[gmx-users] g_msd bug

[Sławomir Stachura]

No -it is not a typo - my cluster allows me to use higher amount of memory than 10%. Information I received from administrator of the cluster :

>> [root at isei ~]#top
>>
>> top - 13:52:23 up 30 days,  3:00, 76 users,  load average: 5.85, 17.19,
>> 13.08
>> Tasks: 2825 total,   1 running, 2815 sleeping,   1 stopped,   7 zombie
>> Cpu(s):  0.1%us,  0.7%sy,  0.0%ni, 97.2%id,  1.9%wa,  0.0%hi,  0.1%si,
>> 0.0%st
>> Mem:  527077804k total, 526482844k used,   594960k free,     8016k buffers
>> Swap: 141596792k total, 141407504k used,   189288k free,   294092k cached
>>
>>     PID USER      PR  NI  VIRT  RES  SHR  S %CPU %MEM    TIME+  COMMAND
>> 28381 stachura  34  19  307g 252g 1392 D        2.2     97.5     202:57.50 g_msd

It's all I have. Anyone has ever encountered such situation?

Best wishes,
   Slawomir



Wiadomość napisana przez chris.neale at utoronto.ca w dniu 2011-06-27, o godz. 17:12:

> 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,
> 
> --
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