First, thank you very much to the community for all the helpful
information on Friday.
I'm now encountering an intermittent error with one of our
applications (mpiblast). It's integrated with the cluster scheduler
(SGE), and all of the directories involved are XSan volumes re-
exported via NFS to the compute nodes.
Sometimes, jobs will fail because they cannot find their startup
directory:
Can't start from current directory: No such file or directory
sh: -c: line 1: unexpected EOF while looking for matching `''
sh: -c: line 4: syntax error: unexpected end of file
This persists even if I insert "sleep" or "while (!(-e /the/
appropriate/directory)) {sleep;}}" in my submission script. In fact,
I can pause the job and log in to check whether the directory exists
is mounted on the compute node, and it *is*.
This is, however, intermittent. Sometimes jobs work fine.
Occasionally, I will have a job work, but I get these in the STDERR:
shell-init: could not get current directory: getcwd: cannot access
parent directories: No such file or directory.
Other jobs work fine. It's only when a single parallel job tries to
start on many of the cluster nodes at the same time that it
*sometimes* can't find its startup directory (or the home directory
of the submitting user).
Any advice or insight would be appreciated.
-Chris Dwan
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