<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none"><!--P{margin-top:0;margin-bottom:0;} p
{margin-top:0;
margin-bottom:0}--></style>
</head>
<body dir="ltr" style="font-size:12pt;color:#000000;background-color:#FFFFFF;font-family:Calibri,Arial,Helvetica,sans-serif;">
<p>Dear phenix community,</p>
<p><br>
</p>
<p>I am trying to get phenix to run with rosetta on my Ubuntu 16.04 station.</p>
<p><br>
</p>
<p>I am running the latest official phenix version (phenix-1.13-2998) and and compiled rosetta 3.7 (2016.32.58837) using scons as described:</p>
<p><a href="https://www.phenix-online.org/documentation/reference/rosetta_install.html">https://www.phenix-online.org/documentation/reference/rosetta_install.html</a></p>
<p><a href="https://www.rosettacommons.org/docs/latest/build_documentation/Build-Documentation">https://www.rosettacommons.org/docs/latest/build_documentation/Build-Documentation</a></p>
<p><br>
</p>
<p>Then ran rosetta.build_phenix_interface.</p>
<p><br>
</p>
<p>All went without error but running rosetta.run_tests then gave the segmentation fault below. Defining variables as suggested did not help.<br>
</p>
<p><br>
</p>
<p>I found a similar question in the phenixbb archives but no resolution: </p>
<p><a href="http://www.phenix-online.org/pipermail/phenixbb/2013-October/020274.html" target="_blank" title="Ctrl+Click or tap to follow the link">http://www.phenix-online.org/pipermail/phenixbb/2013-October/020274.html</a></p>
<p><br>
</p>
<p>Any suggestions on how to move forward greatly appreciated!</p>
<p><br>
</p>
<p>Cheers,</p>
<p>Joseph.</p>
<p><br>
</p>
<p>_________________________________________________________________________________________________________<br>
</p>
<p><br>
</p>
<p><br>
</p>
<p>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>
Traceback (most recent call last):<br>
File "/usr/local/phenix-1.13-2998/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 305, in <module><br>
run(sys.argv[1:], create_dir=True)<br>
File "/usr/local/phenix-1.13-2998/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run<br>
debug=params.output.debug)<br>
File "/usr/local/phenix-1.13-2998/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__<br>
self.run_jobs()<br>
File "/usr/local/phenix-1.13-2998/modules/phenix/phenix/rosetta/refine.py", line 388, in run_jobs<br>
check_result(result)<br>
File "/usr/local/phenix-1.13-2998/modules/phenix/phenix/rosetta/refine.py", line 379, in check_result<br>
raise RuntimeError("Aborted due to error in job %d." % result.job_id)<br>
RuntimeError: Aborted due to error in job 1.<br>
<br>
</p>
<p><br>
</p>
<div id="Signature">
<div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
<br>
<font size="2">Joseph S. Brock | PhD<br>
Researcher<br>
Drew Lab<br>
Department of Biochemistry and Biophysics<br>
Stockholm University</font><br>
</div>
</div>
</body>
</html>