Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2
On Thu, Feb 19, 2004 at 12:24:53PM +0100, Michael Banck wrote: > On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote: > > For me PyMol on SuSE 8.2 crashed always when raytracing a line element. > > That seems to be identical to Debian Bug #229080 > (http://bugs.debian.org/229080) > > > The stock compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I > > got the same crash with gcc 3.3.1, but not with gcc 2.95. I have not > > tried it on SUSE 9 yet, installing and using gcc 2.95 (for PyMol only) > > solved the problem for me. See PyMol bugreport 806361. > > Thanks for the information, I will see whether that helps on Debian, > too. For the record, the current gcc-3.3 in Debian testing/unstable seems to work fine again for rendering sticks and lines, so I uploaded 0.95-1 using the standard gcc on all architectures again. Michael
RE: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2
Morri has a good point: The standalone pymol-0_xx-bin-linux-libc6-i386.tgz binary builds should be capable of running on virtually any current x86-based Linux system: RH, SUSE, Debian, Fedora, or whatever. So, if you're having trouble with compilation or use of distribution-specific packages on Linux and simply want to use PyMOL as a standalone tool, then downloading those binaries is an easy way to get going. Installation is trivial and you don't need root privileges. 1) tar zxvf pymol-(version)-bin-linux-libc6-i386.tgz 2) cd pymol 3) ./setup.sh 4) ./pymol.com Cheers, Warren FYI: those builds are built using GCC 2.96 under RedHat 6.2 for maximum compatibility -- they're not the fastest PyMOL binaries in the world, but they do run without a hassle. > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Morri Feldman > Sent: Thursday, February 19, 2004 3:18 PM > To: Michael Banck > Cc: pymol users > Subject: Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2 > > Hi Michael, > > I downloaded pymol-0_93-bin-linux-libc6-i386.tgz to my Debian machine. > When I run this copy rather than the .deb version I am able > to ray trace lines without a crash. > > Best, > Morri > > On Thu, 19 Feb 2004, Michael Banck wrote: > > > On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote: > > > For me PyMol on SuSE 8.2 crashed always when raytracing a > line element. > > > > That seems to be identical to Debian Bug #229080 > > (http://bugs.debian.org/229080) > > > > > The stock compiler on SuSE 8.2 is gcc 3.3 20030226 > (prerelease). I > > > got the same crash with gcc 3.3.1, but not with gcc 2.95. I have > > > not tried it on SUSE 9 yet, installing and using gcc 2.95 > (for PyMol > > > only) solved the problem for me. See PyMol bugreport 806361. > > > > Thanks for the information, I will see whether that helps > on Debian, > > too. > > > > > > Michael > > > > > > --- > > SF.Net is sponsored by: Speed Start Your Linux Apps Now. > > Build and deploy apps & Web services for Linux with a free DVD > > software kit from IBM. Click Now! > > http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click > > ___ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > --- > SF.Net is sponsored by: Speed Start Your Linux Apps Now. > Build and deploy apps & Web services for Linux with a free > DVD software kit from IBM. Click Now! > http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2
Hi Michael, I downloaded pymol-0_93-bin-linux-libc6-i386.tgz to my Debian machine. When I run this copy rather than the .deb version I am able to ray trace lines without a crash. Best, Morri On Thu, 19 Feb 2004, Michael Banck wrote: > On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote: > > For me PyMol on SuSE 8.2 crashed always when raytracing a line element. > > That seems to be identical to Debian Bug #229080 > (http://bugs.debian.org/229080) > > > The stock compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I > > got the same crash with gcc 3.3.1, but not with gcc 2.95. I have not > > tried it on SUSE 9 yet, installing and using gcc 2.95 (for PyMol only) > > solved the problem for me. See PyMol bugreport 806361. > > Thanks for the information, I will see whether that helps on Debian, > too. > > > Michael > > > --- > SF.Net is sponsored by: Speed Start Your Linux Apps Now. > Build and deploy apps & Web services for Linux with > a free DVD software kit from IBM. Click Now! > http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2
Michael, * Michael Banck [2004-02-19 12:24] wrote: > On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote: > > For me PyMol on SuSE 8.2 crashed always when raytracing a line element. > > That seems to be identical to Debian Bug #229080 > (http://bugs.debian.org/229080) > > > The stock compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I > > got the same crash with gcc 3.3.1, but not with gcc 2.95. I have not > > tried it on SUSE 9 yet, installing and using gcc 2.95 (for PyMol only) > > solved the problem for me. See PyMol bugreport 806361. > > Thanks for the information, I will see whether that helps on Debian, > too. Just as another data point. I use the CVS version of PyMOL (currently version 0.94) under Debian testing (using gcc-3.3.3 20040125). I haven't seen any crashes. (In case it makes a difference: Athlon XP+ 2500 and Radeon 9500 Pro graphics). Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associatephone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2
On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote: > For me PyMol on SuSE 8.2 crashed always when raytracing a line element. That seems to be identical to Debian Bug #229080 (http://bugs.debian.org/229080) > The stock compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I > got the same crash with gcc 3.3.1, but not with gcc 2.95. I have not > tried it on SUSE 9 yet, installing and using gcc 2.95 (for PyMol only) > solved the problem for me. See PyMol bugreport 806361. Thanks for the information, I will see whether that helps on Debian, too. Michael
Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2
Dear Buz, > I've been using Pymol 0.93 on SuSE Linux 8.2 for a few hours now, and I'm > having trouble ray tracing graphics. > Each time I start the ray tracer Pymol quits with a segmentation fault > error; I guess you are running into a compiler bug (or a bug in PyMol which gets exposed only by some compiler versions). For me PyMol on SuSE 8.2 crashed always when raytracing a line element. The stock compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I got the same crash with gcc 3.3.1, but not with gcc 2.95. I have not tried it on SUSE 9 yet, installing and using gcc 2.95 (for PyMol only) solved the problem for me. See PyMol bugreport 806361. Thomas -- Thomas Siegmund, Ph.D. DeveloGen AG Bioinformatics and Data Management Phone: +49(551) 505 58 651 E-Mails können unvollständig oder fehlerhaft oder manipuliert sein. Sie dienen daher stets nur der Information. Rechtsverbindliche Willenserklärungen müssen in Schriftform, d.h. mindestens per Telefax mit Unterschrift des Erklärenden, abgegeben werden, um wirksam zu sein. Unsere E-Mails sind stets vertraulich und nur für den angegebenen Adressaten bestimmt. Andere Empfänger werden gebeten, diese Nachricht zu löschen. Jede unberechtigte Weiterleitung ist untersagt. Trotz ergriffener Vorsichtsmaßnahmen gegen Viren kann keine Haftung für etwaige Schäden aus der Verwendung dieser E-Mail übernommen werden. E-mails may be incomplete or be subject to change without notice. Therefore the content of this E-mail is not binding unless confirmed by letter or by telefax with signature of the author. Our E-mails are confidential and dedicated to the intended recipient only. If you are not an intended recipient, please delete the original message and all copies. Any unauthorized distribution is strictly prohibited. Although precautions have been taken to prevent the existence of viruses in this E-mail, the company cannot accept any responsibility for any damage arising out of or from the use of this E-mail.