<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">Hi,<br>
<br>
Could you file an issue on redmine.gromacs.org and attach the tpr,
trr and ndx files and paste the command line?<br>
If a single trr frame is enough to reproduce the issue, please
attach a trr file wiht a single frame.<br>
<br>
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>
<br>
Thanks for reporting this.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 2017-01-24 21:42, Edgar Galicia wrote:<br>
</div>
<blockquote
cite="mid:CACC2841vfX3Gn8xQymUxFJFm-u56Rd96_PvdZdv7YXKGrqFUNA@mail.gmail.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<div dir="ltr">
<div>
<div>Dear community,<br>
<br>
</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><br>
edgar@edgar:TE_380$ gmx order -f nvt3mixmd.trr -s nvt3mix.tpr
-n order.ndx -d z -sl 200 -szonly<br>
:-) GROMACS - gmx order, VERSION 5.1.4 (-:<br>
<br>
GROMACS is written by:<br>
Emile Apol Rossen Apostolov Herman J.C.
Berendsen Par Bjelkmar <br>
Aldert van Buuren Rudi van Drunen Anton Feenstra
Sebastian Fritsch <br>
Gerrit Groenhof Christoph Junghans Anca Hamuraru
Vincent Hindriksen<br>
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner <br>
Per Larsson Justin A. Lemkul Magnus Lundborg
Pieter Meulenhoff <br>
Erik Marklund Teemu Murtola Szilard Pall
Sander Pronk <br>
Roland Schulz Alexey Shvetsov Michael Shirts
Alfons Sijbers <br>
Peter Tieleman Teemu Virolainen Christian Wennberg
Maarten Wolf <br>
and the project leaders:<br>
Mark Abraham, Berk Hess, Erik Lindahl, and David van
der Spoel<br>
<br>
Copyright (c) 1991-2000, University of Groningen, The
Netherlands.<br>
Copyright (c) 2001-2015, The GROMACS development team at<br>
Uppsala University, Stockholm University and<br>
the Royal Institute of Technology, Sweden.<br>
check out <a moz-do-not-send="true"
href="http://www.gromacs.org">http://www.gromacs.org</a> for
more information.<br>
<br>
GROMACS is free software; you can redistribute it and/or
modify it<br>
under the terms of the GNU Lesser General Public License<br>
as published by the Free Software Foundation; either version
2.1<br>
of the License, or (at your option) any later version.<br>
<br>
GROMACS: gmx order, VERSION 5.1.4<br>
Executable: /usr/local/gromacs/bin/gmx<br>
Data prefix: /usr/local/gromacs<br>
Command line:<br>
gmx order -f nvt3mixmd.trr -s nvt3mix.tpr -n order.ndx -d z
-sl 200 -szonly<br>
<br>
Taking z axis as normal to the membrane<br>
Dividing box in 200 slices.<br>
<br>
Only calculating Sz<br>
Reading file nvt3mix.tpr, VERSION 5.1.4 (single precision)<br>
Using following groups: <br>
Groupname: C1 First atomname: C1 First atomnr 0<br>
Groupname: C2 First atomname: C2 First atomnr 1<br>
Groupname: C3 First atomname: C3 First atomnr 2<br>
Groupname: C4 First atomname: C4 First atomnr 3<br>
Groupname: C5 First atomname: C5 First atomnr 4<br>
Groupname: C6 First atomname: C6 First atomnr 5<br>
Groupname: C7 First atomname: C7 First atomnr 6<br>
<br>
trn version: GMX_trn_file (single precision)<br>
Reading frame 0 time 0.000 Number of elements in
first group: 900<br>
Box divided in 200 slices. Initial width of slice: 0.100000<br>
Last frame 10000 time 20000.000 <br>
<br>
Read trajectory. Printing parameters to file<br>
Atom 1 Tensor: x=-0.000581845 , y=-0.000266539, z=0.000848428<br>
Atom 2 Tensor: x=-0.00055126 , y=-0.000262139, z=0.000813441<br>
Atom 3 Tensor: x=-0.000471739 , y=-0.000138164, z=0.000609943<br>
Atom 4 Tensor: x=-0.000227096 , y=-0.000174483, z=0.000401621<br>
