Subject: Indys with 8-bit graphics - summary

From: "Graham W. Mullier" <[email-masked]>
Date: Tue, 7 Jun 1994 10:18:23 +0000 (BST)

my original query was:

> Dear netters,
>  
> We are thinking of buying an SG Indy with base-level graphics (i.e. 8-bit)
> to supplement the other workstations we have. We don't think we need
> blistering 3-D graphics performance with this machine because we already have
> an Indigo2 Extreme to do the more complex work for us.
>  
> We want to be able to run Sybyl, plus perhaps the CSD graphical interface,
> Spartan and Oxford Molecular's Cameleon. With Sybyl we would be using it
> mostly for small-molecule stuff plus some molecular spreadsheet work.
>  
> Our problem is that we haven't been able to see a demo machine yet, and hence
> we can't decide whether the 8-bit graphics will be good enough for our
> purposes.
>  
> SO: do any of you have experience of a base-level Indy? What's the minimum
> specification that we should be looking at, in your opinion?

and the responses seem to be in favour of using 8-bit graphics,
although some people clearly believe that 8-bit is unusable.

We did (finally) get a chance to compare an 8-bit Indy with
a 24-bit Indy, both running Sybyl. The decision was that, for us,
8-bit graphics would be good enough. Remember that we already
have high quality devices (a ps390 with stereo, plus 2 SGs at
Elan/Extreme level), so the only requirement is something to replace
our tired old Personal Iris 4D/20.

And now, those responses in full (well, apart from some trivial editing
indicated by [...]):
--------------------------------------------------------------
Date: Fri, 20 May 1994 08:13:17 -0400
From: "Jeffrey L. Nauss" <[email-masked]>
Subject: Re:  CCL:Is anyone using 8-bit Indys for modelling?
To: "Graham W. Mullier" <mullier>

Can't help you with your problem but I would be interested in  
any responses you may get.  We are considering getting an Indy to  
run Biosym's InsightII.

Thanks....
                                                Jeff Nauss

****************************************************************************
*  UU    UU             Jeffrey L. Nauss, PhD                              *
*  UU    UU             Director, Molecular Modeling Services              *
*  UU    UU             Department of Chemistry                            *
*  UU    UU CCCCCCC     University of Cincinnati                           *
*   UU  UU CCCCCCCC     Cincinnati, OH 45221-0172                          *
*    UUUU CC                                                               *
*         CC            Telephone: 513-556-0148    Fax: 513-556-9239       *
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*          CCCCCCCC     e-mail: [email-masked]                    *
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****************************************************************************

--------------------------------------------------------------
Date: Fri, 20 May 94 12:55 GMT
From: "ADRIAN STEVENS, DEPT. OF CHEMISTRY, UNI. OF PORTSMOUTH" <[email-masked]>
To: MULLIER <MULLIER>
Subject: 8-bit Indy Workstation - Yes!

Dear Graham Mullier,

I noted that you are looking at the Indy workstation with an interest to
acquire.  You wanted to know about whether other chemists have used this
machine to do modelling.  As a postgrad for the Uni. of Portsmouth,
I am engaged in a modelling study of zeolites.  We use an Indy workstation
to perform all our molecular modelling and Monte Carlo calcs., etc.  We    
have a 1Gig HDD together with a secondary 1Mb CPU cache.  The processor
used is a 100MHz R4000 chip.  In addition we have set up a 128Mb swap space
to compliment the 64Mb RAM.  We have NOT chosen the 24bit graphics, instead
we stayed with the standard 8bit supplied.

This setup is used to run the Biosym software InsightII with some other extras
It has remained an excellent machine throughout all the systems investigated
and can quite happily model the very vast 4000+ atom systems of zeolites.

The graphics speed and quality is more than adequate for the requirements
and does not present any refresh slowdown.

It is my personal oppinion - and treat it as thus - that the setup above
is the very least that should be considered for all but the most demanding
of applications.  The HDD is sufficient for our purposes but will vary     
depending on your needs.

[...]

Adrian.

