Subject: Summary: OpenGL on Linux and Insight/Sybyl

From: Malcolm Gillies <[email-masked]>
Date: Thu, 06 Jul 2000 12:49:21 +0200

I've compiled a (slightly edited) list of replies to my question, as
well as some ensuing discussions.

Thank you to everyone who responded.

The general impression I gained is that hardware accelerated OpenGL
on Linux has similar performance to SGI for many molecular graphics
applications, and that people who are using it are quite satisfied.
In particular, various in-house and non-commercial programs are
reported to work well.

Unfortunately, noone seems to have succeeded in getting MSI Insight
(aka Biosym InsightII) working with a remote Linux OpenGL display.
At first glance, this appears to be a minor problem with Insight
recognizing the remote display type correctly, but there may also be
other more subtle difficulties to overcome. I'd be interested to know
MSI's response to this problem.

I received one clear report that Sybyl can be used in the way I
propose, though apparently there is a problem with object selection.
Given that Tripos are supporting configurations using a PC X server
with OpenGL (e.g.  Exceed 3D), I would expect that fixes or
workarounds shouldn't be too difficult.

I didn't hear from anyone who is using the new SGI Visual
Workstations.
--
Malcolm Gillies <[email-masked]>
PhD student, computational medicinal chemistry
Dept Medicinal Chemistry, Faculty of Pharmacy,
Utrecht University, The Netherlands
------- Messages

Date:         Mon, 03 Jul 2000 11:55:21 +0200
From:         Malcolm Gillies
Subject:      CCL:OpenGL on Linux and Insight/Sybyl - any experiences?
Message-Id:   <[email-masked]>

I'm interested in hearing about any experiences using Linux with an
X server supporting OpenGL/GLX as a remote display for modelling
programs such as MSI Insight or Tripos Sybyl.

In particular, I'd like to hear if the following kind of setup is
workable in practise:

* Insight running on SGI
* Linux 2.2.* kernel on x86
* Nvidia video card (GeForce 256/GeForce 2 GTS/Quadro)
* Nvidia OpenGL Linux reference drivers and Xfree86

But I'm also interested in information on other video cards, drivers,
or the new SGI Visual Workstations (VPro graphics) under Linux.

If this sort of configuration is practical, then it could be a cheap way
of expanding a modelling lab with extra workstations for light use by
students, etc.

------- Message 2

Date:         Mon, 03 Jul 2000 14:29:59 +0200
From:         Sigismondo Boschi
Message-Id:   <[email-masked]>

Dear Malcolm,

I have installed the glx module for the Matrox G400. It is a module
in development, for Xfree 3.x You can find it and information about
it at http://www.matroxusers.com/

It works quite fine interfacing MSI cerius2 (InsightII does not
recognize it giving the error "Couldn't get initial visual in
app_init_display" indeed!  Xvision for windows does the same) running
both on IBM rs6000 (SP) and Origin2000. The main lack is the "depth
cueing". For the rest it works fine, very fast rendering atoms and
isosurfaces, comparable with an SGI O2. The PC is a PentiumIII
450MHz, Linux Redhat 6.1, XFree86 3.3.5, matrox G400 single-head
16MB.  Also other software runs fine: gaussview and gOpenMol for
example.

Checking now the site "matroxusers" I have found they have included
the DRI driver (direct rendering interface) also for this board in
the very new Xfree86 4.0.1. More information at
http://www.xfree86.org and in particular
http://www.xfree86.org/4.0.1/RELNOTES.html

Actually I have not tried it: I have found it just now. I will let
you know if in the next days I will be able to try it.

Please, post the summary to CCL!  Thanks

Kind regards

   Sigismondo

-- 
 -------------------------------------------------------------------------
|Sigismondo Boschi, Ph.D.                |tel: +39 051 6171559            |
|CINECA (High Performance Systems)       |fax: +39 051 6137273 - 6132198  |
|via Magnanelli, 6/3                     |                                |
|40033 Casalecchio di Reno (BO) ITALY    |WWW: http://www.cineca.it       |
 -------------------------------------------------------------------------

------- Message 3

Date:         Mon, 03 Jul 2000 09:27:47 -0400
From:         "Bienstock.Rachelle"
Message-Id:   <[email-masked]>

Malcolm:

Although I am by no means an expert in this area, it was my
impression that the MSI Insight software package currently available
will not run on Linux.  First, because it is commercial software
package, you are only given the executibles which are currently only
sold and available as compiled code under Irix.  MSI is working on a
commerical version which will be available for Linix.  You may want
to consult with MSI to see when this will be available.

