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From: Joris B. <be...@or...> - 2007-07-13 09:24:17
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Dear all, We have two molecular modeling PCs with 3D emitters (and CRT monitors). One runs the linux distribution Redhat (Gnome) and the other one Suse (KDE). It seems to us that the one running Suse/KDE is much faster than the one running Redhat/Gnome. Faster in the sense of rotating big surface rendered hexamers, 60mers. These are equivalent machines with one year old Athlon64, 4GB RAM and Nvidia Fx1400 graphic cards. (unfortunately i cannot switch to Suse since i cannot get Insight/Discovery Studio to run under Suse). I do not want to start a linux distribution war but we are curious under which distribution pymol is developed/tested and what people generally are using to run pymol (with 3D capability!)?? Thanks a lot for the info. Best wishes, Joris Beld Laboratory of Organic Chemistry Swiss Federal Institute of Technology Zürich Switzerland |
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From: Maciek P. <ma...@ja...> - 2007-07-13 10:17:06
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I accidentaly sent my reply to your private address first -- sorry. Resending to the list. 2007/7/13, Joris Beld <be...@or...>: > We have two molecular modeling PCs with 3D emitters (and CRT monitors). > One runs the linux distribution Redhat (Gnome) and the other one Suse > (KDE). It seems to us that the one running Suse/KDE is much faster than > the one running Redhat/Gnome. Faster in the sense of rotating big > surface rendered hexamers, 60mers. These are equivalent machines with > one year old Athlon64, 4GB RAM and Nvidia Fx1400 graphic cards. > (unfortunately i cannot switch to Suse since i cannot get > Insight/Discovery Studio to run under Suse). Try to check if both machines have the same drivers for NVidia video cards (paste output of `glxinfo' command at terminal if you are unable to figure it out). NVidia company's drivers that give best performance and utilize 3D acceleration are closed-source, so distributions which have religious approach to Free Software tend not to include it and use less efficient free/open source drivers (as in vanilla Debian, or as I would expect from Red Hat -- at least from freely available Red Hat that I remember, and from currently available Fedora, I'm not sure about Red Hat Enterprise). Distributions that are focused more on user experience than on ideology (such as Ubuntu or as I would expect from SuSE) include rather closed-source NVidia's drivers. If your RH box uses open-source drivers, try to download drivers from nvidia.com and install them manually. Their installation script is automated and usually works right out of the box. Also, please send distribution versions so that I can comment on it -- Red Hat Enterprise, as far as I know, tends to use old versions of packages since they are tested and stable. I personally use PyMOL (not that I use it much) on PLD Linux Distribution (http://www.pld-linux.org/) which I also co-develop, but this is a very specific distribution tailored for power users and experienced administrators. There is repared .spec file for PyMOL in distro's CVS repository so that users can compile open-source line of PyMOL in automated way and install results in their system as an RPM package, which makes managing system much easier. Regards, Maciek -- -><- This signature intentionally left blank. -><- |
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From: Mathias W. <m....@un...> - 2007-07-13 10:48:00
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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 |
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From: Forlani R. <rob...@ni...> - 2007-07-13 11:58:47
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=20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf=20 > Of Mathias W. > Sent: 13 July 2007 12:48 > To: PyM...@li... > Subject: Re: [PyMOL] best linux distribution to run pymol >=20 > Joris Beld schrieb: > > Dear all, >=20 > > (unfortunately i cannot switch to Suse since i cannot get=20 > > Insight/Discovery Studio to run under Suse). >=20 > This due to the ignorance of the accelrys developers. Even=20 > the newest version of DS (1.7) does not run on modern=20 > Distributions using glibc-2.4 or higher. They say that they=20 > 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=20 > glibc-2.4 system and to find the bug which is preventing it=20 > from running (I don't think they are still using=20 > linuxthreads). As of the time DS 1.7 was released glibc-2.4=20 > was already widely spread and so I call this ignorance. I got=20 > a test version of DS 1.7 and I don't want to use an old linux=20 > just because of this modelling program. As you pointed out=20 > you end up with the situation that you cannot run any other=20 > newer program (or only with great effort)... >=20 > -- > Mad =20 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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From: Joris B. <be...@or...> - 2007-07-15 12:19:38
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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 > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
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From: DeLano S. <de...@de...> - 2007-07-15 19:59:53
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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
-------------------------------------------------------------------------
This SF.net email is sponsored by DB2 Express
Download DB2 Express C - the FREE version of DB2 express and take
control of your XML. No limits. Just data. Click to get it now.
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_______________________________________________
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From: Martin <mar...@gm...> - 2007-07-16 07:14:39
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Am Freitag, 13. Juli 2007 schrieb Joris Beld: Gruezi Boris, > I do not want to start a linux distribution war but we are curious under > which distribution pymol is developed/tested and what people generally > are using to run pymol (with 3D capability!)?? > Thanks a lot for the info. Every recent distribution should give you good 3D performance if drivers ar= e=20 set up correctly. I can share OpenSUSE packages (slightly older) than the= =20 officially available deb's for ubuntu (in gutsy). They should also work/be= =20 available for Debian as well.=20 Best Martin =2D-=20 =46alls dir die Antwort zu ungenau erscheint, k=F6nnte es an der =46ragestellung liegen. (Daniel Fass in de.org.ccc) |
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From: Praedor A. <pr...@ya...> - 2007-07-16 12:59:47
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On Monday 16 July 2007 03:14:32 Martin H=F6fling wrote: > Am Freitag, 13. Juli 2007 schrieb Joris Beld: > > Gruezi Boris, > > > I do not want to start a linux distribution war but we are curious under > > which distribution pymol is developed/tested and what people generally > > are using to run pymol (with 3D capability!)?? > > Thanks a lot for the info. > > Every recent distribution should give you good 3D performance if drivers > are set up correctly. I can share OpenSUSE packages (slightly older) than > the officially available deb's for ubuntu (in gutsy). They should also > work/be available for Debian as well. I've never had problems at all with Mandriva.=20 praedor =2D-=20 Reichstag fire is to Hitler as 9/11 is to Bush |
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