[gmx-users] Error in gmx trjcat
Syed Azeem
syedazeemullah186 at gmail.com
Tue Apr 17 16:32:15 CEST 2018
Hey Mark,
Still the same problem persists.
GROMACS: gmx check, VERSION 5.1.4
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Command line:
gmx check -f new2.xtc -m report.tex
Checking file new2.xtc
Reading frame 0 time 100000.000
# Atoms 10174
Precision 0.001 (nm)
Reading frame 8000 time 180000.000 *** Error in `gmx':
munmap_chunk(): invalid pointer: 0x00000000021a5680 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7fa4f0d337e5]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x1a8)[0x7fa4f0d40698]
/usr/local/gromacs/bin/../lib/libgromacs.so.1(xdr3dfcoord+0x1387)[0x7fa4f1d461d7]
/usr/local/gromacs/bin/../lib/libgromacs.so.1(read_next_xtc+0x1bd)[0x7fa4f1d6839d]
/usr/local/gromacs/bin/../lib/libgromacs.so.1(read_next_frame+0x267)[0x7fa4f1d64977]
/usr/local/gromacs/bin/../lib/libgromacs.so.1(chk_trj+0x58d)[0x7fa4f20bb19d]
/usr/local/gromacs/bin/../lib/libgromacs.so.1(gmx_check+0x2da)[0x7fa4f20be56a]
/usr/local/gromacs/bin/../lib/libgromacs.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x334)[0x7fa4f1add4c4]
gmx(main+0x8c)[0x40c98c]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fa4f0cdc830]
gmx(_start+0x29)[0x40cb19]
======= Memory map: ========
00400000-0043d000 r-xp 00000000 08:07 2646598
/usr/local/gromacs/bin/gmx
0063c000-0063d000 r--p 0003c000 08:07 2646598
/usr/local/gromacs/bin/gmx
0063d000-0063e000 rw-p 0003d000 08:07 2646598
/usr/local/gromacs/bin/gmx
0063e000-0063f000 rw-p 00000000 00:00 0
02167000-02207000 rw-p 00000000 00:00 0 [heap]
7fa4f0471000-7fa4f0492000 r-xp 00000000 08:07 2098798
/usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7fa4f0492000-7fa4f0691000 ---p 00021000 08:07 2098798
/usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7fa4f0691000-7fa4f0692000 r--p 00020000 08:07 2098798
/usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7fa4f0692000-7fa4f0693000 rw-p 00021000 08:07 2098798
/usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7fa4f0693000-7fa4f06ab000 r-xp 00000000 08:07 2623397
/lib/x86_64-linux-gnu/libpthread-2.23.so
7fa4f06ab000-7fa4f08aa000 ---p 00018000 08:07 2623397
/lib/x86_64-linux-gnu/libpthread-2.23.so
7fa4f08aa000-7fa4f08ab000 r--p 00017000 08:07 2623397
/lib/x86_64-linux-gnu/libpthread-2.23.so
7fa4f08ab000-7fa4f08ac000 rw-p 00018000 08:07 2623397
/lib/x86_64-linux-gnu/libpthread-2.23.so
7fa4f08ac000-7fa4f08b0000 rw-p 00000000 00:00 0
7fa4f08b0000-7fa4f08b7000 r-xp 00000000 08:07 2639498
/lib/x86_64-linux-gnu/librt-2.23.so
7fa4f08b7000-7fa4f0ab6000 ---p 00007000 08:07 2639498
/lib/x86_64-linux-gnu/librt-2.23.so
7fa4f0ab6000-7fa4f0ab7000 r--p 00006000 08:07 2639498
/lib/x86_64-linux-gnu/librt-2.23.so
7fa4f0ab7000-7fa4f0ab8000 rw-p 00007000 08:07 2639498
/lib/x86_64-linux-gnu/librt-2.23.so
7fa4f0ab8000-7fa4f0abb000 r-xp 00000000 08:07 2623462
/lib/x86_64-linux-gnu/libdl-2.23.so
7fa4f0abb000-7fa4f0cba000 ---p 00003000 08:07 2623462
/lib/x86_64-linux-gnu/libdl-2.23.so
7fa4f0cba000-7fa4f0cbb000 r--p 00002000 08:07 2623462
/lib/x86_64-linux-gnu/libdl-2.23.so
7fa4f0cbb000-7fa4f0cbc000 rw-p 00003000 08:07 2623462
/lib/x86_64-linux-gnu/libdl-2.23.so
7fa4f0cbc000-7fa4f0e7c000 r-xp 00000000 08:07 2623402
/lib/x86_64-linux-gnu/libc-2.23.so
7fa4f0e7c000-7fa4f107c000 ---p 001c0000 08:07 2623402
/lib/x86_64-linux-gnu/libc-2.23.so
7fa4f107c000-7fa4f1080000 r--p 001c0000 08:07 2623402
/lib/x86_64-linux-gnu/libc-2.23.so
7fa4f1080000-7fa4f1082000 rw-p 001c4000 08:07 2623402
/lib/x86_64-linux-gnu/libc-2.23.so
7fa4f1082000-7fa4f1086000 rw-p 00000000 00:00 0
7fa4f1086000-7fa4f109c000 r-xp 00000000 08:07 2626206
/lib/x86_64-linux-gnu/libgcc_s.so.1
7fa4f109c000-7fa4f129b000 ---p 00016000 08:07 2626206
/lib/x86_64-linux-gnu/libgcc_s.so.1
7fa4f129b000-7fa4f129c000 rw-p 00015000 08:07 2626206
/lib/x86_64-linux-gnu/libgcc_s.so.1
7fa4f129c000-7fa4f13a4000 r-xp 00000000 08:07 2621457
/lib/x86_64-linux-gnu/libm-2.23.so
7fa4f13a4000-7fa4f15a3000 ---p 00108000 08:07 2621457
/lib/x86_64-linux-gnu/libm-2.23.so
7fa4f15a3000-7fa4f15a4000 r--p 00107000 08:07 2621457
/lib/x86_64-linux-gnu/libm-2.23.so
7fa4f15a4000-7fa4f15a5000 rw-p 00108000 08:07 2621457
/lib/x86_64-linux-gnu/libm-2.23.so
7fa4f15a5000-7fa4f1717000 r-xp 00000000 08:07 2100941
