Question

Has anyone compiled and used MEME 4.x for use in a parallel computation environment, based upon operation with a Sun Grid Engine (SGE) cluster?

I can compile the suite and its tests pass. However, when I attempt to use the -p n option, to specify n computation nodes, I get several error messages:

/gridware/codine/util/arch: Command not found.
/gridware/codine/util/arch: Command not found.
/gridware/codine/util/arch: Command not found.
/gridware/codine/util/arch: Command not found.
1: Command not found.

We do not have /gridware/codine/util/arch, but we do have /gridengine/sgi/util/arch.

I tried looking around MEME's source code, particularly at meme.c and mp.h, but there are no references to these paths.

I'm wondering if I am missing makefile directives. Here is my ./configure statement:

./configure --prefix=/home/areynolds/proj/meme/meme_4.3.0_build --with-url="http://meme.nbcr.net/meme" --enable-openmp --enable-debug

Is MPI a requirement; are there directives I am missing for MPI?

Thank you for any advice.

Answer 1

This may not be overly useful but it very much sounds like a configuration problem.

Usually there is configure flag that needs to be set to point to the libraries, something like:

--with-mpidir=MPIDIR
--with-mpicc=MPICC

It also appears that the MEME suite does not support Open MPI (as per install notes).

I would also recommend posting on the MEME user forum:

https://www.nbcr.net/forum/viewforum.php?f=5