Subject: Re: Re: [gmx-users] Gromacs 4 bug?
Antoine.Fortune at ujf-grenoble.fr
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).
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.
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
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 !
Ingenieur Modelisation Moleculaire
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