Adding basic profiling tests (#56)

* Adding basic profiling tests

* Fixing gmon path

* Adding pandas to profiling tests

* Sorting function names in profiling tests

* Adding averaging in profiling tests

* Updating timing tests to be a percentage of runtime

.github/workflows/ersem.yml

@@ -45,7 +45,7 @@ jobs:
         - name: Building and installing GOTM-FABM-ERSEM
           run: |
               branch=$(git branch --show-current)
-              ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-build.sh $branch
+              ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-build.sh -b $branch
         - name: Running tutorial
           run: |
               ./github-actions/gotm-fabm-ersem/gotm-tut-config-setup.sh
@@ -55,7 +55,8 @@ jobs:
         - name: Running gotm tests
           run: |
               python -m pip install pytest
-              pytest github-actions/gotm-fabm-ersem
+              pytest github-actions/gotm-fabm-ersem/test_state_variables.py github-actions/gotm-fabm-ersem/test_gotm.py
+
   build-fabm0d-gotm-ersem-debian:
     runs-on: ubuntu-latest
     steps:
@@ -80,3 +81,24 @@ jobs:
           run: |
               python -m pip install pytest
               pytest github-actions/fabm0d-gotm-ersem
+  build-gotm-profilling:
+    runs-on: ubuntu-latest
+    steps:
+        - uses: actions/checkout@v2
+        - name: Setup python
+          uses: actions/setup-python@v2
+          with:
+              python-version: '3.x'
+        - name: Installing GOTM-FABM-ERSEM dependences
+          run: ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-dep-debian.sh 
+        - name: Building and installing GOTM-FABM-ERSEM
+          run: |
+              branch=$(git branch --show-current)
+              ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-build.sh -f "-DCMAKE_Fortran_FLAGS="-pg""
+        - name: Running config
+          run: |
+              ./github-actions/gotm-fabm-ersem/gotm-profiling.sh
+        - name: Running gotm profilling
+          run: |
+              python -m pip install pytest pandas
+              pytest -s github-actions/gotm-fabm-ersem/test_profiling.py

github-actions/fabm0d-gotm-ersem/fabm0d-gotm-ersem-build.sh

@@ -1,5 +1,15 @@
 #!/bin/bash
-BRANCH=${1:-master}
+
+BRANCH="master"
+CMAKE_FLAG=""
+while getopts ":b:f:" flag; do
+    case "${flag}" in
+        b) BRANCH=${OPTARG};;
+        f) CMAKE_FLAG=${OPTARG};;
+    esac
+done
+
+CPU="$(nproc)"
 
 echo "Cloning ERSEM"
 git clone https://github.com/pmlmodelling/ersem.git
@@ -16,5 +26,5 @@ cd ersem && git checkout $BRANCH && cd ..
 
 echo "Building FABM-GOTM-ERSEM"
 mkdir build && cd build
-cmake ../fabm/src/drivers/0d -DGOTM_BASE=../gotm -DFABM_ERSEM_BASE=../ersem
-make install
+cmake ../fabm/src/drivers/0d -DGOTM_BASE=../gotm -DFABM_ERSEM_BASE=../ersem $CMAKE_FLAG
+make install -j $CPU

github-actions/gotm-fabm-ersem/gotm-fabm-ersem-build.sh

@@ -1,5 +1,14 @@
 #!/bin/bash
-BRANCH=${1:-master}
+BRANCH="master"
+CMAKE_FLAG=""
+while getopts ":b:f:" flag; do
+    case "${flag}" in
+        b) BRANCH=${OPTARG};;
+        f) CMAKE_FLAG=${OPTARG};;
+    esac
+done
+
+CPU="$(nproc)"
 
 echo "Cloning ERSEM"
 git clone https://github.com/pmlmodelling/ersem.git
@@ -16,5 +25,5 @@ cd ersem && git checkout $BRANCH && cd ..
 
 echo "Building GOTM-FABM-ERSEM"
 mkdir build && cd build
-cmake ../gotm -DFABM_BASE=../fabm -DFABM_ERSEM_BASE=../ersem
-make install
+cmake ../gotm -DFABM_BASE=../fabm -DFABM_ERSEM_BASE=../ersem $CMAKE_FLAG
+make install -j $CPU

github-actions/gotm-fabm-ersem/gotm-profiling.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+echo "Cloning config repo"
+git clone https://github.com/pmlmodelling/ersem-setups.git
+
+cd ersem-setups/L4
+
+echo "Running GOTM with repo configuration"
+for i in {1..5}
+do
+    ~/local/gotm/bin/gotm
+    gprof -b -Q  ~/local/gotm/bin/gotm gmon.out | awk -v OFS=',' '{print $1,$2,$3,$4,$5,$6,$7}' | sed -e '1,3d' > gprof_$i.csv
+done