Re: [scipion-users] Scipion 3.0.9 cryosparc2 plugin pyem error

[David M. <dma...@ub...>]

Hi Wolfgang,

Please, check /cssbsw/em/scipion/3.0/software/em/xmipp/xmipp.conf and /cssbsw/em/scipion/3.0/software/em/xmipp/xmippEnv.json to find a hint of which java had used to compile the dataViewer.

Thanks,

<http://ucm.es/>
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On Mon, Sep 13, 2021 at 3:23 PM Lugmayr, Wolfgang <w.l...@uk...<mailto:w.l...@uk...>> 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...<mailto:pc...@cn...>>
To: "Mailing list for Scipion users" <sci...@li...<mailto: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<http://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


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