[gmx-developers] 4.6 beta2: segfault in grompp (with pulling + free-energy)

[Shirts, Michael (mrs5pt)]

Hi, all-

Likely an issue with the logic path when dt != 0 created when rationalizing
some of the other lambda code integration.  I'll have time to check this out
later this afternoon.  Upload input files to redmine if possible to make
sure I'm reproducing the same errors.

Best,
~~~~~~~~~~~~
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434)-243-1821


> From: Jochen Hub <jhub at gwdg.de>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Wed, 12 Dec 2012 10:59:23 +0100
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Subject: [gmx-developers] 4.6 beta2: segfault in grompp (with pulling +
> free-energy)
> 
> Hi,
> 
> grompp gives a segfault with pulling and free-energy=yes.
> 
> The reason is that ir->fepvals->all_lambda[efptMASS] in readpull.c:302
> is NULL. See:
> 
> (gdb) p ir->fepvals->all_lambda[efptMASS]
> $5 = (double *) 0x0
> 
> I use 4.6-beta2-dev-20121211-031485c. The error does not occur in 4.5.5.
> 
> Is the error obvious, or do you need a redmine?
> 
> Cheers,
> Jochen
> 
> Here is the backtrace:
> 
> Program received signal EXC_BAD_ACCESS, Could not access memory.
> Reason: KERN_INVALID_ADDRESS at address: 0x0000000000000000
> 0x0000000100028e67 in set_pull_init (ir=0x101801000, mtop=0x101505440,
> x=0x10cc81000, box=0x7fff5fbff3c8, oenv=0x101500b50, bStart=0) at
> /Users/jhub/src/gmx/gromacs/src/kernel/readpull.c:302
> 302       lambda =
> ir->fepvals->all_lambda[efptMASS][ir->fepvals->init_fep_state];
> (gdb) bt
> #0  0x0000000100028e67 in set_pull_init (ir=0x101801000,
> mtop=0x101505440, x=0x10cc81000, box=0x7fff5fbff3c8, oenv=0x101500b50,
> bStart=0) at /Users/jhub/src/gmx/gromacs/src/kernel/readpull.c:302
> #1  0x0000000100009957 in cmain (argc=1, argv=0x7fff5fbff778) at
> /Users/jhub/src/gmx/gromacs/src/kernel/grompp.c:1694
> #2  0x0000000100009dde in main (argc=13, argv=0x7fff5fbff778) at
> /Users/jhub/src/gmx/gromacs/src/kernel/main.c:29
> 
> -- 
> ---------------------------------------------------
> Dr. Jochen Hub
> Computational Molecular Biophysics Group
> Institute for Microbiology and Genetics
> Georg-August-University of Göttingen
> Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
> Phone: +49-551-39-14189
> http://cmb.bio.uni-goettingen.de/
> ---------------------------------------------------
> -- 
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.