[gmx-users] error after 1ns of md run during production

sucharita csisd at nus.edu.sg
Wed Mar 12 04:12:27 CET 2014

I have done the subscription, hope my email will be accepted.
Sucharita Dey,PhD, Research Fellow, Cancer Science Institute of Singapore, National University of Singapore. 14, Medical Drive,  #12-01, Singapore 117599. Tel: (65) 90355220, email: csisd at nus.edu.sg
From: Sucharita Dey
Sent: Wednesday, March 12, 2014 11:02 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: error after 1ns of md run during production

Hello gmx-users,

I am running gromacs in a cluster using mpi code, version is 4.5.5, getting
the below mentioned error after 1ns run of the production run, before that I
have successfully done 50 ps of equilibration. And I checked it is fine. Is
the error because of the version? Please help.

Following is taken from the log file giving the error:

Reading file /hpctmp/csisd/UTX_M//new/UTX_M-final.tpr, VERSION 4.5.5 (single

Will use 16 particle-particle and 8 PME only nodes
This is a guess, check the performance at the end of the log file
Making 2D domain decomposition 8 x 2 x 1

WARNING: This run will generate roughly 7742 Mb of data

starting mdrun 'Protein in water'
25000000 steps,  50000.0 ps.

Step 685356, time 1370.71 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 761119.299726, max 9567121.000000 (between atoms 2442 and 2443)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2442   2443   90.0    0.1090 1042816.2500      0.1090
Wrote pdb files with previous and current coordinates
[cheetah-c59:mpi_rank_7][error_sighandler] Caught error: Segmentation fault
(signal 11)
[cheetah-c59:mpi_rank_6][error_sighandler] Caught error: Segmentation fault
(signal 11)

Program mdrun_mpi, VERSION 4.5.5
Source code file: pme.c, line: 538

Fatal error:
3 particles communicated to PME node 2 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Please note,  just to check, I ran the same md for 5ns in my PC which has gromacs 4.6.3, and it is running till now uninterrupted (already covered 3ns)


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