<div dir="ltr">Hi,<div><br></div><div>Edgar reported this at <a href="https://redmine.gromacs.org/issues/2104">https://redmine.gromacs.org/issues/2104</a>, and I have confirmed, but I need input from whoever designed the slicing functionality, please.</div><div><br></div><div>Mark</div></div><br><div class="gmail_quote"><div dir="ltr">On Wed, Jan 25, 2017 at 11:16 AM Berk Hess <<a href="mailto:hess@kth.se">hess@kth.se</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000" class="gmail_msg">
<div class="m_2678032118505192040moz-cite-prefix gmail_msg">Hi,<br class="gmail_msg">
<br class="gmail_msg">
Could you file an issue on <a href="http://redmine.gromacs.org" class="gmail_msg" target="_blank">redmine.gromacs.org</a> and attach the tpr,
trr and ndx files and paste the command line?<br class="gmail_msg">
If a single trr frame is enough to reproduce the issue, please
attach a trr file wiht a single frame.<br class="gmail_msg">
<br class="gmail_msg">
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).<br class="gmail_msg">
<br class="gmail_msg">
Thanks for reporting this.<br class="gmail_msg">
<br class="gmail_msg">
Cheers,<br class="gmail_msg">
<br class="gmail_msg">
Berk</div></div><div bgcolor="#FFFFFF" text="#000000" class="gmail_msg"><div class="m_2678032118505192040moz-cite-prefix gmail_msg"><br class="gmail_msg">
<br class="gmail_msg">
On 2017-01-24 21:42, Edgar Galicia wrote:<br class="gmail_msg">
</div></div><div bgcolor="#FFFFFF" text="#000000" class="gmail_msg">
<blockquote type="cite" class="gmail_msg">
<div dir="ltr" class="gmail_msg">
<div class="gmail_msg">
<div class="gmail_msg">Dear community,<br class="gmail_msg">
<br class="gmail_msg">
</div>
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.</div>
<div class="gmail_msg"><br class="gmail_msg">
edgar@edgar:TE_380$ gmx order -f nvt3mixmd.trr -s nvt3mix.tpr
-n order.ndx -d z -sl 200 -szonly<br class="gmail_msg">
:-) GROMACS - gmx order, VERSION 5.1.4 (-:<br class="gmail_msg">
<br class="gmail_msg">
GROMACS is written by:<br class="gmail_msg">
Emile Apol Rossen Apostolov Herman J.C.
Berendsen Par Bjelkmar <br class="gmail_msg">
Aldert van Buuren Rudi van Drunen Anton Feenstra
Sebastian Fritsch <br class="gmail_msg">
Gerrit Groenhof Christoph Junghans Anca Hamuraru
Vincent Hindriksen<br class="gmail_msg">
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner <br class="gmail_msg">
Per Larsson Justin A. Lemkul Magnus Lundborg
Pieter Meulenhoff <br class="gmail_msg">
Erik Marklund Teemu Murtola Szilard Pall
Sander Pronk <br class="gmail_msg">
Roland Schulz Alexey Shvetsov Michael Shirts
Alfons Sijbers <br class="gmail_msg">
Peter Tieleman Teemu Virolainen Christian Wennberg
Maarten Wolf <br class="gmail_msg">
and the project leaders:<br class="gmail_msg">
Mark Abraham, Berk Hess, Erik Lindahl, and David van
der Spoel<br class="gmail_msg">
<br class="gmail_msg">
Copyright (c) 1991-2000, University of Groningen, The
Netherlands.<br class="gmail_msg">
Copyright (c) 2001-2015, The GROMACS development team at<br class="gmail_msg">
Uppsala University, Stockholm University and<br class="gmail_msg">
the Royal Institute of Technology, Sweden.<br class="gmail_msg">
check out <a href="http://www.gromacs.org" class="gmail_msg" target="_blank">http://www.gromacs.org</a> for
more information.<br class="gmail_msg">
<br class="gmail_msg">
GROMACS is free software; you can redistribute it and/or
modify it<br class="gmail_msg">
under the terms of the GNU Lesser General Public License<br class="gmail_msg">
as published by the Free Software Foundation; either version
2.1<br class="gmail_msg">
of the License, or (at your option) any later version.<br class="gmail_msg">
