[gmx-developers] gmx_order error

Edgar Galicia galicia.andres at gmail.com
Tue Jan 24 21:42:07 CET 2017 

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 (-:

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     Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par
Bjelkmar
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra   Sebastian Fritsch
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 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.
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check out http://www.gromacs.org for more information.

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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 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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