Rachelle

------- Message 4

Date:         Mon, 03 Jul 2000 09:54:06 -0400
From:         "Bienstock.Rachelle"
Message-Id:   <[email-masked]>

> I'm aware that neither Insight nor Sybyl will run on Linux. What I'm
> actually proposing is that the software continue to run on an SGI
> machine, but with a remote Linux X server as display.

Yes, I guess it should work.  Actually, I know at several
universities they have been running the MSI Insight software using
the Hummingbird Exceed software on the PC as an X-terminal emulator.

------- Message 5

Date:         Mon, 03 Jul 2000 10:07:00 -0400
From:         "Bienstock.Rachelle"
Message-Id:   <[email-masked]>

> Right, the crux of the question is if they are using -opengl graphics or
> -axxess X graphics; the latter has been possible for some time, but comes
> at the cost of much more primitive graphics.
> 
> Do you know if they are using a version of Exceed which supports OpenGL
> graphics (I think it's called Exceed 3D)?

You know,I believe it was using the Axxess X graphics. At one time I
had thought of setting this up (to run the software at home on my PC)
and received lots of replies from people who were using the Insight
II software this way with Exceed.

If you search the Comp. Chem. archives you may find some info.
Everyone told me though that the software ran so slowly that it was
almost to the point of being unusuable- i.e.  rotating large
molecules etc.

------- Message 6

Date:         Mon, 03 Jul 2000 09:40:34 -0400
From:         Zsolt Zsoldos
Message-Id:   <[email-masked]>

Dear Malcolm,

My experience is not with Nvidia card, so I cannot comment on its
performance.  However, we have an SGI Indigo2 Impact and a number of
Linux computers. One of the Linux machines have an ELSA Gloria L/MX
graphics card and we use it with the XiG 3D Accelerated-X OpenGL
driver and X server combination (see http://www.xig.com/). This
combination on a 2.2.5-15smp kernel 2x350MHz Pentium II computer can
provide a very comparable performance to the Impact.  We use it with
our own modelling package, not Insight or Sybyl as we are a
computational chemistry software company ourselves. We use standard
OpenGL/GLX graphics in our software which runs on both the SGI and
the Linux-PC.  We use it in every combination (running the software
on either platform with both local and remote display) and each
combination works fine for the OpenGL graphics. On the other hand, we
experience some color mapping problems with non-OpenGL graphics
(menubars, button colors etc) wen running on Linux and remote
displaying on SGI.  But this might be to do with the Java Swing
library.

The mentioned XiG X server provides drivers for a large number of 3D
accelerated OpenGL cards, including the cheap Permedia2 based cards,
like Diamond FireGL 10 00Pro.  Those definitely provide a very cheap
alternative to SGI with usable performance.

I hope you find this information useful.  I'd be very interested to
see a summary of the replies you get, especially if you hear anything
about the SGI Visual Workstations graphics under Linux.

Best regards,
Zsolt

- -- 
Zsolt Zsoldos, PhD.                                         
Simbiosys Inc.                    phone: 1 - 416 - 741-4263
135 Queen's Plate Dr., Unit 355     fax: 1 - 416 - 741-5084
Toronto, Ont, M9W 6V1, Canada      http://www.simbiosys.ca/

------- Message 7

Date:         Mon, 03 Jul 2000 10:56:56 -0300
From:         antonio luiz oliveira de noronha
Message-Id:   <[email-masked]>
In-Reply-To:  <[email-masked]>

Mr. Gillies
	In my lab we use Linux MANDRAKE 7.1 and we had in our
workstations TRIPOS/SYBYL and MSI/INSIGHTII. Both work fine with the
linux box. Our video card is pretty simple, it's a Trident with 2 M.
Also, vwe only use the PCs with linux as terminals, but work very
fine!

Best Regards!!

