.................. checking for v4.2.2 of CCP4 library checking for compiled PHENIX components configuring PHENIX components with optimization setting up environment compiling PHENIX components - this might take an hour compilation of PHENIX components failed from compile_phenix.log: Processing: "/usr/local/phenix-1.3b-rc3/docutils/libtbx_refresh.py" Processing: "/usr/local/phenix-1.3b-rc3/docutils/tools" scons: Reading SConscript files ... RuntimeError: Cannot find a supported Fortran compiler on PATH: Supported compilers are: ifort, g77, gfortran To resolve this problem update PATH or install a supported compiler.: File "/usr/local/phenix-1.3b-rc3/build/mac-ppc-osx/SConstruct", line 7: SConscript("ccp4lib_422_cci/SConscript") File "/usr/local/phenix-1.3b-rc3/scons/src/engine/SCons/Script/SConscript.py", line 596: return apply(method, args, kw) File "/usr/local/phenix-1.3b-rc3/scons/src/engine/SCons/Script/SConscript.py", line 533: return apply(_SConscript, [self.fs,] + files, subst_kw) File "/usr/local/phenix-1.3b-rc3/scons/src/engine/SCons/Script/SConscript.py", line 256: exec _file_ in call_stack[-1].globals File "/usr/local/phenix-1.3b-rc3/ccp4lib_422_cci/SConscript", line 114: + " compiler.") usr+sys time: 3.10 seconds, ticks: 1127611, micro-seconds/tick: 2.749 wall clock time: 6.86 seconds thanks Melody On Wed, Mar 5, 2008 at 12:37 AM, Peter Zwart wrote:

Can you send the exact message?

P

2008/3/4, Melody Lin :

...

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 [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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 :

...

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 [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

-----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

...

Can you send the exact message?

P

2008/3/4, Melody Lin :

...

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

...

...

Could anyone suggest what problem this is? Did I download

Peter Zwart wrote: the compilation. the wrong tar

...

...

file?

Your input is greatly appreciated!

Best, Yan

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb