Re: [ccp4bb]: NFS Performance

[Ethan Merritt <merritt@u.washington.edu>]

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One more potentially relevant data point.
We have had recurring problems with denzo/HKL2000 running on
a linux box but accessing image files on a volume NFS-mounted from
a Tru64 server.  Other programs, even disk-intensive ones, do not
seem to trigger the problem - but I don't recall that arp/Warp has been
monitored for this setup.  In our case the problem shows up on the
server end (Tru64) as well as the client end.  I'm not clear on whether 
that is the same as the case you are reporting or not.

I have wondered if the problem is triggered by application programs 
using mmap() to access large files rather than normal read/write/seek 
calls.  I'm not sure how to test this without source code however.  
Does bonnie test mmap access?


On Wednesday 17 April 2002 11:47, Kay Diederichs wrote:
>
> To Peter and all other contributors to this thread -
>
> I would like to clarify that the NFS performance problem exists
> despite the IRIX server running the latest 6.5.15m, and the Linux
> side being patched with Myklebust's NFS patches (for 2.4.17). The
> problem is also not sensitive to NFS2 or NFS3 mounts, and changing
> rsize, wsize does not help either. By the way, with NFS3 rsize and
> wsize are as high as 32768 by default (look at /proc/mounts).
>
> I have been using bonnie and other benchmarks for years and I'm quite
> satisfied with NFS performance and stability of both Linux and SGI. I
> find that on a 100Mbit switched network, both read and write
> performance can reach the upper limit given by the network speed,
> i.e. almost 10MB/s.
>
> However, the problem shows when running SOLVE or some components of
> arp/Warp. In both cases, CPU usage drops to below 1% during certain
> I/O situations, and these long-running jobs simply don't advance. It
> appears as if g77-compiled programs trigger some kind of drastic
> performance killer.
>
> I believe that neither arp/Warp (I asked Victor about it) nor SOLVE
> (setting SOLVETMPDIR to a local directory does _not_ help) honour
> CCP4_SCR -  if they would the problem would probably not surface.
>
> Maybe someone (Tassos?) could come up with a small piece of code that
> exhibits the problem - in that case it would be possible to
> investigate. But both programs are not open source so it's not easy
> to identify where the problem arises.
>
> Kay
> ----- Original Message -----
> From: "Peter Brick" <p.brick@ic.ac.uk>
> To: <ccp4bb@dl.ac.uk>
> Sent: Wednesday, April 17, 2002 7:52 PM
> Subject: RE: [ccp4bb]: NFS Performance
>
> > ***  For details on how to be removed from this list visit the  ***
> > ***          CCP4 home page http://www.ccp4.ac.uk         ***
> >
> > Hi
> >
> > >> check out the linux NFS kernel patches at
> > >> http://www.fys.uio.no/~trondmy/src/2.4.18/
> > >
> > >Also note that there may be relevant patches on the Irix end:
> > >
> > >http://www.lib.uaa.alaska.edu/linux-kernel/archive/2002-Week-14/07
> > >65.html
> >
> > This problem may be specific to SGI.
> >
> > I set up NFS using default values - and avoid patching Linux
> > kernels if I can help it.
> >
> > I've used Bonnie to check NFS performance between Linux and Compaq
> > Alpha machines.
> >  RH7.2 with autofs and  TruUnix 5.1a automount  all with default
>
> parameters.
>
> >  Bonnie reports sequential (character putc()) o/p rates of:
> >
> > Local file
> >
> > Compaq: 23 MB/s
> > Linux: 17.9 MB/s
> >
> > NFS
> >
> > Linux to Linux: 10.2 MB/s
> > Compaq to Linux (scratch file):  9.9 MB/s
> > Linux to Compaq (scratch file):  4.1 MB/s
> >
> > With 2GB scratch file but 1GB of RAM I can't avoid the effects of
> > caching.
> >
> > Some of the numbers don't make much sense  - on my Alpha local
> > block io gives a worse rate than char io while on a PC it is twice
> > as fast.
> >
> > Peter
> > --
> > Peter Brick,
> > Blackett Laboratory, Department of Biological Sciences,
> > Imperial College, Prince Consort Road, London SW7 2BW, UK
> > Tel: 020-7594-7704  Fax: 020-7589-0191

-- 
Ethan A Merritt       merritt@u.washington.edu
Biomolecular Structure Center Box 357742
University of Washington, Seattle, WA 98195
phone: (206)543-1421
FAX:   (206)685-7002