From: Noel F. <noe...@me...> - 2006-08-22 03:47:55
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Hi all, Recently I finally managed to install the Nvidia driver (NVIDIA-Linux-x86-1.0-7182-pkg1) for the graphics card (Quadro2 Pro/AGP/SSE2) on my Fedora Core 5 box. When I try and run pymol it crashed after I load a pdb file and try and either right or left click on the main display. Here is the output from the pymol run: PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC. A current PyMOL Maintenance and/or Support Subscription may be required for legal use of this Build beyond a finite honor-system evaluation period. Please visit http://www.pymol.org/funding.html for more information. This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6. OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: Quadro2 Pro/AGP/SSE2 GL_VERSION: 1.5.3 NVIDIA 71.82 Adapting to Quadro hardware. PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC. A current PyMOL Maintenance and/or Support Subscription may be required for legal use of this Build beyond a finite honor-system evaluation period. Please visit http://www.pymol.org/funding.html for more information. This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6. HEADER SCOP/ASTRAL domain d1a5ug2 [29269] 08-MAY-03 0000 CmdLoad: "/home/fauxn/results/SCOP_90_results/d1a5ug2.pdb" loaded as "d1a5ug2". /home/fauxn/software/pymol/pymol: line 14: 7203 Segmentation fault $PYMOL_PATH/pymol.exe "$@" Any pointers welcome! Cheers Noel -- PhD Student Department of Biochemistry and Molecular Biology Monash University Clayton, Victoria Australia Ph: +61 3 9905 1418 e-mail: noe...@me... website: http://vbc.med.monash.edu.au/~fauxn |
From: Noel F. <noe...@me...> - 2006-08-24 23:56:10
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HI all, This is a follow on from the e-mail below. Frequently I'm also getting this error when pymol crashes: *** glibc detected *** /home/fauxn/software/pymol/pymol.exe: double free or corruption (!prev): 0x0aaef170 *** ======= Backtrace: ========= /lib/libc.so.6[0xc69d88] /lib/libc.so.6(__libc_free+0x78)[0xc6d25f] /usr/lib/libGL.so.1[0x5bd8e5a] ======= Memory map: ======== 00101000-001fa000 r-xp 00000000 fd:00 11326935 /usr/lib/libX11.so.6.2.0 001fa000-001fe000 rwxp 000f9000 fd:00 11326935 /usr/lib/libX11.so.6.2.0 001fe000-00200000 rwxp 00000000 00:0f 1254 /dev/zero 00200000-00214000 r-xp 00000000 fd:00 12931879 /home/fauxn/software/pymol/ext/lib/python2.4/site-packages/Numeric/_numpy.so 00214000-00216000 rwxp 00013000 fd:00 12931879 /home/fauxn/software/pymol/ext/lib/python2.4/site-packages/Numeric/_numpy.so 00216000-00219000 r-xp 00000000 fd:00 12905453 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/time.so 00219000-0021b000 rwxp 00002000 fd:00 12905453 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/time.so 0021b000-00224000 r-xp 00000000 fd:00 12905473 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/_socket.so 00224000-00227000 rwxp 00009000 fd:00 12905473 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/_socket.so 00227000-0022c000 r-xp 00000000 fd:00 12905440 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/struct.so 0022c000-0022d000 rwxp 00004000 fd:00 12905440 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/struct.so 0022d000-00231000 r-xp 00000000 fd:00 12905478 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/operator.so 00231000-00232000 rwxp 00004000 fd:00 12905478 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/operator.so 00232000-00234000 rwxp 00000000 00:0f 1254 /dev/zero 00234000-00236000 rwxp 00000000 00:0f 1254 /dev/zero 00236000-00238000 rwxp 00000000 00:0f 1254 /dev/zero 00238000-0023a000 rwxp 00000000 00:0f 1254 /dev/zero 0023a000-0023c000 rwxp 00000000 00:0f 1254 /dev/zero 0023c000-0023e000 rwxp 00000000 00:0f 1254 /dev/zero 0023e000-00240000 rwxp 00000000 00:0f 1254 /dev/zero 00240000-00242000 rwxp 00000000 00:0f 1254 /dev/zero 00242000-0024b000 rwxp 00000000 00:0f 1254 /dev/zero 0027c000-00280000 r-xp 00000000 fd:00 12905441 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/collections.so 00280000-00281000 rwxp 00003000 fd:00 12905441 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/collections.so 002b3000-002b6000 r-xp 00000000 fd:00 12905457 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/_random.so 002b6000-002b7000 rwxp 00002000 fd:00 12905457 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/_random.so 002f3000-002f4000 r-xp 002f3000 00:00 0 [vdso] 002f4000-0030d000 r-xp 00000000 fd:00 1669685 /lib/ld-2.4.so 0030d000-0030e000 r-xp 00018000 fd:00 1669685 /lib/ld-2.4.so 0030e000-0030f000 rwxp 00019000 fd:00 1669685 /lib/ld-2.4.so 00311000-00a87000 r-xp 00000000 fd:00 11326754 /usr/lib/libGLcore.so.1.0.7182 00a87000-00aa3000 rwxp 00775000 fd:00 