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Adds example Clinical Workflows for low/med/high/dgx spec systems
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| metadata: | ||
| name: totalsegmentator-argo-template | ||
| generateName: totalsegmentator-argo-template- | ||
| namespace: argo | ||
| spec: | ||
| templates: | ||
| - name: totalsegmentator | ||
| inputs: | ||
| artifacts: | ||
| - name: input-dicom | ||
| path: /var/monai/input | ||
| s3: | ||
| accessKeySecret: | ||
| name: my-minio-cred | ||
| key: accesskey | ||
| secretKeySecret: | ||
| name: my-minio-cred | ||
| key: secretkey | ||
| key: argo/inputs/artifacts/input-dicom | ||
| outputs: | ||
| artifacts: | ||
| - name: output | ||
| path: /var/monai/output | ||
| s3: | ||
| bucket: bucket1 | ||
| accessKeySecret: | ||
| name: my-minio-cred | ||
| key: accesskey | ||
| secretKeySecret: | ||
| name: my-minio-cred | ||
| key: secretkey | ||
| key: /var/monai/output | ||
| metadata: {} | ||
| container: | ||
| name: '' | ||
| image: ghcr.io/gstt-csc/totalsegmentator-aide/map:0.1.2 | ||
| command: | ||
| - /bin/bash | ||
| - '-c' | ||
| args: | ||
| - python3 -u /opt/monai/app/app.py | ||
| resources: | ||
| limits: | ||
| cpu: '20' | ||
| memory: 128Gi | ||
| nvidia.com/gpu: '1' | ||
| requests: | ||
| cpu: '0' | ||
| memory: '0' | ||
| nvidia.com/gpu: '1' | ||
| imagePullPolicy: IfNotPresent | ||
| podSpecPatch: >- | ||
| {"initContainers":[{"name":"init","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}],"containers":[{"name":"wait","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}]} | ||
| entrypoint: totalsegmentator | ||
| arguments: {} |
55 changes: 55 additions & 0 deletions
55
app/workflows/totalsegmentator-argo-template-high-resource.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| metadata: | ||
| name: totalsegmentator-argo-template | ||
| generateName: totalsegmentator-argo-template- | ||
| namespace: argo | ||
| spec: | ||
| templates: | ||
| - name: totalsegmentator | ||
| inputs: | ||
| artifacts: | ||
| - name: input-dicom | ||
| path: /var/monai/input | ||
| s3: | ||
| accessKeySecret: | ||
| name: my-minio-cred | ||
| key: accesskey | ||
| secretKeySecret: | ||
| name: my-minio-cred | ||
| key: secretkey | ||
| key: argo/inputs/artifacts/input-dicom | ||
| outputs: | ||
| artifacts: | ||
| - name: output | ||
| path: /var/monai/output | ||
| s3: | ||
| bucket: bucket1 | ||
| accessKeySecret: | ||
| name: my-minio-cred | ||
| key: accesskey | ||
| secretKeySecret: | ||
| name: my-minio-cred | ||
| key: secretkey | ||
| key: /var/monai/output | ||
| metadata: {} | ||
| container: | ||
| name: '' | ||
| image: ghcr.io/gstt-csc/totalsegmentator-aide/map:0.1.2 | ||
| command: | ||
| - /bin/bash | ||
| - '-c' | ||
| args: | ||
| - python3 -u /opt/monai/app/app.py | ||
| resources: | ||
| limits: | ||
| cpu: '8' | ||
| memory: 64000Mi | ||
| nvidia.com/gpu: '1' | ||
| requests: | ||
| cpu: '0' | ||
| memory: '0' | ||
| nvidia.com/gpu: '1' | ||
| imagePullPolicy: IfNotPresent | ||
| podSpecPatch: >- | ||
| {"initContainers":[{"name":"init","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}],"containers":[{"name":"wait","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}]} | ||
| entrypoint: totalsegmentator | ||
| arguments: {} |