Email: [email-masked]

Adrian Stevens,
Department of Chemistry,
University of Portsmouth,
St. Michael's building,
White Swan Road,
Ports., Hants., UK.  

--------------------------------------------------------------
Date: Fri, 20 May 1994 08:21:35 -0500 (EST)
From: "LEONORE A. FINDSEN" <[email-masked]>
Subject: Re: CCL:Is anyone using 8-bit Indys for modelling?
To: mullier

Graham

Well, I haven't gotten one, but since I will be purchasing an Indy after I move
to my new position, I have looked into it. This is mostly from my e-mail
corresponding with Still's group (MacroModel). I have seen a demo for the
24-bit graphics and 19" screen and the resolution there is very good. What they
said is that if you want reasonable looking graphics, you really need the
24-bit graphics. This is especially true if you want to get the large 19"
screen. The number of pixels is the same for both machines so the large screen
will give you lower resolution. However, the graphics are poor even with the
8-bit graphics and the standard 16" screen. What I have decided to get is the
24-bit graphics with the 19" screen. However, this will be my top-end graphics
device that will be available on the island (see below) so I do need the better
resolution.

I hope this helps,
Leonore

new address: Department of Chemistry
             University of Hawaii at Hilo
             Hilo, Hawaii 96720

-------------------------------------------------------------------------------
Leonore A. Findsen  |e-mail:[email-masked]|For I am a cat, &
College of Pharmacy |      :[email-masked]      |since when has a
University of Toledo| voice:(419) 537-2729                  |cat given a
Toledo, OH  43606   |    FAX:(419) 537-4940                 |straight answer
-------------------------------------------------------------------------------

--------------------------------------------------------------
Date: Fri, 20 May 94 08:45:49 CDT
From: Brad Thompson <[email-masked]>
Message-Id: <[email-masked]>
To: mullier
Subject: Re: CCL:Is anyone using 8-bit Indys for modelling?

Sorry -- this is a request, not a reply.
  
We're in a similar position, in that we're considering getting an
Indy (SGI Indy 4600PC) to run Spartan 3.0 and related stuff.  If
you get any really worthwhile replies, would you let me know?
  
                    | H. Bradford Thompson   [Brad]
[email-masked]       | Scholar in Residence, Chemistry & Physics
                    | Gustavus Adolphus College, St. Peter MN 56082-1498

--------------------------------------------------------------
From: Peter Shenkin <[email-masked]>
Message-Id: <[email-masked]>
Date: Fri, 20 May 1994 10:48:35 -0400
In-Reply-To: "Graham W. Mullier" <[email-masked]>
        "CCL:Is anyone using 8-bit Indys for modelling?" (May 20,  9:35am)
To: "Graham W. Mullier" <mullier>
Subject: Re: CCL:Is anyone using 8-bit Indys for modelling?

I have an 8-bit, low-resolution Indigo.  I use it for molecular
visualization, though not with Sybyl.

The dithering you get with 8-bit graphics gives an ugly and
annoying display, and the low resolution is annoying, too --
especially since not all applications have appropriate X resources
to display reasonably to the low-res display;  this is particularly
true if you have the combination of low resolution and 19" monitor,
which I do.

I'd recommend strongly that you get high-res, 24-bit graphics, even
if you get no 3D graphics acceleration hardware.  If, however, you
do go with low-resolution graphics, get the 16", not the 19" monitor.

I have no personal experience with the combination of 8-bit with
high-resolution graphics, but the dithering thing will affect this
combination as well;  it just makes the display much less attractive,
and much less fun to use.

        -P.
--  
*********** After the revolution, everyone will have a home page. ***********
Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ.,
New York, NY  10027;     [email-masked];     (212) 854-5143
*****************************************************************************

--------------------------------------------------------------
Date: Fri, 20 May 1994 16:59:36 +0200
From: [email-masked]
To: mullier
Subject: Re: 8-bit Indy

I have no experience with Indies but I have tested SYBYL, INSIGHT and
PROSIMULATE on an 8-bit Indigo (R3000, Irix 4.0.5.f, 32 MB Ram) for about
3 weeks and my impression was that for the applications you mentioned an
8-bit machine should work fine. Even my RNA hammerheads with 50-70 nucleotides
haven't brought the machine down as long as I avoided using spacefil models
or connolly surfaces.

