I cannot get Desmond jobs to run under the SGE queueing system. What can I do?

Errors can occur with older versions of the SGE queueing system. The minimum recommended version is 6.0u8, and we strongly advise updating SGE to at least this version.

If this is not possible, you must configure SGE to use ssh for communication, by adding the following lines in your cluster configuration:

rsh_daemon /usr/sbin/sshd -i
rsh_command /usr/bin/ssh
rlogin_command /usr/bin/ssh

See http://gridengine.sunsource.net/howto/qrsh_qlogin_ssh.html for more information. Earlier versions of SGE used rsh by default. If you try to use rsh, you are likely to see the following error message:

rcmd: socket: Permission denied

Even with the use of ssh, running Desmond under an earlier version of SGE will produce core files in your home directory, due to the failure of an SGE job execution daemon. This is an SGE issue which is fixed by upgrading.

Keywords: Desmond, SGE, queue

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