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fa4f1717000-7fa4f1917000 ---p 00172000 08:07 2100941
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fa4f1917000-7fa4f1921000 r--p 00172000 08:07 2100941
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fa4f1921000-7fa4f1923000 rw-p 0017c000 08:07 2100941
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fa4f1923000-7fa4f1927000 rw-p 00000000 00:00 0
7fa4f1927000-7fa4f2c74000 r-xp 00000000 08:07 2646399
/usr/local/gromacs/lib/libgromacs.so.1.4.0
7fa4f2c74000-7fa4f2e73000 ---p 0134d000 08:07 2646399
/usr/local/gromacs/lib/libgromacs.so.1.4.0
7fa4f2e73000-7fa4f2e92000 r--p 0134c000 08:07 2646399
/usr/local/gromacs/lib/libgromacs.so.1.4.0
7fa4f2e92000-7fa4f2eb4000 rw-p 0136b000 08:07 2646399
/usr/local/gromacs/lib/libgromacs.so.1.4.0
7fa4f2eb4000-7fa4f2ebe000 rw-p 00000000 00:00 0
7fa4f2ebe000-7fa4f2ee4000 r-xp 00000000 08:07 2623394
/lib/x86_64-linux-gnu/ld-2.23.so
7fa4f30ba000-7fa4f30c3000 rw-p 00000000 00:00 0
7fa4f30e1000-7fa4f30e3000 rw-p 00000000 00:00 0
7fa4f30e3000-7fa4f30e4000 r--p 00025000 08:07 2623394
/lib/x86_64-linux-gnu/ld-2.23.so
7fa4f30e4000-7fa4f30e5000 rw-p 00026000 08:07 2623394
/lib/x86_64-linux-gnu/ld-2.23.so
7fa4f30e5000-7fa4f30e6000 rw-p 00000000 00:00 0
7fff72b83000-7fff72ba4000 rw-p 00000000 00:00 0 [stack]
7fff72bc5000-7fff72bc8000 r--p 00000000 00:00 0 [vvar]
7fff72bc8000-7fff72bca000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
[vsyscall]
Aborted (core dumped)
> Hi,
>
> I meant to run
>
> gmx check -f 100cat.xtc
>
> gmx check -f new2.xtc
>
> on the separate files, to find out e.g. whether they are trajectories that
> have matching numbers of particles, etc.
>
> Mark
>
> On Tue, Apr 17, 2018 at 1:13 PM Syed Azeem <syedazeemullah186 at gmail.com>
> wrote:
>
>> > Hi,
>> >
>> > What does gmx check report on the two input .xtc files?
>>
>> Hey Mark,
>>
>> Thanks for the reply. I did gmx check on both the .xtc files. Now,
>> even this command is yielding the same error.
>>
>> My command: gmx check -f 100cat.xtc -f2 new2.xtc -m report.tex
>>
>> error:
>>
>> x[10172] ( 2.76900e+00 2.10100e+00 4.70000e-01) - ( 1.20700e+00
>> 2.27200e+00 2.63000e-01)
>> x[10173] ( 3.96200e+00 2.91800e+00 2.63000e-01) - ( 5.89000e-01
>> 4.41200e+00 4.86000e-01)
>> box[ 0] ( 4.72250e+00 0.00000e+00 0.00000e+00) - ( 4.72142e+00
>> 0.00000e+00 0.00000e+00)
>> box[ 1] ( 0.00000e+00 4.72250e+00 0.00000e+00) - ( 0.00000e+00
>> 4.72142e+00 0.00000e+00)
>> box[ 2] ( 0.00000e+00 0.00000e+00 4.72250e+00) - ( 0.00000e+00
>> 0.00000e+00 4.72142e+00)
>> *** Error in `gmx': munmap_chunk(): invalid pointer: 0x0000000002139380
>> ***
>> ======= Backtrace: =========
>> /lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7fce776767e5]
>> /lib/x86_64-linux-gnu/libc.so.6(cfree+0x1a8)[0x7fce77683698]
>>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(xdr3dfcoord+0x1387)[0x7fce786891d7]
>>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(read_next_xtc+0x1bd)[0x7fce786ab39d]
>>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(read_next_frame+0x267)[0x7fce786a7977]
>>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(comp_trx+0x127)[0x7fce78a0c9e7]
>>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(gmx_check+0x42e)[0x7fce78a016be]
>>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x334)[0x7fce784204c4]
>> gmx(main+0x8c)[0x40c98c]
>> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fce7761f830]
>> gmx(_start+0x29)[0x40cb19]
>> ======= Memory map: ========
>> 00400000-0043d000 r-xp 00000000 08:07 2646598
>> /usr/local/gromacs/bin/gmx
>> 0063c000-0063d000 r--p 0003c000 08:07 2646598
>> /usr/local/gromacs/bin/gmx
>> 0063d000-0063e000 rw-p 0003d000 08:07 2646598
>> /usr/local/gromacs/bin/gmx
>> 0063e000-0063f000 rw-p 00000000 00:00 0
>> 020dc000-0219b000 rw-p 00000000 00:00 0
>> [heap]
>> 7fce76db4000-7fce76dd5000 r-xp 00000000 08:07 2098798
>> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
>> 7fce76dd5000-7fce76fd4000 ---p 00021000 08:07 2098798
>> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
>> 7fce76fd4000-7fce76fd5000 r--p 00020000 08:07 2098798
>> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
>> 7fce76fd5000-7fce76fd6000 rw-p 00021000 08:07 2098798
>> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
>> 7fce76fd6000-7fce76fee000 r-xp 00000000 08:07 2623397