Regards,

                        Peter Reinert

--------------------------------------------------------------
Date: Fri, 20 May 94 09:18:00 -0600
From: "Darrell R. Davis" <[email-masked]>
To: mullier
Subject: CCL:Is anyone using 8-bit Indys for modelling?

We bought 6 Indys: We were told that the 8 bit Indys would not work
well for modelling. Biosym actually had a lengthy release describing
the problems and we were convinced.  We went with 5 24 bit PCs and 1
24 bit SC.  These work well with Biosyms Insight/Discover software
which is what we used to demo the machines.  SGI has a real good deal
on PC to SC upgrade at the moment so we will probably move all of our
machines to SC level.

I also have and Indigo2 XZ and it doesn't pain me that much to use the
Indys.   

--------------------------------------------------------------
 Darrell R. Davis  
 Medicinal Chemistry  
 University of Utah  
--------------------------------------------------------------

--------------------------------------------------------------
From: Csonka Gabor <[email-masked]>
Message-Id: <[email-masked]>
To: mullier
Subject: Indy 8-bit

Hello,

Indy is working fine with SYBYL, Macromodel, Spartan etc.
8-bit is satisfactory. Minimum RAM is 32 MB, minimum
processor is MIPS 4600, best processor is MIPS 4400SC
150 MHz. The 4000PC processor is rather slow.

Hope this helps
----------------------------------------------------------
Gabor I. Csonka                 Budapest University of Technology
Tel/FAX: (361) 18.12.177        Inorganic Chemistry Dept. Ch. Bldg
[email-masked]  H-1111, Bp. Szent Gellert ter 4
----------------------------------------------------------

--------------------------------------------------------------
Date: Fri, 20 May 94 11:46:58 -0400
From: George Seibel <[email-masked]>
To: mullier
Subject: 8-bit Indys
Reply-To: [email-masked]

I looked at the original 8-bit indigo as a molecular modeling
machine.  SGI's GL routines fake the "extra bits" by dithering the
image.  It works pretty well on continuous tone photographic-type
images, as long as you aren't too particular.  It works pretty poorly
for depth-cued stick figures.  However, it may be a reasonable choice
for your application anyway.  Small molecule stuff is not usually that
demanding, graphics-wise.  Spartan uses a lot of polygon-based graphics,
which should work ok, aside from the fancy transparency stuff which is
not that useful anyway.  CSD's graphical interface is pretty rudimentary;
most of it is 2D, so that would work fine.  the "3D" part of it, as it
were, is an open question.  You have an Indigo already... my opinion
is that an 8bit Indy is better than nothing, and would be useful for
enough work to make it a not-ridiculous choice.  The only thing that
would make me say "don't do it" is if you really want to do a lot of
depth-cued 3D graphics on it.

George Seibel, SmithKline Beecham
[email-masked]

--------------------------------------------------------------
Date: Fri, 20 May 94 09:17:48 -0700
From: Brian Karlak <[email-masked]>
To: mullier
Subject: Indys

We just bought an Indy to supplement our Indigo2ex as well.  We, however, got
the 24-bit color instead of the 8-bit color.  We didn't feel that the 8-bit
would be adequate for any 3D rendering in Sybyl (even, say, capped sticks mode)
The 24-bit seems to do just fine, except with one wierd bug: sometimes the
molecules come out as Escher-like figures.  When in one static position, the
molecules look just fine; upon rotation, however, different parts of the  
molecule rotate in different directions!  A phenyl may appear to be rotating  
into the screen, but the hydrogens on the phenyls seem to be rotating *out* of
the screen!  Only the shading seems to be affected, though; bond angles and
torsions remain constant.  It's a weird and disconcerting effect, though.

