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mpirun unable to find SU2_PRT

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Old   May 6, 2017, 03:45
Default mpirun unable to find SU2_PRT
  #1
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Ole Pfeifle
Join Date: Feb 2017
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Apollinaris is on a distinguished road
Dear all,

I just set up SU2 with parallel support, but keep getting some errors related to mpi. First the output says that the mpi local host could not be started "mpd: command not found", and then that mpirun was unable to execute SU2_PRT. The first error remains, when I remove the call to SU2_PRT from the pbs file.

Here the error message:

Quote:
/opt/ud/openmpi-1.8.8/bin/mpirun


Job started at
/var/opt/ud/torque-4.2.10/mom_priv/jobs/62679.hpc12.hpc.SC: line 26: mpd: command not found
************************************************** **************************
* hwloc has encountered what looks like an error from the operating system.
*
* L3 (cpuset 0x000003f0) intersects with NUMANode (P#0 cpuset 0x0000003f) without inclusion!
* Error occurred in topology.c line 942
*
* The following FAQ entry in a recent hwloc documentation may help:
* What should I do when hwloc reports "operating system" warnings?
* Otherwise please report this error message to the hwloc user's mailing list,
* along with the output+tarball generated by the hwloc-gather-topology script.
************************************************** **************************
--------------------------------------------------------------------------
mpirun was unable to find the specified executable file, and therefore
did not launch the job. This error was first reported for process
rank 0; it may have occurred for other processes as well.

NOTE: A common cause for this error is misspelling a mpirun command
line parameter option (remember that mpirun interprets the first
unrecognized command line token as the executable).

Node: n12-01
Executable: SU2_PRT
--------------------------------------------------------------------------
8 total processes failed to start
My .bashrc includes all SU2 paths from the /.configure:

Quote:
export SU2_RUN="/home/opfeifle/SU2/bin"
export SU2_HOME="/home/opfeifle/SU2"
export PATH=$PATH:$SU2_RUN
export PYTHONPATH=$PYTHONPATH:$SU2_RUN
And from my pbs script:

Quote:
module load mpi/openmpi-1.8.8-gnu
which mpirun

cd /home/opfeifle/RUNS/STRAIGHT_DUCT

echo " "
echo " "
echo "Job started at"
mpd &
sleep 5s
mpirun -n 8 SU2_PRT straight_duct.cfg
mpirun -n 8 SU2_CFD straight_duct.cfg
mpirun -n 8 SU2_SOL straight_duct.cfg
SU2 was installed with the /.configure options --prefix=/home/opfeifle/SU2 --enable-mpi --with-cc=/opt/ud/openmpi-1.8.8/bin/mpicc --with-cxx=/opt/ud/openmpi-1.8.8/bin/mpicxx CXXFLAGS="-O3"
where the paths were taken from "which mpirun"

Am I missing anything in my path for running mpd?

Any help would be much appreciated!!

With kind regards,
Apollinaris
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Old   May 10, 2017, 05:31
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Tim Albring
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It seems like you are using a very old version and its hard to give any advice on that. Can you try to upgrade ?
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