[maker-devel] Maker-Error when started with OpenMPI

[Rainer Rutka]

Hi everybody.

My name is Rainer. I am an administrator for our HPC-Systems at our
university in Konstanz, Baden-Wuertemberg/Germany.
The procect is called bwHPC-C5.

See: https://www.bwhpc-c5.de/en/index.php

I try to get Maker running on our bwUniCluster since weeks. Unfortunately
i get errors while running a Maker job in the MPI-environment.

BUILD STATUS

==============================================================================
STATUS MAKER v2.31.9
==============================================================================
PERL Dependencies: VERIFIED
External Programs: VERIFIED
External C Libraries: VERIFIED
MPI SUPPORT: ENABLED
MWAS Web Interface: DISABLED
MAKER PACKAGE: CONFIGURATION OK

MODULES / INCLUDES / COMPILERS

# knbw03 20170117 r.rutka Initial revision knbw02 of module version 2.31.9
#
##### (B) Dependencies:
#
# conflict: any other maker version
# module load compiler/gnu/5.2
# module load mpi/openmpi/2.0-gnu-5.2
[...]

MPI/MOAB SUBMIT

[...]
### Queues ###
#MSUB -q fat
#MSUB -l nodes=1:ppn=16
#MSUB -l mem=20gb
#MSUB -l walltime=50:00:00
#
[...]
echo " "
echo "### Loading MAKER module:"
echo " "
module load bio/maker/2.31.9
[ "$MAKER_VERSION" ] || { echo "ERROR: Failed to load module 
'bio/maker/2.31.9'."; exit 1; }
echo "MAKER_VERSION = $MAKER_VERSION"
module list
[...]
echo " "
echo "### Runing Maker example"
echo " "
export LD_PRELOAD=${MPI_LIB_DIR}/libmpi.so
export OMPI_MCA_mpi_warn_on_fork=0

echo "LD_PRELOAD=${LD_PRELOAD}"
#
# "STATUS: Processing and indexing input FASTA files..."
#
mpiexec -mca btl ^openib -n 16 maker
[...]


E R R O R S
=======
[...]
LD_PRELOAD=/opt/bwhpc/common/mpi/openmpi/2.0.1-gnu-5.2/lib/libmpi.so
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
[uc1n338:113607] *** Process received signal ***
[uc1n338:113607] Signal: Segmentation fault (11)
[uc1n338:113607] Signal code: Address not mapped (1)
[uc1n338:113607] Failing at address: 0x4b0
[uc1n338:113608] *** Process received signal ***
[uc1n338:113608] Signal: Segmentation fault (11)
[uc1n338:113608] Signal code: Address not mapped (1)
[uc1n338:113608] Failing at address: 0x4b0
[uc1n338:113621] *** Process received signal ***
[uc1n338:113621] Signal: Segmentation fault (11)
[uc1n338:113621] Signal code: Address not mapped (1)
[uc1n338:113621] Failing at address: 0x4b0
--------------------------------------------------------------------------
mpiexec noticed that process rank 2 with PID 113608 on node uc1n338 
exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
[...]

WHATS WRONG HERE!?

Thank you for your help!

All the best ,

Rainer

-- 
Rainer Rutka
University of Konstanz
Communication, Information, Media Centre (KIM)
* High-Performance-Computing (HPC)
* KIM-Support and -Base-Services
Room: V511
78457 Konstanz, Germany
+49 7531 88-5413

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