Update mpirun and fix CI partly (#71)

* Updated readme and mpirun options * Added venv to testreadme workflow * Forgot to activate venv * Add venv (might have missed some) * Updated readme and mpirun options * Added venv to testreadme workflow * Forgot to activate venv * Add venv (might have missed some)
UM-Bridge · May 17, 2024 · 180bbe2 · 180bbe2
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diff --git a/.github/workflows/benchmark-analytic-banana.yml b/.github/workflows/benchmark-analytic-banana.yml
@@ -53,9 +53,12 @@ jobs:
        -
         name: Dependencies
         run: |
-          sudo apt update && DEBIAN_FRONTEND="noninteractive" sudo apt install -y python3-pip && pip3 install pytest umbridge
+          sudo apt update && DEBIAN_FRONTEND="noninteractive" sudo apt install -y python3-pip python3-venv && \
+          python3 -m venv venv && . venv/bin/activate && \
+          pip3 install pytest umbridge
        -
         name: Validate output
         run: |
+          . venv/bin/activate && \
           cd benchmarks/analytic-banana/ && \
           python3 test_output.py http://localhost:4243
diff --git a/.github/workflows/benchmark-analytic-donut.yml b/.github/workflows/benchmark-analytic-donut.yml
@@ -53,9 +53,12 @@ jobs:
        -
         name: Dependencies
         run: |
-          sudo apt update && DEBIAN_FRONTEND="noninteractive" sudo apt install -y python3-pip && pip3 install pytest umbridge
+          sudo apt update && DEBIAN_FRONTEND="noninteractive" sudo apt install -y python3-pip python3-venv && \
+          python3 -m venv venv && . venv/bin/activate && \
+          pip3 install pytest umbridge
        -
         name: Validate output
         run: |
+          . venv/bin/activate && \
           cd benchmarks/analytic-donut/ && \
           python3 test_output.py http://localhost:4243
diff --git a/.github/workflows/benchmark-analytic-funnel.yml b/.github/workflows/benchmark-analytic-funnel.yml
@@ -53,9 +53,12 @@ jobs:
        -
         name: Dependencies
         run: |
-          sudo apt update && DEBIAN_FRONTEND="noninteractive" sudo apt install -y python3-pip && pip3 install pytest umbridge
+          sudo apt update && DEBIAN_FRONTEND="noninteractive" sudo apt install -y python3-pip python3-venv && \
+          python3 -m venv venv && . venv/bin/activate && \
+          pip3 install pytest umbridge
        -
         name: Validate output
         run: |
+          . venv/bin/activate && \
           cd benchmarks/analytic-funnel/ && \
           python3 test_output.py http://localhost:4243
diff --git a/.github/workflows/benchmark-analytic-gaussian-mixture.yml b/.github/workflows/benchmark-analytic-gaussian-mixture.yml
@@ -53,9 +53,12 @@ jobs:
        -
         name: Dependencies
         run: |
-          sudo apt update && DEBIAN_FRONTEND="noninteractive" sudo apt install -y python3-pip && pip3 install pytest umbridge
+          sudo apt update && DEBIAN_FRONTEND="noninteractive" sudo apt install -y python3-pip python3-venv && \
+          python3 -m venv venv && . venv/bin/activate && \
+          pip3 install pytest umbridge
        -
         name: Validate output
         run: |
+          . venv/bin/activate && \
           cd benchmarks/analytic-gaussian-mixture/ && \
           python3 test_output.py http://localhost:4243
diff --git a/.github/workflows/benchmark-cuqi-ct.yml b/.github/workflows/benchmark-cuqi-ct.yml
@@ -53,9 +53,12 @@ jobs:
        -
         name: Dependencies
         run: |
-          sudo apt update && DEBIAN_FRONTEND="noninteractive" sudo apt install -y python3-pip && pip3 install pytest numpy cuqipy umbridge
+          sudo apt update && DEBIAN_FRONTEND="noninteractive" sudo apt install -y python3-pip python3-venv && \
+          python3 -m venv venv && . venv/bin/activate && \
+          pip3 install pytest umbridge
