A while ago I asked for information and opinions on
workstations for molecular biolgists. This is a slightly
edited summary of the replies that were directly mailed
to me.
Thanks to all who responded!
Your opinions have been very useful to us.
CG
Carl-Georg Meinhof
Dept. of Genetics,
University of Freiburg
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>From ted at NMSU.Edu Wed Sep 18 17:13:04 1991
a friend in our lab recommended i send you mail about your recent
posting.
together with one server. We thought about buying SUN SPARCstations
because we were under the impression that these machines are the
most widespread in the field.
well, they are pretty much the most widespread in all fields. some
more than others.
In terms of compatibility this is a very important argument because
we will depent largely on software which is freely available.
this is probably the single most important argument for or against.
Now it seems that SUN is lagging behind in its technology while
other systems (IBM's RS6000, HP, NEXT) offer more bang for the
buck.
they certainly are not lagging behind next. hp and ibm do have
somewhat faster machines available, although that is likely to change
soon. the market tends to seesaw back and forth as each of the major
players make their moves.
we have both suns and rs/6000's here on campus and we recently had an
hp workstation on loan.
my experience is that the rs/6000's are a little faster than our
admittedly older sparcs and for the most part about even with the
latest offerings from sun. the system administration of rs/6000's is
decidedly nastier than working on suns and porting software is kind of
tricky. much of the publicly available software won't work without
moderate to extensive modifications.
the hp was a much better situation. the system administration was
relatively painless. the system was about twice as fast as the ipx
machine from sun and should be about the same as the upcoming machines
or a larger sparc. software ported relatively painlessly, although
some important software was missing (the automounter, some kernel
calls and other similar stuff). my impression was that most software
would port relatively easily.
the interface software was based heavily on motif (which only hp does
worth a damn), while sun's stuff is based on open look. you should
have roughly equal performance either way. suns interface development
tool is more mature, while hp's may be more capable.
Is there as much software for molecular biologists developed for
these machines as for SPARCstations?
certainly not. i would guess that 90% of the workstation software
already runs on suns (either it was developed there, or has been
ported to there), while the hp machine (don't even consider the ibm)
is new enough that most software just can't have been ported yet.
How much do they differ in terms of source code compatibility?
the hp and sun are close enough you can live with it. the ibm is off
in left field to some extent, although you can live with that if you
have a very good software person to do your porting.
Is it a big disadvantage that SUN is not part of OSF?
i would say that it is a disadvantage to be a member, frankly. the
software that has come out of osf has so far been of much lower
quality than it should have been.
From: bill at connection (Bill Poitras
As far as software compatibility, I find Sun workstations to be the best.
They may be lagging in MIPS and MFLOPS, but almost every piece of freely
availible software has been run on a Sun workstation. Since the RS/6000
and HP machines are new, thier development environments are not as strong
as Sun. Sun OS 4.1.1 comes with better versions of tools, plus is more
based on BSD unix than AIX for the RS/6000 is. This means better
utilities. I don't know if current free modeling packages (MM2, MOPAC)
run on Sun workstations well, I assume they do.
+-----------------+---------------------------+-----------------------------+
| Bill Poitras | Polygen Corporation | {princeton bu}!polygen!bill |
| (bill) | Waltham, MA USA | - This space for rent - |
| | FAX (617)890-8694 | bill at polygen.com |
+-----------------+---------------------------+-----------------------------+
From: Bob Beason <BEASON%GENESEO.BITNET at ibm.ruf.uni-freiburg.de
Hi,
Have you looked at the new Sun IPX workstation? It is a SparcStation 2 with
the graphics accel. built onto the motherboard, but has only 2 SBus slots.
The price is quite a bit less than the Sparc 2. Sun is becoming more
aggressive with their pricing now with the competition. You would still
have the advantage of compatibility for software.
