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When I run Desmond, Jaguar, or QSite jobs on a cluster with an Infiniband network, the jobs fail with the following in the log file. How do I fix this?
libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes.
This will severely limit memory registrations.

The jobs are failing because of limits that are set in your shell. Have a look at the OpenMPI FAQs #14 and #15 listed here:

Of particular importance is the fact that shell limits can be set in many places (limits.conf, PAM, even the resource manager daemons e.g. SGE, LSF, etc.). Simply logging into a computer and testing the limits via ulimit -a (or equivalent) may yield inaccurate results.

To truly test the shell limits in the environment of a cluster job, submit a simple batch script to the queue that prints out ulimit -a.

You can increase the limit for RLIMIT_MEMLOCK by adding the following command in the shell startup files:

bash: ulimit -l unlimited
csh/tcsh: limit memorylocked unlimited

Related Articles:

#1481: My parallel Jaguar calculation failed with an "out of memory" error. What is the problem?

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