Running meme suite FIMO in parallel

Question

[Marouen Ben Guebila]

I have meme suite FIMO 5.0.5 installed on ubuntu 18.04. I installed OpenMPI to run FIMO in parallel.

When I type in

mpirun --version

I get

mpirun (Open MPI) 4.0.1

Report bugs to http://www.open-mpi.org/community/help/

But when I launch FIMO, only one process is running in htop. when I reinstalled FIMO, it actually fails to install the parallel version

Makefile:599: recipe for target 'meme' failed make[2]: *** [meme]
Error 1 make[2]: Leaving directory
'/home/ubuntu/meme-5.0.5/src/parallel'

When I traced back the error I found the following errors

undefined reference to `mpInit' meme.c:(.text+0x86): undefined
reference to `mpMyID' meme.c:(.text+0x96): undefined reference to
`mpNodes' meme.c:(.text+0x155): undefined reference to `mpMyID'
meme.c:(.text+0x164): undefined reference to `mpMyID'
meme.c:(.text+0x18a): undefined reference to `mpFinalize'

Much appreciate any help on this

Answer 1

[Marouen Ben Guebila]

so I could get it to install without warnings through downgrading to 5.0.4 version. But I couldn't get FIMO to run in parallel, the reason being that FIMO does not have a parallel implementation. MEME allows that through the -p option.

[ATpoint]

Yeah, I was already surprised that you mentioned parallel fimo. Is is pretty fast in my experience, so usually it only takes seconds for standard tasks, and if one wants to scan multiple PFMs you can parallelize with GNU parallel.