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Warning

Iceberg reaches end-of-life on 30th November 2020. If you are running jobs on Iceberg then you need to take urgent action to ensure that your jobs/scripts will run on ShARC or Bessemer. If you have never used ShARC or Bessemer then now is the time to test your scripts. Not all software on Iceberg is available on ShARC/Bessemer.

Knime

KNIME Analytics Platform is an open solution for data-driven innovation, helping you discover the potential hidden in your data, mine for fresh insights, or predict new futures.

Interactive Usage

After connecting to iceberg (see Establishing a SSH connection), start an interactive session with the qrshx command.

The latest version of Knime including all of the extensions can be loaded with

module load apps/knime

Alternatively, you can load a specific version of Knime excluding all of the extensions using one of the following

module load apps/knime/3.1.2

With extensions

module load apps/knime/3.1.2ext

Knime can then be run with

$ knime

Batch usage

There is a command line option allowing the user to run KNIME in batch mode:

knime -application org.knime.product.KNIME_BATCH_APPLICATION -nosplash -workflowDir="<path>"
  • -application org.knime.product.KNIME_BATCH_APPLICATION launches the KNIME batch application.

  • -nosplash does not show the initial splash window.

  • -workflowDir=”<path>” provides the path of the directory containing the workflow.

Full list of options:

  • -nosave do not save the workflow after execution has finished

  • -reset reset workflow prior to execution

  • -failonloaderror don’t execute if there are errors during workflow loading

  • -updateLinks update meta node links to latest version

  • -credential=name[;login[;password]] for each credential enter credential name and optional login/password

  • -masterkey[=…] prompt for master password (used in e.g. database nodes),if provided with argument, use argument instead of prompting

  • -preferences=… path to the file containing eclipse/knime preferences,

  • -workflowFile=… ZIP file with a ready-to-execute workflow in the root of the ZIP

  • -workflowDir=… directory with a ready-to-execute workflow

  • -destFile=… ZIP file where the executed workflow should be written to if omitted the workflow is only saved in place

  • -destDir=… directory where the executed workflow is saved to if omitted the workflow is only saved in place

  • -workflow.variable=name,value,type define or overwrite workflow variable’name’ with value ‘value’ (possibly enclosed by quotes). The’type’ must be one of “String”, “int” or “double”.

The following return codes are defined:

  • 0 upon successful execution

  • 2 if parameters are wrong or missing

  • 3 when an error occurs during loading a workflow

  • 4 if an error during execution occurred

Installation Notes

These notes are primarily for administrators of the system.

Version 3.1.2 without extensions

  • Download with wget https://download.knime.org/analytics-platform/linux/knime_3.1.2.linux.gtk.x86_64.tar.gz

  • Move to /usr/local/extras/knime_analytics/3.1.2

  • Unzip tar -xvzf knime_3.1.2.linux.gtk.x86_64.tar.gz

The modulefile is at /usr/local/extras/modulefiles/apps/knime/3.1.2

contains

#%Module1.0

proc ModulesHelp { } {
        puts stderr " Adds KNIME to your PATH environment variable and necessary libraries"
}

prepend-path PATH /usr/local/extras/knime_analytics/3.1.2

Version 3.1.2 with extensions

  • Download with wget https://download.knime.org/analytics-platform/linux/knime-full_3.1.2.linux.gtk.x86_64.tar.gz

  • Move to /usr/local/extras/knime_analytics/3.1.2ext

  • Unzip tar -xvzf knime-full_3.1.2.linux.gtk.x86_64.tar.gz

The modulefile is at /usr/local/extras/modulefiles/apps/knime/3.1.2ext

contains

#%Module1.0

proc ModulesHelp { } {
        puts stderr " Adds KNIME to your PATH environment variable and necessary libraries"
}

prepend-path PATH /usr/local/extras/knime_analytics/3.1.2ext