Task #12578
closed
Support #12249: Need installed KNIME 3.6 and R 3.4 including the listed plugins
Need installed FSKlab plugin for KNIME and the provided Testworkflow in Dataminer tested
100%
Description
Hello Andrea,
as requested before in the other ticket above, I would like to ask you to install our latest version of FSKlab plugin on the dataminer.
You can test if it works with my Dataminer FSKtestworkflow in https://aginfra.d4science.org/group/rakip_portal/data-miner
Please tell me the outcame of your tests.
The version currently installed is old and not properly installed (0.1.0.201808131056)
THX
Lars
Files
Updated by Andrea Dell'Amico over 6 years ago
- Assignee changed from Andrea Dell'Amico to _InfraScience Systems Engineer
Updated by Andrea Dell'Amico over 6 years ago
(I do not have access to that VRE, FYI).
Updated by Andrea Dell'Amico over 6 years ago
- Status changed from New to In Progress
- % Done changed from 0 to 50
The one I get installed is 1.2.1.201809271338. I'm adding a cron job that (re)installs the plugin daily. By tomorrow it will be installed on every dataminer.
Updated by Andrea Dell'Amico over 6 years ago
- Status changed from In Progress to Feedback
- % Done changed from 50 to 100
- Infrastructure Pre-Production, Production added
Scripts and cron job have been installed. I tested the procedure on the dev environment and the plugin installed successfully, the cron job will do the same on the production servers.
Updated by Lars Valentin over 6 years ago
- File RLOG7637da67-4773-445d-a900-1fcbd2d618f6.txt RLOG7637da67-4773-445d-a900-1fcbd2d618f6.txt added
Andrea Dell'Amico wrote:
Scripts and cron job have been installed. I tested the procedure on the dev environment and the plugin installed successfully, the cron job will do the same on the production servers.
I just checked my FSKX test workflow in the dataminer and I still receive the failing log with old nodes and issues. Could you please test my workflow in the dataminer.
I attach the log file again.
Updated by Leonardo Candela over 6 years ago
I assume the DM algorithm you are using for testing purposes is FSKX T E X T (available at)
I tried to execute it by myself and I confirm it fails ... from the log I see a number of issues including:
...
"org.osgi.framework.BundleException: Could not resolve module: com.knime.enterprise.client.openejb [33]"
[14] " Unresolved requirement: Require-Bundle: com.knime.enterprise.server.rest.api; bundle-version=\"[4.7.0,5.0.0)\""
...
"org.osgi.framework.BundleException: Could not resolve module: de.bund.bfr.knime.fsklab.metadata.model [921]"
[440] " Bundle was not resolved because of a uses contraint violation."
[441] " org.osgi.service.resolver.ResolutionException: Uses constraint violation. Unable to resolve resource de.bund.bfr.knime.fsklab.metadata.model [osgi.identity; type=\"osgi.bundle\"; version:Version=\"0.1.0.201808131056\"; osgi.identity=\"de.bund.bfr.knime.fsklab.metadata.model\"; singleton:=\"true\"] because it is exposed to package 'org.w3c.dom.events' from resources org.eclipse.osgi [osgi.identity; type=\"osgi.bundle\"; version:Version=\"3.12.100.v20180210-1608\"; osgi.identity=\"org.eclipse.osgi\"; singleton:=\"true\"] and org.w3c.dom.events [osgi.identity; type=\"osgi.bundle\"; version:Version=\"3.0.0.draft20060413_v201105210656\"; osgi.identity=\"org.w3c.dom.events\"] via two dependency chains."
...
The workflow is invoked by DM as follows
/usr/local/bin/knime -reset -consoleLog -nosplash -application org.knime.product.KNIME_BATCH_APPLICATION -workflowFile=simple_FSK_testworkflow.knwf -destFile=workflow.zip -workflow.variable=dummy,"dummy",String
Updated by Andrea Dell'Amico over 6 years ago
- Status changed from Feedback to In Progress
- % Done changed from 100 to 80
The installation of the plugin failed because of a bug in my script that only shows up when run by cron. I'm fixing it now, I'm also adding the run of the simple_FSK workflow to immediately check the installation.
