Owens

HOWTO: Install your own Perl modules

While we provide a number of Perl modules, you may need a module we do not provide. If it is a commonly used module, or one that is particularly difficult to compile, you can contact OSC Help for assistance, but we have provided an example below showing how to build and install your own Perl modules. Note, these instructions use "bash" shell syntax; this is our default shell, but if you are using something else (csh, tcsh, etc), some of the syntax may be different.

NWChem

NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.

Availability and Restrictions

Versions

The following versions of NWChem are available on OSC clusters:

Messages from sbatch

sbatch messages

shell warning

Submitting a job without specifying the proper shell will return a warning like below:

sbatch: WARNING: Job script lacks first line beginning with #! shell. Injecting '#!/bin/bash' as first line of job script.

Errors

If an error is encountered, the job is rejected.

Not specifying a project account

It is required to specify an account for a job to run. Please use the --account=<project-code> option to do this.

Owens

TIP: Remember to check the menu to the right of the page for related pages with more information about Owens' specifics.

OSC's Owens cluster being installed in 2016 is a Dell-built, Intel® Xeon® processor-based supercomputer.

ARM MAP

ARM MAP is a full scale profiler for HPC programs. We recommend using ARM MAP after reviewing reports from ARM Performance Reports. MAP supports pthreads, OpenMP, and MPI software on CPU, GPU, and MIC based architectures.

ARM Performance Reports

ARM Performance Reports is a simple tool used to generate a single-page HTML or plain text report that presents the overall performance characteristics of HPC applications. It supports pthreads, OpenMP, or MPI code on CPU, GPU, and MIC based architectures.

Schrodinger

The Schrodinger molecular modeling software suite includes a number of popular programs focused on drug design and materials science but of general applicability, for example Glide, Jaguar, and MacroModel.  Maestro is the graphical user interface for the suite.  It allows the user to construct and graphically manipulate both simple and complex chemical structures, to apply molecular mechanics and dynamics techniques to evaluate the energies and geometries of molecules in vacuo or in solution, and to display and examine graphically the results of the modeling calculations.

OpenMPI

MPI is a standard library for performing parallel processing using a distributed memory model. The Ruby, Owens, and Pitzer clusters at OSC can use the OpenMPI implementation of the Message Passing Interface (MPI).

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