[gmx-users] Error in gmx trjcat
Mark Abraham
mark.j.abraham at gmail.com
Tue Apr 17 14:40:49 CEST 2018
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
> >>
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