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Subject: [OMPI users] MPI can not open file?
From: Bernhard Knapp (bernhard.knapp_at_[hidden])
Date: 2009-04-07 07:05:04


Hi

I am trying to get a parallel job of the gromacs software started. MPI
seems to boot fine but unfortunately it seems not to be able to open a
specified file although it is definitly in the directory where the job
is started. I also changed the file permissions to 777 but it does not
affect the result. Any suggestions?

cheers
Bernhard

[bknapp_at_quoVadis04 testSet]$ mpirun -np 8 -machinefile
/home/bknapp/scripts/machinefile.txt mdrun -np 8 -nice 0 -s
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr -o
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.trr -c
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.pdb -g
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.log -e
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.edr -v
bknapp_at_192.168.0.103's password:
NNODES=8, MYRANK=1, HOSTNAME=quoVadis04
NNODES=8, MYRANK=3, HOSTNAME=quoVadis04
NNODES=8, MYRANK=7, HOSTNAME=quoVadis04
NNODES=8, MYRANK=0, HOSTNAME=quoVadis03
NNODES=8, MYRANK=4, HOSTNAME=quoVadis03
NNODES=8, MYRANK=6, HOSTNAME=quoVadis03
NODEID=4 argc=16
NNODES=8, MYRANK=2, HOSTNAME=quoVadis03
NODEID=1 argc=16
NODEID=3 argc=16
NODEID=7 argc=16
NODEID=2 argc=16
NODEID=6 argc=16
NODEID=0 argc=16

--------------------------------------------------------------------------
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.
--------------------------------------------------------------------------

-------------------------------------------------------
Program mdrun, VERSION 4.0.3
Source code file: gmxfio.c, line: 736

Can not open file:
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr
-------------------------------------------------------

"I Need a Little Poison" (Throwing Muses)

Error on node 0, will try to stop all the nodes
Halting parallel program mdrun on CPU 0 out of 8

gcq#108: "I Need a Little Poison" (Throwing Muses)

--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 3777 on
node 192.168.0.103 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------

[bknapp_at_quoVadis04 testSet]$ ll
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr
-rwxrwxrwx 1 bknapp bknapp 6118424 2009-03-13 09:44
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr