Knime Executor script fails

KNIME Server
1

Hi When updatting to the latest version of the executor on Ubuntu server with console only display it fails with the below message. I have tried this several times and it is not clear how to proceed beyond this. Should I remove one of the extensions that it is complaining about? If so are there any instructions to do this under Linux on the terminal? I do not need the Erlwood chem extension.

Thanks in anticipation.

Nick

Errors:

!ENTRY org.eclipse.equinox.p2.director 4 10054 2020-05-01 17:28:29.611
!MESSAGE Cannot complete the install because of a conflicting dependency.
!SUBENTRY 1 org.eclipse.equinox.p2.director 4 0 2020-05-01 17:28:29.612
!MESSAGE Software being installed: KNIME Distance Matrix 4.1.1.v202001312017 (org.knime.features.distmatrix.feature.group 4.1.1.v202001312017)
!SUBENTRY 1 org.eclipse.equinox.p2.director 4 0 2020-05-01 17:28:29.612
!MESSAGE Software currently installed: Erlwood Knime Open Source Cheminformatics 3.3.0.v201701271222 (org.erlwood.features.cheminformatics.base.feature.group 3.3.0.v201701271222)
!SUBENTRY 1 org.eclipse.equinox.p2.director 4 1 2020-05-01 17:28:29.613
!MESSAGE Only one of the following can be installed at once:
!SUBENTRY 2 org.eclipse.equinox.p2.director 4 0 2020-05-01 17:28:29.613
!MESSAGE KNIME Distance Matrix Extension 4.1.0.v201911251600 (org.knime.distmatrix 4.1.0.v201911251600)
!SUBENTRY 2 org.eclipse.equinox.p2.director 4 0 2020-05-01 17:28:29.614
!MESSAGE KNIME Distance Matrix Extension 4.1.1.v202001312017 (org.knime.distmatrix 4.1.1.v202001312017)
!SUBENTRY 2 org.eclipse.equinox.p2.director 4 0 2020-05-01 17:28:29.614
!MESSAGE KNIME Distance Matrix Extension 3.7.2.v201904170930 (org.knime.distmatrix 3.7.2.v201904170930)
!SUBENTRY 1 org.eclipse.equinox.p2.director 4 1 2020-05-01 17:28:29.615
!MESSAGE Cannot satisfy dependency:
!SUBENTRY 2 org.eclipse.equinox.p2.director 4 0 2020-05-01 17:28:29.616
!MESSAGE From: Erlwood Knime Open Source Cheminformatics 3.3.0.v201701271222 (org.erlwood.features.cheminformatics.base.feature.group 3.3.0.v201701271222)
!SUBENTRY 2 org.eclipse.equinox.p2.director 4 0 2020-05-01 17:28:29.616
!MESSAGE To: org.erlwood.knime.cheminformatics [3.3.0.v201701271213]
!SUBENTRY 1 org.eclipse.equinox.p2.director 4 1 2020-05-01 17:28:29.616
!MESSAGE Cannot satisfy dependency:
!SUBENTRY 2 org.eclipse.equinox.p2.director 4 0 2020-05-01 17:28:29.617
!MESSAGE From: Erlwood Knime Open Source Cheminformatics 3.3.0.v201701271213 (org.erlwood.knime.cheminformatics 3.3.0.v201701271213)
!SUBENTRY 2 org.eclipse.equinox.p2.director 4 0 2020-05-01 17:28:29.617
!MESSAGE To: bundle org.knime.distmatrix [3.0.0,4.0.0)
!SUBENTRY 1 org.eclipse.equinox.p2.director 4 1 2020-05-01 17:28:29.617
!MESSAGE Cannot satisfy dependency:
!SUBENTRY 2 org.eclipse.equinox.p2.director 4 0 2020-05-01 17:28:29.617
!MESSAGE From: KNIME Distance Matrix 4.1.1.v202001312017 (org.knime.features.distmatrix.feature.group 4.1.1.v202001312017)
!SUBENTRY 2 org.eclipse.equinox.p2.director 4 0 2020-05-01 17:28:29.617
!MESSAGE To: org.knime.distmatrix [4.1.1.v202001312017]
May 01, 2020 5:28:30 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener unregister
INFO: Removing the extensions for bundle 306
May 01, 2020 5:28:30 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener unregister
INFO: Removing the extensions for bundle 307

2

Hi @Cnik,

welcome to the KNIME community.

From which executor version are you coming from? If it is a version less than 4.0 you have to install a fresh executor build, as it is a major version update.

Please have a look at the topic “Installing a new KNIME Server Executor” here: https://docs.knime.com/2019-12/server_update_guide/index.html#knime-executor

And for detailed instructions here:
https://docs.knime.com/2019-12/server_admin_guide/index.html#knime-executor-installation

Please use the KNIME Server Executor tar.gz-build from this site for the installation:
https://www.knime.com/knimecom-product-downloads-2019-12

Cheers,
Michael

3

Thanks for the response.

It is from version 4.1 I think - the server was installed with version 4.

Is installing a new executor the easiest way forward?

Thanks,

Nick

4

Hey Nick,

no, it should be easier to uninstall the erlwood extension.

First: stop the server and check, that no executor instances are still running.
Change directory to the main executor folder. Have a look at your installed extensions, grep erlwood:

./knime -application org.eclipse.equinox.p2.director -nosplash -consolelog -lir|grep erlwood

You should see two lines.
Now uninstall them from the executor:

./knime -application org.eclipse.equinox.p2.director -nosplash -consolelog -u org.erlwood.features.cheminformatics.base.feature.group,org.erlwood.knime.cheminformatics -d <knime-installation-folder>

I took the extension names from your error messages,please use the names you get from the list of extensions as described above and change the <knime-installation-folder> to the absolute path of your executer installation.

Afterwards you should be able to run the update-rmi.sh skript without errors.

Hope this solves your issue.

Cheers,
Michael

5

Many Thanks for the answer. Sorry for the late response. This worked to uninstall the required packages very well. I really appreciated the informative content. It was good to learn a little more about how it all works.

Ultimately this did not do the business though. I eventually “cheated” a little by remote connecting with putty with xming to provide an xserver and ran the graphical tools. It then managed to find and work around the issues which I had. The issues seem to have been related to 3.7 version not having been removed by the upgrade script when I last upgraded. Hopefully a useful feedback. Let me know if I can provide you any more info. As a Windows admin and Linux semi-pro at best it’s been a challenge!

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