>> /lib/x86_64-linux-gnu/libpthread-2.23.so
>> 7fce76fee000-7fce771ed000 ---p 00018000 08:07 2623397
>> /lib/x86_64-linux-gnu/libpthread-2.23.so
>> 7fce771ed000-7fce771ee000 r--p 00017000 08:07 2623397
>> /lib/x86_64-linux-gnu/libpthread-2.23.so
>> 7fce771ee000-7fce771ef000 rw-p 00018000 08:07 2623397
>> /lib/x86_64-linux-gnu/libpthread-2.23.so
>> 7fce771ef000-7fce771f3000 rw-p 00000000 00:00 0
>> 7fce771f3000-7fce771fa000 r-xp 00000000 08:07 2639498
>> /lib/x86_64-linux-gnu/librt-2.23.so
>> 7fce771fa000-7fce773f9000 ---p 00007000 08:07 2639498
>> /lib/x86_64-linux-gnu/librt-2.23.so
>> 7fce773f9000-7fce773fa000 r--p 00006000 08:07 2639498
>> /lib/x86_64-linux-gnu/librt-2.23.so
>> 7fce773fa000-7fce773fb000 rw-p 00007000 08:07 2639498
>> /lib/x86_64-linux-gnu/librt-2.23.so
>> 7fce773fb000-7fce773fe000 r-xp 00000000 08:07 2623462
>> /lib/x86_64-linux-gnu/libdl-2.23.so
>> 7fce773fe000-7fce775fd000 ---p 00003000 08:07 2623462
>> /lib/x86_64-linux-gnu/libdl-2.23.so
>> 7fce775fd000-7fce775fe000 r--p 00002000 08:07 2623462
>> /lib/x86_64-linux-gnu/libdl-2.23.so
>> 7fce775fe000-7fce775ff000 rw-p 00003000 08:07 2623462
>> /lib/x86_64-linux-gnu/libdl-2.23.so
>> 7fce775ff000-7fce777bf000 r-xp 00000000 08:07 2623402
>> /lib/x86_64-linux-gnu/libc-2.23.so
>> 7fce777bf000-7fce779bf000 ---p 001c0000 08:07 2623402
>> /lib/x86_64-linux-gnu/libc-2.23.so
>> 7fce779bf000-7fce779c3000 r--p 001c0000 08:07 2623402
>> /lib/x86_64-linux-gnu/libc-2.23.so
>> 7fce779c3000-7fce779c5000 rw-p 001c4000 08:07 2623402
>> /lib/x86_64-linux-gnu/libc-2.23.so
>> 7fce779c5000-7fce779c9000 rw-p 00000000 00:00 0
>> 7fce779c9000-7fce779df000 r-xp 00000000 08:07 2626206
>> /lib/x86_64-linux-gnu/libgcc_s.so.1
>> 7fce779df000-7fce77bde000 ---p 00016000 08:07 2626206
>> /lib/x86_64-linux-gnu/libgcc_s.so.1
>> 7fce77bde000-7fce77bdf000 rw-p 00015000 08:07 2626206
>> /lib/x86_64-linux-gnu/libgcc_s.so.1
>> 7fce77bdf000-7fce77ce7000 r-xp 00000000 08:07 2621457
>> /lib/x86_64-linux-gnu/libm-2.23.so
>> 7fce77ce7000-7fce77ee6000 ---p 00108000 08:07 2621457
>> /lib/x86_64-linux-gnu/libm-2.23.so
>> 7fce77ee6000-7fce77ee7000 r--p 00107000 08:07 2621457
>> /lib/x86_64-linux-gnu/libm-2.23.so
>> 7fce77ee7000-7fce77ee8000 rw-p 00108000 08:07 2621457
>> /lib/x86_64-linux-gnu/libm-2.23.so
>> 7fce77ee8000-7fce7805a000 r-xp 00000000 08:07 2100941
>> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
>> 7fce7805a000-7fce7825a000 ---p 00172000 08:07 2100941
>> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
>> 7fce7825a000-7fce78264000 r--p 00172000 08:07 2100941
>> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
>> 7fce78264000-7fce78266000 rw-p 0017c000 08:07 2100941
>> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
>> 7fce78266000-7fce7826a000 rw-p 00000000 00:00 0
>> 7fce7826a000-7fce795b7000 r-xp 00000000 08:07 2646399
>> /usr/local/gromacs/lib/libgromacs.so.1.4.0
>> 7fce795b7000-7fce797b6000 ---p 0134d000 08:07 2646399
>> /usr/local/gromacs/lib/libgromacs.so.1.4.0
>> 7fce797b6000-7fce797d5000 r--p 0134c000 08:07 2646399
>> /usr/local/gromacs/lib/libgromacs.so.1.4.0
>> 7fce797d5000-7fce797f7000 rw-p 0136b000 08:07 2646399
>> /usr/local/gromacs/lib/libgromacs.so.1.4.0
>> 7fce797f7000-7fce79801000 rw-p 00000000 00:00 0
>> 7fce79801000-7fce79827000 r-xp 00000000 08:07 2623394
>> /lib/x86_64-linux-gnu/ld-2.23.so
>> 7fce799fd000-7fce79a06000 rw-p 00000000 00:00 0
>> 7fce79a24000-7fce79a26000 rw-p 00000000 00:00 0
>> 7fce79a26000-7fce79a27000 r--p 00025000 08:07 2623394
>> /lib/x86_64-linux-gnu/ld-2.23.so
>> 7fce79a27000-7fce79a28000 rw-p 00026000 08:07 2623394
>> /lib/x86_64-linux-gnu/ld-2.23.so
>> 7fce79a28000-7fce79a29000 rw-p 00000000 00:00 0
>> 7ffc72305000-7ffc72326000 rw-p 00000000 00:00 0
>> [stack]
>> 7ffc7233b000-7ffc7233e000 r--p 00000000 00:00 0
>> [vvar]
>> 7ffc7233e000-7ffc72340000 r-xp 00000000 00:00 0
>> [vdso]
>> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
>> [vsyscall]
>> Aborted (core dumped)
>>
>> >
>> > Mark
>> >
>> > On Tue, Apr 17, 2018 at 12:06 PM Syed Azeem
>> > <syedazeemullah186 at gmail.com
>> >
>> > wrote:
>> >
>> >> Hey all,
>> >>
>> >> I'm experiencing an error while using trjcat command. Initially, I ran
>> >> a simulation for 50 ns and then extended till 100ns. After extension,
>> >> I concatenated the trajectories of both the runs using gmx trjcat.
