[gmx-users] Error in writing trajectory files using HPC (vGromacs 2018.2)
Budheswar Dehury
bude at kemi.dtu.dk
Tue Oct 16 16:12:14 CEST 2018
Dear All,
I am going through very bad phase while analyzing huge trajectories (23 GB, POPC membrane protein systems: Atoms: 201382) using HPC system installed at HPC facility of Denmark Technical University, Denmark. I have checked the trajectory, which seems fine with the gmx check command...
Though it reads the trajectories but while writing the compressed forms after reading all the frames, it shows the following error..
*** Error in `gmx': munmap_chunk(): invalid pointer: 0x00007f76c609386e ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7f574)[0x7f76c3fa6574]
/appl/gromacs/2018.2/XeonE5-2680v2/bin/../lib64/libgromacs.so.3(_Z8done_topP10t_topology+0x39)[0x7f76c5263f59]
/appl/gromacs/2018.2/XeonE5-2680v2/bin/../lib64/libgromacs.so.3(gmx_trjconv+0x1a3a)[0x7f76c54e6ffa]
/appl/gromacs/2018.2/XeonE5-2680v2/bin/../lib64/libgromacs.so.3(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x261)[0x7f76c5143ca1]
gmx[0x40e58c]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f76c3f493d5]
gmx[0x40e651]
======= Memory map: ========
00400000-0043f000 r-xp 00000000 00:bb 70350544 /appl/gromacs/2018.2/XeonE5-2680v2/bin/gmx
0063e000-0063f000 r--p 0003e000 00:bb 70350544 /appl/gromacs/2018.2/XeonE5-2680v2/bin/gmx
0063f000-00640000 rw-p 0003f000 00:bb 70350544 /appl/gromacs/2018.2/XeonE5-2680v2/bin/gmx
01506000-01d83000 rw-p 00000000 00:00 0 [heap]
7f76c1ca5000-7f76c1ce3000 r-xp 00000000 00:bb 64559031 /appl/gcc/7.3.0/lib64/libquadmath.so.0.0.0
7f76c1ce3000-7f76c1ee3000 ---p 0003e000 00:bb 64559031 /appl/gcc/7.3.0/lib64/libquadmath.so.0.0.0
7f76c1ee3000-7f76c1ee4000 rw-p 0003e000 00:bb 64559031 /appl/gcc/7.3.0/lib64/libquadmath.so.0.0.0
7f76c1ee4000-7f76c2003000 r-xp 00000000 08:05 518663 /usr/lib64/libgfortran.so.3.0.0
7f76c2003000-7f76c2203000 ---p 0011f000 08:05 518663 /usr/lib64/libgfortran.so.3.0.0
7f76c2203000-7f76c2204000 r--p 0011f000 08:05 518663 /usr/lib64/libgfortran.so.3.0.0
7f76c2204000-7f76c2206000 rw-p 00120000 08:05 518663 /usr/lib64/libgfortran.so.3.0.0
7f76c2206000-7f76c220f000 r-xp 00000000 08:05 516182 /usr/lib64/libltdl.so.7.3.0
7f76c220f000-7f76c240e000 ---p 00009000 08:05 516182 /usr/lib64/libltdl.so.7.3.0
7f76c240e000-7f76c240f000 r--p 00008000 08:05 516182 /usr/lib64/libltdl.so.7.3.0
7f76c240f000-7f76c2410000 rw-p 00009000 08:05 516182 /usr/lib64/libltdl.so.7.3.0
7f76c2410000-7f76c241a000 r-xp 00000000 08:05 515617 /usr/lib64/libnuma.so.1
7f76c241a000-7f76c261a000 ---p 0000a000 08:05 515617 /usr/lib64/libnuma.so.1
7f76c261a000-7f76c261b000 r--p 0000a000 08:05 515617 /usr/lib64/libnuma.so.1
7f76c261b000-7f76c261c000 rw-p 0000b000 08:05 515617 /usr/lib64/libnuma.so.1
