[gmx-users] gmx distance -- gmx: double free or corruption
Christopher Neale
chris.neale at alum.utoronto.ca
Fri Dec 2 21:27:13 CET 2016
Posted:
https://redmine.gromacs.org/issues/2086
Thanks Mark.
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abraham at gmail.com>
Sent: 29 November 2016 09:27:34
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] gmx distance -- gmx: double free or corruption
Hi,
That looks like something can be improved in the code, but it's hard to say
what. Can you open another Redmine issue with repo files please? If a
single pdb frame reproduces it, then that would likely be best.
I see you've tried to use -sf to simplify common subexpressions - that's
likely a good idea in general. See e.g. gmx help selections evaluation.
Mark
On Fri, Nov 25, 2016 at 8:45 PM Christopher Neale <
chris.neale at alum.utoronto.ca> wrote:
> Please ignore the mention of this being an amber trajectory. I can
> reproduce the exact same behaviour by gmx distance -s my.pdb -f my.pdb , so
> the issue can be reproduced on the information in a PDB file alone (and
> that pdb looks just fine in VMD).
>
> Thank you,
> Chris.
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of
> Christopher Neale <chris.neale at alum.utoronto.ca>
> Sent: 25 November 2016 14:33:51
> To: Discussion list for GROMACS users
> Subject: [gmx-users] gmx distance -- gmx: double free or corruption
>
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> Dear Users:
>
> I am having trouble with gmx distance crashing in gromacs 5.1.2. I am
> trying to analyze the distance of different peptide residues from the
> center of a lipid bilayer. have CA atoms on residues 2-20 and also on
> residues 22-40 (2 peptides). If I try to do residues 2-20 it works fine. If
> I try to do residues 22 to 40, I get a memory error. Funny thing is, I
> narrowed it down to see that 22-36 is OK but 22-37 fails, then when I try
> 37 alone it is OK, and selections of 26-40 also work. Please note that all
> these tests were repeated 2x on an allocation with 128 GB of memory, so I
> don’t think I’m just describing a stochastic failure.
>
> I didn’t try newer versions of gromacs, but there is nothing in the
> release notes for any newer version that mentions “distance” or “select”
> that seems to be related to this.
>
> ## I run like this:
> inpstr=$(for((i=22;i<=40;i++)); do echo -n "com of (residue $i and name
> CA) plus com of (resname POPC or resname POPS) plus "; done|sed "s/plus
> $//")
> gmx distance -s gromacs.tpr -f gromacs.xtc -n index.ndx -select "$inpstr"
> -oxyz depthB.xvg
>
> I’ve also tried giving gmx distance a .pdb as input to the -s option,
> where I first ran gmx editconf -resnr 1 just to avoid any issues with
> possible double residue counting in the .tpr file, and the result is the
> same crash.
>
> I checked that the .pdb and the .xtc have the same number of atoms with
> gmx check and I also ran gmx select on these groups to ensure that an atom
> was picked up in all cases (it was). Also, VMD loading the .pdb extracted
> from the .tpr and the .xtc gives a sensible trajectory.
>
> As a final note, the simulation was actually run in amber. I then used a
> plugin-aware version go gmx trjconv to read in the amber netcdf trajectory
> file and output a gromacs .xtc file, which I used in a non-plugin-aware
> version of gromacs for the analyses. The .tpr was generated for the same
> system (actually, I generated the gromacs .tpr from a grompp -pp .top file
> that was used in amber tool parmed gromber to set up the amber run).
>
> ## The output (with error) is this:
>
> :-) GROMACS - gmx distance, VERSION 5.1.2 (-:
>
> GROMACS is written by:
> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par
> Bjelkmar
> Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
> Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent
> Hindriksen
> Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner
> Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
> Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
> Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
> Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
> and the project leaders:
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2015, The GROMACS development team at
> Uppsala University, Stockholm University and
> the Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> GROMACS is free software; you can redistribute it and/or modify it
> under the terms of the GNU Lesser General Public License
> as published by the Free Software Foundation; either version 2.1
> of the License, or (at your option) any later version.
