Trouble with ABySS, Paired-End, parallel, mpirun cannot find ABYSS-P

[Lucas Swanson]

Hello,

I am trying to use ABySS 1.2.2 to assemble some transcriptome data for
use with the Trans-ABySS pipeline and seem to be having a problem. The
error message I am getting is:

[sdats1:17144] mca: base: component_find: unable to open
/hpc/store/COMPBIO/lswanson/Trans-ABySS/openmpi-1.4.3/lib/openmpi/mca_plm_tm:
perhaps a missing symbol, or compiled for a different version of Open
MPI? (ignored)
[sdats1:17144] mca: base: component_find: unable to open
/hpc/store/COMPBIO/lswanson/Trans-ABySS/openmpi-1.4.3/lib/openmpi/mca_ras_tm:
perhaps a missing symbol, or compiled for a different version of Open
MPI? (ignored)
--------------------------------------------------------------------------
mpirun was unable to launch the specified application as it could not
find an executable:

Executable: ABYSS-P
Node: sdats1

while attempting to start process rank 0.
--------------------------------------------------------------------------
make: *** [C42-assembly-1.fa] Error 133

The script I am using to launch ABySS is:

#!/bin/sh
#PBS -m ea
#PBS -M lucas.a...@gmail.com
#PBS -S /bin/sh
#PBS -l mem=300mb
#PBS -l arch=x86_64
#PBS -l walltime=72:00:00
abyss_path=/hpc/store/COMPBIO/lswanson/Trans-ABySS/abyss-1.2.2/bin
mpi_path=/hpc/store/COMPBIO/lswanson/Trans-ABySS/openmpi-1.4.3/bin
export PATH=$abyss_path:$mpi_path:$PATH
cd $PBS_O_INITDIR
# get read sequence file paths from "in" file
export in=`paste -sd' ' in`
export JOB_NAME=${PBS_JOBNAME%-$PBS_ARRAYID}
export SGE_TASK_ID=$PBS_ARRAYID
mkdir k$PBS_ARRAYID && cd k$PBS_ARRAYID && \
abyss-pe np=64 OVERLAP_OPTIONS=--no-scaffold
SIMPLEGRAPH_OPTIONS=--no-scaffold E=0 n=10 v=-v

The commands I used to install ABySS are:

./configure --prefix
/hpc/store/COMPBIO/lswanson/Trans-ABySS/abyss-1.2.2/ --with-mpi
/hpc/store/COMPBIO/lswanson/Trans-ABySS/openmpi-1.4.3/bin
CPPFLAGS=-I/hpc/store/COMPBIO/lswanson/Trans-ABySS/sparsehash-1.9/include
make
make install

Do I have to use some special option to build ABYSS-P?
I am not really sure what is going on with the "mca: base:
component_find:" warnings, when I look in
/hpc/store/COMPBIO/lswanson/Trans-ABySS/openmpi-1.4.3/lib/openmpi/ I
can see the following files:
mca_plm_tm.la
mca_plm_tm.so
mca_ras_tm.la
mca_ras_tm.so

Should I be doing anything special when installing OpenMPI?

Any light you can shed will be greatly appreciated.

~Thanks,
Lucas Swanson