[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
>>
>>
>>     
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>   




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