[gmx-developers] gmx_order error
Mark Abraham
mark.j.abraham at gmail.com
Wed Feb 1 14:28:27 CET 2017
Hi,
Edgar reported this at https://redmine.gromacs.org/issues/2104, and I have
confirmed, but I need input from whoever designed the slicing
functionality, please.
Mark
On Wed, Jan 25, 2017 at 11:16 AM Berk Hess <hess at kth.se> wrote:
> Hi,
>
> Could you file an issue on redmine.gromacs.org and attach the tpr, trr
> and ndx files and paste the command line?
> If a single trr frame is enough to reproduce the issue, please attach a
> trr file wiht a single frame.
>
> It is more likely that we write an array out of bounds which then causes a
> segv at the free. We can fix this. If you want to try to fix it yourself, I
> would suggest to compile in debug mode and use valgrind (or some other
> memory debugger).
>
> Thanks for reporting this.
>
> Cheers,
>
> Berk
>
>
> On 2017-01-24 21:42, Edgar Galicia wrote:
>
> Dear community,
>
> I am having problems when running "gmx_order" utility. When I give the
> command -sl to divide the box into slices the utility works properly only
> for certain values and for others not.
>
> edgar at edgar:TE_380$ gmx order -f nvt3mixmd.trr -s nvt3mix.tpr -n
> order.ndx -d z -sl 200 -szonly
> :-) GROMACS - gmx order, VERSION 5.1.4 (-:
>
> 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 order, VERSION 5.1.4
> Executable: /usr/local/gromacs/bin/gmx
> Data prefix: /usr/local/gromacs
> Command line:
> gmx order -f nvt3mixmd.trr -s nvt3mix.tpr -n order.ndx -d z -sl 200
> -szonly
>
> Taking z axis as normal to the membrane
> Dividing box in 200 slices.
>
> Only calculating Sz
> Reading file nvt3mix.tpr, VERSION 5.1.4 (single precision)
> Using following groups:
> Groupname: C1 First atomname: C1 First atomnr 0
> Groupname: C2 First atomname: C2 First atomnr 1
> Groupname: C3 First atomname: C3 First atomnr 2
> Groupname: C4 First atomname: C4 First atomnr 3
> Groupname: C5 First atomname: C5 First atomnr 4
> Groupname: C6 First atomname: C6 First atomnr 5
> Groupname: C7 First atomname: C7 First atomnr 6
>
> trn version: GMX_trn_file (single precision)
> Reading frame 0 time 0.000 Number of elements in first group:
> 900
> Box divided in 200 slices. Initial width of slice: 0.100000
> Last frame 10000 time 20000.000
>
> Read trajectory. Printing parameters to file
> Atom 1 Tensor: x=-0.000581845 , y=-0.000266539, z=0.000848428
> Atom 2 Tensor: x=-0.00055126 , y=-0.000262139, z=0.000813441
> Atom 3 Tensor: x=-0.000471739 , y=-0.000138164, z=0.000609943
> Atom 4 Tensor: x=-0.000227096 , y=-0.000174483, z=0.000401621
> Atom 5 Tensor: x=-0.000493846 , y=-1.93626e-05, z=0.00051325
> *** Error in `gmx': free(): invalid next size (normal): 0x0000000000feeaa0
> ***
> ======= Backtrace: =========
> /lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f5164ce17e5]
> /lib/x86_64-linux-gnu/libc.so.6(+0x7fe0a)[0x7f5164ce9e0a]
> /lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f5164ced98c]
>
> /usr/local/gromacs/bin/../lib/libgromacs.so.1(calc_order+0x1f07)[0x7f5165e5d1c7]
>
> /usr/local/gromacs/bin/../lib/libgromacs.so.1(gmx_order+0x872)[0x7f5165e5f962]
>
> /usr/local/gromacs/bin/../lib/libgromacs.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x334)[0x7f5165a8a4c4]
> gmx(main+0x8c)[0x40c98c]
> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f5164c8a830]
> gmx(_start+0x29)[0x40cb19]
> ======= Memory map: ========
> 00400000-0043d000 r-xp 00000000 08:12 4599583
> /usr/local/gromacs/bin/gmx
> 0063c000-0063d000 r--p 0003c000 08:12 4599583
> /usr/local/gromacs/bin/gmx
> 0063d000-0063e000 rw-p 0003d000 08:12 4599583
> /usr/local/gromacs/bin/gmx
> 0063e000-0063f000 rw-p 00000000 00:00 0
> 00f59000-01034000 rw-p 00000000 00:00 0
> [heap]
> 7f5160000000-7f5160021000 rw-p 00000000 00:00 0
> 7f5160021000-7f5164000000 ---p 00000000 00:00 0
> 7f516441f000-7f5164440000 r-xp 00000000 08:12 4063562
> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
> 7f5164440000-7f516463f000 ---p 00021000 08:12 4063562
> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
> 7f516463f000-7f5164640000 r--p 00020000 08:12 4063562
> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
> 7f5164640000-7f5164641000 rw-p 00021000 08:12 4063562
> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
> 7f5164641000-7f5164659000 r-xp 00000000 08:12 8528645
> /lib/x86_64-linux-gnu/libpthread-2.23.so
> 7f5164659000-7f5164858000 ---p 00018000 08:12 8528645
> /lib/x86_64-linux-gnu/libpthread-2.23.so
> 7f5164858000-7f5164859000 r--p 00017000 08:12 8528645
> /lib/x86_64-linux-gnu/libpthread-2.23.so
> 7f5164859000-7f516485a000 rw-p 00018000 08:12 8528645
> /lib/x86_64-linux-gnu/libpthread-2.23.so
> 7f516485a000-7f516485e000 rw-p 00000000 00:00 0
> 7f516485e000-7f5164865000 r-xp 00000000 08:12 8528634
> /lib/x86_64-linux-gnu/librt-2.23.so
> 7f5164865000-7f5164a64000 ---p 00007000 08:12 8528634
> /lib/x86_64-linux-gnu/librt-2.23.so
> 7f5164a64000-7f5164a65000 r--p 00006000 08:12 8528634
> /lib/x86_64-linux-gnu/librt-2.23.so
> 7f5164a65000-7f5164a66000 rw-p 00007000 08:12 8528634
> /lib/x86_64-linux-gnu/librt-2.23.so
> 7f5164a66000-7f5164a69000 r-xp 00000000 08:12 8528638
> /lib/x86_64-linux-gnu/libdl-2.23.so
> 7f5164a69000-7f5164c68000 ---p 00003000 08:12 8528638
> /lib/x86_64-linux-gnu/libdl-2.23.so
> 7f5164c68000-7f5164c69000 r--p 00002000 08:12 8528638
> /lib/x86_64-linux-gnu/libdl-2.23.so
> 7f5164c69000-7f5164c6a000 rw-p 00003000 08:12 8528638
> /lib/x86_64-linux-gnu/libdl-2.23.so
> 7f5164c6a000-7f5164e29000 r-xp 00000000 08:12 8528639
> /lib/x86_64-linux-gnu/libc-2.23.so
> 7f5164e29000-7f5165029000 ---p 001bf000 08:12 8528639
> /lib/x86_64-linux-gnu/libc-2.23.so
> 7f5165029000-7f516502d000 r--p 001bf000 08:12 8528639
> /lib/x86_64-linux-gnu/libc-2.23.so
> 7f516502d000-7f516502f000 rw-p 001c3000 08:12 8528639
> /lib/x86_64-linux-gnu/libc-2.23.so
> 7f516502f000-7f5165033000 rw-p 00000000 00:00 0
> 7f5165033000-7f5165049000 r-xp 00000000 08:12 8524211
> /lib/x86_64-linux-gnu/libgcc_s.so.1
> 7f5165049000-7f5165248000 ---p 00016000 08:12 8524211
> /lib/x86_64-linux-gnu/libgcc_s.so.1
> 7f5165248000-7f5165249000 rw-p 00015000 08:12 8524211
> /lib/x86_64-linux-gnu/libgcc_s.so.1
> 7f5165249000-7f5165351000 r-xp 00000000 08:12 8528644
> /lib/x86_64-linux-gnu/libm-2.23.so
> 7f5165351000-7f5165550000 ---p 00108000 08:12 8528644
> /lib/x86_64-linux-gnu/libm-2.23.so
> 7f5165550000-7f5165551000 r--p 00107000 08:12 8528644
> /lib/x86_64-linux-gnu/libm-2.23.so
> 7f5165551000-7f5165552000 rw-p 00108000 08:12 8528644
> /lib/x86_64-linux-gnu/libm-2.23.so
> 7f5165552000-7f51656c4000 r-xp 00000000 08:12 4068136
> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
> 7f51656c4000-7f51658c4000 ---p 00172000 08:12 4068136
> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
> 7f51658c4000-7f51658ce000 r--p 00172000 08:12 4068136
> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
> 7f51658ce000-7f51658d0000 rw-p 0017c000 08:12 4068136
> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
> 7f51658d0000-7f51658d4000 rw-p 00000000 00:00 0
> 7f51658d4000-7f5166c1f000 r-xp 00000000 08:12 4596601
> /usr/local/gromacs/lib/libgromacs.so.1.4.0
> 7f5166c1f000-7f5166e1e000 ---p 0134b000 08:12 4596601
> /usr/local/gromacs/lib/libgromacs.so.1.4.0
> 7f5166e1e000-7f5166e3d000 r--p 0134a000 08:12 4596601
> /usr/local/gromacs/lib/libgromacs.so.1.4.0
> 7f5166e3d000-7f5166e5f000 rw-p 01369000 <013-690%2000> 08:12
> 4596601 /usr/local/gromacs/lib/libgromacs.so.1.4.0
> 7f5166e5f000-7f5166e69000 rw-p 00000000 00:00 0
> 7f5166e69000-7f5166e8f000 r-xp 00000000 08:12 8528591
> /lib/x86_64-linux-gnu/ld-2.23.so
> 7f516700f000-7f5167072000 rw-p 00000000 00:00 0
> 7f516708b000-7f516708e000 rw-p 00000000 00:00 0
> 7f516708e000-7f516708f000 r--p 00025000 08:12 8528591
> /lib/x86_64-linux-gnu/ld-2.23.so
> 7f516708f000-7f5167090000 rw-p 00026000 08:12 8528591
> /lib/x86_64-linux-gnu/ld-2.23.so
> 7f5167090000-7f5167091000 rw-p 00000000 00:00 0
> 7fff2a900000-7fff2a922000 rw-p 00000000 00:00 0
> [stack]
> 7fff2a9ec000-7fff2a9ee000 r--p 00000000 00:00 0
> [vvar]
> 7fff2a9ee000-7fff2a9f0000 r-xp 00000000 00:00 0
> [vdso]
> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
> [vsyscall]
> Aborted (core dumped)
>
> My guess is that memory is not been deallocated properly. If you would
> have any suggestion for me to correct this issue I would appreciate it very
> much.
>
> Greetings,
> Edgar
>
>
>
> --
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