[gmx-users] g_msd bug

[chris.neale at utoronto.ca]

600 GB of memory? I highly doubt that you have that much memory  
available. Are you sure that this is not a typo? Can you please post  
evidence that you have >=600 GB of memory available? It is common for  
clusters to disallow an individual process from using >10% of the  
total memory on a head-node, which makes 600 MB more likely, in which  
case you can try submitting your job to a compute node.

-- original message --

Hello,
thank you for your reply. I have used following command :

g_msd  -n POPC.ndx  -lateral z -o POPC_msd.xvg -mol POPC_diff.xvg

Trajectory has 10000 frames and the system it was ran on is Fedora Red  
Hat 5.4.
Indeed my network administrator was very unhappy about comsumed memory.

Regards,
    Slawomir





Wiadomo¶æ napisana przez Tsjerk Wassenaar w dniu 2011-06-27, o godz. 15:40:

[Hide Quoted Text]
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 S³awomir 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,