Updating ptyrex_basic workflow to use latest container

Author: fallars

e02/schema/ptyrex_Schema.json

@@ -16,18 +16,11 @@
             "title": "Scan number",
             "type": "integer"
         },
-        "proj_start": {
+        "proj_number": {
             "default": null,
             "maximum": 10000000,
             "minimum": 0,
-            "title": "Proj Start",
-            "type": "integer"
-        },
-        "proj_end": {
-            "default": null,
-            "maximum": 10000000,
-            "minimum": 0,
-            "title": "Proj End",
+            "title": "Proj Number",
             "type": "integer"
         },
         "nprocs": {
@@ -40,7 +33,7 @@
         "memory": {
             "type": "string",
             "pattern": "^[0-9]+[GMK]i$",
-            "default": "16Gi"
+            "default": "32Gi"
         }
     },
     "title": "RexSubmission"

e02/schema/ptyrex_ui.json

@@ -23,22 +23,17 @@
             },
             {
               "type": "Control",
-              "label": "Projection start number",
-              "scope": "#/properties/proj_start"
+              "label": "Projection number",
+              "scope": "#/properties/proj_number"
             },
             {
               "type": "Control",
-              "label": "Projection end number",
-              "scope": "#/properties/proj_end"
-            },
-            {
-              "type": "Control",
-              "label": "Number of Processors",
+              "label": "Requested number of Processors",
               "scope": "#/properties/nprocs"
             },
             {
               "type": "Control",
-              "label": "Amount of memory",
+              "label": "Requested memory",
               "scope": "#/properties/memory"
             }
           ]

e02/templates/ptyrex_basic.yaml

@@ -22,15 +22,11 @@ spec:
         configMapKeyRef:
          name: sessionspaces
          key: data_directory
-  ##
   volumes:
   - name: session
     hostPath:
       path: "{{`{{ workflows.parameters.visitdir}}`}}"
       type: Directory
-  ##
-  #should claim and use a volume called workflows within the visit directory called workflows
-  ##
   volumeClaimTemplates:
   - metadata:
       name: tmpdir
@@ -40,50 +36,77 @@ spec:
         requests:
           storage: 1Gi
       storageClassName: netapp
-  ##
   templates:
-    - name: ptyrex-container
-      steps:
-      - - name: ptyrex
-          template: ptyrex
-  ##
-    - name: ptyrex
-      inputs:
-        parameters:
-        - name: config_json
-          value: "{{`{{workflows.parameters.config_json}}`}}"
-        - name: scan_number
-          value: "{{`{{workflows.parameters.scan_number}}`}}"
-        - name: projection_start
-          value: "{{`{{workflows.parameters.proj_start}}`}}"
-        - name: projection_end
-          value: "{{`{{workflows.parameters.proj_end}}`}}"
-        - name: nprocs
-          value: "{{`{{workflows.parameters.nprocs}}`}}"
-        - name: memory
-          value: "{{`{{ workflow.parameters.memory }}`}}" 
-      script:
-        image: gitlab.diamond.ac.uk:5050/scisoft/ptychography/dimtools/mib2x #I am using this image to test the workflow generates its inputs correctly not to run anything at the moment
-        imagePullPolicy: Always
-        env:
-          - name: BLOSC_NTHREADS
-            value: "{{`{{ inputs.parameters.nprocs }}`}}"
-          - name: OMP_NUM_THREADS
-            value: "{{`{{ inputs.parameters.nprocs }}`}}"
-        volumeMounts:
-        - name: tmpdir
-          mountPath: /tmp
-        - name: session
-          mountPath: "{{`{{workflows.parameters.visitdir}}`}}"
-        command: [sh]
-        source: |
-          #!/bin/sh
-          set -e
-
-          cmd=("python mpiexec -np nprocs ptyrex_recon -c {{`{{workflows.parameters.config_json}}`}} -s {{`{{workflows.parameters.scan_number}}`}} -p {{`{{workflows.parameters.projection_start}}`}}-{{`{{workflows.parameters.projection_end}}`}}")
-          echo "Executing: ${cmd[@]}"
-          #exec "${cmd[@]}"
-
-
+  - name: ptyrex-container
+    inputs:
+      parameters:
+      - name: config_json
+        value: "{{`{{workflow.parameters.config_json}}`}}"
+      - name: scan_number
+        value: "{{`{{workflow.parameters.scan_number}}`}}"
+      - name: projection_start
+        value: "{{`{{workflow.parameters.proj_number}}`}}"
+      - name: nprocs
+        value: "{{`{{workflow.parameters.nprocs}}`}}"
+      - name: memory
+        value: "{{`{{ workflow.parameters.memory }}`}}" 
+    container:
+      image: gitlab.diamond.ac.uk:5050/scisoft/ptychography/dimtools/ptyrex:latest
+      imagePullPolicy: Always
+      env:
+      - name: CUPY_CACHE_DIR
+        value: /tmp/.cupy/kernel_cache
+      - name: MKL_NUM_THREADS
+        value: "1"
+      - name: NUMEXPR_NUM_THREADS
+        value: "1"
+      - name: OMP_NUM_THREADS
+        value: "1"
+      command: 
+      - "/opt/conda/bin/mpirun"
+      args: 
+      - "-np"
+      - "{{`{{ inputs.parameters.nprocs }}`}}"
+      - "/home/ptyrex_recon"
+      - "-c"
+      - "{{`{{ inputs.parameters.config_json }}`}}"
+      - "-s"
+      - "{{`{{ inputs.parameters.scan_number }}`}}"
+      - "-p"
+      - "{{`{{ inputs.parameters.proj_number }}`}}"
 
+      volumeMounts:
+      - name: tmpdir
+        mountPath: /tmp
+      - name: session
+        mountPath: "{{`{{ workflow.parameters.visitdir }}`}}"
+    podSpecPatch: |
+      containers:
+      - name: main
+        resources:
+          requests:
+            cpu: "{{`{{ inputs.parameters.nprocs }}`}}"
+            memory: "{{`{{ inputs.parameters.memory }}`}}"
+            nvidia.com/gpu: "{{`{{ inputs.parameters.nprocs }}`}}"
+          limits:
+            cpu: "{{`{{ inputs.parameters.nprocs }}`}}"
+            memory: "{{`{{ inputs.parameters.memory }}`}}"
+            nvidia.com/gpu: "{{`{{ inputs.parameters.nprocs }}`}}"
+    tolerations:
+    - key: nvidia.com/gpu
+      operator: Exists
+      effect: NoSchedule
+    - key: nodetype
+      operator: Equal
+      value: gpu
+      effect: NoSchedule
+    - key: nodegroup
+      operator: Equal
+      value: workflows
+      effect: NoSchedule
+    volumes:
+    - name: session
+      hostPath:
+        path:  "{{`{{ workflow.parameters.visitdir }}`}}"
+        type: Directory