[phenixbb] Problem with BOOST_ADAPTBX_FPE_DEFAULT and BOOST_ADAPTBX_SIGNALS_DEFAULT

Sam Stampfer Samuel.Stampfer at tufts.edu
Tue Aug 25 15:25:11 PDT 2009


Thanks for everyone's help!  I got the refinement working in version 1.4-125
and am all set.
-Sam

On Tue, Aug 25, 2009 at 4:19 PM, Ben Eisenbraun <bene at crystal.harvard.edu>wrote:

> There's version 1.4-125 in the SBGrid software tree.  Did you try it?  Is
> that version too old?
>
> You should ask Katya to update her user list.  You're not in our database.
>
> -ben
>
> 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 at 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 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
>
>
>
> --
> | Ben Eisenbraun                              | Tools Sysadmin         |
> | Structural Biology Grid                     | http://sbgrid.org      |
> | Harvard Medical School                      | http://hms.harvard.edu |
>
>
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