Pass max dp3 threads to dp3 issue21

steps/applybeam.cwl

@@ -4,6 +4,12 @@ id: applybeam
 baseCommand:
   - DP3
 inputs:
+  - id: max_dp3_threads
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: numthreads=
+      separate: false
   - id: msin
     type: Directory
     inputBinding:

steps/applycal.cwl

@@ -4,6 +4,13 @@ id: applycal
 baseCommand:
   - DP3
 inputs:
+  - id: max_dp3_threads
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: numthreads=
+      separate: false
+    doc: Number of threads DP3 is allowed to use.
   - id: msin
     type: Directory
     inputBinding:

steps/ddecal.cwl

@@ -9,6 +9,12 @@ arguments:
   - steps=[ddecal,count]
 
 inputs:
+  - id: max_dp3_threads
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: numthreads=
+      separate: false
   - id: msin
     type: Directory
     doc: Input Measurement Set

steps/dp3_make_parset_target.cwl

@@ -3,6 +3,8 @@ cwlVersion: v1.2
 id: make_parset
 label: define_parset
 inputs:
+  - id: numthreads
+    type: int?
   - id: raw_data
     type: boolean?
     default: false

steps/dp3_prep_cal.cwl

@@ -4,6 +4,12 @@ id: dp3
 baseCommand:
   - DP3
 inputs:
+  - id: max_dp3_threads
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: numthreads=
+      separate: false
   - id: parset
     type: File?
     inputBinding:
@@ -116,4 +122,4 @@ stderr: DP3_err.log
 requirements:
   - class: InlineJavascriptRequirement
   - class: ResourceRequirement
-    coresMin: 8
\ No newline at end of file
+    coresMin: 8

steps/dp3_prep_target.cwl

@@ -4,6 +4,12 @@ id: dp3
 baseCommand:
   - DP3
 inputs:
+  - id: max_dp3_threads
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: numthreads=
+      separate: false
   - id: parset
     type: File?
     inputBinding:
@@ -172,4 +178,4 @@ stderr: DP3_err.log
 requirements:
   - class: InlineJavascriptRequirement
   - class: ResourceRequirement
-    coresMin: 4
\ No newline at end of file
+    coresMin: 4

steps/filter_predict.cwl

@@ -4,6 +4,12 @@ id: predict
 baseCommand:
   - DP3
 inputs:
+  - id: max_dp3_threads
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: numthreads=
+      separate: false
   - id: msin
     type: Directory
     inputBinding:
@@ -128,4 +134,4 @@ hints:
   - class: DockerRequirement
     dockerPull: astronrd/linc
 stdout: filter_predict.log
-stderr: filter_predict_err.log
\ No newline at end of file
+stderr: filter_predict_err.log

steps/gaincal.cwl

@@ -6,6 +6,12 @@ id: gaincal
 baseCommand:
   - DP3
 inputs:
+  - id: max_dp3_threads
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: numthreads=
+      separate: false
   - id: msin
     type: Directory
     inputBinding:

steps/predict.cwl

@@ -4,6 +4,12 @@ id: predict
 baseCommand:
   - DP3
 inputs:
+  - id: max_dp3_threads
+    type: int?
+    inputBinding:
+      position: 0
+      prefix: numthreads=
+      separate: false
   - id: msin
     type: Directory
     inputBinding:
@@ -105,4 +111,4 @@ hints:
   - class: DockerRequirement
     dockerPull: astronrd/linc
 stdout: predict_cal.log
-stderr: predict_cal_err.log
\ No newline at end of file
+stderr: predict_cal_err.log

workflows/linc_calibrator.cwl

@@ -168,6 +168,8 @@ steps:
     label: initial_flags_join
   - id: prep
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin
         source:
           - msin
@@ -181,8 +183,6 @@ steps:
         source: flagunconverged
       - id: demix
         source: demix
-      - id: max_dp3_threads
-        source: max_dp3_threads
       - id: memoryperc
         source: memoryperc
       - id: flag_baselines
@@ -258,6 +258,8 @@ steps:
     label: concat_logfiles_RefAnt
   - id: pa
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin
         source:
           - prep/msout
@@ -288,6 +290,8 @@ steps:
     label: PA
   - id: fr
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin
         source:
           - pa/msout
@@ -318,6 +322,8 @@ steps:
     label: FR
   - id: bp
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin
         source:
           - fr/msout

workflows/linc_calibrator/apply_calibrate_bp.cwl

@@ -3,6 +3,8 @@ cwlVersion: v1.2
 id: apply_calibrate
 label: apply_calibrate
 inputs:
+  - id: max_dp3_threads
+    type: int?
   - id: msin
     type: Directory
   - id: do_smooth
@@ -52,6 +54,8 @@ outputs:
 steps:
   - id: applyPA
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin
         source: msin
       - id: msin_datacolumn
@@ -73,6 +77,8 @@ steps:
     label: applyPA
   - id: applyBP
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin
         source: applyPA/msout
       - id: msin_datacolumn
@@ -96,6 +102,8 @@ steps:
     label: applyBP
   - id: applybeam
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin
         source: applyBP/msout
       - id: msin_datacolumn
@@ -123,6 +131,8 @@ steps:
     label: applybeam
   - id: applyFR
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin
         source: applybeam/msout
       - id: msin_datacolumn
@@ -157,6 +167,8 @@ steps:
     label: BLsmooth
   - id: calib_cal
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin
         source: BLsmooth/msout
       - id: msin_datacolumn