Updated by Lars Valentin over 6 years ago
Thank you for testing. As stated above FSK seems to be still installed in Version=\"0.1.0.201808131056\" as you see in line 441. Could you please install the latest version and test this workflow in the dataminer again to check if you were successful?
As a reminder from previous advises, you need to uninstall the old plugins before installing the new version! If that procedure was messed up I had to manually delete the old plugin version in the plugin folder.
I have no clue about the other issues.
Updated by Andrea Dell'Amico over 6 years ago
Lars Valentin wrote:
Thank you for testing. As stated above FSK seems to be still installed in Version=\"0.1.0.201808131056\" as you see in line 441. Could you please install the latest version and test this workflow in the dataminer again to check if you were successful?
As a reminder from previous advises, you need to uninstall the old plugins before installing the new version! If that procedure was messed up I had to manually delete the old plugin version in the plugin folder.
That's what the script is doing, the commands are the same ones used in the ansible role but limited to your plugin. The version that you'll find installed is the one I wrote about yesterday in the parent ticket, if you didn't change it since yesterday evening.
Updated by Lars Valentin over 6 years ago
great, I am looking forward that this will lead to a finally working version. Please let me know if it runs in the dataminer with my testworkflow.
How about the other Plugins - is this now a version which only comes with the FSK-plugin to do a step by step solution?
Updated by Andrea Dell'Amico over 6 years ago
Lars Valentin wrote:
great, I am looking forward that this will lead to a finally working version. Please let me know if it runs in the dataminer with my testworkflow.
The new plugin has been installed everywhere. The script that will executed every night runs the following command to verify that the plugin has been installed correctly:
/usr/local/bin/knime -nosplash -clean -application org.knime.product.KNIME_BATCH_APPLICATION -workflowDir="/opt/knime/knime_workflows/simple_FSK_testworkflow"
Its execution succeeded on all the dataminer. The contents of /opt/knime/knime_workflows/simple_FSK_testworkflow are (some directories are the result of the executions):
# ls -la /opt/knime/knime_workflows/simple_FSK_testworkflow/ total 100 drwxr-xr-x 9 root root 4096 Oct 2 13:30 . drwxr-xr-x 4 root root 48 Oct 1 19:52 .. drwxr-xr-x 2 root root 6 Oct 2 13:30 .artifacts drwxr-xr-x 2 root root 39 Oct 2 13:30 files drwxr-xr-x 5 root root 66 Oct 2 13:30 FSK Runner (#2) drwxr-xr-x 2 root root 30 Oct 2 13:30 FSKXReader01_workingDirectory16499 drwxr-xr-x 4 root root 53 Oct 2 13:30 FSKX Reader (#1) drwxr-xr-x 3 root root 40 Oct 2 13:30 FSKX Writer (#3) drwxr-xr-x 3 root root 40 Oct 2 13:30 Image Port Writer (#4) -rw-r--r-- 1 root root 45445 Sep 14 10:03 knime.log -rw-r--r-- 1 root root 289 Sep 14 10:03 .project -rw-r--r-- 1 root root 204 Oct 2 13:30 .savedWithData -rw-r--r-- 1 root root 5166 Oct 2 13:30 workflow.knime -rw-r--r-- 1 root root 29947 Sep 14 10:03 workflow.svg
The same workflow run from the dataminer fails, with the same error you reported before, but it seems to me that's something that should be investigated by @g.panichi@isti.cnr.it or @gianpaolo.coro@isti.cnr.it, because the same workflow run from the command line works correctly. The dataminer execution string is:
/usr/local/bin/knime -reset -consoleLog -nosplash -application org.knime.product.KNIME_BATCH_APPLICATION -workflowFile=simple_FSK_testworkflow.knwf -destFile=workflow.zip -workflow.variable=dummy,"dummy",String
The execution with the same variables from the command line completes correctly:
/usr/local/bin/knime -reset -consoleLog -nosplash -application org.knime.product.KNIME_BATCH_APPLICATION -workflowDir="/opt/knime/knime_workflows/simple_FSK_testworkflow" -workflow.variable=dummy,"dummy",String
The result log is the following, the result image is attached:
INFO main BatchExecutor ===== Executing workflow /opt/knime/knime_workflows/simple_FSK_testworkflow ===== WARN main BatchExecutor The workflow variable is potentially unused (not defined in workflow): "dummy" (STRING) SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. INFO main BatchExecutor Workflow execution done Finished in 8 secs (8462ms) INFO main BatchExecutor ============= Workflow executed sucessfully ===============
How about the other Plugins - is this now a version which only comes with the FSK-plugin to do a step by step solution?
