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Improve k8s volume size calculations #141

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johnbradley opened this issue Jan 29, 2019 · 1 comment
Closed

Improve k8s volume size calculations #141

johnbradley opened this issue Jan 29, 2019 · 1 comment

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@johnbradley
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PR #140 uses the job's volume size for the job-data, output-data, tmpout volume sizes.
The /tmp volume is hard coded to be 1 G.
Need to come up with more accurate sizes for these.

@johnbradley
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I had a job that failed due to /tmp filling up.
The workflow failed running gatk4 SortSam resulting in a No space left on device error .

Related code:

TMP_VOLUME_SIZE_IN_G = 1

def create_tmp_persistent_volume(self):
self.cluster_api.create_persistent_volume_claim(
self.names.tmp,
storage_size_in_g=TMP_VOLUME_SIZE_IN_G,
storage_class_name=self.storage_class_name,
labels=self.default_metadata_labels,
)

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