From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Thu Mar 17 2022 - 10:30:10 CDT
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!uaA1akGwaqs-P8XEytTJ4h4aCCjOilth8piRb7GQOTe75yX89aM8Q3gg5iexu7U2jg$
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,
>
> <https://urldefense.com/v3/__https://iith.ac.in/__;!!DZ3fjg!oDwYdoHGz8MPL249x_2pZpZIV0AN7SfdSE9L4lWPuxIIwx_eKxnIXFNDWCU96GPgRg$>
>
>
>
> Sruthi Sundaresan
>
> Ph.D. Research Scholar
>
> C/o Dr. Thenmalarchelvi Rathinavelan
>
> Molecular Biophysics Lab, Department of Biotechnology
>
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-- Josh Vermaas Assistant Professor MSU-DOE Plant Research Laboratory, Department of Biochemistry and Molecular Biology Michigan State University https://urldefense.com/v3/__https://vermaaslab.github.io/__;!!DZ3fjg!uaA1akGwaqs-P8XEytTJ4h4aCCjOilth8piRb7GQOTe75yX89aM8Q3gg5icRSLJC9g$
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