workflows/linc_calibrator/apply_calibrate_fr.cwl

@@ -3,6 +3,8 @@ cwlVersion: v1.2
 id: apply_calibrate
 label: apply_calibrate
 inputs:
+  - id: max_dp3_threads
+    type: int?
   - id: msin
     type: Directory
   - id: do_smooth
@@ -40,6 +42,8 @@ outputs:
 steps:
   - id: applyFR
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin
         source: msin
       - id: msin_datacolumn
@@ -74,6 +78,8 @@ steps:
     label: BLsmooth
   - id: calib_cal
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin
         source: BLsmooth/msout
       - id: msin_datacolumn

workflows/linc_calibrator/apply_calibrate_pa.cwl

@@ -3,6 +3,8 @@ cwlVersion: v1.2
 id: apply_calibrate
 label: apply_calibrate
 inputs:
+  - id: max_dp3_threads
+    type: int?
   - id: msin
     type: Directory
   - id: do_smooth
@@ -44,6 +46,8 @@ outputs:
 steps:
   - id: applyPA
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin
         source: msin
       - id: msin_datacolumn
@@ -65,6 +69,8 @@ steps:
     label: applyPA
   - id: applybeam
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin_datacolumn
         default: CORRECTED_DATA
       - id: msout_datacolumn
@@ -105,6 +111,8 @@ steps:
     label: BLsmooth
   - id: calib_cal
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin
         source: BLsmooth/msout
       - id: msin_datacolumn

workflows/linc_calibrator/bp.cwl

@@ -3,6 +3,8 @@ cwlVersion: v1.2
 id: bp
 label: BP
 inputs:
+  - id: max_dp3_threads
+    type: int?
   - id: max_separation_arcmin
     type: float?
     default: 1.0
@@ -348,6 +350,8 @@ steps:
     label: write_solutions
   - id: apply_calibrate_bp
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin
         source: msin
       - id: do_smooth

workflows/linc_calibrator/dp3_prep_cal.cwl

@@ -3,6 +3,9 @@ cwlVersion: v1.2
 id: dp3_prep_cal
 label: dp3_prep_cal
 inputs:
+  - id: max_dp3_threads
+    type: int?
+    default: 10
   - id: baselines_to_flag
     type: string[]?
     default: []
@@ -118,6 +121,8 @@ steps:
     label: make_parset
   - id: dp3_execute
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: parset
         source: define_parset/output
       - id: msin

workflows/linc_calibrator/fr.cwl

@@ -3,6 +3,8 @@ cwlVersion: v1.2
 id: fr
 label: FR
 inputs:
+  - id: max_dp3_threads
+    type: int?
   - id: flagunconverged
     type: boolean?
     default: false
@@ -235,6 +237,8 @@ steps:
     label: write_solutions
   - id: apply_calibrate_fr
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin
         source: msin
       - id: do_smooth

workflows/linc_calibrator/pa.cwl

@@ -3,6 +3,8 @@ cwlVersion: v1.2
 id: pa
 label: PA
 inputs:
+  - id: max_dp3_threads
+    type: int?
   - id: flagunconverged
     type: boolean?
     default: false
@@ -313,6 +315,8 @@ steps:
     label: write_solutions
   - id: apply_calibrate_pa
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin
         source: msin
       - id: do_smooth

workflows/linc_calibrator/predict_calibrate.cwl

@@ -3,6 +3,9 @@ cwlVersion: v1.2
 id: predict_calibrate
 label: predict_calibrate
 inputs:
+  - id: max_dp3_threads
+    type: int?
+    default: 10
   - id: msin
     type: Directory
   - id: do_smooth
@@ -57,6 +60,8 @@ steps:
     label: BLsmooth
   - id: predict
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin
         source: BLsmooth/msout
       - id: msin_datacolumn
@@ -77,6 +82,8 @@ steps:
     run: ../../steps/predict.cwl
   - id: calib_cal
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin
         source: predict/msout
       - id: msin_datacolumn

workflows/linc_calibrator/prep.cwl

@@ -141,6 +141,8 @@ steps:
     label: select_only_first
   - id: dp3_prep_cal
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: baselines_to_flag
         default: []
         source:
@@ -200,6 +202,8 @@ steps:
       - msin
   - id: predict_calibrate
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin
         linkMerge: merge_flattened
         source:

workflows/linc_target.cwl

@@ -286,6 +286,8 @@ steps:
     label: prep
   - id: gsmcal
     in:
+      - id: max_dp3_threads
+        source: max_dp3_threads
       - id: msin
         source:
           - prep/msout
@@ -388,4 +390,4 @@ steps:
 requirements:
   - class: SubworkflowFeatureRequirement
   - class: ScatterFeatureRequirement
-  - class: MultipleInputFeatureRequirement
\ No newline at end of file
+  - class: MultipleInputFeatureRequirement