> - BatchJobs: is there support, or are there any plans to support the
> HTCondor infrastructure [1], and will this back-end be supported in
> BiocParallel?
We don't have access to a system running condor, otherwise we would
have implemented support already. I'd either need a temporary account
on the system or the following information:
* a minimal condor template to run an R script, including
+ job name being set
+ log file defined
+ resources specified (at least walltime and memory)
* command to submit the job description file to the scheduler
+ format of returned batch ids assigned by the scheduler
(usually whitespace-delimited list in stdout)
+ exit code on success (should be 0)
+ [optional] temporary error codes
* command to list batch ids
+ preferably only jobs of current user
+ exact output format
+ exit code on success (should be 0)
+ [optional] temporary error codes
* command to kill a job given its batch id
+ exit code on success (should be 0)
+ [optional] temporary error codes
For comparison, see the implementations on
<https://github.com/tudo-r/BatchJobs/wiki/Cluster-Functions>.
To get the exit codes in sh/bash/zsh, execute the respective command
and then "echo $?". We use the temporary error codes to trigger a
sleep-retry-loop. Maybe your cluster admins know some or the condor
documentation provides a table of exit codes.
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
