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Bug #2619

Updated by Mark Abraham over 1 year ago

Hi,

this is gmx 2018.2 on:
uname -a
Linux rcpetemp1 4.4.0-131-generic #157-Ubuntu SMP Thu Jul 12 15:51:36 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
compiled with: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=on && make && make install

given a pdb file (as included further below as text) i see:

<pre>
prompt> gmx trjconv -f a3.pdb -o a3.trr

:-) GROMACS - gmx trjconv, 2018.2 (-:

GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra
Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru
Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl
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) 2001-2017, 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 trjconv, version 2018.2
Executable: /home/micb/local/gmx-2018.2-bin/bin/gmx
Data prefix: /home/micb/local/gmx-2018.2-bin
Working dir: /home/micb/current/A2-JnJ-ASD/ff/apis/05-fogal1
Command line:
gmx trjconv -f a3.pdb -o a3.trr

Will write trr: Trajectory in portable xdr format
Reading frame 0 time 0.000 Reading frames from pdb file
Precision of a3.pdb is 0.0001 (nm)
'', 21 atoms 0 time 0.000
Last frame 0 time 0.000

*** Error in `gmx': munmap_chunk(): invalid pointer: 0x00007f09afee9f30 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f09b59ef7e5]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x1a8)[0x7f09b59fc698]
/home/micb/local/gmx-2018.2-bin/bin/../lib/libgromacs.so.3(_Z8done_topP10t_topology+0x36)[0x7f09b68932d6]
/home/micb/local/gmx-2018.2-bin/bin/../lib/libgromacs.so.3(gmx_trjconv+0x173d)[0x7f09b6b3d92d]
/home/micb/local/gmx-2018.2-bin/bin/../lib/libgromacs.so.3(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x334)[0x7f09b677c764]
gmx[0x40e19c]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f09b5998830]
gmx[0x40e279]
======= Memory map: ========
00400000-0043f000 r-xp 00000000 09:00 159132051 /home/micb/local/gmx-2018.2-bin/bin/gmx
0063e000-0063f000 r--p 0003e000 09:00 159132051 /home/micb/local/gmx-2018.2-bin/bin/gmx
0063f000-00640000 rw-p 0003f000 09:00 159132051 /home/micb/local/gmx-2018.2-bin/bin/gmx
00640000-00641000 rw-p 00000000 00:00 0
00ae5000-00b89000 rw-p 00000000 00:00 0 [heap]
7f09adb18000-7f09adb56000 r-xp 00000000 09:00 118883017 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f09adb56000-7f09add55000 ---p 0003e000 09:00 118883017 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f09add55000-7f09add56000 r--p 0003d000 09:00 118883017 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f09add56000-7f09add57000 rw-p 0003e000 09:00 118883017 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f09add57000-7f09add94000 r-xp 00000000 09:00 119015649 /usr/lib/atlas-base/atlas/libblas.so.3.0
7f09add94000-7f09adf94000 ---p 0003d000 09:00 119015649 /usr/lib/atlas-base/atlas/libblas.so.3.0
7f09adf94000-7f09adf95000 rw-p 0003d000 09:00 119015649 /usr/lib/atlas-base/atlas/libblas.so.3.0
7f09adf95000-7f09ae0be000 r-xp 00000000 09:00 118884583 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f09ae0be000-7f09ae2bd000 ---p 00129000 09:00 118884583 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f09ae2bd000-7f09ae2be000 r--p 00128000 09:00 118884583 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f09ae2be000-7f09ae2c0000 rw-p 00129000 09:00 118884583 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f09ae2c0000-7f09ae657000 r-xp 00000000 09:00 119015650 /usr/lib/atlas-base/libatlas.so.3.0
7f09ae657000-7f09ae857000 ---p 00397000 09:00 119015650 /usr/lib/atlas-base/libatlas.so.3.0
7f09ae857000-7f09ae85e000 rw-p 00397000 09:00 119015650 /usr/lib/atlas-base/libatlas.so.3.0
7f09ae85e000-7f09ae87f000 r-xp 00000000 09:00 119015654 /usr/lib/atlas-base/libcblas.so.3.0
7f09ae87f000-7f09aea7f000 ---p 00021000 09:00 119015654 /usr/lib/atlas-base/libcblas.so.3.0
7f09aea7f000-7f09aea80000 rw-p 00021000 09:00 119015654 /usr/lib/atlas-base/libcblas.so.3.0
7f09aea80000-7f09aea89000 r-xp 00000000 09:00 118888640 /usr/lib/x86_64-linux-gnu/libltdl.so.7.3.1
7f09aea89000-7f09aec88000 ---p 00009000 09:00 118888640 /usr/lib/x86_64-linux-gnu/libltdl.so.7.3.1
7f09aec88000-7f09aec89000 r--p 00008000 09:00 118888640 /usr/lib/x86_64-linux-gnu/libltdl.so.7.3.1
7f09aec89000-7f09aec8a000 rw-p 00009000 09:00 118888640 /usr/lib/x86_64-linux-gnu/libltdl.so.7.3.1
7f09aec8a000-7f09aec94000 r-xp 00000000 09:00 118884840 /usr/lib/x86_64-linux-gnu/libnuma.so.1.0.0
7f09aec94000-7f09aee93000 ---p 0000a000 09:00 118884840 /usr/lib/x86_64-linux-gnu/libnuma.so.1.0.0
7f09aee93000-7f09aee94000 r--p 00009000 09:00 118884840 /usr/lib/x86_64-linux-gnu/libnuma.so.1.0.0
7f09aee94000-7f09aee95000 rw-p 0000a000 09:00 118884840 /usr/lib/x86_64-linux-gnu/libnuma.so.1.0.0
7f09aee95000-7f09aeeb6000 r-xp 00000000 09:00 118883416 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f09aeeb6000-7f09af0b5000 ---p 00021000 09:00 118883416 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f09af0b5000-7f09af0b6000 r--p 00020000 09:00 118883416 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f09af0b6000-7f09af0b7000 rw-p 00021000 09:00 118883416 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f09af0b7000-7f09af696000 r-xp 00000000 09:00 119015633 /usr/lib/atlas-base/atlas/liblapack.so.3.0
7f09af696000-7f09af896000 ---p 005df000 09:00 119015633 /usr/lib/atlas-base/atlas/liblapack.so.3.0
7f09af896000-7f09af89b000 rw-p 005df000 09:00 119015633 /usr/lib/atlas-base/atlas/liblapack.so.3.0
7f09af89b000-7f09af8bb000 r-xp 00000000 09:00 119015632 /usr/lib/atlas-base/libf77blas.so.3.0
7f09af8bb000-7f09afaba000 ---p 00020000 09:00 119015632 /usr/lib/atlas-base/libf77blas.so.3.0
7f09afaba000-7f09afabb000 rw-p 0001f000 09:00 119015632 /usr/lib/atlas-base/libf77blas.so.3.0
7f09afabb000-7f09afaf4000 r-xp 00000000 09:00 118884449 /usr/lib/x86_64-linux-gnu/libhwloc.so.5.6.8
7f09afaf4000-7f09afcf3000 ---p 00039000 09:00 118884449 /usr/lib/x86_64-linux-gnu/libhwloc.so.5.6.8
7f09afcf3000-7f09afcf4000 r--p 00038000 09:00 118884449 /usr/lib/x86_64-linux-gnu/libhwloc.so.5.6.8
7f09afcf4000-7f09afcf5000 rw-p 00039000 09:00 118884449 /usr/lib/x86_64-linux-gnu/libhwloc.so.5.6.8
7f09afcf5000-7f09b50f5000 r-xp 00000000 09:00 116922177 /usr/local/cuda-9.2/lib64/libcufft.so.9.2.148
7f09b50f5000-7f09b52f4000 ---p 05400000 09:00 116922177 /usr/local/cuda-9.2/lib64/libcufft.so.9.2.148
7f09b52f4000-7f09b5302000 rw-p 053ff000 09:00 116922177 /usr/local/cuda-9.2/lib64/libcufft.so.9.2.148
7f09b5302000-7f09b534f000 rw-p 00000000 00:00 0
7f09b534f000-7f09b5356000 r-xp 00000000 09:00 273060910 /lib/x86_64-linux-gnu/librt-2.23.so
7f09b5356000-7f09b5555000 ---p 00007000 09:00 273060910 /lib/x86_64-linux-gnu/librt-2.23.so
7f09b5555000-7f09b5556000 r--p 00006000 09:00 273060910 /lib/x86_64-linux-gnu/librt-2.23.so
7f09b5556000-7f09b5557000 rw-p 00007000 09:00 273060910 /lib/x86_64-linux-gnu/librt-2.23.so