>> >>
>> >> Then, again I extended the run from 100 ns to 500 ns. Finally, I tried
>> >> to concatenate the previously concatenated 100 ns trajectory file with
>> >> the final (500 ns) trajectory. This step yielded an error (pasted
>> >> below).
>> >>
>> >> GROMACS: gmx trjcat, VERSION 5.1.4
>> >> Executable: /usr/local/gromacs/bin/gmx
>> >> Data prefix: /usr/local/gromacs
>> >> Command line:
>> >> gmx trjcat -f 100cat.xtc new2.xtc -o cat500.xtc
>> >>
>> >> Reading frame 1 time 100010.000
>> >>
>> >> Summary of files and start times used:
>> >>
>> >> File Start time Time step
>> >> ---------------------------------------------------------
>> >> 100cat.xtc 0.000 ps 10.000 ps
>> >> new2.xtc 100000.000 ps 10.000 ps
>> >>
>> >> Reading frame 0 time 0.000
>> >>
>> >> Continue writing frames from 100cat.xtc t=0 ps, frame=0
>> >> Last frame 10000 time 100000.000 -> frame 9000 time
>> >> 90000.000
>> >> ps
>> >> Reading frame 0 time 100000.000
>> >> lasttime 99990
>> >>
>> >> Continue writing frames from new2.xtc t=100000 ps, frame=10000
>> >> *** Error in `gmx': munmap_chunk(): invalid pointer:
>> >> 0x0000000001455380 ***s
>> >> ======= Backtrace: =========
>> >> /lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f929a9a07e5]
>> >> /lib/x86_64-linux-gnu/libc.so.6(cfree+0x1a8)[0x7f929a9ad698]
>> >>
>> >>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(xdr3dfcoord+0x1387)[0x7f929b9b31d7]
>> >>
>> >>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(read_next_xtc+0x1bd)[0x7f929b9d539d]
>> >>
>> >>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(read_next_frame+0x267)[0x7f929b9d1977]
>> >>
>> >>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(gmx_trjcat+0x32c2)[0x7f929bb64842]
>> >>
>> >>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x334)[0x7f929b74a4c4]
>> >> gmx(main+0x8c)[0x40c98c]
>> >> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f929a949830]
>> >> gmx(_start+0x29)[0x40cb19]
>> >> ======= Memory map: ========
>> >> 00400000-0043d000 r-xp 00000000 08:07 2646598
>> >> /usr/local/gromacs/bin/gmx
>> >> 0063c000-0063d000 r--p 0003c000 08:07 2646598
>> >> /usr/local/gromacs/bin/gmx
>> >> 0063d000-0063e000 rw-p 0003d000 08:07 2646598
>> >> /usr/local/gromacs/bin/gmx
>> >> 0063e000-0063f000 rw-p 00000000 00:00 0
>> >> 013f8000-014b7000 rw-p 00000000 00:00 0
>> >> [heap]
>> >> 7f929a0de000-7f929a0ff000 r-xp 00000000 08:07 2098798
>> >> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
>> >> 7f929a0ff000-7f929a2fe000 ---p 00021000 08:07 2098798
>> >> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
>> >> 7f929a2fe000-7f929a2ff000 r--p 00020000 08:07 2098798
>> >> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
>> >> 7f929a2ff000-7f929a300000 rw-p 00021000 08:07 2098798
>> >> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
>> >> 7f929a300000-7f929a318000 r-xp 00000000 08:07 2623397
>> >> /lib/x86_64-linux-gnu/libpthread-2.23.so
>> >> 7f929a318000-7f929a517000 ---p 00018000 08:07 2623397
>> >> /lib/x86_64-linux-gnu/libpthread-2.23.so
>> >> 7f929a517000-7f929a518000 r--p 00017000 08:07 2623397
>> >> /lib/x86_64-linux-gnu/libpthread-2.23.so
>> >> 7f929a518000-7f929a519000 rw-p 00018000 08:07 2623397
>> >> /lib/x86_64-linux-gnu/libpthread-2.23.so
>> >> 7f929a519000-7f929a51d000 rw-p 00000000 00:00 0
>> >> 7f929a51d000-7f929a524000 r-xp 00000000 08:07 2639498
>> >> /lib/x86_64-linux-gnu/librt-2.23.so
>> >> 7f929a524000-7f929a723000 ---p 00007000 08:07 2639498
>> >> /lib/x86_64-linux-gnu/librt-2.23.so
>> >> 7f929a723000-7f929a724000 r--p 00006000 08:07 2639498
>> >> /lib/x86_64-linux-gnu/librt-2.23.so
>> >> 7f929a724000-7f929a725000 rw-p 00007000 08:07 2639498
>> >> /lib/x86_64-linux-gnu/librt-2.23.so
>> >> 7f929a725000-7f929a728000 r-xp 00000000 08:07 2623462
>> >> /lib/x86_64-linux-gnu/libdl-2.23.so
>> >> 7f929a728000-7f929a927000 ---p 00003000 08:07 2623462
>> >> /lib/x86_64-linux-gnu/libdl-2.23.so
>> >> 7f929a927000-7f929a928000 r--p 00002000 08:07 2623462
>> >> /lib/x86_64-linux-gnu/libdl-2.23.so
>> >> 7f929a928000-7f929a929000 rw-p 00003000 08:07 2623462
>> >> /lib/x86_64-linux-gnu/libdl-2.23.so
>> >> 7f929a929000-7f929aae9000 r-xp 00000000 08:07 2623402
>> >> /lib/x86_64-linux-gnu/libc-2.23.so
