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Re: [scipion-users] Scipion 3.0.9 cryosparc2 plugin pyem error
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From: Pablo C. <pc...@cn...> - 2021-09-13 15:52:14
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Thanks for confirming it fixed Now, for the dataViewer, you might not need to recompile. Probably just setting JAVA_HOME in the scipion config file to a newer java runtime might work. scipion3 config --show will show you the config file. If not present add JAVA_HOME to it pointing to a modern java runtime. Not sure how you got there! On 13/9/21 15:22, Lugmayr, Wolfgang wrote: > Hi Pablo, > > yes the fix below worked on an Ab-Inito job with Scipion 3.0.9 and > cryoSPARC 3.2.0+210831 > > The "view data in cryoSPARC" open the webbrowser with the correct page > (when logged already in in cryoSPARC web). > > The dataViewer has a problem on CentOS Stream (also latest updates today): > > java -Xmx4g -d64 > -Djava.library.path=/cssbsw/em/scipion/3.0/software/em/xmipp/lib > -Dplugins.dir=/cssbsw/em/scipion/3.0/software/em/xmipp/bindings/java/imagej/plugins > -cp > lib/*:/cssbsw/em/scipion/3.0/software/em/xmipp/bindings/java/imagej/*:/cssbsw/em/scipion/3.0/software/em/xmipp/bindings/java/lib/* > xmipp.viewer.scipion.ScipionViewer -i > "Runs/007753_ProtCryoSparcInitialModel/classes3D.sqlite" --mode > metadata --visible enabled id _size _representative._filename > --render _representative._filename --scipion 47401 7828 > Error: A JNI error has occurred, please check your installation and > try again > Exception in thread "main" java.lang.UnsupportedClassVersionError: > xmipp/viewer/scipion/ScipionViewer has been compiled by a more recent > version of the Java Runtime (class file version 60.0), this version of > the Java Runtime only recognizes class file versions up to 52.0 > > $ rpm -qa | grep jdk > java-1.8.0-openjdk-headless-1.8.0.302.b08-0.el8_4.x86_64 > copy-jdk-configs-3.7-4.el8.noarch > java-latest-openjdk-devel-16.0.1.0.9-3.rolling.el8.x86_64 > java-1.8.0-openjdk-1.8.0.302.b08-0.el8_4.x86_64 > java-latest-openjdk-headless-16.0.1.0.9-3.rolling.el8.x86_64 > java-latest-openjdk-16.0.1.0.9-3.rolling.el8.x86_64 > > Will a re-compile Xmipp help, is this a binary distribution problem or > shall i set a different JDK version as default? > > Cheers, > Wolfgang > > > ------------------------------------------------------------------------ > *From: *"Pablo Conesa" <pc...@cn...> > *To: *"Mailing list for Scipion users" > <sci...@li...> > *Sent: *Monday, 13 September, 2021 14:26:00 > *Subject: *Re: [scipion-users] Scipion 3.0.9 cryosparc2 plugin pyem error > > Hi Wolfgang!, This has been reported before and I believe is cause by > a partial update of pwem. > > I hope this fixes your issue but have no confirmation. Would be nice > to get feedback: > > > scipion3 run pip uninstall pyem > > scipion3 run pip install > git+https://github.com/asarnow/pyem.git@ed0527f98657d21d887357426b74e5240d477fae > > > > On 13/9/21 12:18, Lugmayr, Wolfgang wrote: > > Hi, > > I updated Scipion 3.0 and all plugins to the latest version. > > I run an initial model job from Scipion and with the cryoSPARC webinterface the result seems to be ok. > > But then I get the error: > Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2' > > I have only relion 3.1.2 on this dedicated node. > > here are the last log lines: > 00027: Got J6 for JobId > 00028: Running: /cssbsw/em/scipion/3.0/cryosparc/cryosparc_master/bin/cryosparcm cli 'enqueue_job("P1","J6","default", "cssbuke001.desy.de", [0], "False")' > 00029: Removing intermediate results... > 00030: FINISHED: processStep, step 2, time 2021-09-13 12:12:48.450747 > 00031: STARTED: createOutputStep, step 3, time 2021-09-13 12:12:48.540652 > 00032: Creating the output... > 00033: Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2' > 00034: FAILED: createOutputStep, step 3, time 2021-09-13 12:12:51.351945 > 00035: *** Last status is failed > 00036: ------------------- PROTOCOL FAILED (DONE 3/3) > > Cheers, > Wolfgang > > > _______________________________________________ > scipion-users mailing list > sci...@li... <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
