AW: residue_rmsd.tcl segmentation fault

From: Norman Geist (
Date: Fri Apr 04 2014 - 03:18:08 CDT


Von: Axel Kohlmeyer []
Gesendet: Freitag, 4. April 2014 10:04
An: Norman Geist
Cc: John Xi; Namd Mailing List
Betreff: Re: namd-l: residue_rmsd.tcl segmentation fault




On Fri, Apr 4, 2014 at 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


if you are willing to live with a massive performance drop, then you *can*
use swap like RAM. if you put swap space on a RAID-0 made from SSDs, the
performance drop is not that massive at all and when you have exploited the
maximum RAM capacity of a mainboard, this may be the only option without
having to go for an extremely expensive option.


I've seen some OS to decide different. Even if swap isn't full it will kill
processes trying to alloc memory under some conditions. And the bad is, it's
doing it "race condition like" including all other running processes, not
only the current memory consuming one. I've seen the OS to kill some
background procs cause they were trying to alloc some memory, when there was
no left due a large VMD.


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.


that is not quite true. on Linux allocated memory is generally flagged as
copy-on-write, thus a fork will not cost you that much unless you modify
that RAM.


Open a VMD and load data until its using some more of the half of your
memory. Now try "exec ls". It will fail due not enough memory, in fact with
OpenSuse 13.1 and older it's doing so, even if considering swap would bring
enough memory. So this proves both my comments. Maybe it's different in
other distros. I've seen this problem on a machine having 128 GB of ram.
Little more than 64 GB where used by VMD and I could't use STRIDE from VMD
as it is called by "exec" and failes with a message like "not enough memory"
in VMD console.







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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Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy. 
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