<br class="gmail_msg">
GROMACS: gmx order, VERSION 5.1.4<br class="gmail_msg">
Executable: /usr/local/gromacs/bin/gmx<br class="gmail_msg">
Data prefix: /usr/local/gromacs<br class="gmail_msg">
Command line:<br class="gmail_msg">
gmx order -f nvt3mixmd.trr -s nvt3mix.tpr -n order.ndx -d z
-sl 200 -szonly<br class="gmail_msg">
<br class="gmail_msg">
Taking z axis as normal to the membrane<br class="gmail_msg">
Dividing box in 200 slices.<br class="gmail_msg">
<br class="gmail_msg">
Only calculating Sz<br class="gmail_msg">
Reading file nvt3mix.tpr, VERSION 5.1.4 (single precision)<br class="gmail_msg">
Using following groups: <br class="gmail_msg">
Groupname: C1 First atomname: C1 First atomnr 0<br class="gmail_msg">
Groupname: C2 First atomname: C2 First atomnr 1<br class="gmail_msg">
Groupname: C3 First atomname: C3 First atomnr 2<br class="gmail_msg">
Groupname: C4 First atomname: C4 First atomnr 3<br class="gmail_msg">
Groupname: C5 First atomname: C5 First atomnr 4<br class="gmail_msg">
Groupname: C6 First atomname: C6 First atomnr 5<br class="gmail_msg">
Groupname: C7 First atomname: C7 First atomnr 6<br class="gmail_msg">
<br class="gmail_msg">
trn version: GMX_trn_file (single precision)<br class="gmail_msg">
Reading frame 0 time 0.000 Number of elements in
first group: 900<br class="gmail_msg">
Box divided in 200 slices. Initial width of slice: 0.100000<br class="gmail_msg">
Last frame 10000 time 20000.000 <br class="gmail_msg">
<br class="gmail_msg">
Read trajectory. Printing parameters to file<br class="gmail_msg">
Atom 1 Tensor: x=-0.000581845 , y=-0.000266539, z=0.000848428<br class="gmail_msg">
Atom 2 Tensor: x=-0.00055126 , y=-0.000262139, z=0.000813441<br class="gmail_msg">
Atom 3 Tensor: x=-0.000471739 , y=-0.000138164, z=0.000609943<br class="gmail_msg">
Atom 4 Tensor: x=-0.000227096 , y=-0.000174483, z=0.000401621<br class="gmail_msg">
Atom 5 Tensor: x=-0.000493846 , y=-1.93626e-05, z=0.00051325<br class="gmail_msg">
*** Error in `gmx': free(): invalid next size (normal):
0x0000000000feeaa0 ***<br class="gmail_msg">
======= Backtrace: =========<br class="gmail_msg">
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f5164ce17e5]<br class="gmail_msg">
/lib/x86_64-linux-gnu/libc.so.6(+0x7fe0a)[0x7f5164ce9e0a]<br class="gmail_msg">
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f5164ced98c]<br class="gmail_msg">
/usr/local/gromacs/bin/../lib/libgromacs.so.1(calc_order+0x1f07)[0x7f5165e5d1c7]<br class="gmail_msg">
/usr/local/gromacs/bin/../lib/libgromacs.so.1(gmx_order+0x872)[0x7f5165e5f962]<br class="gmail_msg">
/usr/local/gromacs/bin/../lib/libgromacs.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x334)[0x7f5165a8a4c4]<br class="gmail_msg">
gmx(main+0x8c)[0x40c98c]<br class="gmail_msg">
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f5164c8a830]<br class="gmail_msg">
gmx(_start+0x29)[0x40cb19]<br class="gmail_msg">
======= Memory map: ========<br class="gmail_msg">
00400000-0043d000 r-xp 00000000 08:12
4599583 /usr/local/gromacs/bin/gmx<br class="gmail_msg">
0063c000-0063d000 r--p 0003c000 08:12
4599583 /usr/local/gromacs/bin/gmx<br class="gmail_msg">
0063d000-0063e000 rw-p 0003d000 08:12
4599583 /usr/local/gromacs/bin/gmx<br class="gmail_msg">
0063e000-0063f000 rw-p 00000000 00:00 0 <br class="gmail_msg">
00f59000-01034000 rw-p 00000000 00:00
0 [heap]<br class="gmail_msg">
7f5160000000-7f5160021000 rw-p 00000000 00:00 0 <br class="gmail_msg">
7f5160021000-7f5164000000 ---p 00000000 00:00 0 <br class="gmail_msg">
7f516441f000-7f5164440000 r-xp 00000000 08:12
4063562
/usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0<br class="gmail_msg">
