Config for key "layoutInfos" not found

#1

Dear all,

I updated to knime analytics 4.1 and knime server to 4.10. I am trying to execute some workflows and I get the error below in the knime portal. I have already replaced old style wrapped metanodes with components and the legacy quick nodes with widgets. Although I cannot open the visual layout editor of the components (your operating system is using an outdated browser…update the libwebkit* packages, this is a separate issue) I have configured the components using the basic layout (only a couple of quickform nodes present). I get similar errors for the knime example workflows, such as 07_Visualize_Scatterplot_on_file.

Do you know what is going on?

Many thanks,

Panos

–
Errors loading workflow ‘substanceIdentityDataMatrix’: Status: DataLoadError: substanceIdentityDataMatrix 0 loaded with error during data load
Status: DataLoadError: substanceIdentityDataMatrix 0
Status: Error: wrapped node with ID suffix 5365
Status: Error: Could not load Wrapped Metanode layout information: Config for key “layoutInfos” not found.
Status: Error: wrapped node with ID suffix 5647
Status: Error: Could not load Wrapped Metanode layout information: Config for key “layoutInfos” not found.
Status: DataLoadError: File Reader 0:1
Status: DataLoadError: Unable to load port content for node “File Reader”: Unknown table identifier: container_table_compressed
Status: DataLoadError: State has changed from EXECUTED to CONFIGURED
Status: DataLoadError: Table Creator 0:3185
Status: DataLoadError: Unable to load port content for node “Table Creator”: Unknown table identifier: container_table_compressed
Status: DataLoadError: State has changed from EXECUTED to CONFIGURED
Status: DataLoadError: File Reader 0:5237
Status: DataLoadError: Unable to load port content for node “File Reader”: Unknown table identifier: container_table_compressed
Status: DataLoadError: State has changed from EXECUTED to IDLE
Status: DataLoadError: File Reader 0:5238
Status: DataLoadError: Unable to load port content for node “File Reader”: Unknown table identifier: container_table_compressed
Status: DataLoadError: State has changed from EXECUTED to IDLE
Status: DataLoadError: File Reader 0:5453
Status: DataLoadError: Unable to load port content for node “File Reader”: Unknown table identifier: container_table_compressed
Status: DataLoadError: State has changed from EXECUTED to CONFIGURED
Status: DataLoadError: File Reader 0:5566
Status: DataLoadError: Unable to load port content for node “File Reader”: Unknown table identifier: container_table_compressed
Status: DataLoadError: State has changed from EXECUTED to CONFIGURED
Status: Error: Component 0:5647
Status: Error: Node “String Widget” not available from extension “KNIME Quick Forms” (provided by “KNIME AG, Zurich, Switzerland”; plugin “org.knime.js.quickforms” is installed)
Status: Error: Node “List Box Widget” not available from extension “KNIME Quick Forms” (provided by “KNIME AG, Zurich, Switzerland”; plugin “org.knime.js.quickforms” is installed)
Status: Error: Unable to insert connection “[5393(1) -> 5394( 0)]”
Status: DataLoadError: Reference Row Splitter 0:5465
Status: DataLoadError: Unable to load port content for node “Reference Row Splitter”: Unknown table identifier: container_table_compressed
Status: DataLoadError: Advanced MolConverter 0:3186
Status: DataLoadError: Unable to load port content for node “Advanced MolConverter”: Unknown table identifier: rearrange_columns_table_compressed
Status: DataLoadError: JChem Search 0:3364
Status: DataLoadError: Unable to load port content for node “JChem Search”: Unknown table identifier: container_table_compressed
Status: DataLoadError: Column Rename 0:5276
Status: DataLoadError: Unable to load port content for node “Column Rename”: No BufferedDataTable with ID 9634483
Status: DataLoadError: Java Snippet (simple) 0:5240
Status: DataLoadError: Unable to load port content for node “Java Snippet (simple)”: Unknown table identifier: rearrange_columns_table_compressed
Status: DataLoadError: Java Snippet 0:5567