7f76c261c000-7f76c31c5000 r-xp 00000000 00:bb 31025797 /appl/OpenBLAS/0.2.14/XeonE5-2680v2/gcc/lib/libopenblas-r0.2.14.so
7f76c31c5000-7f76c33c5000 ---p 00ba9000 00:bb 31025797 /appl/OpenBLAS/0.2.14/XeonE5-2680v2/gcc/lib/libopenblas-r0.2.14.so
7f76c33c5000-7f76c33d3000 rw-p 00ba9000 00:bb 31025797 /appl/OpenBLAS/0.2.14/XeonE5-2680v2/gcc/lib/libopenblas-r0.2.14.so
7f76c33d3000-7f76c34e2000 rw-p 00000000 00:00 0
7f76c34e2000-7f76c36d0000 r-xp 00000000 00:bb 70339951 /appl/fftw/3.3.8/XeonE5-2680v2/gcc-7.3.0/lib/libfftw3f.so.3.5.8
7f76c36d0000-7f76c38cf000 ---p 001ee000 00:bb 70339951 /appl/fftw/3.3.8/XeonE5-2680v2/gcc-7.3.0/lib/libfftw3f.so.3.5.8
7f76c38cf000-7f76c38e0000 r--p 001ed000 00:bb 70339951 /appl/fftw/3.3.8/XeonE5-2680v2/gcc-7.3.0/lib/libfftw3f.so.3.5.8
7f76c38e0000-7f76c38e1000 rw-p 001fe000 00:bb 70339951 /appl/fftw/3.3.8/XeonE5-2680v2/gcc-7.3.0/lib/libfftw3f.so.3.5.8
7f76c38e1000-7f76c38e8000 r-xp 00000000 08:05 515140 /usr/lib64/librt-2.17.so
7f76c38e8000-7f76c3ae7000 ---p 00007000 08:05 515140 /usr/lib64/librt-2.17.so
7f76c3ae7000-7f76c3ae8000 r--p 00006000 08:05 515140 /usr/lib64/librt-2.17.so
7f76c3ae8000-7f76c3ae9000 rw-p 00007000 08:05 515140 /usr/lib64/librt-2.17.so
7f76c3ae9000-7f76c3aeb000 r-xp 00000000 08:05 515116 /usr/lib64/libdl-2.17.so
7f76c3aeb000-7f76c3ceb000 ---p 00002000 08:05 515116 /usr/lib64/libdl-2.17.so
7f76c3ceb000-7f76c3cec000 r--p 00002000 08:05 515116 /usr/lib64/libdl-2.17.so
7f76c3cec000-7f76c3ced000 rw-p 00003000 08:05 515116 /usr/lib64/libdl-2.17.so
7f76c3ced000-7f76c3d26000 r-xp 00000000 08:05 516184 /usr/lib64/libhwloc.so.5.6.8
7f76c3d26000-7f76c3f25000 ---p 00039000 08:05 516184 /usr/lib64/libhwloc.so.5.6.8
7f76c3f25000-7f76c3f26000 r--p 00038000 08:05 516184 /usr/lib64/libhwloc.so.5.6.8
7f76c3f26000-7f76c3f27000 rw-p 00039000 08:05 516184 /usr/lib64/libhwloc.so.5.6.8
7f76c3f27000-7f76c40ea000 r-xp 00000000 08:05 515110 /usr/lib64/libc-2.17.so
7f76c40ea000-7f76c42e9000 ---p 001c3000 08:05 515110 /usr/lib64/libc-2.17.so
7f76c42e9000-7f76c42ed000 r--p 001c2000 08:05 515110 /usr/lib64/libc-2.17.so
7f76c42ed000-7f76c42ef000 rw-p 001c6000 08:05 515110 /usr/lib64/libc-2.17.so
7f76c42ef000-7f76c42f4000 rw-p 00000000 00:00 0
7f76c42f4000-7f76c430b000 r-xp 00000000 08:05 515136 /usr/lib64/libpthread-2.17.so
7f76c430b000-7f76c450a000 ---p 00017000 08:05 515136 /usr/lib64/libpthread-2.17.so
7f76c450a000-7f76c450b000 r--p 00016000 08:05 515136 /usr/lib64/libpthread-2.17.so
7f76c450b000-7f76c450c000 rw-p 00017000 08:05 515136 /usr/lib64/libpthread-2.17.so
7f76c450c000-7f76c4510000 rw-p 00000000 00:00 0
7f76c4510000-7f76c4526000 r-xp 00000000 00:bb 64558120 /appl/gcc/7.3.0/lib64/libgcc_s.so.1
7f76c4526000-7f76c4725000 ---p 00016000 00:bb 64558120 /appl/gcc/7.3.0/lib64/libgcc_s.so.1
7f76c4725000-7f76c4726000 rw-p 00015000 00:bb 64558120 /appl/gcc/7.3.0/lib64/libgcc_s.so.1
