Dear all,
I've been experiencing problems while trying to run pmemd.MPI in different nodes. We have installed openmpi (version 1.6.3) and amber (version 12).
This is my script:
/opt/openmpi-1.6.3/bin/mpirun -machinefile myhostfile /opt/amber12/bin/pmemd.MPI -O -i md.in -p 39C_1N8R.wat.top -c 39C_1N8R.0.crd -o 39C_1N8R.1.out -r 39C_1N8R.1.crd -x 39C_1N8R.1.trj
And the error I get seems to indicate that something during installation was not set correctly:
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
mpirun has exited due to process rank 0 with PID 25024 on
node node101 exiting improperly. There are two reasons this could occur:
1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.
2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"
This may have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
What should my next step be to fix this? does this look like an openmpi problem or an amber compilation problem? I have to add that during amber12 compilation we got some errors, but all of them "PASSED" so we carried on.
Sorry if this question is too basic, I'm aware I still have a lot to learn..
Thanks very much in advance for your help.
Amparo
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Received on Mon Dec 24 2012 - 06:00:04 PST
