Hi Justin, Thanks, I just posted redmine issue #3204. Will try pull code.
On Thu, Nov 14, 2019 at 6:02 AM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/12/19 6:30 PM, Dave M wrote: > > Hi Justin, > > > > I am having troubles now with domain decompositions when I use openMPI > > mpirun but it works fine when I run on single mpi. My system is quite > large > > (80x80x80) and I defined additional bonds in top file as: > > > > > > [ intermolecular_interactions ] > > > > [ bonds ] > > > > ; ai aj type > > > > 3123 40767 6 4.0047 1000 > > > > 812 41625 6 3.7768 1000 > > > > 1560 42483 6 3.7569 1000 > > > > 2378 43341 6 4.0945 1000 > > > > > > > > I get error like this: > > > > > > Not all bonded interactions have been properly assigned to the domain > > decomposition cells > > > > A list of missing interactions: > > > > Harmonic Pot. of 8 missing 6 > > > > exclusions of -4 missing -4 > > > > > > I saw an old mail thread where Mark suggests to use > > [intermolecular_interactions]. Am already doing it but I still get errors > > (link: > > > https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg37888.html > > ) > > > > > > I use this: > > > > mpirun -np 4 gmx_mpi mdrun -deffnm 03-run -rdd 2 -ntomp 16 > > > > > > With np = 1 it works fine. > > > > > > Would it be possible to overcome this? On single MPI it will take many > > months to get the job done. > > Everything you've posted seems to suggest that the way > [intermolecular_interactions] are designed to function no longer work > properly. A bug report/feature request may be appropriate via Redmine. > > In the meantime, it looks like your only option is to use the pull code, > which does play nicely with domain decomposition. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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.