>
> GROMACS: gmx distance, VERSION 5.1.2
> Executable:
> /oasis/scratch/comet/cneale/temp_project/exec/gromacs-5.1.2/exec_serial/bin/gmx
> Data prefix:
> /oasis/scratch/comet/cneale/temp_project/exec/gromacs-5.1.2/exec_serial
> Command line:
> gmx distance -s gromacs.tpr -f gromacs.xtc -n index.ndx -select 'com of
> (residue 22 and name CA) plus com of (resname POPC or resname POPS) plus
> com of (residue 23 and name CA) plus com of (resname POPC or resname POPS)
> plus com of (residue 24 and name CA) plus com of (resname POPC or resname
> POPS) plus com of (residue 25 and name CA) plus com of (resname POPC or
> resname POPS) plus com of (residue 26 and name CA) plus com of (resname
> POPC or resname POPS) plus com of (residue 27 and name CA) plus com of
> (resname POPC or resname POPS) plus com of (residue 28 and name CA) plus
> com of (resname POPC or resname POPS) plus com of (residue 29 and name CA)
> plus com of (resname POPC or resname POPS) plus com of (residue 30 and name
> CA) plus com of (resname POPC or resname POPS) plus com of (residue 31 and
> name CA) plus com of (resname POPC or resname POPS) plus com of (residue 32
> and name CA) plus com of (resname POPC or resname POPS) plus com of
> (residue 33 and name CA) plus com of (resname POPC or resname POPS) plus
> com of (residue 34 and name CA) plus com of (resname POPC or resname POPS)
> plus com of (residue 35 and name CA) plus com of (resname POPC or resname
> POPS) plus com of (residue 36 and name CA) plus com of (resname POPC or
> resname POPS) plus com of (residue 37 and name CA) plus com of (resname
> POPC or resname POPS) plus com of (residue 38 and name CA) plus com of
> (resname POPC or resname POPS) plus com of (residue 39 and name CA) plus
> com of (resname POPC or resname POPS) plus com of (residue 40 and name CA)
> plus com of (resname POPC or resname POPS) ' -oxyz depthB.xvg
>
> *** glibc detected *** gmx: double free or corruption (!prev):
> 0x00000000019fcbd0 ***
> ======= Backtrace: =========
> /lib64/libc.so.6[0x369ca75f4e]
> /lib64/libc.so.6[0x369ca78cf0]
> /lib64/libc.so.6[0x369ca7bc80]
> /lib64/libc.so.6(realloc+0x158)[0x369ca7bf78]
> gmx(save_realloc+0x35)[0x54abb5]
>
> gmx(_Z24_gmx_sel_lexer_add_tokenPN3gmx17SelectionLocationEPKciP15gmx_sel_lexer_t+0xc3)[0x99b0f3]
>
> gmx(_Z14_gmx_sel_yylexP7YYSTYPEPN3gmx17SelectionLocationEPv+0x8a2)[0x998022]
> gmx[0x966f88]
> gmx(_ZN3gmx19SelectionCollection15parseFromStringERKSs+0x61)[0x967441]
>
> gmx(_ZN3gmx22SelectionOptionManager18convertOptionValueEPNS_22SelectionOptionStorageERKSsb+0x1e)[0x96d82e]
> gmx(_ZN3gmx21AbstractOptionStorage11appendValueERKSs+0x35)[0x51eca5]
> gmx(_ZN3gmx17CommandLineParser5parseEPiPPc+0x335)[0x893065]
