Re: [ccp4bb] CCP4MG can't start
Hi Bill, I commented out the export DISPLAY lines, but it didn't help. What did fix it was reinstalling x11 from the OSX 10.5 CD. Any ideas? I've attached the launch script as a text file. Thanks! Kendall On 7/25/08 12:27 PM, "William G. Scott" <[EMAIL PROTECTED]> wrote: > Hi Kendall: > > I haven't used CCP4Mg^2+ but if it is launched by a shell script that > dumbly sets the DISPLAY variable, then on 10.5 this is equivalent to a > suicide directive, since the new X11 (as of 10.5) sets the DISPLAY > variable using launchd. If this is the case, hack that line out of > the script or put in a conditional test for the operating system > version. > > The latest X11 for 10.5.4 is worth getting too, as it has a lot of > improvements: > > http://xquartz.macosforge.org/trac/wiki/X112.3.0 > > Bill > > William G. Scott > > Contact info: > http://chemistry.ucsc.edu/~wgscott/ > > > On Jul 25, 2008, at 9:18 AM, Kendall Nettles wrote: > >> CCPMG is launching X11 right before it quits. Could it relate to the >> version >> of X11? Coot was not working with the version that updates with the >> OSX, so >> I had to install the Xquartz version to get Coot to work. >> >> Kendall >> >> >> On 7/25/08 10:53 AM, "Jendrek" <[EMAIL PROTECTED]> wrote: >> >>> Hi, >>> >>> I've had the same problem and discovered that in order to start >>> CCP4MG the >>> X11 >>> must be closed. >>> So, just quit your X11 and then start again. It worked fine for me. >>> >>> Andrzej >>> >>> Kendall Nettles wrote: I have tried installing the newest version of CCP4MG 1.1.1, the closedirfix version, and QtMG 1.99.0. In each case, the program does not start. I did get a problem report for pyton, shown below. Mac ppc dual 2.7 GHz, OSX 10.5.4 X11= XQuartz 2.3.0(xorg-server 1.4.2-apple5) Any suggestions would be greatly appreciated! Kendall ccp4mg.txt Description: video/flv
Re: [ccp4bb] CCP4MG can't start
Hi Kendall: I haven't used CCP4Mg^2+ but if it is launched by a shell script that dumbly sets the DISPLAY variable, then on 10.5 this is equivalent to a suicide directive, since the new X11 (as of 10.5) sets the DISPLAY variable using launchd. If this is the case, hack that line out of the script or put in a conditional test for the operating system version. The latest X11 for 10.5.4 is worth getting too, as it has a lot of improvements: http://xquartz.macosforge.org/trac/wiki/X112.3.0 Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Jul 25, 2008, at 9:18 AM, Kendall Nettles wrote: CCPMG is launching X11 right before it quits. Could it relate to the version of X11? Coot was not working with the version that updates with the OSX, so I had to install the Xquartz version to get Coot to work. Kendall On 7/25/08 10:53 AM, "Jendrek" <[EMAIL PROTECTED]> wrote: Hi, I've had the same problem and discovered that in order to start CCP4MG the X11 must be closed. So, just quit your X11 and then start again. It worked fine for me. Andrzej Kendall Nettles wrote: I have tried installing the newest version of CCP4MG 1.1.1, the closedirfix version, and QtMG 1.99.0. In each case, the program does not start. I did get a problem report for pyton, shown below. Mac ppc dual 2.7 GHz, OSX 10.5.4 X11= XQuartz 2.3.0(xorg-server 1.4.2-apple5) Any suggestions would be greatly appreciated! Kendall
