Hi,
Since based on your timings you stop getting a speedup beyond 32
threads, I recommend using a max of 32 threads. :-)
Assuming you have the Ryzen 32-core processor this makes sense -
cpptraj does not benefit from hyperthreading (I think AMD calls it
simultaneous multi-threading but it's essentially the same thing.
-Dan
On Fri, Sep 21, 2018 at 10:57 AM M RCC <mkr3j2c1.gmail.com> wrote:
>
> Thank you Daniel for your suggestion.
> For benchmarking I did the following
> 100 frames [1 out of 6 boxes]
> 4 threads: 218 seconds
> 8 threads: 161 seconds
> 10 threads: 143 seconds
> 12 threads: 133 seconds
> 14 threads: 133 seconds
> 16 threads: 126 seconds
> 32 threads: 118 seconds
> 64 threads: 136 seconds
>
> Am splitting the boxes for calculation. so i think i dont need to worry
> about memory, though i have 120GB of RAM.
>
> Among these in which one i can expect faster performance?
>
> Thanks in advance
>
>
>
>
> On Thu, Sep 20, 2018 at 3:27 PM M RCC <mkr3j2c1.gmail.com> wrote:
>
> >
> > Dear Amber Users,
> >
> > I am trying to run GIST calculation in parallel with 64 core AMD system
> > using Ambertools18.
> > when am using "mpirun -np 64 cpptraj.MPI -i gist.in" , i got error with
> > core dump.
> >
> > then i am using "cpptraj.MPI -i gist.in" (even assigning
> > OMP_NUM_THREADS=64) program is running in only one core.
> >
> > How i can utilise all 64 core for GIST calculation?
> >
> >
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Received on Fri Sep 21 2018 - 10:30:03 PDT