No, there's only the version with all the plugins installed. I did not find any difference between your distribution and ours, after I've found the correct ways to execute the workflows.
Updated by Andrea Dell'Amico over 6 years ago
- File workflow.zip workflow.zip added
I also run the same workflow adding the option -destFile=workflow.zip. The result is attached.
Updated by Andrea Dell'Amico over 6 years ago
I also run successfully:
/usr/local/bin/knime -reset -consoleLog -nosplash -application org.knime.product.KNIME_BATCH_APPLICATION -destFile=workflow.zip -workflowFile=simple_FSK_testworkflow.knwf -workflow.variable=dummy,"dummy",String
So perhaps the problem is that when running from the dataminer, the file simple_FSK_testworkflow.knwf is not in the directory from where the workflow is run? The filename has no absolute path, so it must reside in the same directory from where the command is launched. I also tried to move the workflow file in a different place and run the command using an absolute path: it works.
Updated by Lars Valentin over 6 years ago
Thanks for the effort! If I understand you right the dataminer does not yet behave as expected while KNIME in batch mode itself does work now. Would be great if the experts you mentioned could solve that too.
Regarding the other KNIME plugins from the long list - in my version I did not include them in order to help to find the issue step by step. Thats why I ask if your ANSIBLE routine also did install all the other plugins from our list now or if this is an open task after the issue is fixed and I need to open a ticket for it.
Updated by Andrea Dell'Amico over 6 years ago
Lars Valentin wrote:
Thanks for the effort! If I understand you right the dataminer does not yet behave as expected while KNIME in batch mode itself does work now. Would be great if the experts you mentioned could solve that too.
It's a different problem: knime wants to write inside the knime distribution somehow, when using your plugin (other workflows work fine). So I had success when testing as root, but the execution failed when run by the dataminer user. I fixed that changing the ownership of the knime distribution directory, even if I don't like it.
Now, your workflow still fails, but because of a missing output file. The version executed by the dataminer does not generate the file image.png, while the one you gave me does. So, now the dataminer execution error is:
Knime computation /usr/local/bin/knime -reset -consoleLog -nosplash -application org.knime.product.KNIME_BATCH_APPLICATION -workflowFile=simple_FSK_testworkflow.knwf -destFile=workflow.zip -workflow.variable=dummy,"dummy",Str ing computation finished Logs of the computation [1] "CompilerOracle: exclude javax/swing/text/GlyphView.getBreakSpot" [2] "INFO \t main BatchExecutor\t ===== Executing workflow simple_FSK_testworkflow.knwf =====" [3] "WARN \t main BatchExecutor\t The workflow variable is potentially unused (not defined in workflow): \"dummy\" (STRING)" [4] "INFO \t main BatchExecutor\t Workflow execution done Finished in 8 secs (8218ms)" [5] "INFO \t main BatchExecutor\t Saved workflow availabe at: /home/gcube/tomcat/webapps/wps/ecocfg/rscr_aa0ac843-9b17-4958-8955-1e17c6129cfd/FSKX-Testworkflow/workflow.zip" [6] "INFO \t main BatchExecutor\t ============= Workflow executed sucessfully ===============" Output Parameter:workflow workflow.zip Output Parameter:image image.png file workflow exists? TRUE file image exists? FALSE FALSE Error, the output image(image.png) does not exist!
Please fix the workflow, or the workflow parameters.