Status: DataLoadError: Unable to load port content for node “Java Snippet”: Unknown table identifier: rearrange_columns_table_compressed
Status: DataLoadError: Column Filter 0:5459
Status: DataLoadError: Unable to load port content for node “Column Filter”: No BufferedDataTable with ID 9634493
Status: DataLoadError: Java Snippet (simple) 0:5239
Status: DataLoadError: Unable to load port content for node “Java Snippet (simple)”: Unknown table identifier: rearrange_columns_table_compressed
Status: DataLoadError: Concatenate (Optional in) 0:5241
Status: DataLoadError: Unable to load port content for node “Concatenate (Optional in)”: No BufferedDataTable with ID 9634485
Status: DataLoadError: Column Filter 0:5569
Status: DataLoadError: Unable to load port content for node “Column Filter”: No BufferedDataTable with ID 9634491
Status: DataLoadError: Java Snippet 0:5461
Status: DataLoadError: Unable to load port content for node “Java Snippet”: Unknown table identifier: rearrange_columns_table_compressed
Status: DataLoadError: GroupBy 0:5242
Status: DataLoadError: Unable to load port content for node “GroupBy”: Unknown table identifier: container_table_compressed
Status: DataLoadError: Column Rename 0:5463
Status: DataLoadError: Unable to load port content for node “Column Rename”: No BufferedDataTable with ID 9634497
Status: DataLoadError: Joiner 0:5236
Status: DataLoadError: Unable to load port content for node “Joiner”: Unknown table identifier: container_table_compressed
Status: DataLoadError: Column Filter 0:5462
Status: DataLoadError: Unable to load port content for node “Column Filter”: No BufferedDataTable with ID 9634499
Status: DataLoadError: Java Snippet 0:4866
Status: DataLoadError: Unable to load port content for node “Java Snippet”: Unknown table identifier: rearrange_columns_table_compressed
Status: DataLoadError: String to Date&Time 0:4867
Status: DataLoadError: Unable to load port content for node “String to Date&Time”: Unknown table identifier: rearrange_columns_table_compressed
Status: DataLoadError: Sorter 0:4499
Status: DataLoadError: Unable to load port content for node “Sorter”: Unknown table identifier: container_table_compressed
Status: DataLoadError: Java Snippet (simple) 0:5256
Status: DataLoadError: Unable to load port content for node “Java Snippet (simple)”: Unknown table identifier: rearrange_columns_table_compressed
Status: DataLoadError: Java Snippet 0:5417
Status: DataLoadError: Unable to load port content for node “Java Snippet”: Unknown table identifier: rearrange_columns_table_compressed
Status: DataLoadError: Column Filter 0:5452
Status: DataLoadError: Unable to load port content for node “Column Filter”: No BufferedDataTable with ID 9634508
Status: DataLoadError: Concatenate 0:5464
Status: DataLoadError: Unable to load port content for node “Concatenate”: No BufferedDataTable with ID 9634500
Status: DataLoadError: String to JSON 0:5517
Status: DataLoadError: Unable to load port content for node “String to JSON”: Unknown table identifier: rearrange_columns_table_compressed
Status: DataLoadError: JSON Path 0:5516
Status: DataLoadError: Unable to load port content for node “JSON Path”: Unknown table identifier: rearrange_columns_table_compressed
Status: DataLoadError: Row Splitter 0:5515
Status: DataLoadError: Unable to load port content for node “Row Splitter”: Unknown table identifier: container_table_compressed
Status: DataLoadError: Column Filter 0:5570
Status: DataLoadError: Unable to load port content for node “Column Filter”: No BufferedDataTable with ID 9634512
Status: DataLoadError: Concatenate (Optional in) 0:5568
Status: DataLoadError: Unable to load port content for node “Concatenate (Optional in)”: No BufferedDataTable with ID 9634503
Status: DataLoadError: String to JSON 0:5622
Status: DataLoadError: Unable to load port content for node “String to JSON”: Unknown table identifier: rearrange_columns_table_compressed
Status: Error: Metanode 0:5365
Status: Error: Node “File Download Widget” not available from extension “KNIME Quick Forms” (provided by “KNIME AG, Zurich, Switzerland”; plugin “org.knime.js.quickforms” is installed)

