[gmx-users] g_msd bug

[Dommert Florian]

Hello,

I can also confirm this behaviour. Furthermore if I use an index group,
that just contains 1 molecule and compare the results from an analysis
with the flag -mol and without, then I obtain different results which
should not be the case.

/Flo


On Thu, 2011-07-07 at 09:28 +0200, Ivan Gladich wrote: 
> Dear all,
>   I found the same problem that Sławomir  pointed out 10 days ago about 
> the memory usage in the computation of g_msd.
> 
> 
> I have 100 ns simulation for 2880 water molecules. The trajectory is 
> savede every 1 ps: this means that I have 100000 frame
> 
> I think that there is a strange memory problem only when the option -mol 
> is used
> Indeed, if I use
> 
> g_msd_d -f ../t230.xtc -s ../t230.tpr -n index.ndx -o msdt230.xvg -b 
> 4000 -e 100000 -beginfit 5000 -endfit 25000 -trestart 20 -type x
> 
> the g_msd does not have any problem
> 
> by the way using the option -mol (as Sławomir did in the last e-mails)
> 
> g_msd_d -f ../t230.xtc -s ../t230.tpr -n index.ndx -o msdt230.xvg -b 
> 4000 -e 100000 -beginfit 5000 -endfit 25000 -trestart 20 -type x -mol
> 
> g_msd crashes and memory information (see below) points out that this 
> crash is due by the memory overflow.
> 
> Thanks a lot
> Ivan
> 
> Tasks: 478 total,   5 running, 473 sleeping,   0 stopped,   0 zombie
> Cpu(s):  0.0%us,  0.5%sy, 12.7%ni, 77.7%id,  9.1%wa,  0.0%hi,  0.0%si,  
> 0.0%st
> Mem:  65459256k total, 65382420k used,    76836k free,        0k buffers
> Swap: 32009508k total,  5360348k used, 26649160k free,     6312k cached
> 
> 
> 
> On 06/27/11 15:40, Tsjerk Wassenaar wrote:
> > Hi Slawomir,
> >
> > That's quite a usage of memory! Can you provide more information? Like
> > the number of frames in the trajectory, the command line you used, and
> > the system you ran on?
> >
> > Cheers,
> >
> > Tsjerk
> >
> > 2011/6/27 Sławomir Stachura<stachura.slawomir at gmail.com>:
> >> Hi GMX Users,
> >> I am writting this email, beacause I think the g_msd program in Gromacs 4.5.4 bears a problem. I was calculating the MSD od center of mass of POPC in membrane (system contains 274 POPC lipid molecules in all-atom force field) from 50 ns trajectory and it seems to consume great amount of memory. With  time of calculations the memory reserves are gradually devoured to the extent, in my case,  of over 600 GB (than my administrator of cluster killed the process). It seems that it does not release memory and it's pilling results up with steps  in memory. Have you heard of such case?
> >> Best wishes,
> >>    Slawomir--
> >> gmx-users mailing list    gmx-users at gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-request at gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >
> >
> 
> 
> -- 
> ------
> Ivan Gladich, Ph.D.
> Postdoctoral Fellow
> Academy of Sciences of the Czech Republic
> Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
> Flemingovo nám. 2.
> 166 10 Praha 6
> Czech Republic
> 
> Tel: +420775504164
> e-mail: ivan.gladich at uochb.cas.cz
> web page:http://www.molecular.cz/~gladich/
> -----
> 


-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 198 bytes
Desc: This is a digitally signed message part
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110707/6d49c2bd/attachment.sig>