Re: [ccp4bb]: CCP4 computing platform

[Bart Hazes <bhazes@ualberta.ca>]

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Different computer hardware, networking gear, cache, RAID etc. all affect the
performance of your computing environment and you can get very involved with
the technology. Fortunately, for the great majority of cases it doesn't seem
to matter that much anymore.

In the "old days" (for me that is the late 80's, early 90's) a faster computer
meant the difference between spending the whole day in the library reading
while the computing was trying to finish a refinement an spending only half a
day in the library. Nowadays it means the difference between drinking a cup of
coffee before refinement completes and finishing only half of it or burning
your palate while trying to keep up with Refmac.

I like the low price of PC/Linux not just because they are cheap. It also
means you don't feel compelled to buy expensive maintenance contracts (Dell
and perhaps others have actually very good 3-year on-site service contracts at
very low cost!), expensive proprietary compilers, and taking a big SGI or
other system, that costed you dearly, out of service is painful. PCs can just
be replaced on a regular basis. I tend to buy one for each new person in the
lab to be their personal workhorse for the duration of their stay. No fights
over diskspace, if it is full they have to clean up their own stuff. NFS has
not been a problem on our network of Linux-only computers.

Tassos has a point regarding maintenance issues in a distributed system. It is
harder to maintain a uniform computing environment, upgrade the OS, keep
regular backups. We are in the less-then-7 category he referred to so it has
not be an issue for us and I think with a bit of planning it should expand
well beyond 7 systems. For backup we use a daily script that fetches files
created or modified that day for backup on a central harddisk. When that
harddisk fills up a full backup is made on tape and the harddisk is cleared.
We don't regularly update the OS on all computers, just wait for the next OS
release unless a problem is actually hurting us. Ignoring security fixes is
not smart but we are behind a local firewall. I have moved to create standard
files to do the sourcing of CCP4's and other packages' setup scripts so that
users at least start out with the same settings.

In short, unless you have an exceptional computing task Pentium 4 and AMD
processors will do a great job. Don't go overboard and buy the cheapest PCs
you can get because I would doubt their reliability. We started out with Dell
PCs and the 3-year on-site warranty (~US$100 for three years!). More recently
we have switched to a shop specialized in Linux workstations (Pentium, AMD,
Alpha, Sun) because Dell doesn't offer AMD processors and this company happens
to have its headoffice in our city (www.harddata.com). Both systems are very
solidly build so we probably stick with them.

Bart

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Assistant Professor
Dept. of Medical Microbiology & Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta, T6G 2H7, Canada
phone:	1-780-492-0042
fax:	1-780-492-7521

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