[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Re: [ccp4bb]: NFS Performance
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
I have been experiencing exactly the same problem for a long time. This
not only affects SOLVE, but also arp/Warp - both of which are
long-running programs.
We work around the problem by using local (temporary) disks for these
programs, but of course this is a major pain.
I seem to remember that the problem does not exist for PGI-compiled CCP4
binaries (the ones that used to be distributed with arp/Warp but which
have since expired ...), which might indicate that this is a g77
buffering problem. Can anybody confirm this?
Kay
Martin Singleton wrote:
>
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
> Dear All
>
> We have recently started using Linux (RedHat 7.2) machines in our SGI
> based network.
> All of our user accounts are held on an NFS exported filesystem from an
> SGI server. This filesystem is mounted on the Linux machine as well as the
> other SGIs. Linux sees the filesystem fine, but there appears to be a
> major performance problem when certain CCP4 programs as well as SOLVE on
> the Linux box requires access to this filesystem. The problem seems to
> occur during read/writes of large binary files, which cause programs to
> slow to a crawl, in some cases increasing the run time by two orders of
> magnitude. I have noticed that the programs processor usage often drops to
> < 1% when this occurs and the machine rapidly runs out of memory (1GB
> real!) If the same process is run on the local (ext3) disc only, or on the
> SGI machines, there are no such problems. Obviously the problem lies with
> the Linux-IRIX disc cross-mounting, but so far I have not been able to see
> where, and the documented NFS options do not seem to help. Has anyone else
> noticed this problem, or suggest any solutions ?
>
> Regards
>
> Martin Singleton
> Cancer Research UK
> Clare Hall Laboratories,
> South Mimms,
> Herts EN6 3LD
> martin.singleton@cancer.org.uk
--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de/~kay
email: Kay.Diederichs @ uni-konstanz.de Tel +49 7531 88 4049 Fax 3183
When replying to my email, please remove the blanks before and after the
"@" !
Fakultaet fuer Biologie, Universitaet Konstanz, Box M656, D-78457
Konstanz