Re: [ccp4bb] CCP4MG can't start
CCPMG is launching X11 right before it quits. Could it relate to the version of X11? Coot was not working with the version that updates with the OSX, so I had to install the Xquartz version to get Coot to work. Kendall On 7/25/08 10:53 AM, "Jendrek" <[EMAIL PROTECTED]> wrote: > Hi, > > I've had the same problem and discovered that in order to start CCP4MG the > X11 > must be closed. > So, just quit your X11 and then start again. It worked fine for me. > > Andrzej > > Kendall Nettles wrote: >> I have tried installing the newest version of CCP4MG 1.1.1, the closedirfix >> version, and QtMG 1.99.0. In each case, the program does not start. I did >> get a problem report for pyton, shown below. >> >> Mac ppc dual 2.7 GHz, OSX 10.5.4 >> X11= XQuartz 2.3.0(xorg-server 1.4.2-apple5) >> >> >> Any suggestions would be greatly appreciated! >> >> Kendall
Re: [ccp4bb] CCP4MG can't start
Hi, I've had the same problem and discovered that in order to start CCP4MG the X11 must be closed. So, just quit your X11 and then start again. It worked fine for me. Andrzej Kendall Nettles wrote: I have tried installing the newest version of CCP4MG 1.1.1, the closedirfix version, and QtMG 1.99.0. In each case, the program does not start. I did get a problem report for pyton, shown below. Mac ppc dual 2.7 GHz, OSX 10.5.4 X11= XQuartz 2.3.0(xorg-server 1.4.2-apple5) Any suggestions would be greatly appreciated! Kendall
[ccp4bb] CCP4MG can't start
I have tried installing the newest version of CCP4MG 1.1.1, the closedirfix version, and QtMG 1.99.0. In each case, the program does not start. I did get a problem report for pyton, shown below. Mac ppc dual 2.7 GHz, OSX 10.5.4 X11= XQuartz 2.3.0(xorg-server 1.4.2-apple5) Any suggestions would be greatly appreciated! Kendall -- Kendall W. Nettles, PhD Assistant Professor Department of Cancer Biology The Scripps Research Institute 5353 Parkside Dr. Jupiter Fl 33458 office 561-799-8851 fax 561-799-8805 cell 561-306-7566 Problem report for python: Process: python [189] Path: /Applications/ccp4mg.app/Contents/MacOS/../ccp4mg-1.1.1/bin/..//pythondist// bin/python Identifier: python Version: ??? (???) Code Type: PPC (Native) Parent Process: sh [160] Date/Time: 2008-07-25 09:12:14.642 -0400 OS Version: Mac OS X 10.5.4 (9E17) Report Version: 6 Exception Type: EXC_BAD_ACCESS (SIGBUS) Exception Codes: KERN_PROTECTION_FAILURE at 0x0020 Crashed Thread: 0 Thread 0 Crashed: 0 libSystem.B.dylib0x96594494 pthread_mutex_lock + 40 1 libSystem.B.dylib0x96592e68 free + 92 2 libSystem.B.dylib0x9662cad8 closedir + 52 3 libfont_cache.dylib 0x029ae724 LoadAllFreeTypeFonts() + 4052 (freetype_font.cc:1009) 4 libfont_cache.dylib 0x029a04b0 FontCache::LoadAllFonts() + 16 (font_info.cc:251) 5 _font_cache.so 0x03a72d70 _wrap_FontCache_LoadAllFonts + 48 (font_cache_wrap_py.cc:3913) 6 org.python.python0x0016f104 _PyEval_SliceIndex + 16528 7 org.python.python0x00171360 PyEval_EvalCodeEx + 2256 8 org.python.python0x001714b0 PyEval_EvalCode + 44 9 org.python.python0x0018d534 PyErr_Display + 1932 10 org.python.python0x0018f42c PyRun_SimpleFileExFlags + 424 11 org.python.python0x001987f0 Py_Main + 1988 12 python 0x257c start + 400 13 python 0x2424 start + 56 Thread 0 