I work on an LSF server and use the bsub command to run the perl script shell in an R script. Here is my command:
bsub -XF -n 1 -R "rusage[mem=16]" -We 60 -J <job_array> -o out.log 'script.pl <script arguments>'
This perl script calls an R script that does some calculations and then prints a PNG graph. R is configured on our LSF cluster in such a way that it does not allow to initiate a PNG device without enabling X11 forwarding. I have X11 redirect enabled, and this works fine as long as I don't want to use Job arrays. According to LSF guidelines, job arrays are not compatible with X11 forwarding.
This will require us to change the scripts for writing to PDF files instead of PNG, however we do not want to change the scripts that we are currently using, as they are part of a larger, public pipeline, and we would not want discrepancies between the public and locally installed versions.
In any case, can we use R to record PNG charts without forwarding X11?
Thanks!
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