Re: [PyMOL] Installing pymol (again)
Brian Goodfellow suggested I use macpymol. I did and it Just Works. I don't know how I managed to overlook that link the first time round... Terry
Re: [PyMOL] Installing pymol (again)
Terry, > Method 1. > - > > In the most straightforward effort, I download pymol-0_99rc6-src.tgz and > run > >python setup.py install >python setup2.py install >./pymol > > as instructed. The first two commands run fine. The ./pymol gets me > > Fatal Python error: Interpreter not initialized (version mismatch?) You've probably tried this already, but what happens if you give a full-path to a single python interpreter (aka /usr/local/bin/python24 instead of python below). Assuming that the pymol launch script is using the same python intpreter, and PYTHON_HOME/PYTHONPATH is set correctly, this might clear up the version mismatch (or at least lead to different errors). > Method 2. > - Can't help you here...maybe one of the OS X experts will chime in. > Method 3: > - Which freeglut target are you using (freeglut or freeglut-static)? You've probably tried the other build target, but if not it may be worth a shot. The command below looks like it's trying to build a static library while linking to a dynamic/shared one...there's probably a way to do this, but it seems like avoiding it might reduce possible sources of problems. Also, what happens when you set up LDFLAGS so that it tries using -bind_at_load? > > I tried to build completely from source (something I've done before). When > building the ext packages, build.com fails building freeglut: > > gcc -g -O2 -o CallbackMaker CallbackMaker-CallbackMaker.o > ../../../src/.libs/libglut.a -lm -L/usr/X11R6/lib -lGL -lGLU -lXext > -lX11 -lXxf86vm > /usr/bin/ld: warning multiple definitions of symbol _glPointParameteri > > /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib(gll_api.o) > definition of _glPointParameteri > /usr/X11R6/lib/libGL.dylib(dri_dispatch.o) definition of > _glPointParameteri > /usr/bin/ld: warning multiple definitions of symbol > _glPointParameteriv > > /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib(gll_api.o) > definition of _glPointParameteriv > /usr/X11R6/lib/libGL.dylib(dri_dispatch.o) definition of > _glPointParameteriv > /usr/bin/ld: warning suggest use of -bind_at_load, as lazy binding may > result in errors or different symbols being used > /usr/bin/ld: Undefined symbols: > _glutBitmapHelvetica12 > _glutBitmap8By13 > _glutBitmap9By15 > _glutBitmapHelvetica10 > _glutBitmapHelvetica18 > _glutBitmapTimesRoman10 > _glutBitmapTimesRoman24 > _glutStrokeMonoRoman > _glutStrokeRoman > symbol _glPointParameteri used from dynamic library > /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib(gll_api.o) > not from earlier dynamic library > /usr/X11R6/lib/libGL.1.dylib(dri_dispatch.o) > symbol _glPointParameteriv used from dynamic library > /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib(gll_api.o) > not from earlier dynamic library > /usr/X11R6/lib/libGL.1.dylib(dri_dispatch.o) Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
[PyMOL] Installing pymol (again)
I'm trying to install pymol on a MacBook Pro (intel). I've tried three
approaches and hit problems on each of them. After several hours of effort
I thought I'd ask here. Details below. I'd be happy to be able to build in
any way, I guess the problem in Method 1 is probably the easiest to solve.
Thanks for any help...
Regards,
Terry
Method 1.
-
In the most straightforward effort, I download pymol-0_99rc6-src.tgz and run
python setup.py install
python setup2.py install
./pymol
as instructed. The first two commands run fine. The ./pymol gets me
Fatal Python error: Interpreter not initialized (version mismatch?)
I have 2 versions of python on my machine. I've tried the above using both
the Darwin ports 2.4 version of python (under /opt) and the system 2.3
version. Both give the same error. It's the "import pymol" line in
__init__.py that's causing the fatal error. I also get this error with an
empty PYTHONPATH. The "pymol" file looks fine in both cases: it runs the
correct python with the correct path to the __init__.py file.
As far as I know the error indicates a problem with conflicting Python
frameworks. But I don't know how to fix it. I thought running the system
python (in both invocations of python setup{,2}.py install) would work, but
it does not. It's not an option for me to uninstall python 2.4.
Method 2.
-
I also downloaded pymol-0_99rc6-bin-macosx-x86-x11.tgz. When I follow the
instructions there, I get
$ ./pymol
dyld: Library not loaded: /usr/X11R6/lib/libGLU.1.dylib
Referenced from:
/Users/terry/s/net/pymol-0_99rc6-bin-macosx-x86-x11/pymol.exe
Reason: image not found
./pymol: line 18: 13684 Trace/BPT trap $PYMOL_PATH/pymol.exe "$@"
and indeed /usr/X11R6/lib/libGLU.1.dylib does not exist. I do have all of
libGLU.1.3.dylib
libGLU.1.dylib -> libGLU.1.3.dylib
libGLU.dylib -> libGLU.1.3.dylib
in /Developer/SDKs/MacOSX10.4u.sdk/usr/X11R6/lib but I was unable to get
these to link (either by putting them into /usr/X11R6/lib, by symlinking to
them, or by setting DYLD_LIBRARY_PATH). The loader finds the libraries but
says:
$ ./pymol
dyld: Library not loaded: /usr/X11R6/lib/libGLU.1.dylib
Referenced from:
/Users/terry/s/net/pymol-0_99rc6-bin-macosx-x86-x11/pymol.exe
Reason: no suitable image found. Did find:
/Developer/SDKs/MacOSX10.4u.sdk/usr/X11R6/lib/libGLU.1.dylib: can't
map
./pymol: line 18: 13765 Trace/BPT trap $PYMOL_PATH/pymol.exe "$@"
Method 3:
-
I tried to build completely from source (something I've done before). When
building the ext packages, build.com fails building freeglut:
gcc -g -O2 -o CallbackMaker CallbackMaker-CallbackMaker.o
../../../src/.libs/libglut.a -lm -L/usr/X11R6/lib -lGL -lGLU -lXext -lX11
-lXxf86vm
/usr/bin/ld: warning multiple definitions of symbol _glPointParameteri
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib(gll_api.o)
definition of _glPointParameteri
/usr/X11R6/lib/libGL.dylib(dri_dispatch.o) definition of _glPointParameteri
/usr/bin/ld: warning multiple definitions of symbol _glPointParameteriv
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib(gll_api.o)
definition of _glPointParameteriv
/usr/X11R6/lib/libGL.dylib(dri_dispatch.o) definition of _glPointParameteriv
/usr/bin/ld: warning suggest use of -bind_at_load, as lazy binding may
result in errors or different symbols being used
/usr/bin/ld: Undefined symbols:
_glutBitmapHelvetica12
_glutBitmap8By13
_glutBitmap9By15
_glutBitmapHelvetica10
_glutBitmapHelvetica18
_glutBitmapTimesRoman10
_glutBitmapTimesRoman24
_glutStrokeMonoRoman
_glutStrokeRoman
symbol _glPointParameteri used from dynamic library
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib(gll_api.o)
not from earlier dynamic library /usr/X11R6/lib/libGL.1.dylib(dri_dispatch.o)
symbol _glPointParameteriv used from dynamic library
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib(gll_api.o)
not from earlier dynamic library /usr/X11R6/lib/libGL.1.dylib(dri_dispatch.o)
collect2: ld returned 1 exit status