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#2

I realised the issue was the knime-server.config file was pointing to an earlier version of the knime platform (3.6). I changed this to point to the latest knime (4.1). No I am getting a different error hen loading a workflow

RMI executor could not be started, see log file for details

Looking at the knime server log file we have:

/srv/knime/knimeExecutor/knime_4.1.0/knime --launcher.suppressErrors --launcher.ini /srv/knime/knimeServer/knimeServerRepository/runtime/runtime_knime-rmi-50100/knime-rmi.ini
Last 5 lines of log output follow:
Knime:
A Java Runtime Environment (JRE) or Java Development Kit (JDK)
must be available in order to run Knime. No Java virtual machine
was found after searching the following locations:
plugins/org.knime.binary.jre.linux.x86_64_1.8.0.152-01/jre/bin
Also check log file in /srv/knime/knimeExecutor/knime_4.1.0/configuration

Which is strange because during the installation I pointed to the correct location of the openJDK bin folder.

I note that I installed manually knime analytics platform with the required server extensions in case this matters.

Regards,

Panos

1 Like
#3

The configuration of the server seems valid, it is using the openJDK you configured during installation.

The knime executor of the server seems misconfigured. There is a knime.ini in /srv/knime/knimeExecutor/knime_4.1.0 that points to plugins/org.knime.binary.jre.linux.x86_64_1.8.0.152-01/jre/bin .

That was the location of the java binary of your knime executor 3.6., the new path has to be plugins/org.knime.binary.jre.linux.x86_64_1.8.0.202-b08/jre/bin .

Please change the path in the mentioned knime.ini ( and /config/knime.ini, if you use it) and restart the server afterwards, it should work.

Best Regards,

Michael

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#4

Dear all,

I would like to add some more information. It seems there is a java version mixup.

In particular:

  1. when I deployed knime server I used a specially downloaded java to avoid dependencies on the system java that may change by the system administrators. I installed
    $./java -version
    openjdk version “1.8.0_232”
    OpenJDK Runtime Environment (AdoptOpenJDK)(build 1.8.0_232-b09)
    OpenJDK 64-Bit Server VM (AdoptOpenJDK)(build 25.232-b09, mixed mode)

This is the java I pointed knime server installer to and the installation went fine.

  1. the system java is
    $ java -version
    openjdk version “1.8.0_222”
    OpenJDK Runtime Environment (build 1.8.0_222-b10)
    OpenJDK 64-Bit Server VM (build 25.222-b10, mixed mode)

  2. The error message in the knime server log complained that the knime executor could not find a java in
    path…/knimeExecutor/knime_4.1.0/plugins/org.knime.binary.jre.linux.x86_64_1.8.0.152-01/jre/bin

  3. In the knime executor we can find the following java

path…/knimeExecutor/knime_4.1.0/plugins/org.knime.binary.jre.linux.x86_64_1.8.0.202-b08/

So there are four versions of java involved here.

The java in 3. above came from a previous installation of knime server probably because I tried to reuse the old knime server repository. I created a new repository and manually copied the old workflows and this has fixed the issue.

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#5

Your Java configuration is valid. The server is running on the OpenJDK version you configured it to use and the KNIME Analytics Platform/Executor doesn’t need an external Java installation as it contains and uses the Open JRE in the plugins folder.

The path …/knimeExecutor/knime_4.1.0/plugins/org.knime.binary.jre.linux.x86_64_1.8.0.152-01/jre/bin was used by the old executor and is now misleading. The path shouldn’t exist anymore on your system after successfully upgrading the executor. This path in the knime.ini has caused the problem with the failing executor.

Is the server running now, are all your problems fixed?

Best Regards,

Michael

1 Like
#6

Hi Michael,

yes, now everything is working. Thank you for your input. This issue can be closed.

Regards,

Panos

1 Like