AW: residue_rmsd.tcl segmentation fault

From: Norman Geist (
Date: Fri Apr 04 2014 - 02:53:45 CDT

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: [] Im Auftrag
von John Xi
Gesendet: Freitag, 4. April 2014 04:49
Betreff: namd-l: residue_rmsd.tcl segmentation fault




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

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

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?






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