Fix git/ownership issues / install numpy

ICB-DCM · Dec 6, 2023 · 19091bd · 19091bd
1 parent 9d36c99
commit 19091bd
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Showing 4 changed files with 10 additions and 3 deletions.
diff --git a/.github/workflows/benchmark_models.yml b/.github/workflows/benchmark_models.yml
@@ -9,6 +9,9 @@ jobs:
     name: benchmark models
     steps:
     - uses: actions/checkout@master
+    - name: chown checkout directory
+      # https://github.com/actions/runner/issues/2033
+      run: chown -R $(id -u):$(id -g) $PWD
 
     - run: echo "PARPE_BASE=$(pwd)" >> $GITHUB_ENV
     - run: echo "PARPE_BUILD=${PARPE_BASE}/build" >> $GITHUB_ENV
@@ -68,6 +71,6 @@ jobs:
     - name: Benchmark models --- tests
       run: |
         cd $PARPE_BASE/benchmark_collection \
-          && AMICI_PARALLEL_COMPILE=4 \
+          && AMICI_PARALLEL_COMPILE="" \
              BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
              $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv ./all.sh
diff --git a/.github/workflows/parpe_tests.yml b/.github/workflows/parpe_tests.yml
@@ -21,6 +21,9 @@ jobs:
 
     steps:
     - uses: actions/checkout@master
+    - name: chown checkout directory
+      # https://github.com/actions/runner/issues/2033
+      run: chown -R $(id -u):$(id -g) $PWD
     - run: git fetch --prune --unshallow
 
     - run: echo "PARPE_BASE=$(pwd)" >> $GITHUB_ENV

diff --git a/container/charliecloud/parpe_base/install.sh b/container/charliecloud/parpe_base/install.sh
@@ -31,6 +31,7 @@ apt-get install -q -y \
   libomp-dev \
   nano \
   python3-dev \
+  python3-numpy \
   python3-pip \
   python3-venv \
   libspdlog-dev \

diff --git a/container/charliecloud/parpe_base/install_parpe.sh b/container/charliecloud/parpe_base/install_parpe.sh
@@ -21,7 +21,7 @@ cmake \
   -DCMAKE_BUILD_TYPE=RelWithDebInfo \
   -DENABLE_PYTHON=ON \
   -DBUILD_TESTS=OFF \
-  .. && make -j12
+  .. && make -j
 
 # install fides optimizer
 cd "$PARPE_BASE/ThirdParty" && ./installFides.sh
@@ -55,7 +55,7 @@ CC=mpicc CXX=mpiCC cmake \
       -DTESTS_MPIEXEC_COMMAND="$mpi_cmd" \
       ..
 
-make -j12 VERBOSE=1
+make -j VERBOSE=1
 
 # MPI settings for python tests
 export PARPE_TESTS_MPIEXEC="mpiexec -n 5 --oversubscribe --allow-run-as-root --mca btl_vader_single_copy_mechanism none --mca btl ^openib --mca oob_tcp_if_include lo --mca btl_tcp_if_include lo --mca orte_base_help_aggregate 0"