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-)!
DeLano Scientific LLC
Subscriber Support Services

From: [] On Behalf Of Joris Beld
Sent: Sunday, July 15, 2007 5:20 AM
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-----
[] On Behalf 
Of Mathias W.
Sent: 13 July 2007 12:48
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)...


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.


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