Hi! Recently I've been simulating a system comprised of water and LiCl ions in different arrangements. Depending on the arrangements I get different responses in terms of performances. The box is tetragonal (but I heard from other people in my lab that they had a performance hit also in cubic boxes, not sure if it's the same as my case anyway).
This is running on 64 processors and I have 51840 atoms. The Li/Cl/H2O are in equal proportions (10368 each). Test1: Water and ions well mixed. Box dimension 30.23817 5.54007 4.84122 A set of DD entries from the log files: DD step 13509999 vol min/aver 0.714 load imb.: force 4.3% pme mesh/force 3.802 DD step 13519999 vol min/aver 0.794 load imb.: force 4.0% pme mesh/force 1.701 DD step 13529999 vol min/aver 0.833 load imb.: force 6.6% pme mesh/force 1.652 DD step 13539999 vol min/aver 0.701 load imb.: force 11.7% pme mesh/force 2.062 DD step 13549999 vol min/aver 0.686 load imb.: force 3.8% pme mesh/force 1.934 DD step 13559999 vol min/aver 0.768 load imb.: force 1.9% pme mesh/force 1.639 DD step 13569999 vol min/aver 0.919 load imb.: force 2.1% pme mesh/force 1.369 Test2: All ions on one side (a cubic crystal) all the water on the other (they are divided in the x direction). Box dimensions 23.03340 6.15600 6.15600 DD load balancing is limited by minimum cell size in dimension X DD step 7569999 vol min/aver 0.868! load imb.: force 39.9% pme mesh/force 1.036 DD load balancing is limited by minimum cell size in dimension X DD step 7579999 vol min/aver 0.869! load imb.: force 43.1% pme mesh/force 1.030 DD load balancing is limited by minimum cell size in dimension X DD step 7589999 vol min/aver 0.868! load imb.: force 41.8% pme mesh/force 1.035 DD load balancing is limited by minimum cell size in dimension X DD step 7599999 vol min/aver 0.869! load imb.: force 41.1% pme mesh/force 1.044 DD load balancing is limited by minimum cell size in dimension X DD step 7609999 vol min/aver 0.868! load imb.: force 40.3% pme mesh/force 1.030 DD load balancing is limited by minimum cell size in dimension X DD step 7619999 vol min/aver 0.869! load imb.: force 43.8% pme mesh/force 1.031 Basically the Test2 is very slow and I would like to find a way to interpret those messages and try fix this issue (tell me if there's something I should read). Thank you, Gabriele -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
