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Desmond and Jaguar parallel jobs fail when sent to an LSF queueing system. What can I do?

April 26, 2017desmond fail Jaguar jobs LSF parallel queueing sent system

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Desmond and Jaguar parallel jobs fail when sent to an LSF queueing system. What can I do?

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MPI parallel jobs may fail when using the LSF queuing system, giving an error in the log file similar to: installation/mmshare-v19103/lib/Linux-x86_64/openmpi/bin/orterun: symbol lookup error: installation/mmshare-v19103/lib/Linux-x86_64/openmpi/lib/openmpi/mca_plm_lsf.so: undefined symbol: lsb_init where installation is the directory that contains your Schrödinger software installation. This failure is due to a bug in OpenMPI that causes problems for tight integration with LSF. This problem has been fixed in Schrödinger Suite 2010, with a patch to the version of Open MPI in the Schrödinger software distribution. If you are using another version of Open MPI and would like to recompile it with the patch included, send email to help@schrodinger.com. Otherwise, the simplest workaround is to disable the tight integration with the LSF queue. Your jobs should still run, but it will be harder for LSF to clean up certain types of job failures (which should be rare). To disable the tight integr