>> >> 7f929aae9000-7f929ace9000 ---p 001c0000 08:07 2623402
>> >> /lib/x86_64-linux-gnu/libc-2.23.so
>> >> 7f929ace9000-7f929aced000 r--p 001c0000 08:07 2623402
>> >> /lib/x86_64-linux-gnu/libc-2.23.so
>> >> 7f929aced000-7f929acef000 rw-p 001c4000 08:07 2623402
>> >> /lib/x86_64-linux-gnu/libc-2.23.so
>> >> 7f929acef000-7f929acf3000 rw-p 00000000 00:00 0
>> >> 7f929acf3000-7f929ad09000 r-xp 00000000 08:07 2626206
>> >> /lib/x86_64-linux-gnu/libgcc_s.so.1
>> >> 7f929ad09000-7f929af08000 ---p 00016000 08:07 2626206
>> >> /lib/x86_64-linux-gnu/libgcc_s.so.1
>> >> 7f929af08000-7f929af09000 rw-p 00015000 08:07 2626206
>> >> /lib/x86_64-linux-gnu/libgcc_s.so.1
>> >> 7f929af09000-7f929b011000 r-xp 00000000 08:07 2621457
>> >> /lib/x86_64-linux-gnu/libm-2.23.so
>> >> 7f929b011000-7f929b210000 ---p 00108000 08:07 2621457
>> >> /lib/x86_64-linux-gnu/libm-2.23.so
>> >> 7f929b210000-7f929b211000 r--p 00107000 08:07 2621457
>> >> /lib/x86_64-linux-gnu/libm-2.23.so
>> >> 7f929b211000-7f929b212000 rw-p 00108000 08:07 2621457
>> >> /lib/x86_64-linux-gnu/libm-2.23.so
>> >> 7f929b212000-7f929b384000 r-xp 00000000 08:07 2100941
>> >> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
>> >> 7f929b384000-7f929b584000 ---p 00172000 08:07 2100941
>> >> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
>> >> 7f929b584000-7f929b58e000 r--p 00172000 08:07 2100941
>> >> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
>> >> 7f929b58e000-7f929b590000 rw-p 0017c000 08:07 2100941
>> >> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
>> >> 7f929b590000-7f929b594000 rw-p 00000000 00:00 0
>> >> 7f929b594000-7f929c8e1000 r-xp 00000000 08:07 2646399
>> >> /usr/local/gromacs/lib/libgromacs.so.1.4.0
>> >> 7f929c8e1000-7f929cae0000 ---p 0134d000 08:07 2646399
>> >> /usr/local/gromacs/lib/libgromacs.so.1.4.0
>> >> 7f929cae0000-7f929caff000 r--p 0134c000 08:07 2646399
>> >> /usr/local/gromacs/lib/libgromacs.so.1.4.0
>> >> 7f929caff000-7f929cb21000 rw-p 0136b000 08:07 2646399
>> >> /usr/local/gromacs/lib/libgromacs.so.1.4.0
>> >> 7f929cb21000-7f929cb2b000 rw-p 00000000 00:00 0
>> >> 7f929cb2b000-7f929cb51000 r-xp 00000000 08:07 2623394
>> >> /lib/x86_64-linux-gnu/ld-2.23.so
>> >> 7f929cd27000-7f929cd30000 rw-p 00000000 00:00 0
>> >> 7f929cd4e000-7f929cd50000 rw-p 00000000 00:00 0
>> >> 7f929cd50000-7f929cd51000 r--p 00025000 08:07 2623394
>> >> /lib/x86_64-linux-gnu/ld-2.23.so
>> >> 7f929cd51000-7f929cd52000 rw-p 00026000 08:07 2623394
>> >> /lib/x86_64-linux-gnu/ld-2.23.so
>> >> 7f929cd52000-7f929cd53000 rw-p 00000000 00:00 0
>> >> 7ffc2b427000-7ffc2b448000 rw-p 00000000 00:00 0
>> >> [stack]
>> >> 7ffc2b4dc000-7ffc2b4df000 r--p 00000000 00:00 0
>> >> [vvar]
>> >> 7ffc2b4df000-7ffc2b4e1000 r-xp 00000000 00:00 0
>> >> [vdso]
>> >> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
>> >> [vsyscall]
>> >> Aborted (core dumped)
>> >>
>> >> How do I overcome the error and concatenate the files?
>> >>
>> >> Best,
>> >> Azeem
>> >> --
>> >> Gromacs Users mailing list
>> >>
>> >> * Please search the archive at
>> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> >> posting!
>> >>
>> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>
>> >> * For (un)subscribe requests visit
>> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> >> send a mail to gmx-users-request at gromacs.org.
>> >>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
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>>
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>>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 17 Apr 2018 12:40:35 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Error in gmx trjcat
> Message-ID:
> <CAMNuMAQ6DhCLkep4XomLzq4NBK8BkL0Q-vrPppNVhVkuNAEdSw at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> I meant to run
>
> gmx check -f 100cat.xtc
>
> gmx check -f new2.xtc
>
> on the separate files, to find out e.g. whether they are trajectories that
> have matching numbers of particles, etc.
>
> Mark
>
> On Tue, Apr 17, 2018 at 1:13 PM Syed Azeem <syedazeemullah186 at gmail.com>
> wrote:
>
>> > Hi,
>> >
>> > What does gmx check report on the two input .xtc files?
>>
>> Hey Mark,
>>
>> Thanks for the reply. I did gmx check on both the .xtc files. Now,
>> even this command is yielding the same error.
