Re: AW: residue_rmsd.tcl segmentation fault

From: John Xi (
Date: Fri Apr 04 2014 - 07:04:45 CDT

Thanks for the explanation and suggestion! I guess reducing the number of frames is the only way out of this problem.  Didn't realize VMD also has a mailing list. Still some people would still run this script after MD. John On Friday, April 4, 2014 3:53 AM, Norman Geist <> wrote: Hi john,   unfortunately you can’t use swap like additional memory. The system will kill processes for being that hungry for memory as swap is only useful to swap out inactive pages. Additionally if the tcl script contains “exec”, you got another problem as TCL does need to fork() to “exec” which duplicates the memory of the parent process. You might want to reduce the number of frames, a stride of 2 can already half the memory usage.   PS: Are you sure that this question is NAMD related?   Norman Geist. [] Im Auftrag von John Xi Gesendet: Freitag, 4. April 2014 04:49 An: Betreff: namd-l: residue_rmsd.tcl segmentation fault   Hi,   I am getting segmentation fault running residue-rmsd.tcl script on a 5.2GB dcd file on a Linux box.  After some googling,  I feel it may be related to system memory issue as suggested previously . Our system has only 4GB of memory and 2GB of swap space. So 2GB more swap space was added to the system. And the output from free command is as following:                          total       used       free     shared    buffers     cached Mem:       3838388     109476      3728912          0       2176      29400 -/+ buffers/cache:          77900       3760488 Swap:      4088204     263952      3824252   So, about 7.5GB of memory could be available for the system.   When the script was run, same problem Segmentation fault came out.   To try to figure out what causes this problem, I monitored the memory usage of system during the reading of dcd file.  When the memory was down to ~20MB, the swap space was called on. I did see the drop of swap space, but only by ~0.2GB, then the segmentation fault came out. The output from free command right before the problem is as following:                         total       used       free     shared    buffers     cached Mem:       3838388    3817844      20544          0        712      25260 -/+ buffers/cache:      3791872      46516 Swap:      4088204      429500    3658704   This seems to suggest the system works fine and the memory for this particular run should be enough (7.5GB vs 5.2GB). Given the exact same script works fine on a 3.2GB dcd file, I have no idea what could be wrong. Can somebody help me out?    Thanks,   John   ________________________________ Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv.

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