Commit fe773e13 authored by Wai Yi Leung's avatar Wai Yi Leung

Spelling fixes

parent ecbab1a8
# Memory behavior biopet
# Memory behaviour biopet
### Calculation
......@@ -7,7 +7,7 @@
- **Resident limit**: (*core_memory* + (0.5 * *retries*)) * *residentFactor*
- **Vmem limit**: (*core_memory* + (0.5 * *retries*)) * (*vmemFactor* + (0.5 * *retries*))
We asume here that the cluster will amplify those values by the number of threads. If this is not the case for your cluster please contact us.
We assume here that the cluster will amplify those values by the number of threads. If this is not the case for your cluster please contact us.
#### Total values
- **Memory limit** (used for java jobs): (*core_memory* + (0.5 * *retries*)) * *threads*
......@@ -20,7 +20,8 @@ We asume here that the cluster will amplify those values by the number of thread
- **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.
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 `core_memory` of 6.0.
### Config
......@@ -37,4 +38,5 @@ In the config there is the possibility to set the resources.
### 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.
In Biopet the number of retries is set to 5. De first retry does not use an increased memory, starting from the 2nd
retry the memory will automatically increase according to the calculations mentioned in [Values per core](#Values per core).
......@@ -4,7 +4,7 @@ pages:
- General:
- Config: 'general/config.md'
- Requirements: 'general/requirements.md'
- Memory behavior: 'general/memory.md'
- Memory behaviour: 'general/memory.md'
- About: 'general/about.md'
- License: 'general/license.md'
- Pipelines:
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