Re: slow down when running 2 simulations on 1 node

From: Julio Maia (jmaia_at_ks.uiuc.edu)
Date: Thu Dec 12 2019 - 13:13:01 CST

Hi,

If you’re not setting the correct affinities, PEs from different replicas might compete for the same cores in your machine.
Please try to set CPU affinities for PEs for each replica and try again. You can check how it’s done here: https://www.ks.uiuc.edu/Research/namd/2.13/ug/node105.html <https://www.ks.uiuc.edu/Research/namd/2.13/ug/node105.html>

Thanks,

> On Dec 12, 2019, at 2:09 AM, Gerald Keller <gerald.keller_at_uni-wuerzburg.de> wrote:
>
> Hi everyone,
>
> in our working group we compute on our own GPU nodes, with no queue system and do not compute on multiple nodes.
> When we calculate two replicas of plain MD runs on 1 node with in total 2 GPUs and 40 CPUs we recognized that the simulation speed slows down when starting the second replica.
>
> 1x NAMD on 1 node using 1 GPU and 18 CPUs:
>
> Info: Benchmark time: 18 CPUs 0.00742875 s/step
> Info: Benchmark time: 18 CPUs 0.0073947 s/step
> Info: Benchmark time: 18 CPUs 0.00747593 s/step
> Info: Benchmark time: 18 CPUs 0.00752931 s/step
> Info: Benchmark time: 18 CPUs 0.00744549 s/step
> Info: Benchmark time: 18 CPUs 0.00746218 s/step
>
> TIMING: 500 CPU: 3.86542, 0.0073741/step Wall: 3.90971, 0.0074047/step
> TIMING: 980 CPU: 7.43293, 0.00730715/step Wall: 7.49914, 0.00738945/step
> TIMING: 1000 CPU: 7.58503, 0.007605/step Wall: 7.65193, 0.0076393/step
> TIMING: 1500 CPU: 11.2973, 0.0073617/step Wall: 11.3969, 0.00763561/step
> TIMING: 2000 CPU: 15.0195, 0.00745355/step Wall: 15.1411, 0.0075375/step
>
>
> 2x NAMD on 1 node 1 GPU and 18 CPUs for each replica:
>
> Info: Benchmark time: 18 CPUs 0.0115988 s/step
> Info: Benchmark time: 18 CPUs 0.0116316 s/step
> Info: Benchmark time: 18 CPUs 0.0118586 s/step
> Info: Benchmark time: 18 CPUs 0.0115375 s/step
> Info: Benchmark time: 18 CPUs 0.0114114 s/step
> Info: Benchmark time: 18 CPUs 0.0117798 s/step
>
> TIMING: 500 CPU: 6.0915, 0.0113823/step Wall: 6.18421, 0.0114815/step
> TIMING: 1000 CPU: 11.8594, 0.0126053/step Wall: 12.0109, 0.0127244/step
> TIMING: 1500 CPU: 17.564, 0.0114935/step Wall: 17.7579, 0.0116048/step
> TIMING: 2000 CPU: 23.3157, 0.0119276/step Wall: 23.5628, 0.0119936/step
>
> If we run 1x NAMD on 1 node using 1 GPU and 18 CPUs and start another simulation with amber on the other GPU, there is no influence on the namd simulation speed.
>
> Does anyone have an idea why this is happening and how to solve that problem? Because of limited resources, somtimes we have to run only one simulation per GPU.
>
> Thank you in advance for your suggestions!
>
> Best regards
> Gerald

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