>>
>> My command: gmx check -f 100cat.xtc -f2 new2.xtc -m report.tex
>>
>> error:
>>
>> x[10172] ( 2.76900e+00 2.10100e+00 4.70000e-01) - ( 1.20700e+00
>> 2.27200e+00 2.63000e-01)
>> x[10173] ( 3.96200e+00 2.91800e+00 2.63000e-01) - ( 5.89000e-01
>> 4.41200e+00 4.86000e-01)
>> box[ 0] ( 4.72250e+00 0.00000e+00 0.00000e+00) - ( 4.72142e+00
>> 0.00000e+00 0.00000e+00)
>> box[ 1] ( 0.00000e+00 4.72250e+00 0.00000e+00) - ( 0.00000e+00
>> 4.72142e+00 0.00000e+00)
>> box[ 2] ( 0.00000e+00 0.00000e+00 4.72250e+00) - ( 0.00000e+00
>> 0.00000e+00 4.72142e+00)
>> *** Error in `gmx': munmap_chunk(): invalid pointer: 0x0000000002139380
>> ***
>> ======= Backtrace: =========
>> /lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7fce776767e5]
>> /lib/x86_64-linux-gnu/libc.so.6(cfree+0x1a8)[0x7fce77683698]
>>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(xdr3dfcoord+0x1387)[0x7fce786891d7]
>>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(read_next_xtc+0x1bd)[0x7fce786ab39d]
>>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(read_next_frame+0x267)[0x7fce786a7977]
>>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(comp_trx+0x127)[0x7fce78a0c9e7]
>>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(gmx_check+0x42e)[0x7fce78a016be]
>>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x334)[0x7fce784204c4]
>> gmx(main+0x8c)[0x40c98c]
>> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fce7761f830]
>> gmx(_start+0x29)[0x40cb19]
>> ======= Memory map: ========
>> 00400000-0043d000 r-xp 00000000 08:07 2646598
>> /usr/local/gromacs/bin/gmx
>> 0063c000-0063d000 r--p 0003c000 08:07 2646598
>> /usr/local/gromacs/bin/gmx
>> 0063d000-0063e000 rw-p 0003d000 08:07 2646598
>> /usr/local/gromacs/bin/gmx
>> 0063e000-0063f000 rw-p 00000000 00:00 0
>> 020dc000-0219b000 rw-p 00000000 00:00 0
>> [heap]
>> 7fce76db4000-7fce76dd5000 r-xp 00000000 08:07 2098798
>> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
>> 7fce76dd5000-7fce76fd4000 ---p 00021000 08:07 2098798
>> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
>> 7fce76fd4000-7fce76fd5000 r--p 00020000 08:07 2098798
>> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
>> 7fce76fd5000-7fce76fd6000 rw-p 00021000 08:07 2098798
>> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
>> 7fce76fd6000-7fce76fee000 r-xp 00000000 08:07 2623397
>> /lib/x86_64-linux-gnu/libpthread-2.23.so
>> 7fce76fee000-7fce771ed000 ---p 00018000 08:07 2623397
>> /lib/x86_64-linux-gnu/libpthread-2.23.so
>> 7fce771ed000-7fce771ee000 r--p 00017000 08:07 2623397
>> /lib/x86_64-linux-gnu/libpthread-2.23.so
>> 7fce771ee000-7fce771ef000 rw-p 00018000 08:07 2623397
>> /lib/x86_64-linux-gnu/libpthread-2.23.so
>> 7fce771ef000-7fce771f3000 rw-p 00000000 00:00 0
>> 7fce771f3000-7fce771fa000 r-xp 00000000 08:07 2639498
>> /lib/x86_64-linux-gnu/librt-2.23.so
>> 7fce771fa000-7fce773f9000 ---p 00007000 08:07 2639498
>> /lib/x86_64-linux-gnu/librt-2.23.so
>> 7fce773f9000-7fce773fa000 r--p 00006000 08:07 2639498
>> /lib/x86_64-linux-gnu/librt-2.23.so
>> 7fce773fa000-7fce773fb000 rw-p 00007000 08:07 2639498
>> /lib/x86_64-linux-gnu/librt-2.23.so
>> 7fce773fb000-7fce773fe000 r-xp 00000000 08:07 2623462
>> /lib/x86_64-linux-gnu/libdl-2.23.so
>> 7fce773fe000-7fce775fd000 ---p 00003000 08:07 2623462
>> /lib/x86_64-linux-gnu/libdl-2.23.so
>> 7fce775fd000-7fce775fe000 r--p 00002000 08:07 2623462
>> /lib/x86_64-linux-gnu/libdl-2.23.so
>> 7fce775fe000-7fce775ff000 rw-p 00003000 08:07 2623462
>> /lib/x86_64-linux-gnu/libdl-2.23.so
>> 7fce775ff000-7fce777bf000 r-xp 00000000 08:07 2623402
>> /lib/x86_64-linux-gnu/libc-2.23.so
>> 7fce777bf000-7fce779bf000 ---p 001c0000 08:07 2623402
>> /lib/x86_64-linux-gnu/libc-2.23.so
>> 7fce779bf000-7fce779c3000 r--p 001c0000 08:07 2623402
>> /lib/x86_64-linux-gnu/libc-2.23.so
>> 7fce779c3000-7fce779c5000 rw-p 001c4000 08:07 2623402
>> /lib/x86_64-linux-gnu/libc-2.23.so
>> 7fce779c5000-7fce779c9000 rw-p 00000000 00:00 0
>> 7fce779c9000-7fce779df000 r-xp 00000000 08:07 2626206
>> /lib/x86_64-linux-gnu/libgcc_s.so.1
>> 7fce779df000-7fce77bde000 ---p 00016000 08:07 2626206
>> /lib/x86_64-linux-gnu/libgcc_s.so.1
>> 7fce77bde000-7fce77bdf000 rw-p 00015000 08:07 2626206
>> /lib/x86_64-linux-gnu/libgcc_s.so.1
>> 7fce77bdf000-7fce77ce7000 r-xp 00000000 08:07 2621457
>> /lib/x86_64-linux-gnu/libm-2.23.so
>> 7fce77ce7000-7fce77ee6000 ---p 00108000 08:07 2621457
>> /lib/x86_64-linux-gnu/libm-2.23.so
>> 7fce77ee6000-7fce77ee7000 r--p 00107000 08:07 2621457
>> /lib/x86_64-linux-gnu/libm-2.23.so
>> 7fce77ee7000-7fce77ee8000 rw-p 00108000 08:07 2621457
>> /lib/x86_64-linux-gnu/libm-2.23.so
>> 7fce77ee8000-7fce7805a000 r-xp 00000000 08:07 2100941
>> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
