, Pitzer
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD generally scales well on OSC platforms and offers a variety of modelling techniques. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR.
Ascend, Owens, Pitzer
MVAPICH2 is a standard library for performing parallel processing using a distributed-memory model.
Ascend, Owens, Pitzer
The storage at OSC consists of servers, data storage subsystems, and networks providing a number of storage services to OSC HPC systems. The current configuration consists of:
Owens
LS-DYNA is a general purpose finite element code for simulating complex structural problems, specializing in nonlinear, transient dynamic problems using explicit integration. LS-DYNA is one of the codes developed at Livermore Software Technology Corporation (LSTC).
Ascend, Owens, Pitzer
The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a classical molecular dynamics code designed for high-performance simulation of large atomistic systems. LAMMPS generally scales well on OSC platforms, provides a variety of modeling techniques, and offers GPU accelerated computation.
Ascend, Owens, Pitzer
The Intel compilers for both C/C++ and FORTRAN.
Availability and Restrictions
Versions
The versions currently available at OSC are:
Owens, Pitzer
A job script is a text file containing job setup information for the batch system followed by commands to be executed. It can be created using any text editor and may be given any name. Some people like to name their scripts something like myscript.job or myscript.sh, but myscript works just as well.
OSC has recently switched schedulers from PBS to Slurm.
Please see the slurm migration pages for information about how to convert commands.
Please see the slurm migration pages for information about how to convert commands.
Batch processing
Efficiently using computing resources at OSC requires using the batch processing system. Batch processing refers to submitting requests to the system to use computing resources.