One other thing you might want to take into consideration is that (as far as I
am aware) the Indy is not technically supported by Tripos.  Supposedly, this
will change soon; Tripos is waiting to be sure that the Indy's IRIX OS is
stable or some such thing.  You may want to call them and ask.

Other than that, the Indy works great.

Brian Karlak
Onyx Pharmaceuticals

"For I am a cat, and since when has a cat given anyone a straight answer?"

--------------------------------------------------------------
From: Slawomir Blonski <[email-masked]>
Subject: Re: CCL:Is anyone using 8-bit Indys for modelling?
To: "Graham W. Mullier" <mullier>
Date: Fri, 20 May 1994 12:35:51 -0400 (EDT)

We have tested Indy with 24-bit graphics. Numerical performance of our MD code
was the same on Indy and on our Indigo 2 Extreme with R4400 processor. Graphics
program, which displays ball-and-stick models with hundreds of atoms, was about
3 times slower on Indy than on Indigo. But it is 24-bit, not 8-bit.

Slawomir Blonski

--------------------------------------------------------------
From: "Walter E. Reiher III" <[email-masked]>
Subject: Re: CCL:Is anyone using 8-bit Indys for modelling?
To: "Graham W. Mullier" <mullier>
Date: Fri, 20 May 1994 11:13:27 -0700 (PDT)

Graham,

[...]

I would suggest that you be certain to check with your preferred
software vendors (at least Tripos, Wavefunction, and Oxford Molecular)
to find out the minimum configuration THEY recommend.  One shouldn't
assume that they support AND CHECK all possible SGI configurations.  Ask
them if they've TRIED the configuration you're interested in.

I also do not have direct experience with a base Indy but did try a base
(8-bit) Indigo when I worked at Tripos, and it doesn't look very good.
It *might* be alright for small molecule work, but your nice Spartan
surfaces will probably look awful.  What looked bad in Sybyl on an 8-bit
Indigo was depth cueing and anything rendered (e.g., capped sticks).  No
depth cueing means forgetting protein displays entirely.  Graphics speed
was OK; shading just doesn't look very good.
     Extra colors, as used in depth cueing, were dithered on the 8-bit
Indigo, and this caused anything shaded to look like mush.  Maybe the
Indy is different, but I would be skeptical unless you hear otherwise.

Good luck,
Wally
========================================================================
Walter E. Reiher III, Ph.D.                            [email-masked]
Consultant in Computational Chemistry
P.O. Box 61056                                        voice 408-720-0240
Sunnyvale, CA 94088                                     fax 408-720-0378

--------------------------------------------------------------
Date: Fri, 20 May 1994 15:24:17 -0400 (EDT)
From: [email-masked]
Subject: 8-bit SGI graphics
To: mullier

We run macromodel and spartan on an 8-bit Indigo Entry without any
problem.  In working with small molecules, I have not felt that the
higher level graphics have mattered when using fancier workstations.

--------------------------------------------------------------
From: Johan Landin <[email-masked]>
Message-Id: <[email-masked]>
Date: Fri, 20 May 1994 23:59:00 -0600
X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail)
To: mullier
Subject: RE: Indy ...

Dear Dr. Mullier,

I think that you should go for an Indy R4600PC which is the latest member of
the Indy family. I have not tested this machine yet but I have used Sybyl on
several models including Indy R4000PC, Indigo R3000 XS, Indigo R4000 Elan and
Indigo^2 R4400. Based on this experience I would suggest the following minimum
configuration:

 Indy R4600PC     (62.8 SPECint92 and 49.9 SPECfp92)
 32 MB memory as an absolute minimum but 48 MB if you can afford it
 8-bit graphics
 16 inch monitor

As all the Z-buffering is done in software instead of hardware, it is very
important to have enough memory. If the performance with solid models is good
enough depends on what you mean with small molecules! If you choose 8-bit
graphics be prepared to that all solid models in Sybyl will look very ugly due
to the 24 bitplane emulation. The appearance of the other programs depends on
if they are able to swith to 8 bit mode or use emulation like Sybyl.