Bob Beason
beason at geneseo.bitnet
From: frist at ccu.UManitoba.C
As the proud owner of a Sparcstation1+, I'll be happy to give you my very
biased opinion.
Scientific computation:
My impression is that the majority of software being written in molecular
biology runs under Unix, and most of that on Sparcs. VMS seems to be
running a close second, but even major VMS packages like GCG are at least
considering a move to Unix. As author of both a general purpose sequence
analysis package and a database package, I have found the SUN environment
to be the best programming environment I have ever worked in. The SUN
languages are implemented very consistently, making it very easy to call
routines written in other languages. The same screen debugger works for C,
Pascal, ModulaII and Fortran.
Productivity:
Having a Sparc on my desktop, I find that I am using it all the time,
because it is such a great productivity tool. Once you have gotten used to
being able to have multple windows open simultaneously on different files
and directories, you will wonder how you used to work without them. When I
was looking at AIX (IBM's Unix) three years ago, they didn't have true
multitasking. The best they could do was to give you multiple sessions, and
you could switch the screen from one session to another, which is a poor
substitute.
Cost:
Although SUN's are pricey at the high end, SUN is very good about
establishing University discounts and site licenses. Also, SUN has now come
out with entry-level workstations that start at the $3-4000 range, so
there's no reason why everyone can't simply have a client SUN on his desk,
accessing a central server.
About the only disadvantage of SUN's is that they are still not a Personal
Computer, in the way that a NeXT is. You still have to be system
administrator for your own machine. However, if you have a client-server
system anyway, you're pretty much committed to having somebody act as
system administrator.
Hope this helps.
===============================================================================
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Department of Plant Science | incompatible with our Abrahamic concept of
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Office phone: 204-474-6085 | begin to use it with love and respect.
FAX: 204-275-5128 | Aldo Leopold, 1948 A SAND COUNTY ALMANAC
===============================================================================
From: krawchuk at cpsc.ucalgary.ca (Brent Krawchuk
By all means, buy NeXT machines.
They are trivial to network together,
fantastically easy to program,
great graphics and is Display Postscript based!
fully BSD unix compatible (runs pretty well everything the sun does),
and by far, the least expensive.
Most of all, the window system is far better than X,
though you can run X if you want to.
(Oh yeah, reads/writes MSDOS disks out of the box, plus there are
packages around to simulate PCs and Macs).
BTW, I have seen impressive molecule modelling programs
for the NeXT which were written in a couple of days, I think.
The NeXT machine is a pleasure to work with.
I have not met -anyone- who doesn't think so.
You definitely won't be disappointed.
I could go on, but I got to get back to work on this gross
SUN Sparcstation 2 ;-)
Bj <brent at cognos.cuc.ab.ca> {NeXTMail preferred}
<krawchuk at cpsc.ucalgary.ca> {In case of bounces.}
From: owhite at NMSU.Ed
my lab at New Mexico State University, has written a variety of
software tools for DNA analysis. all of our software is public domain.
I am quite confident that much of the software that is freely
distributable can be used on most workstations. personally, my only
experience is working on a SPARCstation, and I think of these machines
as incredibly powerful computers. considering the enormous usage of
SPARCstations in many fields computational work, I would regard
purchasing SUN equipment a safe discision.
owen white
From: dank at blacks.jpl.nasa.gov (Dan Kegel
Sun is lagging in technology, but their IPX workstation is quite
reasonably priced for its performance (I just bought one for $10 000,
performance is supposedly same as sparcstation 2). They are lagging
worst in floating point performance; their price/performance there
is about half as good as HP or IBM.
It is not a disadvantage the SUN is not part of OSF; nobody knows yet
what OSF members will do. HP for instance has said it will use the insides
of OSFix but retain the outsides of its own HP/UX operating system,
negating some of the benefits of OSFix.
In any case you should choose the application that you care most about,
and run a benchmark on two machines (say, the Sun IPX and an HP 700-series
workstation). Sorry I don't have any data for yo
