[gmx-users] gmx covar: Segmentation fault

[Oliwia Maria Szklarczyk]

Why is it reading one frame more than the last frame number?… Could that be a bug?

> On 20 Apr 2016, at 16:51, Oliwia Maria Szklarczyk <oliwias at ethz.ch> wrote:
> 
> 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
>