The performance with wireframe models is definitely good enough, this statement
is based on my experience with the Indigo R3000 XS I am writing this letter on,
this machine has lower 2D performance than the proposed Indy. I have found the
Indigo OK for running Sybyl but I am missing the ability to show solid models
as I do not have the Z-buffer hardware option. The ugliness of the emulated
24bit display is something one can live with if there are better displays
nearby.

Hope this helps
                Johan Landin

_________________________________________________________________
Johan Landin                       Tel: +46 31 773 3767, 773 3762
Dept. of Structural Chemistry      Fax: +46 31 41 6108
Medicinaregatan 9
S-413 90 Goteborg, Sweden          Email: [email-masked]

--------------------------------------------------------------

Date: Sun, 22 May 1994 09:19:26 -0600 (CST)
From: Andy Holder <[email-masked]>
Subject: 8-bit graphics
To: mullier

Dear Dr. Mullier,

  Our program AMPAC runs quite well in the 8-bit color environment on an  
SGI.  If you are doing small-moleculae semiempirical work, I think that  
AMPAC is a better choice that Spaqrtan due to our more advanced and  
robust algorithms.  I'll send a packet.

    Andy

p.s.  I'll be happy to provide you with a demo version..

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
                    DR. ANDREW HOLDER
                   President, Semichem

Semichem, Inc.            ||  Internet Addr: [email-masked]
7128 Summit               ||  Phone Number:  (913) 268-3271
Shawnee, KS,  66216       ||  FAX Number:    (913) 268-3445
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

--------------------------------------------------------------
Date: Mon, 23 May 94 08:11:20 -0700
From: Soaring Bear <[email-masked]>
Subject: Re:  CCL:Is anyone using 8-bit Indys for modelling?

It didn't take us long to add graphics card to Indy to operate Insight.
Good Luck,
                   Bear

* UU   UU        SOARING BEAR                            *
* UU   UU        Molecular Modeling Services             *
* UU   UU        Pharmaceutical Sciences, New Pharm 404  *
* UU   UU AA     University of Arizona                   *
*  UU UU AAAA    Tucson, AZ 85721                        *
*       AA  AA         where the sun shines              *
*      AAAAAAAA                                          *
*     AAA    AAA e-mail:[email-masked] *
*     AAA    AAA                                         *

--------------------------------------------------------------
Date: Mon, 23 May 1994 12:26:18 EDT
From: "CBAS25 ::P_BLADON ::CBAS25" <[email-masked]>
To: mullier
Subject: RE: CCL:Is anyone using 8-bit Indys for modelling?

Dear Graham Mullier,

    My only experience with SGI 8-bit machines is a session with limited access
to a Demo 8-bit Indigo (i.e. the original Indigo). I was interested in
porting our own INTERCHEM modelling software to it.

    While it coped fairly well with software written for the 24 bit systems,
the rendering of images involving lighting modes left something to be desired;
the dithering left rather grainy pictures.  The low screen resolution
(1024 x 768) was also a drawback.  So when I came to consider the
Indy systems I decided to go for the 24-bit system, with the 16 inch screen
which has 1280 X 1024 resolution.  

    This has proved perfectly adequate. However, with the z-buffering using  
the main memory animated 3-D images tend to be displayed more slowly than
on the PI-4D-20.  The machine has only the primary cache so I would expect  
a better preformance with the SC processor. When it comes to 2-D display and  
straight computation the machine is a great improvement on the PI-4D-20 which  
I previously used.  Only some minor changes in software were needed when
it was ported to this system.

    The real test is with the software that YOU want to use.  I am not sure
whether the commercial software has been optimised for the 8-bit systems, wou  
would have to check this.

Yours sincerely

Peter Bladon

------------------------------------------------------------------------------

Thanks to everyone who took the time to respond to my query.

Sorry for the delay in producing this summary, I was too busy hill-walking
in Skye.

Graham Mullier, computational chemistry group,
Zeneca Agrochemicals, Jealott's Hill, UK.
[email-masked]

.