In article <1996Sep12.155933 at bphvax>,
Charles A. Alexander <caal at bphvax.biophysics.rochester.edu> wrote:
>>We're presently evaluating the pros and cons of migrating our GCG
>package to a UNIX platform. It seems like a lot of the freeware
>biocomputing apps are being written for UNIX and though I love my VAX
>and VMS System Management, it seems like I would be doing my users a
>disservice by not providing at least the option of other software.
>>We also want to provide molecular modelling tools for the people we
>support and it seems that SGI and SUNS have a lot of tools available for
>these applications as well.
>>Anybody have any recommendations on what kind of machines would be
>able to handle the kind of processing power required for both these
>applications for a peak load of about 10-15 users simultaneously. We
>have a total of about 50 users and growing.
mole.bio.cam.ac.uk is a three year-old SGI Indigo2 with a 150MHz R4400
and 128Mb RAM. Not a stupendous machine at all, and we are looking to
replace it soon. However, we are trying to do what you are doing, but
on a rather larger scale; mole has 1,500 users, with usually 30-40
logged in at any one time during the day. FASTA searches are getting
a bit slow these days, which is why we want a more powerful machine.
However, it seems that an SGI workstation would probably suit you
quite well. However, *don't* to molecular visualisation on the same
machine; you will kill the interactive performance of the remote
users. Our protein modelling group uses SGI Indigo2 machines as well
for their NMR work, and are very happy with them.
I can't speak for Sun machines really, but it seems that the majority
of the bioinformatics world are either using SGI or DEC. We have a
Digital Alpha machine on loan at the moment for evaluation. A 250MHz
ev5 Alpha processor seems to be about on a par with a 195 MHz R10000,
although the R10000 might have a slight edge in our tests.
Having said that, so far I prefer IRIX to DEC Unix. IRIX seems to
have more flexible process sheduling, and this is very important if
you buy a single processor machine which is also going to handle
interactive tasks such as e-mail (which ours does). With
multi-processor machines this is less of a problem because you can
restrict certain functions to certain processors.
>I don't want to start a holy war but should we look at Suns or SGIs ?
You should definitely consider DEC as well. It also gives you the
flexibility to run OpenVMS if your users (or you) decide they loathe
UNIX :-) Or even Windows NT; a fair bit of software seems to be being
ported to it these days.
>Anybody care to share their experiences ? How stable are the OS' and
>how difficult are they to manage.
We used to use VAXen, although this was before I joined. In many ways
UNIX is much more messy than VMS (according to my boss/predecessor),
and it's probably less secure. However, IRIX is pretty stable (as
long as you use a 'standard' version, which at the moment means 5.3 or
6.2). mole runs quite happily for months without a reboot. I only
had to shut it down last week because a hard disk failed (joy!).
>My limited experience tells me that
>SGIs are easier to handle. I'll apologize in advance if my ignorance
Well, I know very little about VMS, so I can't really compare.
>Thanks in advance. BTW, anybody have an updated spec sheet on how GCG
>performs on various platforms ?
Don't trust these things. The comparisons are always totally
ludicrous. In our tests so far, on a Dec AlphaServer 2100 5/250 and
an SGI Indigo2 with a 195MHz R10000 processor, both machines are about
3x as fast as the 150MHz R4400 doing either GCG or Pearson FASTA
searches. From the SGI data I have seen, performance scales rather better
with multiple processors on SGIs than on DECs, but you'd expect SGI
benchmarks to say that, of course.
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