7f5164440000-7f516463f000 ---p 00021000 08:12
4063562
/usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0<br class="gmail_msg">
7f516463f000-7f5164640000 r--p 00020000 08:12
4063562
/usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0<br class="gmail_msg">
7f5164640000-7f5164641000 rw-p 00021000 08:12
4063562
/usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0<br class="gmail_msg">
7f5164641000-7f5164659000 r-xp 00000000 08:12
8528645 /lib/x86_64-linux-gnu/<a href="http://libpthread-2.23.so" class="gmail_msg" target="_blank">libpthread-2.23.so</a><br class="gmail_msg">
7f5164659000-7f5164858000 ---p 00018000 08:12
8528645 /lib/x86_64-linux-gnu/<a href="http://libpthread-2.23.so" class="gmail_msg" target="_blank">libpthread-2.23.so</a><br class="gmail_msg">
7f5164858000-7f5164859000 r--p 00017000 08:12
8528645 /lib/x86_64-linux-gnu/<a href="http://libpthread-2.23.so" class="gmail_msg" target="_blank">libpthread-2.23.so</a><br class="gmail_msg">
7f5164859000-7f516485a000 rw-p 00018000 08:12
8528645 /lib/x86_64-linux-gnu/<a href="http://libpthread-2.23.so" class="gmail_msg" target="_blank">libpthread-2.23.so</a><br class="gmail_msg">
7f516485a000-7f516485e000 rw-p 00000000 00:00 0 <br class="gmail_msg">
7f516485e000-7f5164865000 r-xp 00000000 08:12
8528634 /lib/x86_64-linux-gnu/<a href="http://librt-2.23.so" class="gmail_msg" target="_blank">librt-2.23.so</a><br class="gmail_msg">
7f5164865000-7f5164a64000 ---p 00007000 08:12
8528634 /lib/x86_64-linux-gnu/<a href="http://librt-2.23.so" class="gmail_msg" target="_blank">librt-2.23.so</a><br class="gmail_msg">
7f5164a64000-7f5164a65000 r--p 00006000 08:12
8528634 /lib/x86_64-linux-gnu/<a href="http://librt-2.23.so" class="gmail_msg" target="_blank">librt-2.23.so</a><br class="gmail_msg">
7f5164a65000-7f5164a66000 rw-p 00007000 08:12
8528634 /lib/x86_64-linux-gnu/<a href="http://librt-2.23.so" class="gmail_msg" target="_blank">librt-2.23.so</a><br class="gmail_msg">
7f5164a66000-7f5164a69000 r-xp 00000000 08:12
8528638 /lib/x86_64-linux-gnu/<a href="http://libdl-2.23.so" class="gmail_msg" target="_blank">libdl-2.23.so</a><br class="gmail_msg">
7f5164a69000-7f5164c68000 ---p 00003000 08:12
8528638 /lib/x86_64-linux-gnu/<a href="http://libdl-2.23.so" class="gmail_msg" target="_blank">libdl-2.23.so</a><br class="gmail_msg">
7f5164c68000-7f5164c69000 r--p 00002000 08:12
8528638 /lib/x86_64-linux-gnu/<a href="http://libdl-2.23.so" class="gmail_msg" target="_blank">libdl-2.23.so</a><br class="gmail_msg">
7f5164c69000-7f5164c6a000 rw-p 00003000 08:12
8528638 /lib/x86_64-linux-gnu/<a href="http://libdl-2.23.so" class="gmail_msg" target="_blank">libdl-2.23.so</a><br class="gmail_msg">
7f5164c6a000-7f5164e29000 r-xp 00000000 08:12
8528639 /lib/x86_64-linux-gnu/<a href="http://libc-2.23.so" class="gmail_msg" target="_blank">libc-2.23.so</a><br class="gmail_msg">
7f5164e29000-7f5165029000 ---p 001bf000 08:12
8528639 /lib/x86_64-linux-gnu/<a href="http://libc-2.23.so" class="gmail_msg" target="_blank">libc-2.23.so</a><br class="gmail_msg">
7f5165029000-7f516502d000 r--p 001bf000 08:12
8528639 /lib/x86_64-linux-gnu/<a href="http://libc-2.23.so" class="gmail_msg" target="_blank">libc-2.23.so</a><br class="gmail_msg">
7f516502d000-7f516502f000 rw-p 001c3000 08:12
8528639 /lib/x86_64-linux-gnu/<a href="http://libc-2.23.so" class="gmail_msg" target="_blank">libc-2.23.so</a><br class="gmail_msg">
7f516502f000-7f5165033000 rw-p 00000000 00:00 0 <br class="gmail_msg">
7f5165033000-7f5165049000 r-xp 00000000 08:12
8524211 /lib/x86_64-linux-gnu/libgcc_s.so.1<br class="gmail_msg">
7f5165049000-7f5165248000 ---p 00016000 08:12