Atom 5 Tensor: x=-0.000493846 , y=-1.93626e-05, z=0.00051325<br>
*** Error in `gmx': free(): invalid next size (normal):
0x0000000000feeaa0 ***<br>
======= Backtrace: =========<br>
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f5164ce17e5]<br>
/lib/x86_64-linux-gnu/libc.so.6(+0x7fe0a)[0x7f5164ce9e0a]<br>
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f5164ced98c]<br>
/usr/local/gromacs/bin/../lib/libgromacs.so.1(calc_order+0x1f07)[0x7f5165e5d1c7]<br>
/usr/local/gromacs/bin/../lib/libgromacs.so.1(gmx_order+0x872)[0x7f5165e5f962]<br>
/usr/local/gromacs/bin/../lib/libgromacs.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x334)[0x7f5165a8a4c4]<br>
gmx(main+0x8c)[0x40c98c]<br>
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f5164c8a830]<br>
gmx(_start+0x29)[0x40cb19]<br>
======= Memory map: ========<br>
00400000-0043d000 r-xp 00000000 08:12
4599583 /usr/local/gromacs/bin/gmx<br>
0063c000-0063d000 r--p 0003c000 08:12
4599583 /usr/local/gromacs/bin/gmx<br>
0063d000-0063e000 rw-p 0003d000 08:12
4599583 /usr/local/gromacs/bin/gmx<br>
0063e000-0063f000 rw-p 00000000 00:00 0 <br>
00f59000-01034000 rw-p 00000000 00:00
0 [heap]<br>
7f5160000000-7f5160021000 rw-p 00000000 00:00 0 <br>
7f5160021000-7f5164000000 ---p 00000000 00:00 0 <br>
7f516441f000-7f5164440000 r-xp 00000000 08:12
4063562
/usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0<br>
7f5164440000-7f516463f000 ---p 00021000 08:12
4063562
/usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0<br>
7f516463f000-7f5164640000 r--p 00020000 08:12
4063562
/usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0<br>
7f5164640000-7f5164641000 rw-p 00021000 08:12
4063562
/usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0<br>
7f5164641000-7f5164659000 r-xp 00000000 08:12
8528645 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://libpthread-2.23.so">libpthread-2.23.so</a><br>
7f5164659000-7f5164858000 ---p 00018000 08:12
8528645 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://libpthread-2.23.so">libpthread-2.23.so</a><br>
7f5164858000-7f5164859000 r--p 00017000 08:12
8528645 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://libpthread-2.23.so">libpthread-2.23.so</a><br>
7f5164859000-7f516485a000 rw-p 00018000 08:12
8528645 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://libpthread-2.23.so">libpthread-2.23.so</a><br>
7f516485a000-7f516485e000 rw-p 00000000 00:00 0 <br>
7f516485e000-7f5164865000 r-xp 00000000 08:12
8528634 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://librt-2.23.so">librt-2.23.so</a><br>
7f5164865000-7f5164a64000 ---p 00007000 08:12
8528634 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://librt-2.23.so">librt-2.23.so</a><br>
7f5164a64000-7f5164a65000 r--p 00006000 08:12
8528634 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://librt-2.23.so">librt-2.23.so</a><br>
7f5164a65000-7f5164a66000 rw-p 00007000 08:12
8528634 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://librt-2.23.so">librt-2.23.so</a><br>
7f5164a66000-7f5164a69000 r-xp 00000000 08:12
8528638 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://libdl-2.23.so">libdl-2.23.so</a><br>
7f5164a69000-7f5164c68000 ---p 00003000 08:12
8528638 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://libdl-2.23.so">libdl-2.23.so</a><br>
7f5164c68000-7f5164c69000 r--p 00002000 08:12
8528638 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://libdl-2.23.so">libdl-2.23.so</a><br>
7f5164c69000-7f5164c6a000 rw-p 00003000 08:12
8528638 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://libdl-2.23.so">libdl-2.23.so</a><br>
