[gmx-users] gmx covar: Segmentation fault
Oliwia Maria Szklarczyk
oliwias at ethz.ch
Wed Apr 20 16:59:06 CEST 2016
> Dear All,
>
> Anyone has experience with the covariance analysis program from gromacs? I can’t get rid of the segmentation fault. I run the following:
>
> gmx covar -f md.xtc -s md.tpr -v eigenvec.trr -n sys.ndx
>
> And this is the output:
>
> Choose a group for the least squares fit
> Group 0 ( Ligand) has 121 elements
> Group 1 ( Ligand-C-alpha) has 12 elements
> Group 2 ( EB1) has 1370 elements
> Group 3 ( System) has 88911 elements
> Group 4 ( Protein) has 1491 elements
> Group 5 ( Protein-H) has 1194 elements
> Group 6 ( C-alpha) has 149 elements
> Group 7 ( Backbone) has 446 elements
> Group 8 ( MainChain) has 596 elements
> Group 9 ( MainChain+Cb) has 734 elements
> Group 10 ( MainChain+H) has 739 elements
> Group 11 ( SideChain) has 752 elements
> Group 12 ( SideChain-H) has 598 elements
> Group 13 ( Prot-Masses) has 1491 elements
> Group 14 ( non-Protein) has 87420 elements
> Group 15 ( Water) has 87402 elements
> Group 16 ( SOL) has 87402 elements
> Group 17 ( non-Water) has 1509 elements
> Group 18 ( Ion) has 18 elements
> Group 19 ( NA) has 18 elements
> Group 20 ( Water_and_ions) has 87420 elements
> Select a group: 1
> Selected 1: 'Ligand-C-alpha'
>
> Choose a group for the covariance analysis
> Group 0 ( Ligand) has 121 elements
> Group 1 ( Ligand-C-alpha) has 12 elements
> Group 2 ( EB1) has 1370 elements
> Group 3 ( System) has 88911 elements
> Group 4 ( Protein) has 1491 elements
> Group 5 ( Protein-H) has 1194 elements
> Group 6 ( C-alpha) has 149 elements
> Group 7 ( Backbone) has 446 elements
> Group 8 ( MainChain) has 596 elements
> Group 9 ( MainChain+Cb) has 734 elements
> Group 10 ( MainChain+H) has 739 elements
> Group 11 ( SideChain) has 752 elements
> Group 12 ( SideChain-H) has 598 elements
> Group 13 ( Prot-Masses) has 1491 elements
> Group 14 ( non-Protein) has 87420 elements
> Group 15 ( Water) has 87402 elements
> Group 16 ( SOL) has 87402 elements
> Group 17 ( non-Water) has 1509 elements
> Group 18 ( Ion) has 18 elements
> Group 19 ( NA) has 18 elements
> Group 20 ( Water_and_ions) has 87420 elements
> Select a group: 0
> Selected 0: 'Ligand'
> Calculating the average structure ...
> Last frame 300 time 30000.000
>
> Back Off! I just backed up average.pdb to ./#average.pdb.8#
> Constructing covariance matrix (363x363) ...
> Last frame 300 time 30000.000
> Read 301 frames
>
> Trace of the covariance matrix: 7.96121 (nm^2)
>
> Diagonalizing ...
>
> Sum of the eigenvalues: 7.96121 (nm^2)
> [euler04:19031] *** Process received signal ***
> [euler04:19031] Signal: Segmentation fault (11)
> [euler04:19031] Signal code: Address not mapped (1)
> [euler04:19031] Failing at address: (nil)
> [euler04:19031] [ 0] /lib64/libpthread.so.0(+0xf7e0) [0x7f5112b257e0]
> [euler04:19031] [ 1] /lib64/libc.so.6(fwrite+0x34) [0x7f51120bc974]
> [euler04:19031] [ 2] /cluster/apps/gromacs/5.0.2/x86_64/gcc_4.8.2/openmpi_1.6.5/bin/../lib64/libgromacs_mpi.so.0(gmx_covar+0x3cc9) [0x7f5116c79a69]
> [euler04:19031] [ 3] /cluster/apps/gromacs/5.0.2/x86_64/gcc_4.8.2/openmpi_1.6.5/bin/../lib64/libgromacs_mpi.so.0(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x8a) [0x7f5116a09cfa]
> [euler04:19031] [ 4] gmx_mpi(main+0x85) [0x40cc25]
> [euler04:19031] [ 5] /lib64/libc.so.6(__libc_start_main+0xfd) [0x7f5112073d5d]
> [euler04:19031] [ 6] gmx_mpi() [0x40c419]
> [euler04:19031] *** End of error message ***
> Segmentation fault
>
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