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Hi again, the missing $PHENIX_ROSETTA_PATH/main/source/bin error I reported below can be fixed by redefining these variables in the shell where one runs rosetta.run_tests:<br class="">
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>export PHENIX_ROSETTA_PATH=/usr/local/rosetta/rosetta-2018.33.60351</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>export ROSETTA_BIN=$PHENIX_ROSETTA_PATH/main/source/bin</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>export ROSETTA3_DB=$PHENIX_ROSETTA_PATH/main/database</div>
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<div>and then re-running rosetta.run_tests.</div>
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<div>However, I then get yet another error from Rosetta… will report off-list as that is probably related to my specific installation.</div>
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<div>Best, Luca</div>
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<div class="">Begin forwarded message:</div>
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">From:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">Luca Jovine &lt;<a href="mailto:luca.jovine@ki.se" class="">luca.jovine@ki.se</a>&gt;<br class="">
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Subject:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">Re: [phenixbb] Rosetta installation problems (II)</b><br class="">
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Date:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">7 October 2018 at 11:43:24 CEST<br class="">
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">To:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">Billy Poon &lt;<a href="mailto:BKPoon@lbl.gov" class="">BKPoon@lbl.gov</a>&gt;<br class="">
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Cc:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">PHENIX user mailing list &lt;<a href="mailto:phenixbb@phenix-online.org" class="">phenixbb@phenix-online.org</a>&gt;<br class="">
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<div class="">On 6 Oct 2018, at 21:45, Billy Poon &lt;<a href="mailto:BKPoon@lbl.gov" class="">BKPoon@lbl.gov</a>&gt; wrote:</div>
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<div dir="ltr" class="">Hi Luca,
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<div class="">Please try the latest version of Rosetta 3.10. There was a bug with macOS 10.13.6 that is fixed. I have tested Rosetta 3.10 on macOS 10.13.6 and Xcode 10. The rosetta.run_tests step completes without using massive amounts of memory. Also, if you
 use the GUI for phenix.rosetta_refine, please use the latest nightly build, dev-3283. There was a bug where the final R-values are not stored, which caused the GUI to crash.</div>
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<div class=""><span style="font-size:12.8000001907349px" class="">Billy K. Poon</span><br class="">
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<div class="">Research Scientist, Molecular Biophysics and Integrated Bioimaging</div>
<div class="">Lawrence Berkeley National Laboratory</div>
<div class="">1 Cyclotron Road, M/S 33R0345</div>
<div class="">Berkeley, CA 94720</div>
<div class="">Tel: (510) 486-5709</div>
<div class="">Fax: (510) 486-5909</div>
<div class="">Web:&nbsp;<a href="https://phenix-online.org/" class="">https://phenix-online.org</a></div>
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<div class="">Hi Billy,</div>
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<div class="">Thanks for the follow-up, I tried and confirm that the combination of Rosetta 3.10 &#43; PHENIX dev-3283 indeed works fine on Mac OS 10.13.6.</div>
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<div class="">However, I then tried the same on ubuntu (16.04) and in this case I got the following:</div>
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<div class="">&gt; echo $PHENIX_ROSETTA_PATH</div>
<div class="">/usr/local/rosetta/rosetta-2018.33.60351</div>
<div class="">&gt; which rosetta.run_tests</div>
<div class="">/usr/local/phenix/phenix-dev-3283/build/bin/rosetta.run_tests</div>
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<div class="">&gt; rosetta.run_tests</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>(...)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>End of input processing</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Traceback (most recent call last):</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>&nbsp;File &quot;/usr/local/phenix/phenix-dev-3283/build/../modules/phenix/phenix/command_line/rosetta_refine.py&quot;, line 304, in &lt;module&gt;</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>&nbsp; &nbsp;run(sys.argv[1:], create_dir=True)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>&nbsp;File &quot;/usr/local/phenix/phenix-dev-3283/build/../modules/phenix/phenix/command_line/rosetta_refine.py&quot;, line 143, in run</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>&nbsp; &nbsp;scripts_cmd = phenix.rosetta.refine.find_scripts_command()</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>&nbsp;File &quot;/usr/local/phenix/phenix-dev-3283/modules/phenix/phenix/rosetta/refine.py&quot;, line 26, in find_scripts_command</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>&nbsp; &nbsp;return find_rosetta_command(&quot;rosetta_scripts.python.&quot;, **kwds)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>&nbsp;File &quot;/usr/local/phenix/phenix-dev-3283/modules/phenix/phenix/rosetta/refine.py&quot;, line 50, in find_rosetta_command</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>&nbsp; &nbsp;rosetta_cmd = search_path(rosetta_bin)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>&nbsp;File &quot;/usr/local/phenix/phenix-dev-3283/modules/phenix/phenix/rosetta/refine.py&quot;, line 31, in search_path</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>&nbsp; &nbsp;for node in os.listdir(path) :</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>OSError: [Errno 2] No such file or directory: '$PHENIX_ROSETTA_PATH/main/source/bin'</div>
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<div class="">...but directory $PHENIX_ROSETTA_PATH/main/source/bin does exist, and it’s populated:</div>
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<div class="">ls -l $PHENIX_ROSETTA_PATH/main/source/bin</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>total 2292</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>lrwxrwxrwx 1 luca luca &nbsp;92 Oct &nbsp;7 10:29 AbinitioRelax.default.linuxgccrelease -&gt; ../build/src/release/linux/4.15/64/x86/gcc/5.4/default/AbinitioRelax.default.linuxgccrelease</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>(...)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>lrwxrwxrwx 1 luca luca 101 Oct &nbsp;7 10:54 zinc_statistic_generator.python.linuxgccrelease -&gt; ../build/src/release/linux/4.15/64/x86/gcc/5.4/python/zinc_statistic_generator.python.linuxgccrelease</div>
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<div class="">Do you have any idea of why this happens?&nbsp;</div>
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<div class="">Thanks again,</div>
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<div class="">Luca</div>
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