Re: [gmx-users] parallel processing

Hi, On Sat, Dec 3, 2016 at 6:34 PM abhisek Mondal wrote: > Hello Mark, > > I had gone through the page. Not finding any solution there. > > My architecture is: > Architecture: x86_64 > CPU op-mode(s):32-bit, 64-bit > Byte Order:Little Endian

Re: [gmx-users] parallel processing

Hello Mark, I had gone through the page. Not finding any solution there. My architecture is: Architecture: x86_64 CPU op-mode(s):32-bit, 64-bit Byte Order:Little Endian CPU(s):16 On-line CPU(s) list: 0-15 Thread(s) per core:1 Core(s) per socket:

Re: [gmx-users] parallel processing

Hi, Please check out http://manual.gromacs.org/documentation/2016.1/user-guide/mdrun-performance.html. Your first sample command is woefully inefficient, but for em this likely doesn't matter. Mark On Fri, 2 Dec 2016 09:01 abhisek Mondal wrote: > But if I want to run

Re: [gmx-users] parallel processing

But if I want to run the same job in 4 nodes (available cores= 4*16) then how would this work ? On Fri, Dec 2, 2016 at 2:20 PM, wrote: > Hi Abhisek, > > You would need to use another version of gromacs with mpi rather than > thread-mpi (installed by adding

Re: [gmx-users] parallel processing

Hi Abhisek, You would need to use another version of gromacs with mpi rather than thread-mpi (installed by adding DGMX_MPI=ON to the cmake command). You could then use the following command mpirun -np 4 gmx_mpi mdrun -ntomp 16 -npme 0 -v -deffnm em I'm not sure why you are specifying -npme 0

[gmx-users] parallel processing

Hi, I'm running gromacs on a cluster configuration as follows: 1 node = 16 cores I'm able to use single node with "gmx mdrun -ntmpi 4 -ntomp 16 -npme 0 -v -deffnm em" command. How can I be able to run on multiple node (I have 20 nodes available) ? "-nt" is not doing good here. -- Abhisek