From: John Xi (jxi2014_at_yahoo.com)
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 <norman.geist_at_uni-greifswald.de> 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.
Von:owner-namd-l_at_ks.uiuc.edu
[mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von John Xi
Gesendet: Freitag, 4. April 2014 04:49
An: namd-l_at_ks.uiuc.edu
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
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