Thanks for everyone's help! I got the refinement working in version 1.4-125 and am all set.<br>-Sam<br><br><div class="gmail_quote">On Tue, Aug 25, 2009 at 4:19 PM, Ben Eisenbraun <span dir="ltr"><<a href="mailto:bene@crystal.harvard.edu">bene@crystal.harvard.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">There's version 1.4-125 in the SBGrid software tree. Did you try it? Is<br>
that version too old?<br>
<br>
You should ask Katya to update her user list. You're not in our database.<br>
<br>
-ben<br>
<div><div></div><div class="h5"><br>
On Tue, Aug 25, 2009 at 04:13:44PM -0400, Sam Stampfer wrote:<br>
> I couldn't get the source code to compile- the final message was: "error:<br>
> configuration step incomplete, exiting". Any ideas?<br>
> Thanks,<br>
> -Sam<br>
><br>
> [A copy of my problem is pasted here]:<br>
><br>
> I'm running the latest complete version of phenix (version 1.4-147, on Linux<br>
> 2.6-x86 64). When I run my .csh file I get the following error (with the 4<br>
> previous lines included):<br>
><br>
><br>
> /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python(PyDict_SetItem+0x1fd)<br>
> [0x446bdd]<br>
><br>
> /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python<br>
> [0x4396e4]<br>
><br>
> /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python<br>
> [0x4470a9]<br>
> /lib64/libc.so.6 [0x30fca322a0]<br>
> Segmentation fault (Python and libc call stacks above)<br>
> This crash may be due to a problem in any imported<br>
> Python module, including modules which are not part<br>
> of the cctbx project. To disable the traps leading<br>
> to this message, define these environment variables<br>
> (e.g. assign the value 1):<br>
> BOOST_ADAPTBX_FPE_DEFAULT<br>
> BOOST_ADAPTBX_SIGNALS_DEFAULT<br>
> This will NOT solve the problem, just mask it, but<br>
> may allow you to proceed in case it is not critical.<br>
><br>
> When I type the command "setenv BOOST_ADAPTBX_FPE_DEFAULT 1" and then run my<br>
> .csh file, it runs for a slightly longer period of time before ending with a<br>
> different error:<br>
><br>
> 311240e000-3112410000 rw-p 0000e000 fd:00 14237822<br>
> /lib64/libbz2.so.1.0.4<br>
> 2ad973412000-2ad973414000 rw-p 2ad973412000 00:00 0<br>
> 2ad973429000-2ad97346d000 rw-p 2ad973429000 00:00 0<br>
> 2ad97346e000-2ad9734af000 rw-p 2ad97346e000 00:00 0<br>
> 2ad9734e1000-2ad973563000 rw-p 2ad9734e1000 00:00 0<br>
> 2ad973563000-2ad973567000 r-xp 00000000 fd:00 5727920<br>
> /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so<br>
> 2ad973567000-2ad973666000 ---p 00004000 fd:00 5727920<br>
> /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so<br>
> 2ad973666000-2ad973668000 rw-p 00003000 fd:00 5727920<br>
> /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so<br>
> 2ad973668000-2ad97366d000 r-xp 00000000 fd:00 5727941<br>
> /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/select.so<br>
> 2ad97366d000-2ad97376c000 ---p 00005000 fd:00 5727941<br>
> /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lAbort<br>
><br>
> However, the file ran fine and successfully output an improved .pdb file<br>
> without any BOOST-related problems on my PI's Mac- she is running version 95<br>
> of Phenix (which I was unable to obtain for linux- is it available<br>
> somewhere?)<br>
><br>
> Can you help me with this?<br>
><br>
> Thanks!<br>
><br>
> -Sam<br>
><br>
><br>
> On Tue, Aug 25, 2009 at 3:28 PM, Ralf W. Grosse-Kunstleve<br>
> <<a href="mailto:rwgk@cci.lbl.gov">rwgk@cci.lbl.gov</a>>wrote:<br>
><br>
> > Could you try with a source installation?<br>
> ><br>
> ><br>
> > <a href="https://www.phenix-online.org/download/phenix/nightly/?version=1.4-147&show_source=1" target="_blank">https://www.phenix-online.org/download/phenix/nightly/?version=1.4-147&show_source=1</a><br>
> ><br>
> > I recommend you rm -rf the binary installation before ./install from<br>
> > sources.<br>
> > Add<br>
> > --nproc=N<br>
> > to the ./install command to use all N cpus in your machine for the<br>
> > installation.<br>
> ><br>
> > Let me know if the problem persists.<br>
> ><br>
> > Ralf<br>
> > _______________________________________________<br>
> > phenixbb mailing list<br>
> > <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
> > <a href="http://www.phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><br>
> ><br>
<br>
> _______________________________________________<br>
> phenixbb mailing list<br>
> <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
> <a href="http://www.phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><br>
<br>
<br>
<br>
</div></div><font color="#888888">--<br>
| Ben Eisenbraun | Tools Sysadmin |<br>
| Structural Biology Grid | <a href="http://sbgrid.org" target="_blank">http://sbgrid.org</a> |<br>
| Harvard Medical School | <a href="http://hms.harvard.edu" target="_blank">http://hms.harvard.edu</a> |<br>
<br>
</font></blockquote></div><br>