> gmx(_ZN3gmx35TrajectoryAnalysisCommandLineRunner3runEiPPc+0x1c9)[0x74bb49]
>
> gmx(_ZN3gmx35TrajectoryAnalys+0xommandLineRunner4Impl23RunnerCommandLineModule3runEiPPc4c)[0x74b8bc]
> gmx(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x295)[0x4aca25]
> gmx(main+0xc5)[0x4922d5]
> /lib64/libc.so.6(__libc_start_main+0xfd)[0x369ca1ed5d]
> gmx[0x4920c9]
> ======= Memory map: ========
> 00400000-01647000 r-xp 00000000 54c:64a02 1891512467004187318
> /oasis/scratch/comet/cneale/temp_project/exec/gromacs-5.1.2/exec_serial/bin/gmx
> 01846000-01874000 rw-p 01246000 54c:64a02 1891512467004187318
> /oasis/scratch/comet/cneale/temp_project/exec/gromacs-5.1.2/exec_serial/bin/gmx
> 01874000-0187f000 rw-p 00000000 00:00 0
> 019e3000-01a25000 rw-p 00000000 00:00 0
> [heap]
> 369c600000-369c620000 r-xp 00000000 08:01 4718636
> /lib64/ld-2.12.so
> 369c81f000-369c820000 r--p 0001f000 08:01 4718636
> /lib64/ld-2.12.so
> 369c820000-369c821000 rw-p 00020000 08:01 4718636
> /lib64/ld-2.12.so
> 369c821000-369c822000 rw-p 00000000 00:00 0
> 369ca00000-369cb8a000 r-xp 00000000 08:01 4718640
> /lib64/libc-2.12.so
> 369cb8a000-369cd8a000 ---p 0018a000 08:01 4718640
> /lib64/libc-2.12.so
> 369cd8a000-369cd8e000 r--p 0018a000 08:01 4718640
> /lib64/libc-2.12.so
> 369cd8e000-369cd8f000 rw-p 0018e000 08:01 4718640
> /lib64/libc-2.12.so
> 369cd8f000-369cd94000 rw-p 00000000 00:00 0
> 369ce00000-369ce83000 r-xp 00000000 08:01 4718695
> /lib64/libm-2.12.so
> 369ce83000-369d082000 ---p 00083000 08:01 4718695
> /lib64/libm-2.12.so
> 369d082000-369d083000 r--p 00082000 08:01 4718695
> /lib64/libm-2.12.so
> 369d083000-369d084000 rw-p 00083000 08:01 4718695
> /lib64/libm-2.12.so
> 369d200000-369d217000 r-xp 00000000 08:01 4718654
> /lib64/libpthread-2.12.so
> 369d217000-369d417000 ---p 00017000 08:01 4718654
> /lib64/libpthread-2.12.so
> 369d417000-369d418000 r--p 00017000 08:01 4718654
> /lib64/libpthread-2.12.so
> 369d418000-369d419000 rw-p 00018000 08:01 4718654
> /lib64/libpthread-2.12.so
> 369d419000-369d41d000 rw-p 00000000 00:00 0
> 369d600000-369d602000 r-xp 00000000 08:01 4718691
> /lib64/libdl-2.12.so
> 369d602000-369d802000 ---p 00002000 08:01 4718691
> /lib64/libdl-2.12.so
> 369d802000-369d803000 r--p 00002000 08:01 4718691
> /lib64/libdl-2.12.so
> 369d803000-369d804000 rw-p 00003000 08:01 4718691
> /lib64/libdl-2.12.so
> 369da00000-369da07000 r-xp 00000000 08:01 4718655
> /lib64/librt-2.12.so
> 369da07000-369dc06000 ---p 00007000 08:01 4718655
> /lib64/librt-2.12.so
> 369dc06000-369dc07000 r--p 00006000 08:01 4718655
> /lib64/librt-2.12.so
> 369dc07000-369dc08000 rw-p 00007000 08:01 4718655
> /lib64/librt-2.12.so
> 369de00000-369de15000 r-xp 00000000 08:01 4718675
> /lib64/libz.so.1.2.3
> 369de15000-369e014000 ---p 00015000 08:01 4718675
