On Tue, Aug 25, 2009 at 04:13:44PM -0400, Sam Stampfer wrote:
> I couldn't get the source code to compile- the final message was: "error:
> configuration step incomplete, exiting". Any ideas?
> Thanks,
> -Sam
>
> [A copy of my problem is pasted here]:
>
> I'm running the latest complete version of phenix (version 1.4-147, on Linux
> 2.6-x86 64). When I run my .csh file I get the following error (with the 4
> previous lines included):
>
>
> /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python(PyDict_SetItem+0x1fd)
> [0x446bdd]
>
> /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python
> [0x4396e4]
>
> /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python
> [0x4470a9]
> /lib64/libc.so.6 [0x30fca322a0]
> Segmentation fault (Python and libc call stacks above)
> This crash may be due to a problem in any imported
> Python module, including modules which are not part
> of the cctbx project. To disable the traps leading
> to this message, define these environment variables
> (e.g. assign the value 1):
> BOOST_ADAPTBX_FPE_DEFAULT
> BOOST_ADAPTBX_SIGNALS_DEFAULT
> This will NOT solve the problem, just mask it, but
> may allow you to proceed in case it is not critical.
>
> When I type the command "setenv BOOST_ADAPTBX_FPE_DEFAULT 1" and then run my
> .csh file, it runs for a slightly longer period of time before ending with a
> different error:
>
> 311240e000-3112410000 rw-p 0000e000 fd:00 14237822
> /lib64/libbz2.so.1.0.4
> 2ad973412000-2ad973414000 rw-p 2ad973412000 00:00 0
> 2ad973429000-2ad97346d000 rw-p 2ad973429000 00:00 0
> 2ad97346e000-2ad9734af000 rw-p 2ad97346e000 00:00 0
> 2ad9734e1000-2ad973563000 rw-p 2ad9734e1000 00:00 0
> 2ad973563000-2ad973567000 r-xp 00000000 fd:00 5727920
> /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so
> 2ad973567000-2ad973666000 ---p 00004000 fd:00 5727920
> /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so
> 2ad973666000-2ad973668000 rw-p 00003000 fd:00 5727920
> /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so
> 2ad973668000-2ad97366d000 r-xp 00000000 fd:00 5727941
> /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/select.so
> 2ad97366d000-2ad97376c000 ---p 00005000 fd:00 5727941
> /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lAbort
>
> However, the file ran fine and successfully output an improved .pdb file
> without any BOOST-related problems on my PI's Mac- she is running version 95
> of Phenix (which I was unable to obtain for linux- is it available
> somewhere?)
>
> Can you help me with this?
>
> Thanks!
>
> -Sam
>
>
> On Tue, Aug 25, 2009 at 3:28 PM, Ralf W. Grosse-Kunstleve
> <
rwgk@cci.lbl.gov>wrote:
>
> > Could you try with a source installation?
> >
> >
> >
https://www.phenix-online.org/download/phenix/nightly/?version=1.4-147&show_source=1
> >
> > I recommend you rm -rf the binary installation before ./install from
> > sources.
> > Add
> > --nproc=N
> > to the ./install command to use all N cpus in your machine for the
> > installation.
> >
> > Let me know if the problem persists.
> >
> > Ralf
> > _______________________________________________
> > phenixbb mailing list
> >
phenixbb@phenix-online.org
> >
http://www.phenix-online.org/mailman/listinfo/phenixbb
> >
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