>> 7fce7805a000-7fce7825a000 ---p 00172000 08:07 2100941
>> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
>> 7fce7825a000-7fce78264000 r--p 00172000 08:07 2100941
>> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
>> 7fce78264000-7fce78266000 rw-p 0017c000 08:07 2100941
>> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
>> 7fce78266000-7fce7826a000 rw-p 00000000 00:00 0
>> 7fce7826a000-7fce795b7000 r-xp 00000000 08:07 2646399
>> /usr/local/gromacs/lib/libgromacs.so.1.4.0
>> 7fce795b7000-7fce797b6000 ---p 0134d000 08:07 2646399
>> /usr/local/gromacs/lib/libgromacs.so.1.4.0
>> 7fce797b6000-7fce797d5000 r--p 0134c000 08:07 2646399
>> /usr/local/gromacs/lib/libgromacs.so.1.4.0
>> 7fce797d5000-7fce797f7000 rw-p 0136b000 08:07 2646399
>> /usr/local/gromacs/lib/libgromacs.so.1.4.0
>> 7fce797f7000-7fce79801000 rw-p 00000000 00:00 0
>> 7fce79801000-7fce79827000 r-xp 00000000 08:07 2623394
>> /lib/x86_64-linux-gnu/ld-2.23.so
>> 7fce799fd000-7fce79a06000 rw-p 00000000 00:00 0
>> 7fce79a24000-7fce79a26000 rw-p 00000000 00:00 0
>> 7fce79a26000-7fce79a27000 r--p 00025000 08:07 2623394
>> /lib/x86_64-linux-gnu/ld-2.23.so
>> 7fce79a27000-7fce79a28000 rw-p 00026000 08:07 2623394
>> /lib/x86_64-linux-gnu/ld-2.23.so
>> 7fce79a28000-7fce79a29000 rw-p 00000000 00:00 0
>> 7ffc72305000-7ffc72326000 rw-p 00000000 00:00 0
>> [stack]
>> 7ffc7233b000-7ffc7233e000 r--p 00000000 00:00 0
>> [vvar]
>> 7ffc7233e000-7ffc72340000 r-xp 00000000 00:00 0
>> [vdso]
>> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
>> [vsyscall]
>> Aborted (core dumped)
>>
>> >
>> > Mark
>> >
>> > On Tue, Apr 17, 2018 at 12:06 PM Syed Azeem
>> > <syedazeemullah186 at gmail.com
>> >
>> > wrote:
>> >
>> >> Hey all,
>> >>
>> >> I'm experiencing an error while using trjcat command. Initially, I ran
>> >> a simulation for 50 ns and then extended till 100ns. After extension,
>> >> I concatenated the trajectories of both the runs using gmx trjcat.
>> >>
>> >> Then, again I extended the run from 100 ns to 500 ns. Finally, I tried
>> >> to concatenate the previously concatenated 100 ns trajectory file with
>> >> the final (500 ns) trajectory. This step yielded an error (pasted
>> >> below).
>> >>
>> >> GROMACS: gmx trjcat, VERSION 5.1.4
>> >> Executable: /usr/local/gromacs/bin/gmx
>> >> Data prefix: /usr/local/gromacs
>> >> Command line:
>> >> gmx trjcat -f 100cat.xtc new2.xtc -o cat500.xtc
>> >>
>> >> Reading frame 1 time 100010.000
>> >>
>> >> Summary of files and start times used:
>> >>
>> >> File Start time Time step
>> >> ---------------------------------------------------------
>> >> 100cat.xtc 0.000 ps 10.000 ps
>> >> new2.xtc 100000.000 ps 10.000 ps
>> >>
>> >> Reading frame 0 time 0.000
>> >>
>> >> Continue writing frames from 100cat.xtc t=0 ps, frame=0
>> >> Last frame 10000 time 100000.000 -> frame 9000 time
>> >> 90000.000
>> >> ps
>> >> Reading frame 0 time 100000.000
>> >> lasttime 99990
>> >>
>> >> Continue writing frames from new2.xtc t=100000 ps, frame=10000
>> >> *** Error in `gmx': munmap_chunk(): invalid pointer:
>> >> 0x0000000001455380 ***s
>> >> ======= Backtrace: =========
>> >> /lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f929a9a07e5]
>> >> /lib/x86_64-linux-gnu/libc.so.6(cfree+0x1a8)[0x7f929a9ad698]
>> >>
>> >>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(xdr3dfcoord+0x1387)[0x7f929b9b31d7]
>> >>
>> >>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(read_next_xtc+0x1bd)[0x7f929b9d539d]
>> >>
>> >>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(read_next_frame+0x267)[0x7f929b9d1977]
>> >>
>> >>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(gmx_trjcat+0x32c2)[0x7f929bb64842]
>> >>
>> >>
>> /usr/local/gromacs/bin/../lib/libgromacs.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x334)[0x7f929b74a4c4]
>> >> gmx(main+0x8c)[0x40c98c]
>> >> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f929a949830]
>> >> gmx(_start+0x29)[0x40cb19]
>> >> ======= Memory map: ========
>> >> 00400000-0043d000 r-xp 00000000 08:07 2646598
>> >> /usr/local/gromacs/bin/gmx
>> >> 0063c000-0063d000 r--p 0003c000 08:07 2646598
>> >> /usr/local/gromacs/bin/gmx
>> >> 0063d000-0063e000 rw-p 0003d000 08:07 2646598
>> >> /usr/local/gromacs/bin/gmx
>> >> 0063e000-0063f000 rw-p 00000000 00:00 0
>> >> 013f8000-014b7000 rw-p 00000000 00:00 0
>> >> [heap]
>> >> 7f929a0de000-7f929a0ff000 r-xp 00000000 08:07 2098798
>> >> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
>> >> 7f929a0ff000-7f929a2fe000 ---p 00021000 08:07 2098798
>> >> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
>> >> 7f929a2fe000-7f929a2ff000 r--p 00020000 08:07 2098798
>> >> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
>> >> 7f929a2ff000-7f929a300000 rw-p 00021000 08:07 2098798
