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@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.ne...@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.slawo...@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, > > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
