strange XGboost error on Linux KNIME Executor while adding knode to workflow

I use XGboost in some projects and it worked so far. I restarted Ubuntu Linux 20.04 due to some updates with current KNIME Server and Executor (4.4.1) and afterwards the XGboost nodes do not works anymore both one the Server and KNIME Exectutor started locally. The error is while trying to add the knode to the workflow:
#################################################################
2021-10-18 12:13:12,867 : DEBUG : main : : CreateNodeCommand : : : Node cannot be created.
java.lang.NoClassDefFoundError: ml/dmlc/xgboost4j/java/XGBoostError
at org.knime.xgboost.base.nodes.learner.XGBLearnerNodeModel.collectOutportTypes(XGBLearnerNodeModel.java:109)
[…]
at org.eclipse.equinox.launcher.Main.main(Main.java:1434)
Caused by: java.lang.ClassNotFoundException: An error occurred while automatically activating bundle org.knime.xgboost.libs (1199).
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:126)
[…]
at java.base/java.lang.ClassLoader.loadClass(Unknown Source)
… 57 more
Caused by: org.osgi.framework.BundleException: Exception in org.knime.xgboost.libs.XGBoostPluginActivator.start() of bundle org.knime.xgboost.libs.
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:835)
[…]
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:117)
… 64 more
Caused by: java.lang.UnsatisfiedLinkError: /usr/local/knime/knime-full_4.4.1/plugins/org.knime.xgboost.bin.linux.amd64.cpu_4.4.0.v202104131257/libs/libxgboost4j.so: libgomp.so.1: cannot open shared object file: No such file or directory
[…]
##################################################################

The user has full rights for this lib:
ls -l /usr/local/knime/knime-full_4.4.1/plugins/org.knime.xgboost.bin.linux.amd64.cpu_4.4.0.v202104131257/libs/libxgboost4j.so
-rw-rw-r-- 1 knime knime 3327002 Aug 22 07:42 /home/knime/knime-full_4.4.1/plugins/org.knime.xgboost.bin.linux.amd64.cpu_4.4.0.v202104131257/libs/libxgboost4j.so

I also checked the SHA256 checksum of the large downloaded tar.gz-file and its is also OK.

Do you have and idea why something like this could happen?

Its about “libgomp.so.1”. Somehow I may have removed “libgomp1” via apt/dpkg since there is not depency to that by the system packages.
I suggest that there to be some hint in the error that such an external lib is needed.

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Hi @spider

thanks for the update! Just to confirm: is it working again with the package installed?
I’ll pass on your suggestion regarding the error message to the developers.

Kind regards
Marvin

Yes, it does work. I did some cleanup since the last reboot by removing unused packages using “apt autoremove” and this lib seems be be removed but was still in the RAM so KNIME’s xgboost still worked.
Maybe this lib is also used by other KNIME functions/extensions…

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