Summary: Xmol on O2 SGI
- From: Danilo Gonzalez <fgonzale # - at - #
lauca.usach.cl>
- Organization: Universidad de Santiago de Chile
- Subject: Summary: Xmol on O2 SGI
- Date: Tue, 09 Dec 1997 16:24:07 -0400
Hi!!
I received many answer about the following question:
***********************************************************************
I trying to run XMOL on a SGI O2, but when I run it, an error
message
"Wrong Architecture" appears.
Can anybody help me to solve this problem?
***********************************************************************
In summary, XMOL not run in IRIX 6.X, the solution in only run XMOL in
machine with IRIX 5.X, and run via remote display.... ;^(
Other possibility is to use other alternative program how VMD
ay way, I put it all the answer received.... Thanks again!
*****************
Xmol 1.3.1 has been compiled under old IRIX (even before 5.3) in the
COFF
executable format. Newer IRIX-es (starting with 6.1) no longer support
this format; the executable standard is now ELF. You have to go back to
IRIX 5.3 to run xmol. To make sure type this command:
file xmol
Hope this helps,
Robert Fraczkiewicz
University of Texas Medical Branch
*************************
Dear Fdo Danilo Gonzalez Nilo,
According to my experience, this is because the difference in the IRIX
version. You know SGI O2 runs IRIX6.3 which is very unique. So, try to
compile XMOL on SGI O2 again. Good luck.
Arthur
_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
_/ Arthur Wang Doctoral Candidate _/
_/ Molecular Design Lab _/
_/ Institute of Physical Chemistry, Peking University _/
_/ Beijing 100871, P.R.China _/
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**********************************
Hi,
The short answer is that you can't run Xmol on an O2. The SGI
version of Xmol uses the COFF executable format which is not supported
by
versions of IRIX after 5.3 . Last I heard Xmol was not still being
developed so it is unlikely that it will become available for new
machines
and operating system versions.
Dave Young
youngd2 # - at - # mail.auburn.edu
------------------------------------------------------------------------
Live long and maintain marketable job skills.
------------------------------------------------------------------------
***********************
Hi Danilo,
the problem we all have is that there has been a big change in the
operating
system of SGI. The result is that executable programs which had been
compiled
to the old COFF format are no longer supported since IRIX 6.2 (or 6.0
?).
As you will probably have IRIX 6.4 (or eventually 6.2) you can no longer
execute
programs in this old COFF format.
By the way, you can check your version by entering "/sbin/uname -r"
and
will
probably get an output like "6.2" or "6.4".
Unfortunately the XMol crew doesn't want to spread their program's
source code
(which one could compile for nearly any operating system that is derived
from
UNIX). Additionally, they do not recompile their old version of XMol to
the new
ELF executable format.
In order to work around this problem, we use an old SGI workstation
running on
IRIX 4.0.5 for executing this program and do this with the option
"-display=<another.host.that.runs.on.irix.6.2>:0.0". This is by
now the
only
way to get at least the graphics output and control panels piped to our
new SGI
INDIGO2, where we can use this program.
Your problem is now that you'd need an SGI machine that runs on an old
IRIX...
Hope this helps (or at least answers your question),
Best Regards,
Michael
**********************************************
* Dr. Michael Schimeczek *
* AK Boche *
* FB Chemie der Philipps-Universitaet *
* Hans-Meerwein-Str. *
* D-35032 Marburg/Lahn *
* email: schimi # - at - # sg1512.chemie.uni-marburg.de *
**********************************************
************************
My guess is you are using the wrong executable on the O2. Either find
an
executable for the O2 or recompile XMOL on the O2 itself.
--
Jeffrey L. Nauss, PhD Telephone: 513-556-0148
Dir. Molec. Model. Serv. Fax: 513-556-9239
Department of Chemistry e-mail: Jeffrey.Nauss # - at - # UC.Edu
University of Cincinnati URL http://www.che.uc.edu/~nauss
***********************
Hi,
usually you get an error message like this if you try to run an MIPS4
(R8K/R10K)
executable on a MIPS2 machine (R4K/R5K). In this case you need to
recompile
XMOL for your machine architecture. Normally a MIPS2 executable should
run on a
MIPS4 machine.
Regards
Stefan
Disclaimer: All opinions expressed here are mine, not my employers.
--
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*****************************
Hola
Tambien tenemos una SGI O2 y queremos instalar xmol. De momento xmol lo
tenemos funcionando sin ningun problema en estaciones IBM RS600. No se
como
se resuelve tu problema, pero si lo logras te agradeceria que me lo
contases.
Un saludo
Luis Carballeira
Quimica-Fisica
Universidad de Vigo, Galicia
Espana
*********************************
Hi !
