I'm an intern in a bioinformatic lab for the summer and I just got permission to use a super-computer to do protein disorder jobs. I know how to use this program on my local computer with linux and it's pretty simple. I downloaded it, make install, run the script with the right PATHs to the files I want to use et voilà.
My question is quite simple but since I'm new to all of this, I don't really know where to look : How can I know if I can use this program in parallel? I ask this because apparently I need to know that before I can submit a job. On the supercomputer there are nods with 8 cores. According to my colleagues, knowing if my job is parallelizable is very important since it will determine whether I use one core or all 8, which will affect time and resources.
I hope this makes sense and I'm sorry if it's a dumb question but I'm kind of lost here... Thanks for the help! :)
(the program I use is DISOPRED3, available for free)
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mparadis92 •
If you inspect the run_disopred.pl file at line 20 you can find:
## IMPORTANT: Changing these flags will alter the behaviour of blastpgp ## You may want to use -a n to speed-up the search using n processors, if available my $PSIBLAST_PAR = "-a 1 -b 0 -j 3 -h 0.001";
So, at least this part of the computation can be performed using more than one processor by properly setting parameter a.
Wow I think that's what I need! I looked through all the files but I guess I didn't see this part.... thanks a lot! :)
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The software man page generally has information on how to best parallelize runs. Quite a few use OpenMPI and such, so you could read through their documentation. If the developers have a github repo, you can read through the README there and look at issues. You could also email them.
Sadly there is not a lot of documentation. I searched a lot and couldn't find a definitive answer. I thought maybe there were ways to test this or something. Thanks for the answer!
cross-posted: http://stackoverflow.com/questions/30645791