[gmx-users] Memory issues using -ac option of gmx hbond

[Mark Abraham]

Hi,

To diagnose such issues, explore using fewer frames and more restrictive
selections for the analysis.

Mark

On Mon, 7 Aug 2017 23:55 Smith, Micholas D. <smithmd at ornl.gov> wrote:

> I had a similar problem. Using gromacs 2016.3's hbond tool fixed this.
>
>
> ===================
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Jared
> Sagendorf <sagendor at usc.edu>
> Sent: Monday, August 07, 2017 5:46 PM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Memory issues using -ac option of gmx hbond
>
> I'm trying to analyzing hydrogen bonds between a DNA and protein complex.
> When using the -ac option of gmx hbond, I'm getting segmentation faults
> which look like an out-of-memory problem.
>
> However, I'm giving the process 64gb of memory, and an additional 64gb of
> virtual memory. How memory intenstive is this program??
>
> Note I am using version 5.1.13. A snippet of the output is below
>
> Calculating hydrogen bonds between DNA_interface (919 atoms) and
> Protein_interface (1026 atoms)
> Found 138 donors and 458 acceptors
> Making hbmap structure...done.
> ...
> Found 117 different hydrogen bonds in trajectory
> Found 156 different atom-pairs within hydrogen bonding distance
> Merging hbonds with Acceptor and Donor swapped
> - Reduced number of hbonds from 117 to 116
> - Reduced number of distances from 156 to 156
> Average number of hbonds per timeframe 16.544 out of 31602 possible
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu
> Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media
> J. Phys. Chem. B 110 (2006) pp. 4393-4398
> -------- -------- --- Thank You --- -------- --------
>
> Doing autocorrelation according to the theory of Luzar and Chandler.
> [hpc3338:34436] *** Process received signal ***
> [hpc3338:34436] Signal: Segmentation fault (11)
> [hpc3338:34436] Signal code: Address not mapped (1)
> [hpc3338:34436] Failing at address: 0xfde7c370
> [hpc3338:34436] [ 0] /lib64/libpthread.so.0(+0xf370)[0x7ff5c3810370]
> [hpc3338:34436] [ 1]
>
> /usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(+0x464449)[0x7ff5c4a7b449]
> [hpc3338:34436] [ 2]
>
> /usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(cross_corr+0x39)[0x7ff5c4a7b019]
> [hpc3338:34436] [ 3]
>
> /usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(+0x339bb2)[0x7ff5c4950bb2]
> [hpc3338:34436] [ 4]
>
> /usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(gmx_hbond+0x312e)[0x7ff5c4947aae]
> [hpc3338:34436] [ 5]
>
> /usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x267)[0x7ff5c47b4637]
> [hpc3338:34436] [ 6] gmx_mpi(main+0xba)[0x40bfea]
> [hpc3338:34436] [ 7]
> /lib64/libc.so.6(__libc_start_main+0xf5)[0x7ff5c2c01b35]
> [hpc3338:34436] [ 8] gmx_mpi[0x40be69]
> [hpc3338:34436] *** End of error message ***
>
>
> Am I doing something wrong here?
> --
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