Fwd: About wall clock time

From: Rik Chakraborty (rik.chakraborty01_at_gmail.com)
Date: Mon Oct 16 2017 - 01:20:40 CDT

Dear NAMD experts,

Recently, we have installed a new cluster and the configurations are
following below,

1. Master node with storage node- DELL PowerEdge R730xd Server
2. CPU only node- DELL PowerEdge R430 Server (6 nos.)
3. GPU node- DELL PowerEdge R730 Server (3 nos.)
4. 18 ports Infiniband Switch- Mellanox SX6015
5. 24 ports Gigabit Ethernet switch- D-link make

We have run a NAMD job using this cluster to check *the efiiciency in time
with increasing number of CPU node. Each CPU node has 24 processor. The
details of the given system and the outcomes are listed below,

1. No. of atoms used: 73310
2. Total simulation time: 1ns
3. Time step: 2fs

*No. of nodes*

*Wall Clock Time (s)*

1

27568.892578

2

28083.976562

3

30725.347656

4

33117.160156

5

35750.988281

6

39922.492188

As we can see, wall clock time is increased with the increase of no. of CPU
nodes which is not expected.

So, this is my kind request to check this out and let me know about the
problem.

Thanking you,

Rik Chakraborty
Junior Research Fellow (Project)
Dept. of Biological Sciences
Indian Institute of Science Education and Research, Kolkata
Mohanpur, Dist. Nadia
Pin 721246
West Bengal, India

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