8524211 /lib/x86_64-linux-gnu/libgcc_s.so.1<br class="gmail_msg">
7f5165248000-7f5165249000 rw-p 00015000 08:12
8524211 /lib/x86_64-linux-gnu/libgcc_s.so.1<br class="gmail_msg">
7f5165249000-7f5165351000 r-xp 00000000 08:12
8528644 /lib/x86_64-linux-gnu/<a href="http://libm-2.23.so" class="gmail_msg" target="_blank">libm-2.23.so</a><br class="gmail_msg">
7f5165351000-7f5165550000 ---p 00108000 08:12
8528644 /lib/x86_64-linux-gnu/<a href="http://libm-2.23.so" class="gmail_msg" target="_blank">libm-2.23.so</a><br class="gmail_msg">
7f5165550000-7f5165551000 r--p 00107000 08:12
8528644 /lib/x86_64-linux-gnu/<a href="http://libm-2.23.so" class="gmail_msg" target="_blank">libm-2.23.so</a><br class="gmail_msg">
7f5165551000-7f5165552000 rw-p 00108000 08:12
8528644 /lib/x86_64-linux-gnu/<a href="http://libm-2.23.so" class="gmail_msg" target="_blank">libm-2.23.so</a><br class="gmail_msg">
7f5165552000-7f51656c4000 r-xp 00000000 08:12
4068136
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21<br class="gmail_msg">
7f51656c4000-7f51658c4000 ---p 00172000 08:12
4068136
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21<br class="gmail_msg">
7f51658c4000-7f51658ce000 r--p 00172000 08:12
4068136
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21<br class="gmail_msg">
7f51658ce000-7f51658d0000 rw-p 0017c000 08:12
4068136
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21<br class="gmail_msg">
7f51658d0000-7f51658d4000 rw-p 00000000 00:00 0 <br class="gmail_msg">
7f51658d4000-7f5166c1f000 r-xp 00000000 08:12
4596601
/usr/local/gromacs/lib/libgromacs.so.1.4.0<br class="gmail_msg">
7f5166c1f000-7f5166e1e000 ---p 0134b000 08:12
4596601
/usr/local/gromacs/lib/libgromacs.so.1.4.0<br class="gmail_msg">
7f5166e1e000-7f5166e3d000 r--p 0134a000 08:12
4596601
/usr/local/gromacs/lib/libgromacs.so.1.4.0<br class="gmail_msg">
7f5166e3d000-7f5166e5f000 rw-p <a href="tel:013-690%2000" value="+461369000" class="gmail_msg" target="_blank">01369000</a> 08:12
4596601
/usr/local/gromacs/lib/libgromacs.so.1.4.0<br class="gmail_msg">
7f5166e5f000-7f5166e69000 rw-p 00000000 00:00 0 <br class="gmail_msg">
7f5166e69000-7f5166e8f000 r-xp 00000000 08:12
8528591 /lib/x86_64-linux-gnu/<a href="http://ld-2.23.so" class="gmail_msg" target="_blank">ld-2.23.so</a><br class="gmail_msg">
7f516700f000-7f5167072000 rw-p 00000000 00:00 0 <br class="gmail_msg">
7f516708b000-7f516708e000 rw-p 00000000 00:00 0 <br class="gmail_msg">
7f516708e000-7f516708f000 r--p 00025000 08:12
8528591 /lib/x86_64-linux-gnu/<a href="http://ld-2.23.so" class="gmail_msg" target="_blank">ld-2.23.so</a><br class="gmail_msg">
7f516708f000-7f5167090000 rw-p 00026000 08:12
8528591 /lib/x86_64-linux-gnu/<a href="http://ld-2.23.so" class="gmail_msg" target="_blank">ld-2.23.so</a><br class="gmail_msg">
7f5167090000-7f5167091000 rw-p 00000000 00:00 0 <br class="gmail_msg">
7fff2a900000-7fff2a922000 rw-p 00000000 00:00
0 [stack]<br class="gmail_msg">
7fff2a9ec000-7fff2a9ee000 r--p 00000000 00:00
0 [vvar]<br class="gmail_msg">
7fff2a9ee000-7fff2a9f0000 r-xp 00000000 00:00
0 [vdso]<br class="gmail_msg">
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00
0 [vsyscall]<br class="gmail_msg">
Aborted (core dumped)<br class="gmail_msg">
<br class="gmail_msg">
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.<br class="gmail_msg">
<br class="gmail_msg">
<div class="gmail_msg">Greetings,<br class="gmail_msg">
</div>
Edgar<br class="gmail_msg">
</div>
</div>
<br class="gmail_msg">
<fieldset class="m_2678032118505192040mimeAttachmentHeader gmail_msg"></fieldset>
<br class="gmail_msg">
</blockquote>
<br class="gmail_msg">
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