Question: Tips On Compiling And Using Meme 4.3 With A Sun Grid Engine Computation Cluster
gravatar for Alex Reynolds
9.2 years ago by
Alex Reynolds27k
Seattle, WA USA
Alex Reynolds27k wrote:

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="" --enable-openmp --enable-debug

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

Thank you for any advice.


I was able to successfully build a version of MEME 4.3 that supports OpenMPI.

First, I worked with our sys admin to install OpenMPI 1.4 on each of the SGE nodes (compilation options) and set up an SGE parallel environment called mpi_test:

$ qconf -sp mpi_test
pe_name           mpi_test
slots             120 
user_lists        NONE
xuser_lists       NONE
start_proc_args   /bin/true
stop_proc_args    /bin/true     
allocation_rule   $fill_up
control_slaves    TRUE
job_is_first_task FALSE 
urgency_slots     min

Secondly, I used the following build options for MEME:

$ ./configure --prefix=/home/areynolds/proj/meme/meme_4.3.0_build \ 
--with-url="" \
--enable-openmp \
--enable-debug \
--with-mpicc=/opt/openmpi-1.4/bin/mpicc \

Thirdly, the mpirun and meme_p binaries depend upon shared libraries in the OpenMPI installation. It is necessary to add /opt/openmpi-1.4/lib to your local LD_LIBRARY_PATH environment variable before running qsub.

Finally, I set up a script (called runall.cluster) along the following lines. Runtime options can be adjusted to taste:


# runall.cluster

#$ -N memeCluster64
#$ -S /bin/bash
#$ -pe mpi_test 64
#$ -v -np=64
#$ -cwd
#$ -o "memeCluster64.out"
#$ -e "memeCluster64.err"
#$ -notify
#$ -V

time /opt/openmpi-1.4/bin/mpirun -np 64 \
   /home/areynolds/proj/meme/meme/bin/meme_p \
   /home/areynolds/proj/meme/data/ \
   -oc /home/areynolds/proj/meme/output/ \
   -maxsize 230000 \
   -dna \
   -minw 8 -maxw 12 -allw \
   -p 64

This script is executed directly with qsub and runs the parallelized MEME binary meme_p with the specified options. In this case, it will run on 64 nodes of our computation cluster:

qsub ./runall.cluster

Hopefully this information will help out others.

meme parallel motif • 4.8k views
ADD COMMENTlink modified 7.8 years ago by Timothy Bailey30 • written 9.2 years ago by Alex Reynolds27k

thanks for following up on this, great information

ADD REPLYlink written 8.8 years ago by Istvan Albert ♦♦ 79k

This is the real spirit of Biostar, thanks for sharing this.

ADD REPLYlink written 8.8 years ago by Khader Shameer18k
gravatar for Timothy Bailey
8.8 years ago by
Timothy Bailey30 wrote:

I've put a link on the MEME User Forum to this thread.

ADD COMMENTlink written 8.8 years ago by Timothy Bailey30
gravatar for Istvan Albert
9.2 years ago by
Istvan Albert ♦♦ 79k
University Park, USA
Istvan Albert ♦♦ 79k wrote:

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:


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:

ADD COMMENTlink written 9.2 years ago by Istvan Albert ♦♦ 79k
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