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Re: [scipion-users] deep consensus pickling error
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From: Dmitry A. S. <sem...@gm...> - 2021-04-19 13:52:53
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<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0in; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} pre {mso-style-priority:99; mso-style-link:"HTML Preformatted Char"; margin:0in; font-size:10.0pt; font-family:"Courier New";} span.HTMLPreformattedChar {mso-style-name:"HTML Preformatted Char"; mso-style-priority:99; mso-style-link:"HTML Preformatted"; font-family:"Courier New";} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:8.5in 11.0in; margin:1.0in 1.0in 1.0in 1.0in;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=EN-US link=blue vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><div><p class=MsoNormal><span lang=EN-GB>Dear Carlos Oscar, Pablo, David, Ruben, <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Thank you very much for your fast response.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Currently, deep learning is running.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>A colleague of mine, Christian, kindly looked at the problem.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Let me, please post the errors we had and where we are now.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>May be Christian can comment more on this issue.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Please see the errors here.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><a href="https://yadi.sk/d/KlTeKv1O9UCTQg">https://yadi.sk/d/KlTeKv1O9UCTQg</a><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Sincerely,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>Dmitry<o:p></o:p></span></p></div><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p class=MsoNormal><o:p> </o:p></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='border:none;padding:0in'><b>From: </b><a href="mailto:co...@cn...">Carlos Oscar Sorzano</a><br><b>Sent: </b>Monday, April 19, 2021 12:57 PM<br><b>To: </b><a href="mailto:sci...@li...">Mailing list for Scipion users</a>; <a href="mailto:pc...@cn...">Pablo Conesa</a>; <a href="mailto:rub...@gm...">Rubén Sánchez</a>; <a href="mailto:dma...@ub...">David Maluenda</a><br><b>Subject: </b>Re: [scipion-users] deep consensus pickling error</p></div><p class=MsoNormal><o:p> </o:p></p><p>Dear Dmitry,</p><p>let us see if David or Rubén knows where this environment is coming from.</p><p>Kind regards, Carlos Oscar</p><div><p class=MsoNormal>El 19/04/2021 a las 9:37, Pablo Conesa escribió:<o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p>Hi Dmitry... you have no environment for xmipp_DLTK_v0.3.</p><p>You have a "weird" xmipp_DLTK_v0.3_BACKUP2 /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2</p><p><o:p> </o:p></p><div><p class=MsoNormal>On 17/4/21 8:56, Dmitry A. Semchonok wrote:<o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>Dear colleagues,<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal>During deep consensus pickling I received the following error<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal>Any ideas?<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal>Thank you<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal>Sincerely,<o:p></o:p></p><p class=MsoNormal>Dmitry<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 176 tasks | elapsed: 1.8min<o:p></o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 426 tasks | elapsed: 4.3min<o:p></o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 776 tasks | elapsed: 7.5min<o:p></o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 1226 tasks | elapsed: 11.5min<o:p></o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 1776 tasks | elapsed: 16.7min<o:p></o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 2426 tasks | elapsed: 23.7min<o:p></o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 3176 tasks | elapsed: 32.1min<o:p></o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 4026 tasks | elapsed: 41.4min<o:p></o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 4976 tasks | elapsed: 51.8min<o:p></o:p></p><p class=MsoNormal>[Parallel(n_jobs=12)]: Done 5285 out of 5285 | elapsed: 55.1min