 ___________________________________________________________________
|                                                                   |
|Antonio Luiz Oliveira de Noronha                                   |
|Medicinal Chemistry of Organotin Compounds                         |
|NEQUIM - Medicinal Chemistry Group                                 |
|Chemistry Departament - DQ                                         |
|UFMG - Federal University of Minas Gerais - Brazil                 |
|Av. Antonio Carlos, 6627 - Campus Pampulha                         | 
|CEP 31270-901 - Belo Horizonte - MG - Brazil                       |
|VOICE +55 31 499 5765   -   FAX +55 31 499 5700                    |
|___________________________________________________________________|

------- Message 8

Date:         Mon, 03 Jul 2000 16:03:16 -0300
From:         antonio luiz oliveira de noronha
Message-Id:   <[email-masked]>

Mr. Gillies

	I check it. Yup, the INSIGHT does not work, but the SYBYL
works fine, using the x graphics.

Regards!!

------- Message 9

Date:         Mon, 03 Jul 2000 15:58:52 +0200
From:         Ezequiel Quintana Morales
Message-Id:   <[email-masked]>

Hi,

We use on a daily basis, linux boxes as terminals of SGI's running
Sybyl. We use SuSE Linux starting from 6.2 to 6.4, and Nvidia TNT2
or GeForce 256 DDR video cards. For us that is the best option (the
cheapest).

They all run fine (GeForce better, :-)). The configuration is very
simple and y ou only need to load the iris fonts into the linux
machines. However, we have found that running Sybyl in OGLX mode,
the selection on screen of objects can hung the SGI. In XDEV mode
there is no problem.

Hope this help. If you want more details, please let me know.

Regards,
Ezequiel

- --------------------------------------------------------------------
Dr. Ezequiel Quintana Morales
Instituto de Investigaciones Quimicas
Centro de Investigaciones Cientificas Isla de la Cartuja
c/ Americo Vespucio, s/n
41092 Sevilla
Tel: + 34 95 4489564           Fax: + 34 95 4460565
- --------------------------------------------------------------------

------- Message 10

Date:         Mon, 03 Jul 2000 17:59:12 +0200
From:         Ezequiel Quintana Morales
Message-Id:   <[email-masked]>

Malcolm,

> I guess you are using the Nvidia reference Linux driver. Is it
> reasonably stable?

I don't use the nvidia driver but the one that come with the SuSE
distribution. I tried several: Utah-glx and nvidia drivers but SuSE
in collaboration with UTAH-glx has one which works fine and it's
easier to install (just from the CD).

> > They all run fine (GeForce better, :-)). The configuration is very
> > simple and y ou only need to load the iris fonts into the linux
> > machines. However, we have foun d that running Sybyl in OGLX mode,
> > the selection on screen of objects can hung th e SGI. In XDEV mode
> > there is no problem.
> 
> That's interesting. So the SGI hangs, rather than the X server on
> the Linux machine?
> 
> I was hoping that things would work stably in OGLX mode.

I don't know if you has used Sybyl too much, but it's a very tricky
software. If you select objects using the dialog boxes everything is
ok, but if you need to point with the mouse on the screen Sybyl
crashes and most of the times hangs the computer (OGLX mode).

For TRIAD (NMR module of Sybyl), the best configuration I had tested
is XDM/Fvwm2(or mwm), but never KDM/KDE, and if you want a working
rubber band you need to have activated Num Lock.

> If possible, could you tell me which software versions you are using?
> 
> - Sybyl

6.6

> - Xfree86

3.3.6 (but 3.3.5 and 4.0 are also ok)

> - Nvidia drivers

As I told you before I use the drives which come with SuSE 6.2 and 6.4
(6.1 doesn't have them and I haven't tried 6.3).
For SuSE 6.2 they are:
   glxriva-1.0.8
   mesa-3.0.48
For SuSE 6.4:
   glx-000229-20
   mesa-3.1.35

------- Message 11

Date:         Tue, 04 Jul 2000 11:15:20 +0200
From:         Ezequiel Quintana Morales
Message-Id:   <[email-masked]>

Malcolm,

> I had the impression that the SuSE drivers only support the
> Riva 128/128ZX/TNT/TNT2 graphic boards of NVIDIA, and not the GeForce?

SuSE 6.4 supports also GeForce 256, GeForce 256 DDR and Quadro.