11326754 /usr/lib/libGLcore.so.1.0.7182 00aa3000-00ab8000 rwxp 00aa3000 00:00 0 00aba000-00abb000 r-xp 00000000 fd:00 15615182 /usr/lib/tls/libnvidia-tls.so.1.0.7182 00abb000-00abc000 rwxp 00000000 fd:00 15615182 /usr/lib/tls/libnvidia-tls.so.1.0.7182 00ad3000-00ad7000 r-xp 00000000 fd:00 12905474 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/strop.so 00ad7000-00ad9000 rwxp 00003000 fd:00 12905474 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/strop.so 00b14000-00b17000 r-xp 00000000 fd:00 12905449 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/math.so 00b17000-00b18000 rwxp 00003000 fd:00 12905449 /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/math.so 00b4a000-00b52000 r-xp 00000000 fd:00 11326936 /usr/lib/libXrender.so.1.3.0 00b52000-00b53000 rwxp 00007000 fd:00 11326936 /usr/lib/libXrender.so.1.3.0 00b60000-00b64000 r-xp 00000000 fd:00 11327016 /usr/lib/libXfixes.so.3.0.0 00b64000-00b65000 rwxp 00003000 fd:00 11327016 /usr/lib/libXfixes/home/fauxn/software/pymol/pymol: line 14: 10660 Aborted $PYMOL_PATH/pymol.exe "$@" Dose anyone have any idea's? This occurs when I single click left or right in the main display. On Tuesday 22 August 2006 13:46, Noel Faux wrote: > Hi all, > > Recently I finally managed to install the Nvidia driver > (NVIDIA-Linux-x86-1.0-7182-pkg1) for the graphics card (Quadro2 > Pro/AGP/SSE2) on my Fedora Core 5 box. When I try and run pymol it crashed > after I load a pdb file and try and either right or left click on the main > display. > > Here is the output from the pymol run: > > PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC. > > A current PyMOL Maintenance and/or Support Subscription may be required > for legal use of this Build beyond a finite honor-system evaluation > period. Please visit http://www.pymol.org/funding.html for more > information. > > This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6. > OpenGL graphics engine: > GL_VENDOR: NVIDIA Corporation > GL_RENDERER: Quadro2 Pro/AGP/SSE2 > GL_VERSION: 1.5.3 NVIDIA 71.82 > Adapting to Quadro hardware. > > PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC. > > A current PyMOL Maintenance and/or Support Subscription may be required > for legal use of this Build beyond a finite honor-system evaluation > period. Please visit http://www.pymol.org/funding.html for more > information. > > This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6. > HEADER SCOP/ASTRAL domain d1a5ug2 [29269] 08-MAY-03 0000 > CmdLoad: "/home/fauxn/results/SCOP_90_results/d1a5ug2.pdb" loaded > as "d1a5ug2". > /home/fauxn/software/pymol/pymol: line 14: 7203 Segmentation fault > $PYMOL_PATH/pymol.exe "$@" > > Any pointers welcome! > > Cheers > Noel -- PhD Student Department of Biochemistry and Molecular Biology Monash University Clayton, Victoria Australia Ph: +61 3 9905 1418 e-mail: noe...@me... website: http://vbc.med.monash.edu.au/~fauxn |
From: Noel F. <noe...@me...> - 2006-08-30 03:44:44
Attachments:
pymol_setup.log
|
Hi all, As suggested by Peter, I tried compiling PyMol from src (pymol-0_99rc6-src.tgz). Unfortunately it fell over :( Attached is the output. The error occurs in layer0/Crystal.c. I've look at the file in vim and there does not seem to be anything untowards (weird characters etc...) in it. I tried to compile from pymol-0_99rc1-src.tgz and got the same error. Any pointers?? Many thanks Noel On Friday 25 August 2006 23:49, you wrote: > <snip> > > > Dose anyone have any idea's? This occurs when I single click left or > > right in > > the main display. > > If you're using the binary distribution, try using the source distribution > and see if the problem persists (if compilation fails, then the error > message might provide some information as to what's going on). You could > also try different graphics drivers (if possible). > > Failing that, it sounds like an issue w\ the mouse event listener in the > glut stuff. Unfortunately I don't know of an easy fix or work-around if > this is the case (hopefully Warren will chime in on this). > > Good luck, > > Pete -- PhD Student Department of Biochemistry and Molecular Biology Monash University Clayton, Victoria Australia Ph: +61 3 9905 1418 e-mail: noe...@me... website: http://vbc.med.monash.edu.au/~fauxn |
From: Peter A. M. <pa...@co...> - 2006-08-30 13:54:59
|
