From: Sruthi Sundaresan (bo20resch11002_at_iith.ac.in)
Date: Tue Apr 26 2022 - 08:25:07 CDT
Could you please tell me where I can find this?
On Tue, Apr 26, 2022 at 6:54 PM Vermaas, Josh <vermaasj_at_msu.edu> wrote:
> Do you have CUDASOAintegrate turned on? That is probably the biggest
> switch I’ve seen.
>
>
>
> *From: *Sruthi Sundaresan <bo20resch11002_at_iith.ac.in>
> *Date: *Tuesday, April 26, 2022 at 8:42 AM
> *To: *"Vermaas, Josh" <vermaasj_at_msu.edu>
> *Cc: *"namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>, Ruturaj warake <
> ruturajwarake47_at_gmail.com>
> *Subject: *Re: namd-l: Simulation running slow (1ns/day)
>
>
>
> Thank you!
>
> I am currently running my simulations on NAMD version 3.0 with NVIDIA
> Tesla V100 and the speed has indeed increased significantly (~9ns/day) when
> running on 2 GPUs.
>
>
>
> I went through the blog you shared and checked a few others as well.
> Systems with 10,00,000 atoms could give 15.7ns/day when run on 2 GPUs (
> https://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/
> <https://urldefense.com/v3/__https:/www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/__;!!HXCxUKc!hcW8vvnm85KlyIGYD5FMTQgd9QzsztBHRqLQnjF-Y3DQn4nz_oXPZoyzDSCgya4$>),
> but I am unable to achieve this even though my system is smaller in size.
> Is there any more scope to increase the speed of the simulations?
>
>
>
>
>
> Thanks and regards,
>
>
>
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>
> *Sruthi Sundaresan*
>
> *Ph.D. Research Scholar*
>
> C/o Dr. Thenmalarchelvi Rathinavelan
>
> Molecular Biophysics Lab, Department of Biotechnology
>
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>
>
>
> On Thu, Mar 17, 2022 at 9:00 PM Josh Vermaas <vermaasj_at_msu.edu> wrote:
>
> There are two things I would try:
>
> Running with 20 processors, ideally only the NUMA node that is controlling
> the V100. I've seen instances where performance goes backwards on
> multi-socket systems when using multiple sockets based on the
> QPI/UPI/whatever it is now called interface between the sockets.
>
> NAMD 3.0a9, which will put the whole system on the GPU. Benchmarks I have
> for a 500k atom system on 2 V100s with CUDASOAIntegrate turned on yield
> something like 40ns/day. See
> https://urldefense.com/v3/__https://developer.nvidia.com/blog/delivering-up-to-9x-throughput-with-namd-v3-and-a100-gpu/__;!!DZ3fjg!8ZhTmRUcW7XZRgIQOUwx7Rsf0yitTuZT1JAttBdu7ZR9pXju5aGcfNNyJowcrstNrknsxzZRUPJgUQ-ptqgwNSd8Ts5m2g$
> <https://urldefense.com/v3/__https:/developer.nvidia.com/blog/delivering-up-to-9x-throughput-with-namd-v3-and-a100-gpu/__;!!HXCxUKc!hcW8vvnm85KlyIGYD5FMTQgd9QzsztBHRqLQnjF-Y3DQn4nz_oXPZoyzxrPYNx8$>
> for more details on how NAMD3.0a9 is different than the 2.X versions of
> NAMD.
>
> -Josh
>
> On 3/17/22 8:57 AM, Sruthi Sundaresan wrote:
>
> Hello Ruturaj Sir,
>
> Here's the configuration of the system:
>
>
>
> Architecture: x86_64
> CPU op-mode(s): 32-bit, 64-bit
> Byte Order: Little Endian
> CPU(s): 40
> On-line CPU(s) list: 0-39
> Thread(s) per core: 1
> Core(s) per socket: 20
> Socket(s): 2
> NUMA node(s): 2
> Vendor ID: GenuineIntel
> CPU family: 6
> Model: 85
> Model name: Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz
> Stepping: 7
> CPU MHz: 999.908
> CPU max MHz: 3900.0000
> CPU min MHz: 1000.0000
> BogoMIPS: 5000.00
> Virtualization: VT-x
> L1d cache: 32K
> L1i cache: 32K
> L2 cache: 1024K
> L3 cache: 28160K
> NUMA node0 CPU(s): 0-19
> NUMA node1 CPU(s): 20-39
>
>
>
> On Thu, Mar 17, 2022 at 6:22 PM Ruturaj warake <ruturajwarake47_at_gmail.com>
> wrote:
>
> Hello Shruti ma'am,
>
>
>
> Reason for your problem would be low computer configuration.
>
> Please mention here your computer configuration.
>
> If not then, try to reduce system size.
>
> Thanks.
>
>
>
> On Thu, 17 Mar 2022, 18:19 Sruthi Sundaresan, <bo20resch11002_at_iith.ac.in>
> wrote:
>
> Hi all,
>
> I am currently running my simulations on NAMD version 2.13 with NVIDIA
> Tesla V100. My system consists of 600,000 atoms and I'm able to run only
> 1ns/day. Any suggestions on how to make this run faster?
>
>
>
>
>
> Thanks and regards,
>
>
>
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>
> *Sruthi Sundaresan*
>
> *Ph.D. Research Scholar*
>
> C/o Dr. Thenmalarchelvi Rathinavelan
>
> Molecular Biophysics Lab, Department of Biotechnology
>
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> --
>
> Josh Vermaas
>
> Assistant Professor
>
> MSU-DOE Plant Research Laboratory, Department of Biochemistry and Molecular Biology
>
> Michigan State University
>
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