Regarding the other KNIME plugins from the long list - in my version I did not include them in order to help to find the issue step by step. Thats why I ask if your ANSIBLE routine also did install all the other plugins from our list now or if this is an open task after the issue is fixed and I need to open a ticket for it.
All the plugins you asked have been installed. I'm listing them again:
- org.knime.features.testingapplication.feature.group
- org.knime.features.datageneration.feature.group #KNIME Data Generation http://update.knime.com/analytics-platform/3.6 Lars
- org.knime.features.base.filehandling.feature.group #KNIME File Handling Nodes http://update.knime.com/analytics-platform/3.6 Lars
- org.knime.features.r.feature.group #KNIME Interactive R Statistics Integration http://update.knime.com/analytics-platform/3.6 Lars
- org.knime.features.base.feature.group #KNIME Core http://update.knime.com/analytics-platform/3.6 Lars
- org.knime.features.ext.jfreechart.feature.group #KNIME JFreeChart http://update.knime.com/analytics-platform/3.6 Lars
- org.knime.features.ext.svg.feature.group #KNIME SVG Support http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.ext.webservice.client.feature.group #KNIME Web Service Client http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.virtual.feature.group #KNIME Virtual Nodes http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.ext.textprocessing.feature.group #KNIME Textprocessing http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.ext.textprocessing.language.german.feature.group #KNIME Textprocessing German Language Pack http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.ext.textprocessing.language.spanish.feature.group #KNIME Textprocessing Spanish Language Pack http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.ext.textprocessing.language.french.feature.group #KNIME Textprocessing French Language Pack http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.stats2.feature.group #KNIME Statistics Nodes (Labs) http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.ext.socialmedia.feature.group #KNIME Social Media Connectors (Twitter && Google) http://update.knime.com/analytics-platform/3.6 Matthias
- com.knime.features.reporting.designer.feature.group #KNIME Report Designer http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.webanalytics.feature.group #KNIME Webanalytics http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.python2.feature.group #KNIME Python Integration http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.ext.perl.feature.group #KNIME Perl Integration http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.optimization.feature.group #KNIME Optimization extension http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.ext.osm.feature.group #KNIME Open Street Map Integration http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.network.feature.group #KNIME Network Mining http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.network.distmatrix.feature.group #KNIME Network Mining distance matrix support http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.neighborgram.feature.group #KNIME Neighborgram && ParUni http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.distmatrix.feature.group #KNIME Distance Matrix http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.ext.itemset.feature.group #KNIME Itemset Mining http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.ext.lucene.feature.group #KNIME Indexing and Searching http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.ext.birt.feature.group #KNIME HTML/PDF Writer http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.ext.exttool.feature.group #KNIME External Tool Support http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.arima.feature.group #KNIME Autoregressive integrated moving average (ARIMA) http://update.knime.com/analytics-platform/3.6 Matthias
- org.knime.features.ext.exttool.feature.group #KNIME External Tool Support http://update.knime.com/analytics-platform/3.6 Matthias
- de.bund.bfr.knime.fsklab.feature.feature.group #FSK Lab Feature https://dl.bintray.com/silebat/fsklab_icpmf Lars
# - de.bund.bfr.knime.fsklab.legacy.feature.feature.group #Legacy FSK-Lab nodes https://dl.bintray.com/silebat/fsklab_icpmf Lars
- de.bund.bfr.knime.pmm.base.feature.group #PMM Nodes https://dl.bintray.com/silebat/pmmlab/ Lars
- de.bund.bfr.knime.gis.feature.feature.group #KNIME Nodes for GIS and Graph Visualization http://dl.bintray.com/silebat/generic/ Lars Warenstrominfo
- de.bund.bfr.knime.other.aaw.feat.feature.group #ZoMoPlugin-OtherFeats_aaw https://github.com/SiLeBAT/Other/raw/master/de.bund.bfr.knime.other.aaw.feat/update Alex Mibi-Portal
### - de.bund.bfr.knime.internal.feature.feature.group #Rhome and editable node http://dl.bintray.com/silebat/internal/ Alex RiskRanking
- de.nbi.cibi.feature.feature.group #de.NBI - CIBI Extension http://update.knime.com/community-contributions/3.6 M. Flor
- org.knime.knip.feature.feature.group #KNIME Image Processing http://update.knime.com/community-contributions/3.6 M. Filter AGINFRA
Updated by Andrea Dell'Amico over 6 years ago
- Status changed from In Progress to Feedback
- % Done changed from 80 to 100
Updated by Lars Valentin over 6 years ago
- Status changed from Feedback to In Progress
- % Done changed from 100 to 80
It's a different problem: knime wants to write inside the knime distribution somehow, when using your plugin (other workflows work fine). So I had success when testing as root, but the execution failed when run by the dataminer user. I fixed that changing the ownership of the knime distribution directory, even if I don't like it.
