[gmx-users] error in running systems in parallel

Balasubramani GL glbala87 at imtech.res.in
Thu May 1 08:33:54 CEST 2014


Hai Friends, 

 I have individual input files and directories for my system, i want to
perform REMD(replica exchange MD). when i execute multiple simulation
run mdrun_mpi, gets a error like this: 

I have individual directories called equil0, equil1, equil2, equil3
which contains input/output files under main directory called stage1 ,
when i run this command: 

$ mpirun -np 160 mdrun_mpi -v -multidir equil[0123] 

error pops up: 

NNODES=160, MYRANK=159, HOSTNAME=structure
NODEID=159 argc=7

Back Off! I just backed up md.log to ./#md.log.2#
Getting Loaded...
Reading file topol.tpr, VERSION 4.6.1 (single precision)

Program mdrun_mpi, VERSION 4.5.5
Source code file: tpxio.c, line: 2010

Fatal error:
reading tpx file (topol.tpr) version 83 with version 73 program
For more information and tips for troubleshooting, please check the
website at http://www.gromacs.org/Documentation/Errors

"Alas, You're Welcome" (Prof. Dumbledore in Potter Puppet Pals)

Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 160
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#322: "Alas, You're Welcome" (Prof. Dumbledore in Potter Puppet Pals)

mpirun has exited due to process rank 0 with PID 127928 on
node structure exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).

can somebody suggest me how to fix this error. Your help is greatly

Thanks & Regards, 

Structural & Quatitative Biology Lab, GNRPC,
Institute of Microbial Technology (CSIR),
Sector 39-A, Chandigarh, India-160036.
ph : +91-9876086625/9041280408 
off : 0172-6665475

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