crashed with PPC Thread State 32: srr0: 0x96594494 srr1: 0xd030 dar: 0x0020 dsisr: 0x4000 r0: 0x4d555458 r1: 0xbfffce40 r2: 0xa0bfcab4 r3: 0x0020 r4: 0x r5: 0x r6: 0x80808080 r7: 0x r8: 0x r9: 0x029b32cc r10: 0x6004 r11: 0xa0bfd874 r12: 0x9659446c r13: 0xbfffcfb4 r14: 0x029ad764 r15: 0xbfffd15c r16: 0x090a65c0 r17: 0x r18: 0xbfffcf78 r19: 0x r20: 0xbfffcf4c r21: 0x r22: 0x0001 r23: 0x0001 r24: 0xbfffcf74 r25: 0xbfffd168 r26: 0xbfffd16c r27: 0xbfffd170 r28: 0x0020 r29: 0xa0bf8924 r30: 0x r31: 0x9659447c cr: 0x88248204 xer: 0xlr: 0x9659447c ctr: 0x9659446c vrsave: 0x Binary Images: 0x1000 -0x2fef +python ??? (???) /Applications/ccp4mg.app/Contents/ccp4mg-1.1.1/pythondist/bin/python 0x51000 -0x53fff +_ssl.so ??? (???) /Applications/ccp4mg.app/Contents/ccp4mg-1.1.1/pythondist/lib/python2.3/lib- dynload/_ssl.so 0x9d000 -0x9eff7 +math.so ??? (???) /Applications/ccp4mg.app/Contents/ccp4mg-1.1.1/pythondist/lib/python2.3/lib- dynload/math.so 0xa1000 -0xa2fe7 +libmginterrupt.dylib ??? (???) /Applications/ccp4mg.app/Contents/ccp4mg-1.1.1/lib/libmginterrupt.dylib 0xaf000 -0xb5ff7 +_socket.so ??? (???) /Applications/ccp4mg.app/Contents/ccp4mg-1.1.1/pythondist/lib/python2.3/lib- dynload/_socket.so 0xbb000 -0xbcfff +time.so ??? (???) /Applications/ccp4mg.app/Contents/ccp4mg-1.1.1/pythondist/lib/python2.3/lib- dynload/time.so 0xc -0xc1ff2 +libXau.6.dylib ??? (???) /usr/X11/lib/libXau.6.dylib 0x104000 - 0x1c9ff7 org.python.python 2.3.5 a (2.3.5 a) <0d8cca187f8ff8c4eacf04b69a66f39b> /System/Library/Frameworks/Python.framework/Versions/2.3/Python 0x288000 - 0x28bfff +strop.so ??? (???) /Applications/ccp4mg.app/Contents/ccp4mg-1.1.1/pythondist/lib/python2.3/lib- dynload/strop.so 0x2cf000 - 0x2dbffb +libXpm.4.dylib ??? (???) /usr/X11R6/lib/libXpm.4.dylib 0x2df000 - 0x2edfff +libXext.6.dylib ??? (???) <92d500d9cfda747c5a1c9a3d43c16104> /usr/X11R6/lib/libXext.6.dylib 0x2f9000 - 0x2fcff7 +libXdmcp.6.dylib ??? (???) /usr/X11/lib/libXdmcp.6.dylib 0x68 - 0x685ff0 +libSM.6.dylib ??? (???) /usr/X11R6/lib/libSM.6.dylib 0x689000 - 0x690ff3 +libXi.6.dylib ??? (???) <6e141ddf695eb5b9732d75fb861361f0> /usr/X11R6/lib/libXi.6.dylib 0x693000 - 0x695fff +binascii.so ??? (???) /Applications/ccp4mg.app/Contents/ccp4mg-1.1.1/pythondist/lib/python2.3/lib- dynload/binascii.so 0x6d8000 - 0x713feb +_opengl.so ??? (???) /Applications/ccp4mg.app/Contents/ccp4mg-1.1.1/lib/_opengl.so 0x7da000 - 0x7ebfff +libICE.6.dylib ??? (???) /usr/X11R6/lib/libICE.6.dylib 0x100 - 0x100d
Re: [ccp4bb] ccp4mg can't start
Tim & Yanming, Our first suggestion is to try the latest version (1.0) - a few startup issues were fixed between the two versions. Normally I would encourage you to use the python version distributed with ccp4mg. The C++/Python interface was built against a particular version of Python and probably will not work with others. Liz Tim Grune wrote: Hi Yanming, it looks like ccp4mg looks for python in a specific path within the ccp4mg. Edit the script ccp4mg (you find out where it is with 'which ccp4mg'). Look at the very end of that file for where python is called (probably with some arguments). Make sure it says only 'python', not anything like '/usr/local/ccp4/ccp4mg-0.12.1/bin/..