------- Message 13

Date:         Mon, 03 Jul 2000 16:24:44 +0100
From:         "BAYARD Francois"
Organisation: COMS
Message-Id:   <[email-masked]>

I am also very interested by this topic.
(I use sybyl)

Thanks to forward the answers you will collect.

Francois BAYARD 

Laboratoire COMS - CNRS/CPE UMR 9986
Bat F308  CPE LYON 
43 Bd du 11 Novembre 1918 - BP2077
F-69616 VILLEURBANNE CEDEX - FRANCE       
- -------------------------------
                              http://www.cpe.fr/lcoms
tel    (+33) 4 72 43 18 08  fax    (+33) 4 72 43 17 95

------- Message 15

Date:         Mon, 03 Jul 2000 17:25:25 -0500
From:         John Stone
Message-Id:   <[email-masked]>

Hi Malcolm,
  I saw your post on CCL asking about hardware accelerated OpenGL on
Linux.  We've recently been woking with using the NVidia TNT2,
GeForce 256, and Geforce 2 GTS boards with Linux and XFree 4.0, and
have had some great results.  We are running VMD, our own molecular
visualization tool, which you may have already seen or heard of:
http://www.ks.uiuc.edu/Research/vmd/

Running VMD, a 700MHz Athlon with a GeForce 2 GTS easily doubles an
Onyx2 InfiniteReality2 on rendering speed with a 4,000 atom molecule
displaying in VDW representation.  The GeForce board isn't quite as
fast on lines, and it doesn't have the same hardware antialiasing
that our Onyx2 does, but for $300 US, there's no reason to question
the utility of having a GeForce... :-)

We've also run VMD with some of the other PC video boards that
support hardware 3-D on XFree 4.0, but I'd have to say that the only
ones worth looking at are the NVidia GeForce 2 GTS boards...  For
$300 US, you can get a linux box setup that'll roast most of the SGI
boxes that are out there, certainly so for the kinds of rendering
done in molecular graphics.  There are still a number things that the
SGI machines are better at, but rendering molecules isn't one of
them.  The only thing I can think of that the current generation
NVidia boards lack, that we want to have in our lab, are stereo sync
outputs for use with the CrystalEyes stereo glasses.  Fortunately,
there are some new low-end LCD stereo glasses coming out for PCs that
work with almost any video board, it'll only be a matter of time
before we see support for them in XFree/Linux....

Anyway, if you have questions about Linux and XFree 4.x, or on
getting/using VMD, let us know, and we can help you out.

  John Stone

- -- 

Theoretical Biophysics Group                             
Beckman Institute              http://www.ks.uiuc.edu/~johns/
University of Illinois         Phone:  (217) 244-3349
405 N. Mathews  Ave              FAX:  (217) 244-6078 
Urbana, IL 61801, USA          Unix Is Good For You!!!

------- Message 16

Date:         Tue, 04 Jul 2000 10:30:08 +0200
From:         Stefan Konietzny
Message-Id:   <[email-masked]>

Hi Malcolm,

if it need not to be Linux, you should also try the Hummingbird
Exceed 3D X-Server for Windows.  They send you an evaluation copy
when you ask for.  Of course it's not free, but it worked really fine
with my ErazorIII (TNT2) Card. Most of those programs on our
origin2000 that where denoted "for SGI Workstation only" worked fine
on my PC-Display.  The Linux solution is cheaper, but the Windows
solution is still much cheaper than to buy several SGI's.

Don't blame me for giving the advise to use Windows :-), i'm a Linux
user, but the Exceed-X-Server worked better on my PC than the 3.3.6
plus the appropriate extensions from Nvidia.

Have fun, Stefan.

------- Message 17

Date:         Tue, 04 Jul 2000 13:43:10 +0200
From:         Stefan Konietzny
Message-Id:   <[email-masked]>

Hi Malcolm,

it was Gaussview in OpenGl mode, Cerius2 and InsightII.  It's a few
weeks ago, so i'm not really sure any more.  Further on all those
little programs that our sysop put in the toolchest with the comment
"for SGI only", that are 3D plots of CPU usage etc.

If you like to use Insight without OpenGL in the meantime try (is it
InsightII?) to start it with the --axxess option; that forces the
program not to use OpenGL but usual X-Graphics.

Stefan.

------- End of Forwarded Messages