[phenixbb] problem compiling phenix 1.3 beta rc3

[Schubert, Carsten [PRDUS]]

Running phenix.refine and any other phenix part works for us on RHEL4 Update 6, 2.6.9-67 kernel

Carsten

> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org
> [mailto:phenixbb-bounces at phenix-online.org]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_
sources/iotbx/iotbx/phil.py", 
> 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_
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_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
> 
> 
> 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
> >   
> 
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