From: John Xi (jxi2014_at_yahoo.com)
Date: Thu Apr 03 2014 - 21:49:05 CDT
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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