How to know a program I use is parallelizable?

Question

[mparadis92]

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)

[Ram]

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.

[mparadis92]

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!

[Pierre Lindenbaum]

cross-posted: http://stackoverflow.com/questions/30645791

Answer 1

[Nicola Casiraghi]

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.

[mparadis92]

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! :)