I assume you are running in a non-managed environment and so are using ssh for your launcher? Could you tell us what version of OMPI you are using?

The problem is that ssh drops you in your home directory, not your current working directory. Thus, the path to any file you specify must be relative to your home directory. Alternatively, you can specify the desired current working directory on the mpirun cmd line. Do a "man mpirun" to find the specific option.

I'd have to check, but we may have corrected this in recent versions (or a soon-to-be-released one) so that we automatically move you to the cwd after the daemon is started. However, I know that we didn't do that in some earlier versions - perhaps in the 1.2.x series as well.

Ralph


On Apr 7, 2009, at 5:05 AM, Bernhard Knapp wrote:

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@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@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@quoVadis04 testSet]$ ll 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr
-rwxrwxrwx 1 bknapp bknapp 6118424 2009-03-13 09:44 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr



_______________________________________________
users mailing list
users@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users