55 changes: 55 additions & 0 deletions
55
app/workflows/totalsegmentator-argo-template-low-resource.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| metadata: | ||
| name: totalsegmentator-argo-template | ||
| generateName: totalsegmentator-argo-template- | ||
| namespace: argo | ||
| spec: | ||
| templates: | ||
| - name: totalsegmentator | ||
| inputs: | ||
| artifacts: | ||
| - name: input-dicom | ||
| path: /var/monai/input | ||
| s3: | ||
| accessKeySecret: | ||
| name: my-minio-cred | ||
| key: accesskey | ||
| secretKeySecret: | ||
| name: my-minio-cred | ||
| key: secretkey | ||
| key: argo/inputs/artifacts/input-dicom | ||
| outputs: | ||
| artifacts: | ||
| - name: output | ||
| path: /var/monai/output | ||
| s3: | ||
| bucket: bucket1 | ||
| accessKeySecret: | ||
| name: my-minio-cred | ||
| key: accesskey | ||
| secretKeySecret: | ||
| name: my-minio-cred | ||
| key: secretkey | ||
| key: /var/monai/output | ||
| metadata: {} | ||
| container: | ||
| name: '' | ||
| image: ghcr.io/gstt-csc/totalsegmentator-aide/map:0.1.2 | ||
| command: | ||
| - /bin/bash | ||
| - '-c' | ||
| args: | ||
| - python3 -u /opt/monai/app/app.py | ||
| resources: | ||
| limits: | ||
| cpu: '1' | ||
| memory: 8000Mi | ||
| nvidia.com/gpu: '1' | ||
| requests: | ||
| cpu: '0' | ||
| memory: '0' | ||
| nvidia.com/gpu: '1' | ||
| imagePullPolicy: IfNotPresent | ||
| podSpecPatch: >- | ||
| {"initContainers":[{"name":"init","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}],"containers":[{"name":"wait","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}]} | ||
| entrypoint: totalsegmentator | ||
| arguments: {} |
55 changes: 55 additions & 0 deletions
55
app/workflows/totalsegmentator-argo-template-med-resource.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| metadata: | ||
| name: totalsegmentator-argo-template | ||
| generateName: totalsegmentator-argo-template- | ||
| namespace: argo | ||
| spec: | ||
| templates: | ||
| - name: totalsegmentator | ||
| inputs: | ||
| artifacts: | ||
| - name: input-dicom | ||
| path: /var/monai/input | ||
| s3: | ||
| accessKeySecret: | ||
| name: my-minio-cred | ||
| key: accesskey | ||
| secretKeySecret: | ||
| name: my-minio-cred | ||
| key: secretkey | ||
| key: argo/inputs/artifacts/input-dicom | ||
| outputs: | ||
| artifacts: | ||
| - name: output | ||
| path: /var/monai/output | ||
| s3: | ||
| bucket: bucket1 | ||
| accessKeySecret: | ||
| name: my-minio-cred | ||
| key: accesskey | ||
| secretKeySecret: | ||
| name: my-minio-cred | ||
| key: secretkey | ||
| key: /var/monai/output | ||
| metadata: {} | ||
| container: | ||
| name: '' | ||
| image: ghcr.io/gstt-csc/totalsegmentator-aide/map:0.1.2 | ||
| command: | ||
| - /bin/bash | ||
| - '-c' | ||
| args: | ||
| - python3 -u /opt/monai/app/app.py | ||
| resources: | ||
| limits: | ||
| cpu: '4' | ||
| memory: 16000Mi | ||
| nvidia.com/gpu: '1' | ||
| requests: | ||
| cpu: '0' | ||
| memory: '0' | ||
| nvidia.com/gpu: '1' | ||
| imagePullPolicy: IfNotPresent | ||
| podSpecPatch: >- | ||
| {"initContainers":[{"name":"init","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}],"containers":[{"name":"wait","resources":{"limits":{"cpu":"1","memory":"1000Mi"},"requests":{"cpu":"0","memory":"0Mi"}}}]} | ||
| entrypoint: totalsegmentator | ||
| arguments: {} |