Jaguar jobs submitted to a queuing system produce errors like the following:

jaguar: WARNING fifo_write(): open(): No such file or directory
jaguar: WARNING fifo_write(): Unable to open /tmp/5868.1.all.q/jmonitor14955
Error: Unable to open job control link for writing

What is wrong?

This most likely indicates that the $SCHRODINGER/jaguar run command is being placed in a batch script, and manually submitted to the queue. Schrödinger applications expect to handle the queue submission process for you. For example, you should just be able to do the following directly on the command line:

$SCHRODINGER/jaguar run -HOST host input.in

where host is the actual name of the entry in the schrodinger.hosts file that corresponds to the queue. Jaguar will create its own batch script and it will be submitted to the queue automatically. Because Schrodinger applications expect to handle this process themselves, manual submission can often lead to unexpected behavior.

For this to work properly, a small amount of configuration is required. Mainly, your schrodinger.hosts file will need to be configured for the queue, if is not already. Please see section 6.3 of the Installation Guide for details.

Keywords: queue batch fifo

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