Updating CI (#25)

* trying different ci image

* using python instead of python3

* updated run scripts for using new image

* adding conda

.github/workflows/ci.yml

@@ -1,10 +1,12 @@
 name: CI
 
+
 on:
   push:
     branches:
       - main
   pull_request:
+  workflow_dispatch:
 
 defaults:
   run:
@@ -14,18 +16,23 @@ jobs:
    style:
      runs-on: ubuntu-20.04
      container:
-       image: quay.io/fenicsproject/stable:2019.1.0.r3
-       options: --user 1001 --privileged
-     name: SOUPy Unit Tests
+       image: dcluo28/dibasis:latest
+     name: Repo Test
 
      steps:
         - name: Checkout code
-          uses: actions/checkout@v2
+          uses: actions/checkout@v3
         - name: Checkout hippylib
           run: git clone https://github.com/hippylib/hippylib.git
-        - name: See directory
-          run: pwd && ls
+        - name: Check directory 
+          run: ls 
+        - name: Check user
+          run: whoami 
         - name: Run unit tests 
           run: source .github/workflows/run_tests.sh
         - name: Run examples
           run: source .github/workflows/run_examples.sh
+            # - name: Activate conda 
+          # run: conda init && source ~/.bashrc && conda activate dibasis  
+            # - name: Check conda 
+          # run: conda info 

.github/workflows/run_examples.sh

@@ -1,11 +1,25 @@
 #!/bin/bash
+set -ev 
+
+CONDA_ENV=dibasis
+PYTHON=python
 
 export HIPPYLIB_PATH=$(pwd)/hippylib
+export HIPPYFLOW_PATH=$(pwd)/hippyflow
+
+# This is for running MPI on root in the docker container 
+export OMPI_MCA_btl_vader_single_copy_mechanism=none
+export OMPI_ALLOW_RUN_AS_ROOT=1
+export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 
 # Run poisson example
 cd examples/poisson
 
-python3 driver_poisson_mean.py
+conda init 
+source ~/.bashrc
+conda activate $CONDA_ENV
+
+$PYTHON driver_poisson_mean.py
 
-mpirun -n 2 python3 driver_poisson_mean.py
+mpirun -n 2 --oversubscribe python driver_poisson_mean.py
 

.github/workflows/run_tests.sh

@@ -1,16 +1,27 @@
 #!/bin/bash
 set -ev 
 
-PYTHON=python3
-
+CONDA_ENV=dibasis
+PYTHON=python
 export HIPPYLIB_PATH=$(pwd)/hippylib
 
+# This is for running MPI on root in the docker container 
+export OMPI_MCA_btl_vader_single_copy_mechanism=none
+export OMPI_ALLOW_RUN_AS_ROOT=1
+export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+
 # Run the code
 cd soupy/test
+
+conda init 
+source ~/.bashrc
+conda activate $CONDA_ENV
+
 $PYTHON -m unittest discover -v
 $PYTHON -m unittest discover -v -p 'ptest_*'
 
-mpirun -n 4 $PYTHON ptest_meanVarRiskMeasureSAA.py
-mpirun -n 4 $PYTHON ptest_scipyCostWrapper.py
-mpirun -n 4 $PYTHON ptest_superquantileSAA.py
-mpirun -n 4 $PYTHON ptest_transformedMeanRiskMeasureSAA.py
+mpirun -n 2 --oversubscribe $PYTHON ptest_meanVarRiskMeasureSAA.py
+mpirun -n 2 --oversubscribe $PYTHON ptest_scipyCostWrapper.py
+mpirun -n 2 --oversubscribe $PYTHON ptest_superquantileSAA.py
+mpirun -n 2 --oversubscribe $PYTHON ptest_transformedMeanRiskMeasureSAA.py
+