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Bug #593

trjcat should release the memory again after checking the first frame of all files.

Added by Chris Neale about 7 years ago. Updated about 5 years ago.

Status:
Closed
Priority:
Low
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

trjcat has memory error when joining 28,000 single-frame .xtc files.

Roland suggests that "the memory isn't freed correctly. read_first_frame is allocating the memory for one frame but in most cases it isn't freed. Thus you only see this error with many small files."

David suggests that "The program reads the first frame of all files, and since we roughly have three times compression from xtc to float your figures of 4 vs. 11
Gb. match perfect."

Berk and David pointed out that I could use cat or script the trjcat to go in 10 steps -- if the memory issue can not be dealt with easily, perhaps trjcat could issue an instructive warning message that the user should try these.

original post: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054788.html and there are followups within 24 hours also on the mailing list

Thank you,
Chris.

Associated revisions

Revision c96a340c (diff)
Added by David van der Spoel about 5 years ago

Fixed Bug #593 about memory hole in trjcat.

Fixed by explicitly freeing memory for each frame. Tested to make
sure it does not crash.

Change-Id: Ic0e91b828a1e5a23f38690b4753092a31e6c4db4

History

#1 Updated by Rossen Apostolov about 6 years ago

  • Description updated (diff)
  • Assignee deleted (Erik Lindahl)
  • Target version deleted (git master)

#2 Updated by Rossen Apostolov over 5 years ago

  • Assignee set to David van der Spoel

#3 Updated by Roland Schulz about 5 years ago

  • Priority changed from Normal to Low

#4 Updated by David van der Spoel about 5 years ago

  • Target version set to 4.5.6

Uploaded a patch to gerrit. https://gerrit.gromacs.org/1544

#5 Updated by Roland Schulz about 5 years ago

  • Status changed from New to Closed

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