Re: AW: Using nodelist file causes namd to hang

From: Norman Geist (
Date: Thu Sep 18 2014 - 12:32:23 CDT

This should just show if the two nodes connected directy are faster
than with using the switch, so pointing out if your switch might be
too slow ;) Of course namd can run over hundrets of nodes, but gigabit
is limited...

Am Donnerstag, den 18-09-2014 um 12:35 schrieb Douglas Houston:

Hi Norman,

We have a 802.3ab 1000BASE-T Gigabit Ethernet switch (Netgear
that is dedicated to connecting the nodes of this cluster only (so
additional traffic). Assuming removing this switch will allow two  
nodes to show a speedup relative to one node, would this really  
represent a solution?

It was my understanding that NAMD is at least somewhat
across an ordinary ethernet-linked cluster of nodes. Is this not

Can anyone on this mailing list tell me if they have successfully  
noted a speed increase by running NAMD across an ethernet-linked  
cluster vs. a single node? If so, could they please list their
hardware, e.g. ethernet cards, switch, number of nodes, cores per  
node, size of system benchmarked, etc.


P.S. 64 minutes of simulation runtime across 2 of the nodes results
a total of 390GiB of data transferred between them (according to  
ifconfig) - this equates to about 100 MiB/sec. This is for a  
80,000-atom system. For my small 5,000 atom system it shows about
MiB/sec. Does this mean that, for the large system at least, the  
bandwidth could indeed be saturating (100 MiB/sec being not far
1Gbit/sec)? If this is the case, it is not clear to me why the
transfer rate is so much and if anything can actually be done about

Quoting Norman Geist on Wed, 10 Sep  
2014 15:14:37 +0200:

> Benchmark the timing over two nodes, without the switch. Sometimes
> switches are very slow, especially if other ports are active at the
> time.
> Norman Geist.

Dr. Douglas R. Houston
Institute of Structural and Molecular Biology
Room 3.23, Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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