7f09b5557000-7f09b555a000 r-xp 00000000 09:00 273053355 /lib/x86_64-linux-gnu/libdl-2.23.so
7f09b555a000-7f09b5759000 ---p 00003000 09:00 273053355 /lib/x86_64-linux-gnu/libdl-2.23.so
7f09b5759000-7f09b575a000 r--p 00002000 09:00 273053355 /lib/x86_64-linux-gnu/libdl-2.23.so
7f09b575a000-7f09b575b000 rw-p 00003000 09:00 273053355 /lib/x86_64-linux-gnu/libdl-2.23.so
7f09b575b000-7f09b5773000 r-xp 00000000 09:00 273053349 /lib/x86_64-linux-gnu/libpthread-2.23.so
7f09b5773000-7f09b5972000 ---p 00018000 09:00 273053349 /lib/x86_64-linux-gnu/libpthread-2.23.so
7f09b5972000-7f09b5973000 r--p 00017000 09:00 273053349 /lib/x86_64-linux-gnu/libpthread-2.23.so
7f09b5973000-7f09b5974000 rw-p 00018000 09:00 273053349 /lib/x86_64-linux-gnu/libpthread-2.23.so
7f09b5974000-7f09b5978000 rw-p 00000000 00:00 0
7f09b5978000-7f09b5b38000 r-xp 00000000 09:00 273053351 /lib/x86_64-linux-gnu/libc-2.23.so
7f09b5b38000-7f09b5d38000 ---p 001c0000 09:00 273053351 /lib/x86_64-linux-gnu/libc-2.23.so
7f09b5d38000-7f09b5d3c000 r--p 001c0000 09:00 273053351 /lib/x86_64-linux-gnu/libc-2.23.so
7f09b5d3c000-7f09b5d3e000 rw-p 001c4000 09:00 273053351 /lib/x86_64-linux-gnu/libc-2.23.so
7f09b5d3e000-7f09b5d42000 rw-p 00000000 00:00 0
7f09b5d42000-7f09b5d58000 r-xp 00000000 09:00 273023138 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f09b5d58000-7f09b5f57000 ---p 00016000 09:00 273023138 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f09b5f57000-7f09b5f58000 rw-p 00015000 09:00 273023138 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f09b5f58000-7f09b6060000 r-xp 00000000 09:00 273053343 /lib/x86_64-linux-gnu/libm-2.23.so
7f09b6060000-7f09b625f000 ---p 00108000 09:00 273053343 /lib/x86_64-linux-gnu/libm-2.23.so
7f09b625f000-7f09b6260000 r--p 00107000 09:00 273053343 /lib/x86_64-linux-gnu/libm-2.23.so
7f09b6260000-7f09b6261000 rw-p 00108000 09:00 273053343 /lib/x86_64-linux-gnu/libm-2.23.so
7f09b6261000-7f09b63d3000 r-xp 00000000 09:00 118882804 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f09b63d3000-7f09b65d3000 ---p 00172000 09:00 118882804 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f09b65d3000-7f09b65dd000 r--p 00172000 09:00 118882804 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f09b65dd000-7f09b65df000 rw-p 0017c000 09:00 118882804 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f09b65df000-7f09b65e3000 rw-p 00000000 00:00 0
7f09b65e3000-7f09b9061000 r-xp 00000000 09:00 159131921 /home/micb/local/gmx-2018.2-bin/lib/libgromacs.so.3.2.0
7f09b9061000-7f09b9260000 ---p 02a7e000 09:00 159131921 /home/micb/local/gmx-2018.2-bin/lib/libgromacs.so.3.2.0
7f09b9260000-7f09b927d000 r--p 02a7d000 09:00 159131921 /home/micb/local/gmx-2018.2-bin/lib/libgromacs.so.3.2.0
7f09b927d000-7f09b92a2000 rw-p 02a9a000 09:00 159131921 /home/micb/local/gmx-2018.2-bin/lib/libgromacs.so.3.2.0
7f09b92a2000-7f09b92a6000 rw-p 00000000 00:00 0
7f09b92a6000-7f09b92cc000 r-xp 00000000 09:00 273053347 /lib/x86_64-linux-gnu/ld-2.23.so
7f09b9481000-7f09b948d000 rw-p 00000000 00:00 0
7f09b94c9000-7f09b94cb000 rw-p 00000000 00:00 0
7f09b94cb000-7f09b94cc000 r--p 00025000 09:00 273053347 /lib/x86_64-linux-gnu/ld-2.23.so
7f09b94cc000-7f09b94cd000 rw-p 00026000 09:00 273053347 /lib/x86_64-linux-gnu/ld-2.23.so
7f09b94cd000-7f09b94ce000 rw-p 00000000 00:00 0
7ffc27f8e000-7ffc27fb0000 rw-p 00000000 00:00 0 [stack]
7ffc27fe3000-7ffc27fe6000 r--p 00000000 00:00 0 [vvar]
7ffc27fe6000-7ffc27fe8000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)