        -
         name: Validate output
         run: |
+          . venv/bin/activate && \
           cd benchmarks/cuqi-ct/ && \
           python3 test_output.py http://localhost:4243
diff --git a/.github/workflows/benchmark-deconvolution-1d.yml b/.github/workflows/benchmark-deconvolution-1d.yml
@@ -53,9 +53,12 @@ jobs:
        -
         name: Dependencies
         run: |
-          sudo apt update && DEBIAN_FRONTEND="noninteractive" sudo apt install -y python3-pip && pip3 install pytest numpy cuqipy umbridge
+          sudo apt update && DEBIAN_FRONTEND="noninteractive" sudo apt install -y python3-pip python3-venv && \
+          python3 -m venv venv && . venv/bin/activate && \
+          pip3 install pytest umbridge
        -
         name: Validate output
         run: |
+          . venv/bin/activate && \
           cd benchmarks/deconvolution-1d/ && \
           python3 test_output.py http://localhost:4243
diff --git a/.github/workflows/benchmark-heat-1d.yml b/.github/workflows/benchmark-heat-1d.yml
@@ -53,9 +53,12 @@ jobs:
        -
         name: Dependencies
         run: |
-          sudo apt update && DEBIAN_FRONTEND="noninteractive" sudo apt install -y python3-pip && pip3 install pytest numpy cuqipy umbridge
+          sudo apt update && DEBIAN_FRONTEND="noninteractive" sudo apt install -y python3-pip python3-venv && \
+          python3 -m venv venv && . venv/bin/activate && \
+          pip3 install pytest umbridge
        -
         name: Validate output
         run: |
+          . venv/bin/activate && \
           cd benchmarks/heat-1d/ && \
           python3 test_output.py http://localhost:4242
diff --git a/.github/workflows/model-exahype-tsunami.yml b/.github/workflows/model-exahype-tsunami.yml
@@ -53,9 +53,12 @@ jobs:
        -
         name: Dependencies
         run: |
-          sudo apt update && DEBIAN_FRONTEND="noninteractive" sudo apt install -y python3-pip && pip3 install pytest umbridge
+          sudo apt update && DEBIAN_FRONTEND="noninteractive" sudo apt install -y python3-pip python3-venv && \
+          python3 -m venv venv && . venv/bin/activate && \
+          pip3 install pytest umbridge
        -
         name: Validate output
         run: |
+          . venv/bin/activate && \
           cd models/exahype-tsunami/ && \
           python3 test_output.py http://localhost:4242
diff --git a/.github/workflows/model-l2-sea.yml b/.github/workflows/model-l2-sea.yml
@@ -53,9 +53,12 @@ jobs:
        -
         name: Dependencies
         run: |
-          sudo apt update && DEBIAN_FRONTEND="noninteractive" sudo apt install -y python3-pip && pip3 install pytest umbridge
+          sudo apt update && DEBIAN_FRONTEND="noninteractive" sudo apt install -y python3-pip python3-venv && \
+          python3 -m venv venv && . venv/bin/activate && \
+          pip3 install pytest umbridge
        -
         name: Validate output
         run: |
+          . venv/bin/activate && \
           cd models/l2-sea/ && \
           python3 test_output.py http://localhost:4242
diff --git a/models/gs2/README.md b/models/gs2/README.md
@@ -33,7 +33,7 @@ ApplyHessian | False
 
 Config | Type | Default | Description
 ---|---|---|---
-None | | |
+ranks |int |4 |MPI ranks to run the model
 
 ## Mount directories
 Mount directory | Purpose

diff --git a/models/gs2/server.py b/models/gs2/server.py
@@ -34,8 +34,8 @@ def __call__(self, parameters, config):
                 print(line.rstrip()) # FileInput redirects stdout to file
 
         # Run the model 
-        mpirank = config.get("ranks", 32)
-        os.system(f"mpirun -np {mpirank} /usr/gs2/bin/gs2 {input_file}")
+        mpirank = config.get("ranks", 4)
+        os.system(f"mpirun -n {mpirank} /usr/gs2/bin/gs2 {input_file}")
 
         # Read results using Pyrokinetics package and print output
         gs2_input = input_file