Re: [gmx-users] Multithread run issues

Hi, That user's input can't use OpenMP, like the message says. So try the other options. (And again, don't run mpirun on a thread-MPI mdrun!) Mark On Mon, Oct 10, 2016 at 1:02 PM Mahmood Naderan wrote: > Sorry for the previous incomplete email. > > Program mdrun, VERSION

Re: [gmx-users] Multithread run issues

Sorry for the previous incomplete email. Program mdrun, VERSION 5.1 Source code file: /share/apps/chemistry/gromacs-5.1/src/programs/mdrun/resource-division.cpp, line: 746 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme

Re: [gmx-users] Multithread run issues

>mpirun -np 1 mdrun_mpi -v -ntomp 2 Agree with that. >This is not a problem to solve by running applications differently. You >will have users running jobs with single ranks/processes that use threading >of various kinds to fill the cores. That's a feature, not a bug. Either >configure PBS to

Re: [gmx-users] Multithread run issues

Hi, Yeah, but that run is very likely a) useless because you're just running two copies of the same simulation because you're not running MPI-enabled mdrun b) and even if not, less efficient than the thread-MPI version mdrun -v -nt 2 c) and even if not, likely slightly less efficient than the

Re: [gmx-users] Multithread run issues

OK. I understood the documents. Thing that I want is to see two processes (for example) each consumes 100% cpu. The command for that is mpirun -np 2 mdrun -v -nt 1 ​Thanks Mark.​ Regards, Mahmood -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Multithread run issues

Hi, On Sun, Oct 9, 2016 at 2:06 PM Mahmood Naderan wrote: > Hi, > > Users issue the command "mdrun -v" and that will automatically read input > > files in the working directory. There are two issue with that which I am > > not aware of the solution. > > > > 1- How the

[gmx-users] Multithread run issues

Hi, Users issue the command "mdrun -v" and that will automatically read input files in the working directory. There are two issue with that which I am not aware of the solution. 1- How the number of cores can be changed? 2- Viewing the output of "top" command, it is saying that mdrun uses 400%