Taylor Kaplan wrote:
Hi gromacs users,
I'm running a simulation but I keep getting the following errors.
rogram mdrun_mpi, VERSION 4.5.1
Source code file: gmxfio.c, line: 537
Can not open file:
taExcited.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"That Was Cool" (Beavis and Butthead)
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 4
--------------------------------------------------------------------------
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.
--------------------------------------------------------------------------
gcq#182: "That Was Cool" (Beavis and Butthead)
--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 9680 on
node compute-0-10 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
I don't know why gromacs cannot find my taExcited.tpr file, since it
does exist in my working directory. However I noticed that when gromacs
makes copies of my log files, its putting it in my home directory. This
leads me to believe that it must be looking into the wrong path. This
problem is only recent since gromacs knows where to looking when i
reference my other working files, such as when i run grompp, but mdrun
does not want to open up my .tpr file. Any ideas?
Are you submitting the job to a queue? If so, please provide the entire script
you're using to execute mdrun. Does the problem persist in newer versions of
Gromacs? It's always best to start from the newest available version, rather
than troubleshoot an old one, just to find out the problem has already been
resolved.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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