From: Norman Geist (norman.geist_at_uni-greifswald.de)
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
GS205)
that is dedicated to connecting the nodes of this cluster only (so
no
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
parallelisable
across an ordinary ethernet-linked cluster of nodes. Is this not
the
case?
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
network
hardware, e.g. ethernet cards, switch, number of nodes, cores per
node, size of system benchmarked, etc.
cheers,
Doug
P.S. 64 minutes of simulation runtime across 2 of the nodes results
in
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
60
MiB/sec. Does this mean that, for the large system at least, the
bandwidth could indeed be saturating (100 MiB/sec being not far
off
1Gbit/sec)? If this is the case, it is not clear to me why the
data
transfer rate is so much and if anything can actually be done about
it.
Quoting Norman Geist on Wed, 10 Sep
2014 15:14:37 +0200:
> Benchmark the timing over two nodes, without the switch. Sometimes
the
> switches are very slow, especially if other ports are active at the
same
> time.
>
> Norman Geist.
>
_____________________________________________________
Dr. Douglas R. Houston
Lecturer
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
http://tinyurl.com/douglasrhouston
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