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Bug #521

Segmentation fault at the end of mdrun using old tpr file (version 58) with software version 73.

Added by Maarten Wolf about 9 years ago. Updated about 9 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

Segmentation fault at the end of mdrun using old tpr file (version 58) with software version 73 (git from 25-08-2010). When all steps are completed the segmentation fault occurs. gdb gave the following output:

#0 0x00007f1dd7f88dd1 in xdr_float () from /lib64/libc.so.6
#1 0x00007f1dd7f88c03 in xdr_vector () from /lib64/libc.so.6
#2 0x000000000058a3b6 in do_cpte_reals_low ()
#3 0x000000000058aae7 in do_cpte_matrices ()
#4 0x000000000058b9c2 in do_cpt_ekinstate ()
#5 0x00000000005905aa in write_checkpoint ()
#6 0x000000000052f806 in write_traj ()
#7 0x0000000000430fb2 in do_md ()
#8 0x0000000000425f48 in mdrunner ()
#9 0x0000000000437185 in main ()

When grompping with software version 73 and running with the new tpr file (version 70) no segmentation fault occurs.

test.tpr (346 KB) test.tpr test after membed, version 58 tpr, segmentation fault with version 73 mdrun Maarten Wolf, 08/26/2010 04:16 PM

History

#1 Updated by David van der Spoel about 9 years ago

Please upload the tpr file.

#2 Updated by Teemu Murtola about 9 years ago

This is probably related to bug #522, since the crash is in do_cpte_reals_low(). Since the current version of do_cpte_reals_low() seems to use an uninitialized value for the count to write, I can easily imagine that it will segfault under some conditions.

#3 Updated by Maarten Wolf about 9 years ago

Created an attachment (id=527)
test after membed, version 58 tpr, segmentation fault with version 73 mdrun

#4 Updated by Teemu Murtola about 9 years ago

Now that bug #522 is fixed, the provided tpr file works fine for me (built from commit 1d12211). Haven't tested with earlier versions, though, but it seems probable that the bug is fixed. Please reopen if it still appears.

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