Why is the "bsub" command not automatically visible when using the generic scheduler interface of Parallel Computing Toolbox with LSF Scheduler in MATLAB 7.7 (R2008b)?

I am using the Parallel Computing Toolbox's generic scheduler interface to submit jobs to an LSF scheduler. While submitting a job, I get an error indicating that bsub is not visible on the system path. It does not seem that the shell resource file is being sourced to set up proper paths and environment variables when performing remote passwordless login with OpenSSH 5.1.

Answer 1

[MathWorks Support Team]

There was a change in the behavior between OpenSSH 5.0 and OpenSSH 5.1 that causes resource and setup files to not automatically be sourced. The effect is that the proper environment variables and paths are not configured, which are necessary to make "bsub" visible on the system's executable path.

To workaround this issue, create a wrapper script that sources the necessary resource files, and then calls bsub. Then, replace the calls to "bsub" in the integration scripts with the fully qualified path to that script.

Here is one possible wrapper script called "mybsub" that sources the resource setup file, then forwards all of its arguments to "bsub" (location of the resource file will be different for customers):

#!/bin/csh

source /sandbox/dcttest/LSF_7.0_dctlab/conf/cshrc.lsf

bsub "$1" "$2" "$3" "$4" "$5" "$6" "$7" "$8" "$9"

This file has to be uploaded onto the cluster and made executable, and instances where "bsub" is used and called in the integration scripts must be replaced with the fully qualified path to "mybsub".