From: Stefano Guglielmo (stefano.guglielmo_at_unito.it)
Date: Thu Mar 19 2020 - 10:35:53 CDT
thanks for your advice and sorry for my late reply. I finally managed to
optimize performance for a single simulation.
Now I am trying to run two simulations in parallel using NAMD 2.13
multicore-CUDA version. I used the following option to run the two
+p16 +idlepoll +setcpuaffinity +devices 0 +pemap 0-15
+p16 +idlepoll +setcpuaffinity +devices 1 +pemap 32-47.
For two systems of comparable dimension I observed a sizeable performance
loss when starting the second simulation (from 0.017 s/step to 0.028
s/step). In your opinion is this reasonable or shall I tune some options
differently/use a different version of NAMD?
Thanks in advance for sharing advice,
all the best
Il giorno gio 5 mar 2020 alle ore 22:03 Josh Vermaas <
joshua.vermaas_at_gmail.com> ha scritto:
> Don't forget to compare against multicore builds. On one node with shared
> memory, those builds often win for maximum 1 gpu throughput. Since you have
> 2 on the same node, an smp build without communication threads may win.
> On Thu, Mar 5, 2020, 10:23 AM Victor Kwan <vkwan8_at_uwo.ca> wrote:
>> Hi Stefano,
>> Since you already have a system in mind, you can compare the time it
>> takes to perform a 10ps simulation with different setups.
>> > one or both gpu, number of cores
>> * With NAMD 2.13 comes a large improvement in dual gpu/single node
>> performance and we observe almost linear scaling when going from 1 to 2
>> * 16core/GPU is sufficient, from our experience 6-8core/GPU is the lower
>> * For GPU runs, hyperthreading should not increase affect performance.
>> > pemap/commap options
>> * check the output of nvidia-smi topo matrix - leaving cpu/gpu affinity
>> as default should be fine.
>> On Thu, Mar 5, 2020 at 10:12 AM Stefano Guglielmo <
>> stefano.guglielmo_at_unito.it> wrote:
>>> Dear NAMD users,
>>> I am using a workstation with an AMD Ryzen Threadripper 2990WX 32-Core
>>> Processor, 128 GB RAM and two RTX 2080 Ti cards with NVlink; I am here to
>>> ask for suggestions on what could be the "best" options to run a single
>>> simulation on a 200K atom system with NAMD 2.13 (one or both gpu, number of
>>> cores, hyperthreading or not, pemap/commap options...)
>>> Thanks in advance for your time
>>> Stefano GUGLIELMO PhD
>>> Assistant Professor of Medicinal Chemistry
>>> Department of Drug Science and Technology
>>> Via P. Giuria 9
>>> 10125 Turin, ITALY
>>> ph. +39 (0)11 6707178
>>> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Mail
>>> priva di virus. www.avast.com
-- Stefano GUGLIELMO PhD Assistant Professor of Medicinal Chemistry Department of Drug Science and Technology Via P. Giuria 9 10125 Turin, ITALY ph. +39 (0)11 6707178
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