[gmx-users] gmx covar: Segmentation fault

[Justin Lemkul]

On 4/20/16 10:57 AM, Oliwia Maria Szklarczyk wrote:
> Why is it reading one frame more than the last frame number?… Could that be a bug?
>

No.  Trajectories include t=0, so there's always one more frame than you might 
expect.  The "last frame" is based on index (starting from zero), IIRC.

This is a bug in version 5.0.2 that was fixed forever ago.  Try 5.0.7 or any 
5.1.x version.

-Justin

>> 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
>>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================