//pythondist/bin/python'. Then ccp4mg will use the python of your system. This works for me and ccp4mg does not need its own python installation. Maybe the ccp4mg-developers may want to comment on whether this is a bad idea and may have a negative influence on ccp4mg's performance? Tim -Original Message- From: Yanming Zhang <[EMAIL PROTECTED]> To: Tim Grune <[EMAIL PROTECTED]> Date: Wed, 16 May 2007 01:47:08 -0400 (EDT) Subject: Re: [ccp4bb] ccp4mg can't start Dear Tim, Thanks for your help. python 2.4.2 is the version. Following is the output of ccp4mg -dbx: GNU gdb Red Hat Linux (6.3.0.0-1.132.EL4rh) Copyright 2004 Free Software Foundation, Inc. GDB is free software, covered by the GNU General Public License, and you are welcome to change it and/or distribute copies of it under certain conditions. Type "show copying" to see the conditions. There is absolutely no warranty for GDB. Type "show warranty" for details. This GDB was configured as "i386-redhat-linux-gnu".../usr/local/ccp4/ccp4mg-0.12.1/bin/..//pythondist/bin/python: No such file or directory. (gdb) Starting program: /usr/local/ccp4/ccp4mg-0.12.1/bin/..//python/ui/ui.py -debug opengl command No executable file specified. Use the "file" or "exec-file" command. (gdb) No stack. (gdb) No symbol table is loaded. Use the "file" command Any suggestion? Thanks On Wed, 16 May 2007, Tim Grune wrote: > Hi Yanming, > > which version of python is running on your system(python -V)? Maybe it is too > old? > Otherwise, does 'ccp4mg -dbx' produce any more output? > > On Wednesday 16 May 2007 11:20, you wrote: >> Dear Tim, >> I checked the two files, Both are empty. >> Linux distribution: 2.6.9-42.ELsm >> >> Thanks >> Yanming >> >> On Wed, 16 May 2007, Tim Grune wrote: >>> Could you send the contents of the files >>>/home/yzhang/.CCP4MG/ccp4mg_stdout.txt >>> and >>>/home/yzhang/.CCP4MG/ccp4mg_stderr.txt >>> What Linux distribution are you using? >>> >>> Tim >>> >>> On Wednesday 16 May 2007 10:31, Yanming Zhang wrote: >>>> Dear All, >>>> lately I have a fantacy toward ccp4mg. But either from >>>> ccp4i or typing 'ccp4mg' directly from the prompt(Linux), >>>> I got the following error message: >>>> >>>> Loading fonts.. >>>> ...DONE >>>> Starting graphics thread.. >>>> ...DONE >>>> Parsing command line.. >>>> ...DONE >>>> Redirecting output to /home/yzhang/.CCP4MG/ccp4mg_stdout.txt >>>> Redirecting errors to /home/yzhang/.CCP4MG/ccp4mg_stderr.txt >>>> Started at Fri May 16 09:16:59 2003 >>>> /usr/local/ccp4/ccp4mg-0.12.1/bin/ccp4mg: line 281: 10773 Killed >>>> python $CCP4_MG/python/ui/ui.py $* >>>> >>>> Any quick remedy? >>>> Thanks >>>> Yanming >>> >>> -- >>> Tim Grune >>> Australian Synchrotron >>> 800 Blackburn Road >>> Clayton, VIC 3168 >>> Australia > > -- > Tim Grune > Australian Synchrotron > 800 Blackburn Road > Clayton, VIC 3168 > Australia >
Re: [ccp4bb] ccp4mg can't start