KNIME does need the rights to read and write in its own directories to be fully functional. In my server environment /opt/ knime has the owner and the group 'knime' and KNIME is always only used by the user 'knime'.
As I have no information how the dataminer environment looks like I can't tell you the right settings. But please make sure, that the dataminer matches the rights of KNIME. KNIME does not need root rights!
Now, your workflow still fails, but because of a missing output file. The version executed by the dataminer does not generate the file
image.png, while the one you gave me does. Please fix the workflow, or the workflow parameters.
You are right, I did replace the workflow with the version I sent you, but it still fails in the dataminer. Instead of the normal long list of errors I now receive immedate errors with (permission denied). It looks like that KNIME is not allowed to use its own files. Since no plugins are mentioned, I assume KNIME did not even reach the state to load them.
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> setwd("/home/gcube/tomcat/webapps/wps/config/../ecocfg/rscr_0f1acbb9-8706-42ad-a281-22fb9fe9f2cb/FSKX-Testworkflow")
> gcube_token<<-"6b7d25a8-4ef4-4c71-91e2-013fdf0f1612-843339462"
> gcube_username<<-"lars.valentin"
> gcube_context<<-"/d4science.research-infrastructures.eu/D4Research/RAKIP_portal"
> source('/home/gcube/tomcat/webapps/wps/config/../ecocfg/rscr_0f1acbb9-8706-42ad-a281-22fb9fe9f2cb/FSKX-Testworkflow/7ae0a487-2af5-4e25-8c21-bb01a1169298Main.R')
Machine address:
dataminer2-proto
[1] 0
Input Parameter:dummy dummy
Command: simple_FSK_testworkflow.knwf "dummy"
Adding rights to the files
computation started
software type: Knime-Workflow
dataminer2-proto
Global variables:
globalvariable globalvalue
1 gcube_username lars.valentin
2 gcube_context /d4science.research-infrastructures.eu/D4Research/RAKIP_portal
3 gcube_token 6b7d25a8-4ef4-4c71-91e2-013fdf0f1612-843339462
4 hostname 0
Knime computation
/usr/local/bin/knime -reset -consoleLog -nosplash -application org.knime.product.KNIME_BATCH_APPLICATION -workflowFile=simple_FSK_testworkflow.knwf -destFile=workflow.zip -workflow.variable=dummy,"dummy",String
computation finished
Logs of the computation
[1] "CompilerOracle: exclude javax/swing/text/GlyphView.getBreakSpot"
[2] "!SESSION 2018-10-04 08:43:40.691 -----------------------------------------------"
[3] "eclipse.buildId=unknown"
[4] "java.version=1.8.0_152"
[5] "java.vendor=Oracle Corporation"
[6] "BootLoader constants: OS=linux, ARCH=x86_64, WS=gtk, NL=en_US"
[7] ""
[8] "!ENTRY org.eclipse.osgi 4 0 2018-10-04 08:43:41.185"
[9] "!MESSAGE Error reading configuration: /opt/knime/knime_3.6.0/configuration/org.eclipse.osgi/.manager/.fileTableLock (Permission denied)"
[10] "!STACK 0"
[11] "java.io.FileNotFoundException: /opt/knime/knime_3.6.0/configuration/org.eclipse.osgi/.manager/.fileTableLock (Permission denied)"
[12] "\tat java.io.RandomAccessFile.open0(Native Method)"
[13] "\tat java.io.RandomAccessFile.open(RandomAccessFile.java:316)"
[14] "\tat java.io.RandomAccessFile.<init>(RandomAccessFile.java:243)"
[15] "\tat org.eclipse.osgi.internal.location.Locker_JavaNio.lock(Locker_JavaNio.java:36)"
[16] "\tat org.eclipse.osgi.storagemanager.StorageManager.lock(StorageManager.java:388)"
[17] "\tat org.eclipse.osgi.storagemanager.StorageManager.open(StorageManager.java:701)"