> /lib64/libz.so.1.2.3
> 369e014000-369e015000 r--p 00014000 08:01 4718675
> /lib64/libz.so.1.2.3
> 369e015000-369e016000 rw-p 00015000 08:01 4718675
> /lib64/libz.so.1.2.3
> 2ba3dc377000-2ba3dc379000 rw-p 00000000 00:00 0
> 2ba3dc391000-2ba3dc393000 rw-p 00000000 00:00 0
> 2ba3dc393000-2ba3dc478000 r-xp 00000000 00:1d 42601288
> /opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64/libiomp5.so
> 2ba3dc478000-2ba3dc678000 ---p 000e5000 00:1d 42601288
> /opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64/libiomp5.so
> 2ba3dc678000-2ba3dc683000 rw-p 000e5000 00:1d 42601288
> /opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64/libiomp5.so
> 2ba3dc683000-2ba3dc6ab000 rw-p 00000000 00:00 0
> 2ba3dc6ab000-2ba3dc79e000 r-xp 00000000 08:01 922724
> /opt/gnu/gcc/lib64/libstdc++.so.6.0.20
> 2ba3dc79e000-2ba3dc99d000 ---p 000f3000 08:01 922724
> /opt/gnu/gcc/lib64/libstdc++.so.6.0.20
> 2ba3dc99d000-2ba3dc9a6000 r--p 000f2000 08:01 922724
> /opt/gnu/gcc/lib64/libstdc++.so.6.0.20
> 2ba3dc9a6000-2ba3dc9a8000 rw-p 000fb000 08:01 922724
> /opt/gnu/gcc/lib64/libstdc++.so.6.0.20
> 2ba3dc9a8000-2ba3dc9be000 rw-p 00000000 00:00 0
> 2ba3dc9be000-2ba3dc9d4000 r-xp 00000000 08:01 922663
> /opt/gnu/gcc/lib64/libgcc_s.so.1
> 2ba3dc9d4000-2ba3dcbd3000 ---p 00016000 08:01 922663
> /opt/gnu/gcc/lib64/libgcc_s.so.1
> 2ba3dcbd3000-2ba3dcbd4000 rw-p 00015000 08:01 922663
> /opt/gnu/gcc/lib64/libgcc_s.so.1
> 2ba3dcbd4000-2ba3dcbd9000 rw-p 00000000 00:00 0
> 2ba3e0000000-2ba3e0021000 rw-p 00000000 00:00 0
> 2ba3e0021000-2ba3e4000000 ---p 00000000 00:00 0
> 7fffa657e000-7fffa6595000 rw-p 00000000 00:00 0
> [stack]
> 7fffa65e5000-7fffa65e6000 r-xp 00000000 00:00 0
> [vdso]
> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
> [vsyscall]
> /var/spool/slurmd/job6096391/slurm_script: line 20: 4142 Aborted
> gmx distance -s gromacs.tpr -f gromacs.xtc -n index.ndx -select
> "$inpstr" -oxyz depthB.xvg
>
>
> ##########
>
> I’ve also tried with -sf rather than -select, using a file with contents
> like this:
>
> $ cat my.selection
> bilayer=com of (resname POPC or resname POPS);
> residue 22 and name CA plus bilayer;
> residue 23 and name CA plus bilayer;
> residue 24 and name CA plus bilayer;
> residue 25 and name CA plus bilayer;
> residue 26 and name CA plus bilayer;
> residue 27 and name CA plus bilayer;
> residue 28 and name CA plus bilayer;
> residue 29 and name CA plus bilayer;
> residue 30 and name CA plus bilayer;
> (etc...)
>
> and I get the same type of crash.
>
>
> Finally, I also tried using just POPC not POPC/POPS in the selection to
> cut down on the number of atoms, but it did not help.
>
> Thanks for any advice.
> Chris.
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