Performance on GPU

From: Anup Prasad (anup.prasad_at_monash.edu)
Date: Tue Nov 05 2019 - 07:29:58 CST

Dear NAMD community,

I am using NAMD platform for my MD simulations. I want to use the GPU nodes
on the HPC facility here (CRAY XE) to run my simulations, for which I am
trying to run the "apoa1" benchmark. I compared the simulation output
performance on my HPC facility with given NAMD benchmark results, but got
very poor performance. Based on the NAMD benchmarks for apoa1 I should be
getting a performance of nearly 30 ns/day on the hardware we have here.
However, I am able to get only around 3 ns/day for the same system. I am
using the NAMD config files provided in the benchmark link below.

NAMD benchmark link- https://www.ks.uiuc.edu/Research/namd/benchmarks/

These are the specifications for the GPU nodes at my institute,

*HPC specifications*

*Operating System -- Cray Linux Environment Version - 6.x*

*Cray Programming Environment (CPE) -- Unlimited*

*Intel Parallel Studio XE -- 5 Seats*

*PGI Accelerator -- 2 Seats*

*Workload Manager -- PBS Pro*
*Compute Node - CPU+GPU Node*

*Processor -- 1X BDW 2.1 GHz 18C*

*Accelerator -- 1X P100 16 GiB*

*Memory Per Node -- 64 GB DDR4-2400 with Chipkill technology*

*This is the shell script I use to submit jobs,*

*##############################################################################*

* submitting shell script*

*##############################################################################*

*## Queue it will run in#PBS -N gpu#PBS -q gpuq#PBS -l
select=1:ncpus=18:accelerator=True:vntype=cray_compute#PBS -l
walltime=00:30:00#PBS -l place=pack#PBS -j oemodule load
craype-broadwellmodule load craype-accel-nvidia60module load
namd/2.12/gpu-8.0EXEC=/home/apps/namd/2.12/gpu/8.0/CRAY-XC.cuda.arch.multicore/namd2cd
$PBS_O_WORKDIRtime aprun -n 1 -N 1 -d 18
/home/apps/namd/2.12/gpu/8.0/CRAY-XC.cuda.arch.multicore/namd2 +idlepoll
apoa1_npt_cuda.namd > prod_gpu.log*

*#################################################################################*

*Please help with suggestions. *

*Kind regards*

*Anup Kumar Prasad*

*Ph.D scholar, IITB-Monash Research Academy*

*Indian Institute of Technology Bombay, INDIA*

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