[18] "\tat org.eclipse.osgi.storage.Storage.getChildStorageManager(Storage.java:1776)"
[19] "\tat org.eclipse.osgi.storage.Storage.getInfoInputStream(Storage.java:1793)"
[20] "\tat org.eclipse.osgi.storage.Storage.<init>(Storage.java:132)"
[21] "\tat org.eclipse.osgi.storage.Storage.createStorage(Storage.java:85)"
[22] "\tat org.eclipse.osgi.internal.framework.EquinoxContainer.<init>(EquinoxContainer.java:68)"
[23] "\tat org.eclipse.osgi.launch.Equinox.<init>(Equinox.java:31)"
[24] "\tat org.eclipse.core.runtime.adaptor.EclipseStarter.startup(EclipseStarter.java:303)"
[25] "\tat org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:239)"
[26] "\tat sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)"
[27] "\tat sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)"
[28] "\tat sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)"
[29] "\tat java.lang.reflect.Method.invoke(Method.java:498)"
[30] "\tat org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:653)"
[31] "\tat org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)"
[32] "\tat org.eclipse.equinox.launcher.Main.run(Main.java:1499)"
[33] "\tat org.eclipse.equinox.launcher.Main.main(Main.java:1472)"
[34] "Knime:"
[35] "An error has occurred. See the log file"
[36] "null."
attr(,"status")
[1] 13
Output Parameter:workflow workflow.zip
Output Parameter:image image.png
file workflow exists? FALSE
FALSE Error, the output workflow(workflow.zip) does not exist!
null
at org.eclipse.osgi.internal.framework.EquinoxContainer.<init>(EquinoxContainer.java:70)
at org.eclipse.osgi.launch.Equinox.<init>(Equinox.java:31)
at org.eclipse.core.runtime.adaptor.EclipseStarter.startup(EclipseStarter.java:303)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:239)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:653)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)
at org.eclipse.equinox.launcher.Main.run(Main.java:1499)
at org.eclipse.equinox.launcher.Main.main(Main.java:1472)
Caused by: java.io.FileNotFoundException: /opt/knime/knime_3.6.0/configuration/org.eclipse.osgi/.manager/.fileTableLock (Permission denied)
at java.io.RandomAccessFile.open0(Native Method)
at java.io.RandomAccessFile.open(RandomAccessFile.java:316)
at java.io.RandomAccessFile.<init>(RandomAccessFile.java:243)
at org.eclipse.osgi.internal.location.Locker_JavaNio.lock(Locker_JavaNio.java:36)
at org.eclipse.osgi.storagemanager.StorageManager.lock(StorageManager.java:388)
at org.eclipse.osgi.storagemanager.StorageManager.open(StorageManager.java:701)
at org.eclipse.osgi.storage.Storage.getChildStorageManager(Storage.java:1776)
at org.eclipse.osgi.storage.Storage.getInfoInputStream(Storage.java:1793)
at org.eclipse.osgi.storage.Storage.<init>(Storage.java:132)
at org.eclipse.osgi.storage.Storage.createStorage(Storage.java:85)
at org.eclipse.osgi.internal.framework.EquinoxContainer.<init>(EquinoxContainer.java:68)
... 11 more
Knime: Cannot open display:
Error in eval(ei, envir) : object 'stoptheprocess' not found
Calls: source -> withVisible -> eval -> eval
In addition: Warning message:
running command '/usr/local/bin/knime -reset -consoleLog -nosplash -application org.knime.product.KNIME_BATCH_APPLICATION -workflowFile=simple_FSK_testworkflow.knwf -destFile=workflow.zip -workflow.variable=dummy,"dummy",String' had status 13
Execution halted
null
All the plugins you asked have been installed. I'm listing them again:
great!
