[gmx-users] gmx angle memory consumption

Dallas Warren dallas.warren at monash.edu
Sun Nov 26 22:25:00 CET 2017


GROMACS only writes to a file when the amount of data reaches a
certain threshold, prior to that it is just stored in memory.  I don't
know what that chunk size is.

It may be the manner in which the analysis script stores the
trajectory data in memory?  Hopefully a developer will be able to
provide some insight.  Recommend you do some exploration on what
triggers this, to provide them with further information.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.

On 21 November 2017 at 23:30, Matthias Ernst
<matthias.ernst at physik.uni-freiburg.de> wrote:
> Hi,
> I want to calculate dihedral angles for long trajectories at high
> sampling rates using gmx angle as follows:
> gmx angle -f traj.xtc -n dih_indices.ndx -ov dih.xvg -type dihedral -all
> After some time, it completely fills my RAM without having written
> anything to the output file.  As the system starts swapping, everything
> becomes incredibly slow.
> I thought gmx tools usually process trajectories frame-wise and output
> immediately (or in some chunks), but this seems not to be the case here.
> Could it be gmx angle is storing the values in RAM and only writes them
> out at the end of the analysis?
> Thanks a lot,
> Matthias
> --
> http://phdcomics.com/comics/archive.php?comicid=1936
> --
> 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.

More information about the gromacs.org_gmx-users mailing list