Re: [gmx-users] Error in writing trajectory files using HPC (vGromacs 2018.2)

2018-10-17 Thread Paul bauer 

Hello,

could you open an issue on redmine.gromacs.org to describe the problem, 
with the commands you used and if possible some example files (not full 
length trajectories, but the minimal file that causes the crash).

The same goes for the gmx helix issue you ran into.

Cheers

Paul

On 16/10/2018 16:08, Budheswar Dehury wrote:

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: 0x7f76c609386e ***
=== 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: 
0040-0043f000 r-xp  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
0063f000-0064 rw-p 0003f000 00:bb 70350544   
/appl/gromacs/2018.2/XeonE5-2680v2/bin/gmx
01506000-01d83000 rw-p  00:00 0  [heap]
7f76c1ca5000-7f76c1ce3000 r-xp  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  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 0012 08:05 518663 
/usr/lib64/libgfortran.so.3.0.0
7f76c2206000-7f76c220f000 r-xp  08:05 516182 
/usr/lib64/libltdl.so.7.3.0
7f76c220f000-7f76c240e000 ---p 9000 08:05 516182 
/usr/lib64/libltdl.so.7.3.0
7f76c240e000-7f76c240f000 r--p 8000 08:05 516182 
/usr/lib64/libltdl.so.7.3.0
7f76c240f000-7f76c241 rw-p 9000 08:05 516182 
/usr/lib64/libltdl.so.7.3.0
7f76c241-7f76c241a000 r-xp  08:05 515617 
/usr/lib64/libnuma.so.1
7f76c241a000-7f76c261a000 ---p a000 08:05 515617 
/usr/lib64/libnuma.so.1
7f76c261a000-7f76c261b000 r--p a000 08:05 515617 
/usr/lib64/libnuma.so.1
7f76c261b000-7f76c261c000 rw-p b000 08:05 515617 
/usr/lib64/libnuma.so.1
7f76c261c000-7f76c31c5000 r-xp  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  00:00 0
7f76c34e2000-7f76c36d r-xp  00:bb 70339951   
/appl/fftw/3.3.8/XeonE5-2680v2/gcc-7.3.0/lib/libfftw3f.so.3.5.8
7f76c36d-7f76c38cf000 ---p 001ee000 00:bb 70339951   
/appl/fftw/3.3.8/XeonE5-2680v2/gcc-7.3.0/lib/libfftw3f.so.3.5.8
7f76c38cf000-7f76c38e r--p 001ed000 00:bb 70339951   
/appl/fftw/3.3.8/XeonE5-2680v2/gcc-7.3.0/lib/libfftw3f.so.3.5.8
7f76c38e-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  08:05 515140 
/usr/lib64/librt-2.17.so
7f76c38e8000-7f76c3ae7000 ---p 7000 08:05 515140 
/usr/lib64/librt-2.17.so
7f76c3ae7000-7f76c3ae8000 r--p 6000 08:05 515140 
/usr/lib64/librt-2.17.so
7f76c3ae8000-7f76c3ae9000 rw-p 7000 08:05 515140 
/usr/lib64/librt-2.17.so
7f76c3ae9000-7f76c3aeb000 r-xp  08:05 515116 
/usr/lib64/libdl-2.17.so
7f76c3aeb000-7f76c3ceb000 ---p 2000 08:05 515116 
/usr/lib64/libdl-2.17.so

[gmx-users] Error in writing trajectory files using HPC (vGromacs 2018.2)

2018-10-16 Thread Budheswar Dehury 
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: 0x7f76c609386e ***
=== 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: 
0040-0043f000 r-xp  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
0063f000-0064 rw-p 0003f000 00:bb 70350544   
/appl/gromacs/2018.2/XeonE5-2680v2/bin/gmx
01506000-01d83000 rw-p  00:00 0  [heap]
7f76c1ca5000-7f76c1ce3000 r-xp  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  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 0012 08:05 518663 
/usr/lib64/libgfortran.so.3.0.0
7f76c2206000-7f76c220f000 r-xp  08:05 516182 
/usr/lib64/libltdl.so.7.3.0
7f76c220f000-7f76c240e000 ---p 9000 08:05 516182 
/usr/lib64/libltdl.so.7.3.0
7f76c240e000-7f76c240f000 r--p 8000 08:05 516182 
/usr/lib64/libltdl.so.7.3.0
7f76c240f000-7f76c241 rw-p 9000 08:05 516182 
/usr/lib64/libltdl.so.7.3.0
7f76c241-7f76c241a000 r-xp  08:05 515617 
/usr/lib64/libnuma.so.1
7f76c241a000-7f76c261a000 ---p a000 08:05 515617 
/usr/lib64/libnuma.so.1
7f76c261a000-7f76c261b000 r--p a000 08:05 515617 
/usr/lib64/libnuma.so.1
7f76c261b000-7f76c261c000 rw-p b000 08:05 515617 
/usr/lib64/libnuma.so.1
7f76c261c000-7f76c31c5000 r-xp  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  00:00 0
7f76c34e2000-7f76c36d r-xp  00:bb 70339951   
/appl/fftw/3.3.8/XeonE5-2680v2/gcc-7.3.0/lib/libfftw3f.so.3.5.8
7f76c36d-7f76c38cf000 ---p 001ee000 00:bb 70339951   
/appl/fftw/3.3.8/XeonE5-2680v2/gcc-7.3.0/lib/libfftw3f.so.3.5.8
7f76c38cf000-7f76c38e r--p 001ed000 00:bb 70339951   
/appl/fftw/3.3.8/XeonE5-2680v2/gcc-7.3.0/lib/libfftw3f.so.3.5.8
7f76c38e-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  08:05 515140 
/usr/lib64/librt-2.17.so
7f76c38e8000-7f76c3ae7000 ---p 7000 08:05 515140 
/usr/lib64/librt-2.17.so
7f76c3ae7000-7f76c3ae8000 r--p 6000 08:05 515140 
/usr/lib64/librt-2.17.so
7f76c3ae8000-7f76c3ae9000 rw-p 7000 08:05 515140 
/usr/lib64/librt-2.17.so
7f76c3ae9000-7f76c3aeb000 r-xp  08:05 515116 
/usr/lib64/libdl-2.17.so
7f76c3aeb000-7f76c3ceb000 ---p 2000 08:05 515116 
/usr/lib64/libdl-2.17.so
7f76c3ceb000-7f76c3cec000 r--p 2000 08:05 515116 
/usr/lib64/libdl-2.17.so
7f76c3cec000-7f76c3ced000 rw-p 3000 08:05 515116 
/usr/lib64/libdl-2.17.so
7f76c3ced000-7f76c3d26000 r-xp  08:05 516184 
/usr/lib64/libhwloc.so.5.6.8
7f76c3d26000-7f76c3f25000 ---p