[gmx-users] Error in gmx trjcat

Mark Abraham mark.j.abraham at gmail.com
Tue Apr 17 13:23:27 CEST 2018 

Hi,

What does gmx check report on the two input .xtc files?

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
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