Hi Noel, Which version of gcc are you using? A quick check of google for the unterminated argument list in macro error makes it look like that could be an issues (on my systems, it works for gcc-3.4.5 and 4.0.2; but that's using make instead of python distutils). It looks to me like a c preprocessor issue, rather than something in Crystal.c; specifically dealing with the PRINTF macro in Feedback.h (although it does seem a little strange seeing special characters in a logfile...). You could try 1. checking that you've got all of your development packages installed (you probably do, but it never hurts to check); 2. upgrading (or downgrading) gcc; or 3. customize setup/rules.generic for your system, and build with make (personal preference is for building ext dependencies from ext-0_99rc1-src.tgz as well, but this shouldn't make a difference). Good luck, Pete > Hi all, > > As suggested by Peter, I tried compiling PyMol from src > (pymol-0_99rc6-src.tgz). Unfortunately it fell over :( > > Attached is the output. > > The error occurs in layer0/Crystal.c. I've look at the file in vim and > there > does not seem to be anything untowards (weird characters etc...) in it. > > I tried to compile from pymol-0_99rc1-src.tgz and got the same error. > > Any pointers?? > > Many thanks > > Noel <snip> Pete Meyer Fu Lab BMCB grad student Cornell University |
From: Noel F. <noe...@me...> - 2006-08-31 03:08:33
|
Hi all, On Wednesday 30 August 2006 23:54, Peter Adrian Meyer wrote: > Which version of gcc are you using? gcc (GCC) 4.1.1 20060525 (Red Hat 4.1.1-1) > A quick check of google for the > unterminated argument list in macro error makes it look like that could be > an issues (on my systems, it works for gcc-3.4.5 and 4.0.2; but that's > using make instead of python distutils). It looks to me like a c > preprocessor issue, rather than something in Crystal.c; specifically > dealing with the PRINTF macro in Feedback.h (although it does seem a > little strange seeing special characters in a logfile...). Tried doing the make using the Rules.linux . (did not use the ext package) In the Rule.linux file I changed 2.3 -> 2.4 and added the location of the python .h file etc: PYTHON_EXE = /usr/bin/python PYTHON_INC_DIR = -I$(PYMOL_PATH)/ext/include/python2.4 \ -I$(PYMOL_PATH)/ext/include/python2.4/Numeric -I/usr/include/python2.4/ \ -I/usr/include/python2.4/Numeric I copied Rules.linux to Rules.make under the base pymol dir. It seemed to have compiled ok. In the pymol file I needed to change line 43 to /usr/bin/python $PYMOL_PATH/modules/pymol/__init__.py "$@" so it's poining to the right place for python However when I run it the following errors are thrown: Traceback (most recent call last): File "/home/fauxn/software/pymol-0.99rc6/modules/pymol/__init__.py", line 209, in exec_str exec s in globals(),globals() File "<string>", line 1, in ? File "/home/fauxn/software/pymol-0.99rc6/modules/pymol/__init__.py", line 325, in launch_gui __import__(invocation.options.gui) File "/home/fauxn/software/pymol-0.99rc6/modules/pmg_tk/__init__.py", line 22, in ? from PMGApp import * File "/home/fauxn/software/pymol-0.99rc6/modules/pmg_tk/PMGApp.py", line 27, in ? from Tkinter import * ImportError: No module named Tkinter Have I missed something? The main graphics windows appears. I can load a pdb and view it, but when I try to select an atom/residue an error is thrown: *** glibc detected *** /usr/bin/python: double free or corruption (!prev): 0x087de808 *** Back to square one!!! > > You could try 1. checking that you've got all of your development packages > installed (you probably do, but it never hurts to check); yum search <for devel packages> python-devel.i386 2.4.3-8.FC5 installed python-numeric.i386 23.7-2.2.1 installed tcl-devel.i386 8.4.13-1.1 installed freetype-devel.i386 2.1.10-5.2.1 installed freeglut-devel.i386 2.4.0-4 installed libpng-devel.i386 2:1.2.8-2.2.1 installed libgcc.i386 4.1.1-1.fc5 installed can't find pmw or the zlib-gcc packages through yum. > 2. upgrading (or downgrading) gcc; I'm unsure how to downgrade. > 3. customize setup/rules.generic for your system, and > build with make (personal preference is for building ext dependencies from > ext-0_99rc1-src.tgz as well, but this shouldn't make a difference). Tried to build the ext package but got constant problems: ./build.com tcl ... checking system version (for dynamic loading)... ./configure: line 7624: syntax error near unexpected token `)' ./configure: line 7624: ` OSF*)' make: *** [tcl] Error 2 ./build.com tk ... checking for Tcl configuration... configure: error: /home/fauxn/software/pymol-0.99rc6/ext/src/build/tcl8.4.11/unix directory doesn't contain tclConfig.sh make: *** [tk] Error 1 ./build.com zlib-gcc ... cp: target `/home/fauxn/software/pymol-0.99rc6/ext/include' is not a directory make: *** [zlib-gcc] Error 1 I'm now at a complete loss as how to get pymol running stability on my machine. I'm begining to feel that the best and simplest option is to upgrade my card. Is that really going to fix things if it's a gcc problem? Many Thanks, Noel -- PhD Student Department of Biochemistry and Molecular Biology Monash University Clayton, Victoria Australia Ph: +61 3 9905 1418 e-mail: noe...@me... website: http://vbc.med.monash.edu.au/~fauxn |