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

[Smith, Micholas D.]

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?
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.