Why isn't MEME running in parallel?

[James Johnson]

I'm running MEME like this:

meme.bin test.fa -dna -p 24

However it is only using one processor. What is going wrong? Can you please tell me how I can install MEME to work on multiple processors?

[James Johnson]

The problem with the posted command is that meme.bin is not meant to be run directly! When compiled for for use with MPI there will be 3 programs in the installed bin folder related to MEME but you should be running only one of them, that is the c-shell script meme.

• meme          - This is the program you should be running. It is a c-shell script that calls either meme.bin or meme_p depending on if MPI is installed and you passed the -p option.
• meme.bin  - This is the normal version of MEME and it ignores the -p option because that is only handled by the c-shell script and the MPI command.
• meme_p      -  This is the version of MEME designed to be run by MPI, it will not work if you run it directly!

So the correct command is

meme test.fa -dna -p 24