Re: [PyMOL] best linux distribution to run pymol

[DeLano S. <de...@de...>]

Joris,
 
Given that the vast majority of PyMOL downloads logged are not for Linux
(nearly 10 to 1 against), given the recently splintering of the Linux
desktop market, and given the importance of maintaining backward
compatibility with older Linux distributions, we must take a simple
lowest-common denominator approach toward our precompiled Linux binaries.  
 
Thus, our 32-bit Linux builds are currently prepared in a glibc-2.3
environment using GCC3.  These builds deliver reasonable performance and
compatibility on a wide set of distributions.  Obviously, we cannot prepare
optimized builds for each member of the diverse combinatorial population of
systems (DISTRO x VERSION x RUNTIME x GPU x DRIVER) where it needs to run.
Based on PyMOL usage alone, nearly 90% of our platform-specific effort
should be directed at Windows and Mac, not Linux.  Supporting one Linux
binary out of three total is already an over-allotment of effort.
 
Practically speaking, the only way to achieve top PyMOL performance on Linux
is to build from source code using libraries and compilers optimal for your
specific hardware and distribution.  That is one of the reasons why the
PyMOL open-source code is targeted at Linux 8-)!
 
Cheers,
Warren
 
--
DeLano Scientific LLC
Subscriber Support Services
 


  _____  

From: pym...@li...
[mailto:pym...@li...] On Behalf Of Joris Beld
Sent: Sunday, July 15, 2007 5:20 AM
Cc: pym...@li...
Subject: Re: [PyMOL] best linux distribution to run pymol


Dear all,

Thanks for all the input!
It seems like people do not notice any difference in speed between the
different linux distributions. Also not between KDE or Gnome. That is good
to know. 

Apparently I have some other problem (unrelated to pymol, probably
openGL/glx related) which causes the dramatic difference in speed between
our Redhat (5 fully patched) and Suse (10.2 fully patched). We are using the
latest nvidia drivers from the nvidia website.

Than, about Accelrys/Insight/Discovery Studio. We got Insight/Material
Studio (we do not have the license for DS1.6 or 1.7) to run under Fedora7.
Pymol also runs fine so probably I will switch both machines to Fedora7.
Anyway, thanks again!

Best wishes,

Joris Beld
Laboratory of Organic Chemistry
Swiss Federal Institute of Technology

Forlani Roberto wrote: 

 



  

-----Original Message-----

From: pym...@li... 

[mailto:pym...@li...] On Behalf 

Of Mathias W.

Sent: 13 July 2007 12:48

To: PyM...@li...

Subject: Re: [PyMOL] best linux distribution to run pymol



Joris Beld schrieb:

    

Dear all,

      

(unfortunately i cannot switch to Suse since i cannot get 

Insight/Discovery Studio to run under Suse).

      

This due to the ignorance of the accelrys developers. Even 

the newest version of DS (1.7) does not run on modern 

Distributions using glibc-2.4 or higher. They say that they 

only support RHEL4 which is real old (and uses glibc-2.3).

I guess it would have been no big deal to test DS on a 

glibc-2.4 system and to find the bug which is preventing it 

from running (I don't think they are still using 

linuxthreads). As of the time DS 1.7 was released glibc-2.4 

was already widely spread and so I call this ignorance. I got 

a test version of DS 1.7 and I don't want to use an old linux 

just because of this modelling program. As you pointed out 

you end up with the situation that you cannot run any other 

newer program (or only with great effort)...



--

Mad

    



 

Mathias,

granted that I am not getting money from accelrys ;) I think we should

differentiate between support to different distributions and

compatibility with different distribution.

I have an "unsupported" DS 1.7 running on RHEL 5 (with very nice native

support for nvidia graphics) and a week ago it was running "unsupported"

on a Kubuntu 7.04 (feisty fawn).

At the moment I can not say how pymol is performing on RHEL 5.



Regards,

Roberto





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