Nate,

Thanks, that solves the scramble problem, but I'm still having runtime issues:

  File "build/bdist.macosx-10.3-fat/egg/_cDRMAA.py", line 6, in __bootstrap__ImportError: dlopen(/Users/galaxy/.python-eggs/DRMAA_python-0.2-py2.5-macosx-10.3-fat.egg-tmp/_cDRMAA.so, 2): Symbol not found: _drmaa_control

  Referenced from: /Users/galaxy/.python-eggs/DRMAA_python-0.2-py2.5-macosx-10.3-fat.egg-tmp/_cDRMAA.so  Expected in: dynamic lookup

The only bad message in the egg build was a warning:

gcc -arch i386 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -g -bundle -undefined dynamic_lookup build/temp.macosx-10.3-fat-2.5/cDRMAA_wrap.o -L/common/sge/lib/darwin -ldrmaa -o build/lib.macosx-10.3-fat-2.5/_cDRMAA.so

/usr/bin/ld: for architecture i386

/usr/bin/ld: warning /common/sge/lib/darwin/libdrmaa.dylib cputype (18, architecture ppc) does not match cputype (7) for specified -arch flag: i386 (file not loaded)

Some system details:

Model Name: Xserve

Processor Name: Dual-Core Intel Xeon

System Version: Mac OS X Server 10.4.11 (8S2169)

SGE Version: GE 6.0u11

Any suggestions?

-john 

John Eppley wrote:

Has anyone had success getting galaxy to work with SGE on OS X 10.4?

I cannot get DRMAA_python to compile/scramble. The linker does not recognize the -R flag:

/usr/bin/ld: unknown flag: -R/common/sge/lib/darwin

I can get it to compile by removing that flag, but galaxy dies when it tries to use the library compiled this way.

On Dec 9, 2009, at 10:19 AM, Nate Coraor wrote:

Hi John,

This is a runtime linker issue - OS X (10.4 especially) does runtime linking oddly.  I've committed a fix for it in changeset 3161:b400212305b6, which should be on our public repository in a few days.  Or, you can pull directly from our central dev repo at:

http://bitbucket.org/galaxy/galaxy-central/

Thanks for finding and reporting this.

--nate

_______________________________________________
galaxy-dev mailing list
galaxy-dev@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev