Hi, 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. Any help would be appreciated. -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.
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
Nate Coraor wrote at 10:19 AM on Wednesday, December 9, 2009:
I cannot get DRMAA_python to compile/scramble. The linker does not recognize the -R flag:
John Eppley wrote: 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/
We had the same problem. How can we integrate your fix into a new Galaxy build? I assume that would mean simply downloading and installing your new "DRMAA_python-macosx.py" script in the scripts/scramble directory and then calling it from the right place. Where might that be? Dean A. Snyder Senior Programmer/Analyst Center for Inherited Disease Research (CIDR) Johns Hopkins School of Medicine Bayview Research Campus 333 Cassell Dr, Triad Bldg, Suite 2000 Baltimore, MD 21224 www.cidr.jhmi.edu cell:717 668-3048 office:410-550-4629
Dean Snyder wrote:
We had the same problem. How can we integrate your fix into a new Galaxy build? I assume that would mean simply downloading and installing your new "DRMAA_python-macosx.py" script in the scripts/scramble directory and then calling it from the right place. Where might that be?
Hi Dean, scripts/scramble.py chooses the correct build script automatically, so the following would do it: % SGE_ROOT=/path/to/sge python scripts/scramble.py DRMAA_python --nate
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
On a different system (OSX 10.5 ppc), I get the following: File "build/bdist.macosx-10.5-ppc/egg/_cDRMAA.py", line 6, in __bootstrap__ ImportError: dlopen(/Users/jmeppley/.python-eggs/DRMAA_python-0.2- py2.5-macosx-10.5-ppc.egg-tmp/_cDRMAA.so, 2): Symbol not found: _environ Referenced from: /common/sge/lib/darwin-ppc/libdrmaa.dylib.1.0 Expected in: flat namespace -john On Dec 9, 2009, at 2:09 PM, John Eppley wrote:
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
participants (3)
-
Dean Snyder -
John Eppley -
Nate Coraor