Hi, 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!
Thanks, Mark On Tue, Oct 3, 2017 at 3:05 PM Justin Lemkul <jalem...@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 > that > you're actually allocating an array of type "sortable" which is a pair of > atom > numbers. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > -- > 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-requ...@gromacs.org. > -- 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-requ...@gromacs.org.