</pre>



example pdb:

<pre>
ATOM 1 O ASP 1 2.789 1.249 0.110 0.00 0.00
ATOM 2 C ASP 1 2.347 0.118 0.242 0.00 0.00
ATOM 3 C ASP 1 0.887 -0.207 0.351 0.00 0.00
ATOM 4 O ASP 1 3.087 -1.073 0.270 0.00 0.00
ATOM 5 C ASP 1 4.497 -1.073 0.131 0.00 0.00
ATOM 6 C ASP 1 5.282 -0.057 0.686 0.00 0.00
ATOM 7 C ASP 1 6.668 -0.079 0.525 0.00 0.00
ATOM 8 C ASP 1 7.278 -1.123 -0.167 0.00 0.00
ATOM 9 C ASP 1 6.501 -2.158 -0.690 0.00 0.00
ATOM 10 C ASP 1 5.106 -2.150 -0.534 0.00 0.00
ATOM 11 C ASP 1 4.364 -3.301 -1.114 0.00 0.00
ATOM 12 O ASP 1 4.766 -3.924 -2.081 0.00 0.00
ATOM 13 O ASP 1 3.253 -3.650 -0.431 0.00 0.00
ATOM 14 H ASP 1 0.339 0.696 0.638 0.00 0.00
ATOM 15 H ASP 1 0.721 -0.959 1.127 0.00 0.00
ATOM 16 H ASP 1 0.517 -0.562 -0.613 0.00 0.00
ATOM 17 H ASP 1 4.839 0.768 1.237 0.00 0.00
ATOM 18 H ASP 1 7.273 0.727 0.934 0.00 0.00
ATOM 19 H ASP 1 8.357 -1.134 -0.298 0.00 0.00
ATOM 20 H ASP 1 6.989 -2.975 -1.220 0.00 0.00
ATOM 21 H ASP 1 3.083 -3.100 0.356 0.00 0.00

</pre>


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