residue_rmsd.tcl segmentation fault

From: John Xi (
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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