[gmx-users] restart the mdrun with the checkpoint file

[xianqiang]

 Dear all,

I am trying to use the checkpoint file for the MDrun which war crashed.
However, the following error file was obtained in my log file:

Reading file md_0_2.tpr, VERSION 4.5.5 (single precision)

Reading checkpoint file state.cpt generated: Tue Nov  8 08:06:42 2011


starting mdrun 'Protein in water'
20000000 steps,  20000.0 ps (continuing from step 1685550,   1685.5 ps).
[a02c31n06.pdc.kth.se:20072] 7 more processes have sent help message help-mpi-btl-base.txt / btl:no-nics
[a02c31n06.pdc.kth.se:20072] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

-------------------------------------------------------
Program mdrun, VERSION 4.5.3
Source code file: ../../../gromacs-4.5.3/src/gmxlib/futil.c, line: 459

File input/output error:
state_step1714850.cpt
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"Good Music Saves your Soul" (Lemmy)

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

gcq#311: "Good Music Saves your Soul" (Lemmy)

--------------------------------------------------------------------------
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 20073 on
node a02c31n06.pdc.kth.se exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
~                                                                                        

Anyone can help me with this problem?
Thanks so much,
Xianqiang


--

Xianqiang Sun


Email: xianqiang at theochem.kth.se
Division of Theoretical Chemistry and Biology
School of Biotechnology 
Royal Institute of Technology
S-106 91 Stockholm, Sweden  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111108/b9ba6358/attachment.html>