[gmx-users] gmx covar: Segmentation fault
Justin Lemkul
jalemkul at vt.edu
Wed Apr 20 17:00:34 CEST 2016
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
==================================================
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