I couldn't get the source code to compile- the final message was: "error: 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 2.6-x86 64). When I run my .csh file I get the following error
(with the 4 previous lines included):<br><br><div style="margin-left: 40px;">
/usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python(PyDict_SetItem+0x1fd) [0x446bdd]<br> /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python [0x4396e4]<br> /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python [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></div>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:<br>
<div style="margin-left: 40px;"><br>311240e000-3112410000 rw-p 0000e000 fd:00 14237822 /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 /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 /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 /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 /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 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lAbort<br>
<br></div>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?)<br>
<br>Can you help me with this?<br><br>Thanks!<br><font color="#888888"><br>-Sam</font><br><br><br><div class="gmail_quote">On Tue, Aug 25, 2009 at 3:28 PM, Ralf W. Grosse-Kunstleve <span dir="ltr"><<a href="mailto:rwgk@cci.lbl.gov">rwgk@cci.lbl.gov</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;">Could you try with a source installation?<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>
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</blockquote></div><br>