Parallel netCDF

PnetCDF is a library providing high-performance parallel I/O while still maintaining file-format compatibility with  Unidata's NetCDF, specifically the formats of CDF-1 and CDF-2. Although NetCDF supports parallel I/O starting from version 4, the files must be in HDF5 format. PnetCDF is currently the only choice for carrying out parallel I/O on files that are in classic formats (CDF-1 and 2). In addition, PnetCDF supports the CDF-5 file format, an extension of CDF-2, that supports more data types and allows users to define large dimensions, attributes, and variables (>2B elements).

Amber 14 now available

Friday, September 12, 2014 - 3:45pm

Amber 14 has been installed on Oakley and Glenn; usage is via the modules amber/14 on Oakley and amber14 on Glenn.  For information on available executables and installation details see the software page for Amber or the output of the respective module help command, e.g.: module help amber/14

Jobs requesting Lustre are rejected by qsub

Friday, August 15, 2014 - 11:30pm

On both production clusters, we have begun rejecting jobs that request the use of Lustre or $PFSDIR in order to reduce job failures caused by the triggering of a bug that crashes the filesystem. If you have a GPFS allocation, you may if appropriate want to move your data there in order to maintain productivity while the Lustre service is in a degraded state.

HOWTO: Use ulimit command to set soft limits

This document shows you how to set soft limits using ulimit command.

The ulimit command sets or reports user process resource limits. The default limits are defined and applied when a new user is added to the system. Limits are categorized as either soft or hard. With the ulimit command, you can change your soft limits for the current shell environment, up to the maximum set by the hard limits. You must have root user authority to change resource hard limits.

2014/04 - Invited talk: MVAPICH

The April 2014 HPC Tech Talk (Tuesday, April 22th from 4-5PM) will provide some brief OSC updates, have a user-driven Q&A session, and will close with an invited talk about MPI-3 from the MVAPICH developers from The Ohio State University. To get the WebEX information and add a calendar entry, go here. Slides are available below.


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