[Beowulf] Re: fast file copying

David Mathog mathog at caltech.edu
Fri May 4 08:24:28 PDT 2007

Felix Rauch Valenti wrote:

> On 03/05/07, Alan Louis Scheinine <scheinin at crs4.it> wrote:
> > One possibility is nettee.
> > http://saf.bio.caltech.edu/nettee.html
> As a related side note: If the bandwidth you get is not what you
> expect, it may well be that your switch is bad (or that your disks are
> slow). That was my experience a couple of years ago, so we implemented
> a switch benchmark called "Switchbench", that helps to identify the
> bandwidth bottleneck in a network.

Since both dolly and nettee have been mentioned in this thread, it's
probably appropriate to point out that they are very closely related.
Felix wrote Dolly, and I forked his code and modified it a bit to arrive
at nettee.  

Felix's point about nettee and slow disks is especially relevant when
imaging nodes because historically some of the small linux environments
used for such installations did not set DMA on the disks by default,
and that slowed down the write speed on the disks dramatically.  When
file transfers are being carried out on busy systems it's also a
good idea to put "buffer" or an equivalent program in the output
stream on each node, so that a brief contention for IO writes to
the local disk doesn't slow down the entire chain.  Always use
"buffer" or an equivalent if the local write stream is being piped
through "tar -xf -" or an equivalent dearchiving command, as the
dearchiving step can slow down the write speed if it has to
create a large number of small files in a directory.


David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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