finished<o:p></o:p></p><p class=MsoNormal>[35mFINISHED[0m: extractParticles, step 12, time 2021-04-17 04:05:07.093613<o:p></o:p></p><p class=MsoNormal>[35mSTARTED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 04:05:07.574152<o:p></o:p></p><p class=MsoNormal>[35mFINISHED[0m: joinSetOfParticlesStep, step 13, time 2021-04-17 04:26:59.879548<o:p></o:p></p><p class=MsoNormal>[35mSTARTED[0m: trainCNN, step 14, time 2021-04-17 04:26:59.920444<o:p></o:p></p><p class=MsoNormal>None None None None<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal>$ /usr/local/EMAN_2.21/bin/conda info --env<o:p></o:p></p><p class=MsoNormal># conda environments:<o:p></o:p></p><p class=MsoNormal>#<o:p></o:p></p><p class=MsoNormal>3DFSC /home/panos/.conda/envs/3DFSC<o:p></o:p></p><p class=MsoNormal>cryoassess-0.1.0 /home/panos/.conda/envs/cryoassess-0.1.0<o:p></o:p></p><p class=MsoNormal>cryolo /home/panos/.conda/envs/cryolo<o:p></o:p></p><p class=MsoNormal>xmipp_DLTK_v0.3_BACKUP2 /home/panos/.conda/envs/xmipp_DLTK_v0.3_BACKUP2<o:p></o:p></p><p class=MsoNormal>cryolo /usr/local/EMAN_2.21/envs/cryolo<o:p></o:p></p><p class=MsoNormal>cryolo-1.5.4 /usr/local/EMAN_2.21/envs/cryolo-1.5.4<o:p></o:p></p><p class=MsoNormal>fsc /usr/local/EMAN_2.21/envs/fsc<o:p></o:p></p><p class=MsoNormal>topaz /usr/local/EMAN_2.21/envs/topaz<o:p></o:p></p><p class=MsoNormal>root * /usr/local/EMAN_2.21<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal>>>> 'xmipp_DLTK_v0.3' conda environment not found... (check list above)<o:p></o:p></p><p class=MsoNormal>Traceback (most recent call last):<o:p></o:p></p><p class=MsoNormal> File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 189, in run<o:p></o:p></p><p class=MsoNormal> self._run()<o:p></o:p></p><p class=MsoNormal> File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 240, in _run<o:p></o:p></p><p class=MsoNormal> resultFiles = self._runFunc()<o:p></o:p></p><p class=MsoNormal> File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 236, in _runFunc<o:p></o:p></p><p class=MsoNormal> return self._func(*self._args)<o:p></o:p></p><p class=MsoNormal> File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/protocols/protocol_screen_deepConsensus.py", line 948, in trainCNN<o:p></o:p></p><p class=MsoNormal> env=self.getCondaEnv())<o:p></o:p></p><p class=MsoNormal> File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/xmipp3/base.py", line 204, in getCondaEnv<o:p></o:p></p><p class=MsoNormal> return CondaEnvManager.getCondaEnv(env, envName)<o:p></o:p></p><p class=MsoNormal> File "/opt/Scipion3/software/bindings/xmipp_base.py", line 245, in getCondaEnv<o:p></o:p></p><p class=MsoNormal> envBin = os.path.join(environDir, "bin")<o:p></o:p></p><p class=MsoNormal> File "/usr/lib64/python3.6/posixpath.py", line 80, in join<o:p></o:p></p><p class=MsoNormal> a = os.fspath(a)<o:p></o:p></p><p class=MsoNormal>TypeError: expected str, bytes or os.PathLike object, not NoneType<o:p></o:p></p><p class=MsoNormal>[31mProtocol failed: expected str, bytes or os.PathLike object, not NoneType[0m<o:p></o:p></p><p class=MsoNormal>[35mFAILED[0m: trainCNN, step 14, time 2021-04-17 04:27:00.607417<o:p></o:p></p><p class=MsoNormal>*** Last status is failed<o:p></o:p></p><p class=MsoNormal>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal><br><br><br><o:p></o:p></p><pre>_______________________________________________</pre><pre>scipion-users mailing list</pre><pre><a href="mailto:sci...@li...">sci...@li...</a></pre><pre><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users">https://lists.sourceforge.net/lists/listinfo/scipion-users</a></pre></blockquote><div><p class=MsoNormal>-- <br>Pablo Conesa - <strong><span style='font-family:"Calibri",sans-serif'>Madrid <a href="http://scipion.i2pc.es">Scipion</a> team</span></strong><o:p></o:p></p></div><p class=MsoNormal><br><br><br><o:p></o:p></p><pre>_______________________________________________</pre><pre>scipion-users mailing list</pre><pre><a href="mailto:sci...@li...">sci...@li...</a></pre></blockquote><pre style='mso-margin-top-alt:0in;margin-right:.5in;margin-bottom:5.0pt;margin-left:.5in'><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users">https://lists.sourceforge.net/lists/listinfo/scipion-users</a></pre><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p></div></body></html> |
