[gmx-users] grompp very slow generating .tpr when excluded bonded neighbours is large
mark.j.abraham at gmail.com
Tue Oct 3 17:37:44 CEST 2017
I'm sure we have opportunities to improve this code - please do file a
redmine issue with repro inputs so we can profile and see!
On Tue, Oct 3, 2017 at 3:05 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> On 10/2/17 11:14 PM, Dallas Warren wrote:
> > Thanks for the reply Justin.
> > I am just going to use the largest exclusion bond distance I can, then
> > ignore the RDF of those beyond that distance.
> > Seems curious to me (not actually understanding what grommp is
> > generating) that the list is so large. These are linear molecules, 38
> > atoms, 60 molecules in total.
> It generates a matrix of all possible exclusions, sorts them, then removes
> duplicates. So for nrexcl = 37 you need memory on the order of 37 * 37 *
> 60 * (2
> * sizeof(int)) - the factor of 2 for the atom numbers comes from the fact
> you're actually allocating an array of type "sortable" which is a pair of
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * 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