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Version Dependencies

Info

If you use iserver with AWS clusters in the cloud, the iserver version you are using depends on the ebs_snapshot_id that is set in your ~/.parallelcluster/config. See AWS ParallelCluster Configuration for more details.

iserver Version: 1.2.2 (June 2021)

Changelog

New Features

  • Enable omission of -q option from SGE and UGE submission scripts

Bug Fixes

  • Fixed log message mentioning SGE when Slurm is used
  • Fixed problem with testing.scheduler option so that scheduler tests on startup can now be disabled

Compatibility

All LigandScout versions 4.3 and newer can be used with this version. However, only LigandScout 4.4.6 supports using remote files as conformer generation input.

Compatible with IL KNIME extension versions 1.5.1 and newer.

Full compatibility

This version fully supports all LigandScout Remote features available through LigandScout 4.4.6 or through the most recent versions of the IL KNIME extensions.

iserver Version: 1.2.1 (Jannuary 2021)

Changelog

New Features

  • Implement alternative SGE execution engine to avoid dependence on DRMAA and provide UGE support. This new engine 'sge-cmd' is now recommended for all SGE systems.
  • Support UGE as scheduling system.
  • Allow submitting confgen job with server path as input molecule file
  • Web service endpoint for retrieving possible confgen input molecule files
  • Create web service endpoint to retrieve server version and status
  • Allow wildcards for specifying confgen input and ldb directories in config file
  • Allow all possible idbgen input formats for confgen
  • Add name property idbgen option for confgen jobs
  • All values from application.properties are now trimmed from whitespace automatically
  • Allow to set LigandScout 4 installation path instead of individual executable paths via ligandscout.path
  • Create web service endpoint to retrieve the the used iserver version
  • Implement automated settings validation to point out common configuration problems

Bug Fixes

  • Download of the aggregated server logs was not working on some systems
  • Do not change working directory to the server's installation location with SGE executor so that the behavior can be defined by the user via the config file
  • Confgen sub-job state was not updated to Done in some cases until job was not finished completely
  • Improve parsing of job log files so that errors are recognized better and handled gracefully
  • Include original error causes whenever a problem with the libsize command-line tools occurs
  • Improved processing of conformer generation job results, which improves stability especially for large jobs with thousands of output database chunks.
  • Improve default settings to avoid memory issues that could occur with some molecule libraries
  • Consider configured Slurm partition for determining available cluster resources

Compatibility

All LigandScout versions 4.3 and newer can be used with this version. However, only LigandScout 4.4.6 supports using remote files as conformer generation input.

Compatible with IL KNIME extension versions 1.5.1 and newer.

Full compatibility

This version fully supports all LigandScout Remote features available through LigandScout 4.4.6 or through the most recent versions of the IL KNIME extensions.

iserver Version: 1.2.0 (October 2019)

Changelog

New Features

  • Support for the SLURM scheduling system

Compatibility

Compatible with LigandScout versions 4.3 - 4.4.5.

Compatible with IL KNIME extension versions 1.5.1 and newer.

iserver Version: 1.1.9 (July 2019)

Changelog

New Features

  • The installation folder now includes a new script (update.sh) which allows to automatically update iserver to specific versions.
  • Additional option sge.queue which allows to set a queue that should be used for job submission and for retrieving information about available slots.
  • Logs directory can now be set with logging.directory. Therefore, iserver no longer needs write access to its own installation directory.

Bugfixes

  • Jobs with several thousand sub-jobs caused too many open files on some systems. iserver now closes files immediately after parsing the relevant information, drastically limiting the number of files that have to be open in parallel.
  • SGE option -j n is now used for all jobs. Previously, the progress files would not be created properly if the SGE setup had a different default policy.
  • Improved parsing of libsize output to better deal with unexpected warning messages.

Compatibility

Compatible with LigandScout versions 4.3 - 4.4.5.

Compatible with IL KNIME extension versions 1.5.1 and newer.

iserver Version: 1.1.8 (July 2019)

Version 1.1.8 is an internal version and released only for documentation purposes. Please update directly to iserver version 1.1.9

iserver Version: 1.1.7 (June 2019)

Changelog

New Features

  • iserver now supports restarting of individual failed/canceled sub-jobs. It is also possible to restart all failed sub-jobs at once. Accessible via right-clicking on a failed/canceled sub-job in LigandScout or KNIME. This is especially useful when working with AWS Spot instances, but also improves fault tolerance in general. If parts of a job fail, it is now easily possible to re-run only the failed parts.
  • iserver now creates .submit files in the sub-job directories also when using an SGE cluster. This allows for easily re-submitting jobs and enables manual inspection.
  • Support for the upload of local screening databases (.ldb). There is a new button for this in the "Load Remote Database" dialog in LigandScout 4.4.
  • Automatic refresh of the database list after a remote conformer generation job finished successfully, so the generated database is immediately available for virtual screening.

Bugfixes

  • Previously, iserver sometimes failed to find .ldb databases that were manually moved to another location within the monitored locations
  • Jobs with a large amount of sub-jobs that all failed could not be deleted from the jobs list

Compatibility

Compatible with LigandScout versions 4.3 - 4.4.5.

Compatible with IL KNIME extension versions 1.5.1 and newer.


iserver Version: 1.1.6

Compatibility

Compatible with LigandScout versions 4.3 - 4.4.5.

Compatible with IL KNIME extension versions 1.5.1 and newer.

Compatibility restriction

Even though it is possible to use newever versions of the IL KNIME extensions or LigandScout with this iserver version, we recommend to update to the newest version of iserver. Otherwise, some advanced features introduced with LigandScout 4.4 might not work correctly.


iserver Version: 1.1.5

Compatibility

Compatible with LigandScout versions 4.3 - 4.4.5.

Compatible with IL KNIME extension versions 1.5.1 and newer.

Compatibility restriction

Even though it is possible to use newever versions of the IL KNIME extensions or LigandScout with this iserver version, we recommend to update to the newest version of iserver. Otherwise, some advanced features introduced with LigandScout 4.4 might not work correctly.
Additionally, this version does not yet support the download of non-matching molecules via the activity profiling KNIME node.


iserver Version: 1.1.4

Compatible with LigandScout version 4.2.6.

This version is not yet compatible with the IL KNIME extension.