As far as I know, xmol only runs with irix 5.3. Everything higher won't
work;
If there will be a version running on any irix higher than this, please
tell me !
Cheers
CR
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| Institut fuer Organische Chemie |
| Universitaet Wuerzburg |
| Computational Chemistry Group |
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| Am Hubland | email : rummey # - at - # chemie.uni-wuerzburg.de |
| 97074 Wuerzburg | voice : +49-(0)931-888-4750 |
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***********************
There is only one problem: IRIX-6.x does not longer support
COFF binaries:
$ file /usr/local/bin/xmol
/usr/local/bin/xmol: MIPSEB COFF executable (paged) - version 2.40
There are no chances to get a newer version of xmol ( i had a
correspondence
with the developers of xmol).
You have to use other programs.
Ciao
Bernd Melchers
--
Bernd Melchers | melchers # - at - # FU-Berlin.DE
Freie Universitaet Berlin | "We don't write software, we compose it."
AG Macromelecular Modelling - Prof. Dr. E.W. Knapp
for more information see http://www.chemie.fu-berlin.de/~melchers
**********************
Nobody can help you. IRIX 6.3 (which is the only operating system O2 is
capable of running reliably at the moment) does not support COFF
executables. The only way to make Xmol run under 6.3 is to recompile
it using one of the ELF executable formats 6.3 supports. However,
since Xmol is not supported or developed anymore, and the source
code is not publicly available, this is not possible. Tough luck...
Regards,
/Serge.P
*********************
I'm afraid there is not much you can do about it. As you know, part of
Xmol is distributed as an executable and this has been compiled for
different SGI machines, the newest of them being IRIX 5.x
As far as I know, the Minnesota team who created Xmol do not plan to
upgrade anymore and there we have 1.3.1.1 (if I remember well) as the
latest
version, which does not work on IRIX 6.x machines, thus including SGI
O2.
My suggestion would be: install Xmol in an older machine and then run
it
from your O2 setting the proper DISPLAY.
If anyone else comes up with a Xmol version for IRIX 6.x please let me
know,
I would also be extremelly interested on it (gsastre # - at - # itq.upv.es).
Cheers.
German
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German Sastre URL:
http://www.ri.ac.uk/DFRL/G.Sastre
Instituto de Tecnologia Quimica e-mail:
gsastre # - at - # itq.upv.es
Universidad Politecnica de Valencia Phone: +34
(9)6-387-7803
Camino de Vera s/n; 46071 Valencia (Spain) Fax: +34
(9)6-387-7809
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**********************
Hi Danilo,
I think that happens because you are running IRIX 6.2 or higher. Xmol
is not supported for those platforms. I have not heared that anyone was
still working on it, so it seems unlikely that it will work in the near
future.
Cheers,
Roelant
****************************
Hi,
the problem you have is that IRIX 6.x does not support the elf binary
format any more. Since XMol is not available in the right format (coeff)
you'll have to choose another molecular viewer. You can try VMD
(http://www.ks.uiuc.edu/Research/vmd/), that's what I use.
Cheers,
Dominik
--
------------------------------------------------------------------
Dominik Horinek
Institut fuer physikalische und theoretische Chemie
Universitaet Regensburg
Universitaetsstr. 31, 93053 Regensburg, Deutschland
email: Dominik.Horinek # - at - # chemie.uni-regensburg.de
------------------------------------------------------------------
**************************
Hello,
The reason XMol doesn't work on the O2 is that is was compiled for
IRIX 4. IRIX 6, which the O2s use, doesn't support those binaries any
more. Since XMol is no longer updated and source isn't available, you
will have to use other programs. The one I know the most (because I
helped develop it) is VMD at http://www.ks.uiuc.edu/Research/vmd/ .
Other good, free ones I've heard of are MOLMOL and gOpenMol, which you
should be able to find with a net search program.
Andrew Dalke
dalke # - at - # mag.com
******************
XMOL will not run on an O2. The executable was compiled for an
entirely different binary architecture on earlier SGI's.
Here, we have O2s, Indigo 2s and and Indigo. The only computer
that will run XMOL is the Indigo.
As far as I know, there are no plans to update the executable.
There has been much discussion in CCL about this; there are alternate
packages for many situations.
Dan Strahs
**********************
--
Fdo. Danilo González Nilo
University of Santiago de Chile, Faculty of Chemistry and Biology,
Computational Chemistry Lab.
Phone: (562) 681 2575-Anexo:799 ; Fax: (562) 681 2108
URL : http://quimbio.usach.cl/~danilo/
E-mail: fgonzale # - at - # lauca.usach.cl
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