Updated by Andrea Dell'Amico over 6 years ago
- Status changed from In Progress to Feedback
- % Done changed from 80 to 100
Lars Valentin wrote:
It's a different problem: knime wants to write inside the knime distribution somehow, when using your plugin (other workflows work fine). So I had success when testing as root, but the execution failed when run by the dataminer user. I fixed that changing the ownership of the knime distribution directory, even if I don't like it.
KNIME does need the rights to read and write in its own directories to be fully functional. In my server environment /opt/ knime has the owner and the group 'knime' and KNIME is always only used by the user 'knime'.
As I have no information how the dataminer environment looks like I can't tell you the right settings. But please make sure, that the dataminer matches the rights of KNIME. KNIME does not need root rights!
We usually install as root so that the user cannot mess with the installed software. We do not execute the algorithms as root.
Theconfiguration directory did not have the correct permission'ss yet, it's now OK. The execution now fails with
ERROR KNIME-Worker-0 Node Execute failed: Input file '/tmp/BatchExecutorInput31782/simple_FSK_testworkflow/files/test.fskx' does not exist Oct 04, 2018 10:10:38 AM org.apache.cxf.bus.osgi.CXFExtensionBundleListener unregister INFO: Removing the extensions for bundle 202 Knime: Cannot open display: Error in eval(ei, envir) : object 'stoptheprocess' not found Calls: source -> withVisible -> eval -> eval In addition: Warning message: running command '/usr/local/bin/knime -reset -consoleLog -nosplash -application org.knime.product.KNIME_BATCH_APPLICATION -workflowFile=simple_FSK_testworkflow.knwf -destFile=workflow.zip -workflow.variable=dummy,"dummy",String' had status 4 Execution halted
I see that the workflow file is different from the one I have. This is the one run by the dataminer algorithm:
$ ls -la total 44 drwxr-xr-x 2 gcube gcube 123 Oct 4 10:10 . drwxr-xr-x 3 gcube gcube 30 Oct 4 10:10 .. -rw-r--r-- 1 gcube gcube 226 Oct 4 10:10 globalvariables.csv -rwxrwxrwx 1 gcube gcube 4650 Oct 4 10:10 Main.R -rwxrwxrwx 1 gcube gcube 4615 Oct 4 10:10 simple_FSK_testworkflow.knwf -rwxrwxrwx 1 gcube gcube 14062 Oct 4 10:10 stat_algo.project -rw-r--r-- 1 gcube gcube 5548 Oct 4 10:16 workflow.zip
and this is the one I run after each plugin reinstallation:
ls -l simple_FSK_testworkflow.knwf -rw-r--r-- 1 root root 42927 Oct 4 10:17 simple_FSK_testworkflow.knwf
The one I have executes successfully:
INFO main BatchExecutor ===== Executing workflow simple_FSK_testworkflow.knwf ===== WARN main BatchExecutor The workflow variable is potentially unused (not defined in workflow): "dummy" (STRING) SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. INFO main BatchExecutor Workflow execution done Finished in 8 secs (8648ms) INFO main BatchExecutor Saved workflow availabe at: /home/gcube/workflow.zip INFO main BatchExecutor ============= Workflow executed sucessfully ===============
Updated by Lars Valentin over 6 years ago
I just added the test.fskx file for testing the testworkflow and I get no permission error messages anymore and the Dataminer workflows for FSK run through without complaining about missing FSK nodes.
Looks like we have a working KNIME with FSKlab now! Thank you!
Updated by Pasquale Pagano over 6 years ago
- Status changed from Feedback to Closed
Ok, it seems that we have completed this task. Going to close the ticket.