7f76c4726000-7f76c4753000 r-xp 00000000 00:bb 64559071 /appl/gcc/7.3.0/lib64/libgomp.so.1.0.0
7f76c4753000-7f76c4952000 ---p 0002d000 00:bb 64559071 /appl/gcc/7.3.0/lib64/libgomp.so.1.0.0
7f76c4952000-7f76c4953000 rw-p 0002c000 00:bb 64559071 /appl/gcc/7.3.0/lib64/libgomp.so.1.0.0
7f76c4953000-7f76c4a54000 r-xp 00000000 08:05 515118 /usr/lib64/libm-2.17.so
7f76c4a54000-7f76c4c53000 ---p 00101000 08:05 515118 /usr/lib64/libm-2.17.so
7f76c4c53000-7f76c4c54000 r--p 00100000 08:05 515118 /usr/lib64/libm-2.17.so
7f76c4c54000-7f76c4c55000 rw-p 00101000 08:05 515118 /usr/lib64/libm-2.17.so
7f76c4c55000-7f76c4ddd000 r-xp 00000000 00:bb 64558932 /appl/gcc/7.3.0/lib64/libstdc++.so.6.0.24
7f76c4ddd000-7f76c4fdc000 ---p 00188000 00:bb 64558932 /appl/gcc/7.3.0/lib64/libstdc++.so.6.0.24
7f76c4fdc000-7f76c4fe6000 r--p 00187000 00:bb 64558932 /appl/gcc/7.3.0/lib64/libstdc++.so.6.0.24
7f76c4fe6000-7f76c4fe8000 rw-p 00191000 00:bb 64558932 /appl/gcc/7.3.0/lib64/libstdc++.so.6.0.24
7f76c4fe8000-7f76c4fec000 rw-p 00000000 00:00 0
7f76c4fec000-7f76c6226000 r-xp 00000000 00:bb 70350216 /appl/gromacs/2018.2/XeonE5-2680v2/lib64/libgromacs.so.3.2.0
7f76c6226000-7f76c6425000 ---p 0123a000 00:bb 70350216 /appl/gromacs/2018.2/XeonE5-2680v2/lib64/libgromacs.so.3.2.0
7f76c6425000-7f76c6434000 r--p 01239000 00:bb 70350216 /appl/gromacs/2018.2/XeonE5-2680v2/lib64/libgromacs.so.3.2.0
7f76c6434000-7f76c6455000 rw-p 01248000 00:bb 70350216 /appl/gromacs/2018.2/XeonE5-2680v2/lib64/libgromacs.so.3.2.0
7f76c6455000-7f76c6458000 rw-p 00000000 00:00 0
7f76c6458000-7f76c647a000 r-xp 00000000 08:05 517714 /usr/lib64/ld-2.17.so
7f76c6647000-7f76c6651000 rw-p 00000000 00:00 0
7f76c6676000-7f76c6679000 rw-p 00000000 00:00 0
7f76c6679000-7f76c667a000 r--p 00021000 08:05 517714 /usr/lib64/ld-2.17.so
7f76c667a000-7f76c667b000 rw-p 00022000 08:05 517714 /usr/lib64/ld-2.17.so
7f76c667b000-7f76c667c000 rw-p 00000000 00:00 0
7ffe11b1d000-7ffe11b3f000 rw-p 00000000 00:00 0 [stack]
7ffe11be3000-7ffe11be5000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted
/work3/bude/PS2_G_Secretase/Seed1/Helix
Furthermore, most important thing is that the gmx helix command doesn't work in GROMACS2018.2 version, its showing the segmentation fault..I am unsure about the error...Please help me it fix these error...While I analyzed other helix properties like gmx helixorient, gmx bundle..they are working fine...
Further while defining the Helix in the index should we use atom or amino acid
In case of analysis -ahxstart and -ahxend option what should be the integer (either amino acid number of the first and last position or something else)
Anticipating for a positive reply from your end.
Thanking You
With Warm Regards
Budheswar Dehury
Post-Doctoral Fellow
DTU, Chemistry, Denmark
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