Commit 153351af authored by Peter van 't Hof's avatar Peter van 't Hof

Adding documentation for memory settings

parent c104fdfb
# Memory behavior biopet
### Calculation
- **Default memory per thread**: *core_memory* + (0.5 * *retries*)
- **Memory limit** (used for java jobs): (*core_memory* + (0.5 * *retries*)) * *threads*
- **Resident limit**: (*core_memory* + (0.5 * *retries*)) * *residentFactor*
- **Vmem limit**: (*core_memory* + (0.5 * *retries*)) * (*vmemFactor* + (0.5 * *retries*))
### Defaults
- **core_memory**: 2.0 (in Gb)
- **threads**: 1
- **residentFactor**: 1.2
- **vmemFactor**: 1.4, 2.0 for java jobs
This are de defaults of biopet but each extension in biopet can set their own defaults. As example the *bwa mem* tools use by default 8 threads and corememory of 6.0.
### Config
In the config there is the possibility to set the resources.
- **core_memory**: This overrides the default of the extension
- **threads**: This overrides the default of the extension
- **resident_factor**: This overrides the default of the extension
- **vmem_factor**: This overrides the default of the extension
- **vmem**: Sets a fixed vmem, **When this is set the retries won't raise the *vmem* anymore**
- **memory_limit**: Sets a fixed memory limit, **When this is set the retries won't raise the *memory limit* anymore**
- **resident_limit**: Sets a fixed resident limit, **When this is set the retries won't raise the *resident limit* anymore**
### Retry
In Biopet the number of retries is set to 5. De first retry does not use an increased memory, starting from the 2e retry the memory will automatically increase arcording to the calculations above.
......@@ -4,6 +4,7 @@ pages:
- General:
- Config: 'general/config.md'
- Requirements: 'general/requirements.md'
- Memory behavior: 'general/memory.md'
- About: 'general/about.md'
- License: 'general/license.md'
- Pipelines:
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