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Configure walltime, memory, nodes, ppn, queue per protocol
- Updated templates for local backend
- Updated templates for slurm backend
- Refactored tests to produce output in a test specific subdir (as opposed to overwriting the results with each test.)
- Exit with error when batching is requested as this feature is currently not working pending re-implementation.
- Minor bug fix for SLURM header.ftl template.
- Updated pom.xml and assembly.xml to create tar.gz instead of zip artifact.
- Updated SLURM job header, job footer and submit templates for cluster setup with Quality of Service (QoS)
- Removed custom *_gaf templates, which have been relocated to the respective pipeline repos.
added function that will calculate the duration of each job and put it in a file (in the jobs directory)
- updated header_gaf.ftl
- added footer_gaf.ftl
- updated submit_gaf.ftl
Prepared for Error logging (mailing)
- Further memory reduction by smart handling of all the parameters stored in the environment
Fix #236 The environment string is placed into memory before writing it to files. This causes out of memory errors with large sample sizes
- GoldmanSachs Map and intern Strings for efficient memory usage
- Massive Speed improvements by refactoring code
- Enhanced logging, telling more by telling less
- The batching feature has been disabled for now, due to implementation issues
- The generated dist zip now contains a folder with the following name: molgenis-compute-version. This means you no longer have to change the name, only renaming the zip file should work now
Memory usage improvements
Fix #192 Missing newline between path and environment variables in generated step scripts
Fix #195 user_ prefix and protocol_prefix make the parameter map entities too big
Fix #197 Tests do not test the content of generated scripts
Due to efficiency improvements, the 'tasks' variable now only contains the following fields:
Keep this in mind when creating your own custom submit.ftl