Re: [phenixbb] problem compiling phenix 1.3 beta rc3

-----Original Message----- From: [email protected] [mailto:[email protected]]On Behalf Of Engin Ozkan Sent: Tuesday, March 04, 2008 6:59 PM To: PHENIX user mailing list Subject: Re: [phenixbb] problem compiling phenix 1.3 beta rc3

On a similar matter, our RHEL4 machines cannot run the new version of phenix.refine, giving gcc library version errors. SBGrid personnel informed us that older OS (Fedora < 4 and similar) will not be able to run this software anymore (because of an glibc ABI change). So, we reverted to the older version.

The error we got was this: Traceback (most recent call last): File "/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_sour ces/phenix/phenix/command_line/refine.py", line 1, in <module> from phenix.refinement import command_line File "/scratch/sbgrid/programs/i386-linux/phenix/cci-2008_02_08_161 0/cci_apps_sources/phenix/phenix/command_line/__init__.py", line 1, in <module> File "/nfs/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_

line 1, in <module> File "/scratch/sbgrid/programs/i386-linux/phenix/cci-2008_02_08_161 0/cci_apps_sources/phenix/phenix/command_line/__init__.py", line 3, in <module> File "/scratch/sbgrid/programs/i386-linux/phenix/cci-2008_02_08_161 0/cci_apps_sources/phenix/phenix/command_line/__init__.py", line 1, in <module> File "/nfs/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_

line 1, in <module> File "/nfs/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_

line 2, in <module> File "/nfs/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_

line 1, in <module> File "/nfs/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_

line 45, in <module> File "/nfs/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_

Running phenix.refine and any other phenix part works for us on RHEL4 Update 6, 2.6.9-67 kernel Carsten sources/iotbx/iotbx/phil.py", sources/cctbx/cctbx/array_family/flex.py", sources/scitbx/scitbx/array_family/flex.py", sources/boost_adaptbx/boost/optional.py", sources/boost_adaptbx/boost/python.py", sources/boost_adaptbx/boost/python.py",

line 24, in import_ext ImportError: __import__("boost_python_meta_ext"): /usr/lib/libstdc++.so.6: version `GLIBCXX_3.4.4' not found (required by /programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_build /lib/boost_python_meta_ext.so)

sys.path:

/scratch/sbgrid/programs/i386-linux/phenix/cci-2008_02_08_1610 /cci_apps_sources/phenix/phenix/command_line

/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_sourc es/phenix

/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_sources/elbow

/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_sourc es/PyQuante /programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_sources

/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_sources/tntbx

/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_sources/mmtbx

/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_sources/iotbx

/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_sourc es/PyCifRW

/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_sources/cctbx

/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_sourc es/scitbx

/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_sourc es/boost_adaptbx

/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_sourc es/libtbx /programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_build/lib /programs/i386-linux/haddock/2.0 /programs/i386-linux/eman/1.8/lib

/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_build /base/lib/python25.zip

/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_build /base/lib/python2.5

/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_build /base/lib/python2.5/plat-linux2

/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_build /base/lib/python2.5/lib-tk

/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_build /base/lib/python2.5/lib-dynload

/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_build /base/lib/python2.5/site-packages

Engin

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Can you send the exact message?

P

2008/3/4, Melody Lin :

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Dear all,

I have a problem compiling phenix-1.3beta-rc3 on my Mac OSX tiger ppc. I downloaded the tar file under the sbgrid directory and issued command "sudo ./install" to compile it after unzipping. Everything went OK until the last step when the installer is trying to compile phenix components, ands says it will take an hour, but in 2 minutes it reports failure for

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Could anyone suggest what problem this is? Did I download

Peter Zwart wrote: the compilation. the wrong tar

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file?

Your input is greatly appreciated!

Best, Yan

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