Subject: Re: Re: [gmx-users] Gromacs 4 bug?

Antoine Fortuné Antoine.Fortune at
Mon Dec 15 09:53:43 CET 2008

Hi, all gmx users and devs

Just a (long) word to tell you a meet the same issue as Bernhard :  
mdrun stucks as in an infinite loop or lose some output file pointers  
after a while.

The story :
mdrun hangs after a variable number of steps (40.000 to 260.000  
steps). Outputs are suspended in the shell (mdrun with -v option) as  
in the md log file (idem Bernhard's ouputs) but CPU(s) still runnning  
endless (10 hours before i killed the job). Sometimes it induces a  
complete freeze of the machine and a reboot is needed. No error logged  
(md.log or syslog).

Conditions :
This appends with gromacs 4.0.0 and 4.0.2 recompiled from binaries,  
using mpi  or not (mpi3.3.3-1.x86_64 from gromacs website rpm).  
Computer is an Intel Q9450 at 3.5GHz running OpenSuSE 11.0_x86_64 with  
~400Go free (raid 1 HD) and 4Go DDR3.

Tries :
I first thought this was because of my overclocking parameters but  
other jobs run perfectly with full cpu load over several days and  
mdrun also hangs with standard clock settings. OpenSuSE is stable, no  
problem of any kind with file management or long duration jobs  
(docking jobs running fine).

So now i suspect my md parameters (excessive cutoff distances with PBC  
perhaps or use of temperature and presure coupling ?). As I'm a noob  
in md i first suspect the fault is mine and try to fix it by myself  
(without success for now) before asking help. Still some tries to do  
but ...

"Consolation" :
If Bernhard can run his job with gromacs 3.3 and not with 4.0 perhaps  
i'm not so stupid ...

I follow this thread with interrest !

Antoine Fortuné
Ingenieur Modelisation Moleculaire
Pole Chimie bat. E - BP53 - 38042 GRENOBLE CEDEX 9
Tel : 33+ 0 476635292 - Fax : 33+ 0 476635298

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