Hi Ido,
Ido Tamir wrote:
Hi,
we use qmake to parallelize the illumina/solexa pipeline. Its a make based
system that
operates on many files to generate some output.
However, often under load we get errors like:
error: commlib error: got select error (Connection reset by peer)
error: executing task of job 7980306 failed: failed sending task to
[email protected]: can't find connection
Then we have to restart the pipeline.
I tried the make options -k (keep going) and -i (ignore), and it keeps working,
but the result is broken.
-r is not available for qmake.
Is there a possibility to retry for a certain amount of tries if this error
comes up - and only this
error? Sometimes there are missing files etc... then it should fail.
But this is simply a node not answering in a specified amount of time.
Is there a possibility to extend the timeout?
Setting the gdi_timeout=<timeout> in the global configuration (qconf
-mconf), attribute qmaster_params does increases the receive timeout for
the requests done by qmake (via qrsh -inherit).
See also man page sge_conf.5, section about qmaster_params.
You can try if it helps, but I have doubts.
From the error message "Connection reset by peer" I would guess it
really would require a retry.
You can configure gdi_retries=n, where n > 0, in the global
configuration, attribute qmaster_params to configure a retry of client
request.
Unfortunately this has effect on all clients (qsub, qstat, ...) except
for the qrsh -inherit used by qmake.
I'll file an issue to make sure this gets fixed.
Best regards,
Joachim
Thank you very much for your answers,
ido
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