[phenixbb] problem compiling phenix 1.3 beta rc3
Engin Ozkan
eozkan at stanford.edu
Tue Mar 4 15:58:42 PST 2008
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_sources/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_1610/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_sources/iotbx/iotbx/phil.py",
line 1, in <module>
File
"/scratch/sbgrid/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_sources/phenix/phenix/command_line/__init__.py",
line 3, in <module>
File
"/scratch/sbgrid/programs/i386-linux/phenix/cci-2008_02_08_1610/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_sources/cctbx/cctbx/array_family/flex.py",
line 1, in <module>
File
"/nfs/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_sources/scitbx/scitbx/array_family/flex.py",
line 2, in <module>
File
"/nfs/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_sources/boost_adaptbx/boost/optional.py",
line 1, in <module>
File
"/nfs/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_sources/boost_adaptbx/boost/python.py",
line 45, in <module>
File
"/nfs/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_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_sources/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_sources/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_sources/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_sources/scitbx
/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_sources/boost_adaptbx
/programs/i386-linux/phenix/cci-2008_02_08_1610/cci_apps_sources/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
Peter Zwart wrote:
> Can you send the exact message?
>
> P
>
> 2008/3/4, Melody Lin <xtalin2007 at gmail.com>:
>
>> 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 the compilation.
>> Could anyone suggest what problem this is? Did I download the wrong tar
>> file?
>>
>> Your input is greatly appreciated!
>>
>> Best,
>> Yan
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
More information about the phenixbb
mailing list