[gmx-users] cannot open file

Justin A. Lemkul jalemkul at vt.edu
Sat Jul 30 01:17:12 CEST 2011

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 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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