>> >> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
>> >> 7f929a300000-7f929a318000 r-xp 00000000 08:07 2623397
>> >> /lib/x86_64-linux-gnu/libpthread-2.23.so
>> >> 7f929a318000-7f929a517000 ---p 00018000 08:07 2623397
>> >> /lib/x86_64-linux-gnu/libpthread-2.23.so
>> >> 7f929a517000-7f929a518000 r--p 00017000 08:07 2623397
>> >> /lib/x86_64-linux-gnu/libpthread-2.23.so
>> >> 7f929a518000-7f929a519000 rw-p 00018000 08:07 2623397
>> >> /lib/x86_64-linux-gnu/libpthread-2.23.so
>> >> 7f929a519000-7f929a51d000 rw-p 00000000 00:00 0
>> >> 7f929a51d000-7f929a524000 r-xp 00000000 08:07 2639498
>> >> /lib/x86_64-linux-gnu/librt-2.23.so
>> >> 7f929a524000-7f929a723000 ---p 00007000 08:07 2639498
>> >> /lib/x86_64-linux-gnu/librt-2.23.so
>> >> 7f929a723000-7f929a724000 r--p 00006000 08:07 2639498
>> >> /lib/x86_64-linux-gnu/librt-2.23.so
>> >> 7f929a724000-7f929a725000 rw-p 00007000 08:07 2639498
>> >> /lib/x86_64-linux-gnu/librt-2.23.so
>> >> 7f929a725000-7f929a728000 r-xp 00000000 08:07 2623462
>> >> /lib/x86_64-linux-gnu/libdl-2.23.so
>> >> 7f929a728000-7f929a927000 ---p 00003000 08:07 2623462
>> >> /lib/x86_64-linux-gnu/libdl-2.23.so
>> >> 7f929a927000-7f929a928000 r--p 00002000 08:07 2623462
>> >> /lib/x86_64-linux-gnu/libdl-2.23.so
>> >> 7f929a928000-7f929a929000 rw-p 00003000 08:07 2623462
>> >> /lib/x86_64-linux-gnu/libdl-2.23.so
>> >> 7f929a929000-7f929aae9000 r-xp 00000000 08:07 2623402
>> >> /lib/x86_64-linux-gnu/libc-2.23.so
>> >> 7f929aae9000-7f929ace9000 ---p 001c0000 08:07 2623402
>> >> /lib/x86_64-linux-gnu/libc-2.23.so
>> >> 7f929ace9000-7f929aced000 r--p 001c0000 08:07 2623402
>> >> /lib/x86_64-linux-gnu/libc-2.23.so
>> >> 7f929aced000-7f929acef000 rw-p 001c4000 08:07 2623402
>> >> /lib/x86_64-linux-gnu/libc-2.23.so
>> >> 7f929acef000-7f929acf3000 rw-p 00000000 00:00 0
>> >> 7f929acf3000-7f929ad09000 r-xp 00000000 08:07 2626206
>> >> /lib/x86_64-linux-gnu/libgcc_s.so.1
>> >> 7f929ad09000-7f929af08000 ---p 00016000 08:07 2626206
>> >> /lib/x86_64-linux-gnu/libgcc_s.so.1
>> >> 7f929af08000-7f929af09000 rw-p 00015000 08:07 2626206
>> >> /lib/x86_64-linux-gnu/libgcc_s.so.1
>> >> 7f929af09000-7f929b011000 r-xp 00000000 08:07 2621457
>> >> /lib/x86_64-linux-gnu/libm-2.23.so
>> >> 7f929b011000-7f929b210000 ---p 00108000 08:07 2621457
>> >> /lib/x86_64-linux-gnu/libm-2.23.so
>> >> 7f929b210000-7f929b211000 r--p 00107000 08:07 2621457
>> >> /lib/x86_64-linux-gnu/libm-2.23.so
>> >> 7f929b211000-7f929b212000 rw-p 00108000 08:07 2621457
>> >> /lib/x86_64-linux-gnu/libm-2.23.so
>> >> 7f929b212000-7f929b384000 r-xp 00000000 08:07 2100941
>> >> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
>> >> 7f929b384000-7f929b584000 ---p 00172000 08:07 2100941
>> >> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
>> >> 7f929b584000-7f929b58e000 r--p 00172000 08:07 2100941
>> >> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
>> >> 7f929b58e000-7f929b590000 rw-p 0017c000 08:07 2100941
>> >> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
>> >> 7f929b590000-7f929b594000 rw-p 00000000 00:00 0
>> >> 7f929b594000-7f929c8e1000 r-xp 00000000 08:07 2646399
>> >> /usr/local/gromacs/lib/libgromacs.so.1.4.0
>> >> 7f929c8e1000-7f929cae0000 ---p 0134d000 08:07 2646399
>> >> /usr/local/gromacs/lib/libgromacs.so.1.4.0
>> >> 7f929cae0000-7f929caff000 r--p 0134c000 08:07 2646399
>> >> /usr/local/gromacs/lib/libgromacs.so.1.4.0
>> >> 7f929caff000-7f929cb21000 rw-p 0136b000 08:07 2646399
>> >> /usr/local/gromacs/lib/libgromacs.so.1.4.0
>> >> 7f929cb21000-7f929cb2b000 rw-p 00000000 00:00 0
>> >> 7f929cb2b000-7f929cb51000 r-xp 00000000 08:07 2623394
>> >> /lib/x86_64-linux-gnu/ld-2.23.so
>> >> 7f929cd27000-7f929cd30000 rw-p 00000000 00:00 0
>> >> 7f929cd4e000-7f929cd50000 rw-p 00000000 00:00 0
>> >> 7f929cd50000-7f929cd51000 r--p 00025000 08:07 2623394
>> >> /lib/x86_64-linux-gnu/ld-2.23.so
>> >> 7f929cd51000-7f929cd52000 rw-p 00026000 08:07 2623394
>> >> /lib/x86_64-linux-gnu/ld-2.23.so
>> >> 7f929cd52000-7f929cd53000 rw-p 00000000 00:00 0
>> >> 7ffc2b427000-7ffc2b448000 rw-p 00000000 00:00 0
>> >> [stack]
>> >> 7ffc2b4dc000-7ffc2b4df000 r--p 00000000 00:00 0
>> >> [vvar]
>> >> 7ffc2b4df000-7ffc2b4e1000 r-xp 00000000 00:00 0
>> >> [vdso]
>> >> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
>> >> [vsyscall]
>> >> Aborted (core dumped)
>> >>
>> >> How do I overcome the error and concatenate the files?
>> >>
>> >> Best,
>> >> Azeem
>> >> --
>> >> Gromacs Users mailing list
>> >>
>> >> * Please search the archive at
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>> >> send a mail to gmx-users-request at gromacs.org.
>> >>
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>>
>> * Please search the archive at
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