Hi Yanming, it looks like ccp4mg looks for python in a specific path within the ccp4mg. Edit the script ccp4mg (you find out where it is with 'which ccp4mg'). Look at the very end of that file for where python is called (probably with some arguments). Make sure it says only 'python', not anything like '/usr/local/ccp4/ccp4mg-0.12.1/bin/..//pythondist/bin/python'. Then ccp4mg will use the python of your system. This works for me and ccp4mg does not need its own python installation. Maybe the ccp4mg-developers may want to comment on whether this is a bad idea and may have a negative influence on ccp4mg's performance? Tim -Original Message- From: Yanming Zhang <[EMAIL PROTECTED]> To: Tim Grune <[EMAIL PROTECTED]> Date: Wed, 16 May 2007 01:47:08 -0400 (EDT) Subject: Re: [ccp4bb] ccp4mg can't start Dear Tim, Thanks for your help. python 2.4.2 is the version. Following is the output of ccp4mg -dbx: GNU gdb Red Hat Linux (6.3.0.0-1.132.EL4rh) Copyright 2004 Free Software Foundation, Inc. GDB is free software, covered by the GNU General Public License, and you are welcome to change it and/or distribute copies of it under certain conditions. Type "show copying" to see the conditions. There is absolutely no warranty for GDB. Type "show warranty" for details. This GDB was configured as "i386-redhat-linux-gnu".../usr/local/ccp4/ccp4mg-0.12.1/bin/..//pythondist/bin/python: No such file or directory. (gdb) Starting program: /usr/local/ccp4/ccp4mg-0.12.1/bin/..//python/ui/ui.py -debug opengl command No executable file specified. Use the "file" or "exec-file" command. (gdb) No stack. (gdb) No symbol table is loaded. Use the "file" command Any suggestion? Thanks On Wed, 16 May 2007, Tim Grune wrote: > Hi Yanming, > > which version of python is running on your system(python -V)? Maybe it is too > old? > Otherwise, does 'ccp4mg -dbx' produce any more output? > > On Wednesday 16 May 2007 11:20, you wrote: >> Dear Tim, >> I checked the two files, Both are empty. >> Linux distribution: 2.6.9-42.ELsm >> >> Thanks >> Yanming >> >> On Wed, 16 May 2007, Tim Grune wrote: >>> Could you send the contents of the files >>>/home/yzhang/.CCP4MG/ccp4mg_stdout.txt >>> and >>>/home/yzhang/.CCP4MG/ccp4mg_stderr.txt >>> What Linux distribution are you using? >>> >>> Tim >>> >>> On Wednesday 16 May 2007 10:31, Yanming Zhang wrote: >>>> Dear All, >>>> lately I have a fantacy toward ccp4mg. But either from >>>> ccp4i or typing 'ccp4mg' directly from the prompt(Linux), >>>> I got the following error message: >>>> >>>> Loading fonts.. >>>> ...DONE >>>> Starting graphics thread.. >>>> ...DONE >>>> Parsing command line.. >>>> ...DONE >>>> Redirecting output to /home/yzhang/.CCP4MG/ccp4mg_stdout.txt >>>> Redirecting errors to /home/yzhang/.CCP4MG/ccp4mg_stderr.txt >>>> Started at Fri May 16 09:16:59 2003 >>>> /usr/local/ccp4/ccp4mg-0.12.1/bin/ccp4mg: line 281: 10773 Killed >>>> python $CCP4_MG/python/ui/ui.py $* >>>> >>>> Any quick remedy? >>>> Thanks >>>> Yanming >>> >>> -- >>> Tim Grune >>> Australian Synchrotron >>> 800 Blackburn Road >>> Clayton, VIC 3168 >>> Australia > > -- > Tim Grune > Australian Synchrotron > 800 Blackburn Road > Clayton, VIC 3168 > Australia >
[ccp4bb] ccp4mg can't start
Dear All, lately I have a fantacy toward ccp4mg. But either from ccp4i or typing 'ccp4mg' directly from the prompt(Linux), I got the following error message: Loading fonts.. ...DONE Starting graphics thread.. ...DONE Parsing command line.. ...DONE Redirecting output to /home/yzhang/.CCP4MG/ccp4mg_stdout.txt Redirecting errors to /home/yzhang/.CCP4MG/ccp4mg_stderr.txt Started at Fri May 16 09:16:59 2003 /usr/local/ccp4/ccp4mg-0.12.1/bin/ccp4mg: line 281: 10773 Killed python $CCP4_MG/python/ui/ui.py $* Any quick remedy? Thanks Yanming
