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<p>Dear all,</p>
<p><br>
</p>
<p>I just wanted to post the solution to this incase anybody else runs into a similar problem. I just needed to compile the latest phenix (phenix-1.13-299) from source and now it works with my rosetta installation just fine. After downloading the source installer
I changed into the install directory and ran:</p>
<p><br>
</p>
<p>sudo ./install --prefix=/usr/local/stow --nproc=4 --try-unsupported --source --debug --rosetta --without-pymol (installed in non-standard location so as not to overwrite my binary installation)</p>
<p><br>
</p>
<p>added source statement to .bashrc as instructed:</p>
<p>source /usr/local/stow/phenix-1.13-2998/phenix_env.sh<br>
</p>
<p><br>
</p>
<p><br>
</p>
<p>Since I had already compiled rosetta 3.7 (2016.32.58837) using scons as described:<br>
https://www.phenix-online.org/documentation/reference/rosetta_install.html<br>
https://www.rosettacommons.org/docs/latest/build_documentation/Build-Documentation<br>
<br>
I then ran:<br>
<br>
rosetta.build_phenix_interface_1.13-2998 nproc=4<br>
rosetta.run_tests<br>
</p>
<p><br>
</p>
<p><br>
</p>
<p>Cheers,<br>
</p>
<p>Joseph.<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>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Joseph Brock<br>
<b>Sent:</b> Wednesday, 25 April 2018 10:38 PM<br>
<b>To:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> Phenix.rosetta build Ubuntu 16.04</font>
<div> </div>
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<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>
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