performance of NAMD on KNL

From: jing liang (
Date: Fri Sep 29 2017 - 15:10:04 CDT


I downloaded the NAMD compiled version:

Linux-KNL-multicore (Intel Xeon Phi KNL processor single node)

The node where I am testing NAMD is an Intel Xeon Phi 7250 (Knight's
Each core can use 4 hardware threads. My testing system consisted of 20,000

I did a comparison with other installed versions of NAMD on regular nodes
(not KNL)
which have 28 cores (also intel), these are a SMP and a CUDA versions. The
results are:

Version Time (sec)
SMP (28 threads) 80
GPU (1 Node, 2 GPUs) 50
KNL 160

In the case of KNL, 160 sec. was the best performance I obtained after
several trials
using the setup:

namd2 +ppn68 +setcpuaffinity +pemap 0-67

I wonder if the performance of NAMD in the KNL case is lowered because I am
using the proper setup for running it (ppn, pemap) or maybe because it is a
version what I am using.


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