<div dir="ltr">I'm happy to try to debug this but since I don't ordinarily go through the Rosetta refinement protocol -- that's the protein side, which Frank is expert in -- I will probably need to know what Rosetta command line is generated by the above.</div><br><div class="gmail_quote"><div dir="ltr">On Wed, Aug 22, 2018 at 5:51 PM Billy Poon <<a href="mailto:BKPoon@lbl.gov">BKPoon@lbl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Aaron,<div><br></div><div>This looks like a High Sierra issue since this excessive amount of memory usage is not seen on 10.12. We are tracking this down and will be contacting the Rosetta developers. It looks like any version of Rosetta will cause this problem (I tested back to Rosetta 3.7).</div><div><br clear="all"><div><div dir="ltr" class="m_8866553215370190520gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr">On Wed, Aug 22, 2018 at 4:53 PM Aaron Oakley <<a href="mailto:aarono@uow.edu.au" target="_blank">aarono@uow.edu.au</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word;line-break:after-white-space">
<div>System:<span class="m_8866553215370190520m_-4147157424379606073Apple-tab-span" style="white-space:pre-wrap"> </span>
macOS 10.13.6</div>
<div>Phenix version:<span class="m_8866553215370190520m_-4147157424379606073Apple-tab-span" style="white-space:pre-wrap">
</span>phenix-1.14rc1-3177</div>
<div>Rosetta version:<span class="m_8866553215370190520m_-4147157424379606073Apple-tab-span" style="white-space:pre-wrap">
</span>3.9 (rosetta_src_2018.09.60072_bundle)</div>
<div><br>
</div>
<div>So I rebuilt rosetta 3.9 as root and can now run "Rosetta refinement". However...Rosetta refinement ran for 2 hours, slowly gobbling memory up to a maximum of 25GB before failing (error below).</div>
<div>Also gobbled up disk space, creating a 78 GB file “outtmp.map”.</div>
<div><br>
</div>
<div>A memory leak issue?</div>
<div><br>
</div>
<div>Thanks,</div>
<div><br>
</div>
<div>a++</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier">
RuntimeError : File 'None' not found.</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier">
Traceback:</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier">
File "/Applications/phenix-1.14rc1-3177/modules/cctbx_project/libtbx/runtime_utils.py", line 179, in run</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier">
return_value = self.target()</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier;min-height:14px">
<br>
</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier">
File "/Applications/phenix-1.14rc1-3177/modules/cctbx_project/libtbx/runtime_utils.py", line 74, in __call__</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier">
result = self.run()</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier;min-height:14px">
<br>
</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier">
File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/command_line/rosetta_refine.py", line 304, in run</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier">
return run(args=list(self.args))</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier;min-height:14px">
<br>
</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier">
File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier">
debug=params.output.debug)</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier;min-height:14px">
<br>
</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier">
File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier">
self.run_jobs()</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier;min-height:14px">
<br>
</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier">
File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py", line 388, in run_jobs</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier">
check_result(result)</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier;min-height:14px">
<br>
</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier">
File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py", line 383, in check_result</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier">
raise RuntimeError("File '%s' not found." % result.file_name)</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;font-family:Courier;min-height:14px">
<br>
</div>
</div>
</div>
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