Dear GMX-Users, I'm testing my 256 full hydrated lipid on blue gene. The purpose is to find out the right number for "-npme", as mdrun can not estimate itself successfully.
I met the problem that how to match the maxinum allowed number for DD cells with large number of CPU cores. My simulation box size is about 8x8x9nm^3, with normal LINCS parameter and dds=0.8. The log file said that the maximum allowed number of DD cells is 8x8x9. As far as I understand, DD assigns one core to one cell, so the maximum core I can use in this case for PP part is 8x8x9=576 cores. I then ran with 512 cores with -npme=128. My system runs without problem. What if I want to use more cores? Then I try to increase the "-dds" from 0.8 to 0.9, this leads to an increasing of "the maximum allowed number of DD cells" to 8x10x10. This time is 1024 cores in total and I set -npme=224, then PP part will have 800 cores which are within 10x10x10. The system ran initially but corrupted very soon with warning that "DD cell 2 1 4 could on obtain 56 of the 57 atoms that are connected via constraints from the neighboring cells ...." Therefore the dilemma is if I increase the "-dds", I can meet the requirement for the maximum allowed number of DD cells, but fail the maximum length of constraints in LINCS. Does it mean that for a relative small system, it is not possible to using up to thousand of cores by domain decomposition? I know that if it makes more sense to use thousand of cores for huge system, but if my purpose is simply to speed up the simulation, what should I do? Thank you. Chao -- 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/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/mailing_lists/users.php