7f5164c6a000-7f5164e29000 r-xp 00000000 08:12
8528639 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://libc-2.23.so">libc-2.23.so</a><br>
7f5164e29000-7f5165029000 ---p 001bf000 08:12
8528639 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://libc-2.23.so">libc-2.23.so</a><br>
7f5165029000-7f516502d000 r--p 001bf000 08:12
8528639 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://libc-2.23.so">libc-2.23.so</a><br>
7f516502d000-7f516502f000 rw-p 001c3000 08:12
8528639 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://libc-2.23.so">libc-2.23.so</a><br>
7f516502f000-7f5165033000 rw-p 00000000 00:00 0 <br>
7f5165033000-7f5165049000 r-xp 00000000 08:12
8524211 /lib/x86_64-linux-gnu/libgcc_s.so.1<br>
7f5165049000-7f5165248000 ---p 00016000 08:12
8524211 /lib/x86_64-linux-gnu/libgcc_s.so.1<br>
7f5165248000-7f5165249000 rw-p 00015000 08:12
8524211 /lib/x86_64-linux-gnu/libgcc_s.so.1<br>
7f5165249000-7f5165351000 r-xp 00000000 08:12
8528644 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://libm-2.23.so">libm-2.23.so</a><br>
7f5165351000-7f5165550000 ---p 00108000 08:12
8528644 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://libm-2.23.so">libm-2.23.so</a><br>
7f5165550000-7f5165551000 r--p 00107000 08:12
8528644 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://libm-2.23.so">libm-2.23.so</a><br>
7f5165551000-7f5165552000 rw-p 00108000 08:12
8528644 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://libm-2.23.so">libm-2.23.so</a><br>
7f5165552000-7f51656c4000 r-xp 00000000 08:12
4068136
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21<br>
7f51656c4000-7f51658c4000 ---p 00172000 08:12
4068136
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21<br>
7f51658c4000-7f51658ce000 r--p 00172000 08:12
4068136
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21<br>
7f51658ce000-7f51658d0000 rw-p 0017c000 08:12
4068136
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21<br>
7f51658d0000-7f51658d4000 rw-p 00000000 00:00 0 <br>
7f51658d4000-7f5166c1f000 r-xp 00000000 08:12
4596601
/usr/local/gromacs/lib/libgromacs.so.1.4.0<br>
7f5166c1f000-7f5166e1e000 ---p 0134b000 08:12
4596601
/usr/local/gromacs/lib/libgromacs.so.1.4.0<br>
7f5166e1e000-7f5166e3d000 r--p 0134a000 08:12
4596601
/usr/local/gromacs/lib/libgromacs.so.1.4.0<br>
7f5166e3d000-7f5166e5f000 rw-p 01369000 08:12
4596601
/usr/local/gromacs/lib/libgromacs.so.1.4.0<br>
7f5166e5f000-7f5166e69000 rw-p 00000000 00:00 0 <br>
7f5166e69000-7f5166e8f000 r-xp 00000000 08:12
8528591 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://ld-2.23.so">ld-2.23.so</a><br>
7f516700f000-7f5167072000 rw-p 00000000 00:00 0 <br>
7f516708b000-7f516708e000 rw-p 00000000 00:00 0 <br>
7f516708e000-7f516708f000 r--p 00025000 08:12
8528591 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://ld-2.23.so">ld-2.23.so</a><br>
7f516708f000-7f5167090000 rw-p 00026000 08:12
8528591 /lib/x86_64-linux-gnu/<a
moz-do-not-send="true" href="http://ld-2.23.so">ld-2.23.so</a><br>
7f5167090000-7f5167091000 rw-p 00000000 00:00 0 <br>
7fff2a900000-7fff2a922000 rw-p 00000000 00:00
0 [stack]<br>
7fff2a9ec000-7fff2a9ee000 r--p 00000000 00:00
0 [vvar]<br>
7fff2a9ee000-7fff2a9f0000 r-xp 00000000 00:00
0 [vdso]<br>
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00
0 [vsyscall]<br>
Aborted (core dumped)<br>
<br>
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>
<br>
<div>Greetings,<br>
</div>
Edgar<br>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>