Dear Gromacs users, I have been working with Gromacs v. 5.0.4 by using its MPI/OPENMP – parallelization. While studying outputs of mdrun with input argument ”ntomp” (shell command ”gmx_mpi mdrun -ntomp i” where i = 1,2 or 4), the potential energy values seemed to differ. My typical demo run included 100 steps and the potential energy values were checked for the first (initial) step.
Below, the obtained potential energy values are presented for two different energy groups and for three different ”ntomp” values (unit for potential energy: kJ/mol) System Prot – Sol ntomp: 1 -193754.7 -193733.2 ntomp: 2 -193741.3 -193795.4 ntomp: 4 (”default” run) -193744.7 -193758.7 A more detailed investigation showed that the deviations can be seen in the values of short – range Coulomb forces (other Coulomb short - range values than the values of ”SOL-SOL” system in the ”Prot-Sol” simulations differed less than 1 kJ/mol. The values in "SOL-SOL" system mostly induced the differences). I use ”PME” as ”coulombtype” here, but the potential energy values also differed when using ”cut-off” and again, the differences were noticed especially in the case of the short – range Coulomb forces. The question is: can one expect such differences in potential energy values when using openMP parallelization or is this a simple user error? Gromacs was run in a server for which detailed information is printed below by using command ”lscpu”: " Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 4 On-line CPU(s) list: 0-3 Thread(s) per core: 1 Core(s) per socket: 4 Socket(s): 1 NUMA node(s): 1 Vendor ID: GenuineIntel CPU family: 6 Model: 44 Stepping: 2 CPU MHz: 2400.000 BogoMIPS: 4799.98 Virtualization: VT-x L1d cache: 32K L1i cache: 32K L2 cache: 256K L3 cache: 12288K NUMA node0 CPU(s): 0-3 " For example, the ”default” run (with shell command ”gmx_mpi mdrun”) produces the following info: ” Using 1 MPI process Using 4 OpenMP threads No GPUs detected on host xxx.xxx.jyu.fi ” Thank you. M-J Vesterinen University of Jyväskylä -- 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.