Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

2004-04-08 Thread Michael Banck
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

2004-02-19 Thread Robert Campbell
Michael,

* Michael Banck mba...@gmx.net [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. r...@post.queensu.ca
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

2004-02-19 Thread Morri Feldman
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


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RE: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

2004-02-19 Thread Warren DeLano
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
 
 
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  Build and deploy apps  Web services for Linux with a free DVD 
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[PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

2004-02-18 Thread Buz Barstow
Hi,

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.

I installed Pymol from the source file pymol-0_93-src.tgz.

Each time I start the ray tracer Pymol quits with a segmentation fault error;

/usr/local/pymol/pymol.com: line 2: 29720 Segmentation fault  
/usr/bin/python /usr/lib/python2.2/site-packages/pymol/__init__.py $*

I've tried setting max_threads to 1, and this doesn't resolve the problem. 
I've also downloaded the patch for glibc from SuSE and this doesn't help the 
problem either.

Can anyone help?

Best,

--Buz

 
|-|
Buz Barstow
192 Clark Hall
Cornell University
Ithaca, NY 14853, USA
Email: b...@cornell.edu
Phone: 607 255 8678
Fax: 607 255 8751
|-|



Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

2004-02-18 Thread Thomas Siegmund
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

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