Run make check and make check-short targests (Dev-build)

.github/workflows/spack-dev-build.yml

@@ -0,0 +1,20 @@
+name: spack-dev-build
+
+on:
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+  schedule:
+     - cron:  '0 12 1 * *' # 12:00 UTC on the 1st of every month and on manual dispatch
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Build the Docker image with make checks
+      run: make spack-dev-build
+

Docker-dev-build

@@ -0,0 +1,135 @@
+FROM debian:bullseye
+
+# # which spack version are we using now? Default is develop
+# # but other strings can be given to the docker build command
+# # (for example docker build --build-arg SPACK_VERSION=v0.16.2)
+ARG SPACK_VERSION=develop
+ARG OCT_VERSION=12.1
+RUN echo "Building with spack version ${SPACK_VERSION}"
+
+# Any extra packages to be installed in the host
+ARG EXTRA_PACKAGES
+RUN echo "Installing EXTRA_PACKAGES ${EXTRA_PACKAGES} on container host"
+
+# general environment for docker
+ENV SPACK_ROOT=/home/user/spack \
+	  SPACK=/home/user/spack/bin/spack \
+	  FORCE_UNSAFE_CONFIGURE=1
+
+RUN apt-get -y update
+# Convenience tools, if desired for debugging etc
+# RUN apt-get -y install wget time nano vim emacs git
+
+# From https://github.com/ax3l/dockerfiles/blob/master/spack/base/Dockerfile:
+# install minimal spack dependencies
+RUN apt-get install -y --no-install-recommends \
+              autoconf \
+              build-essential \
+              ca-certificates \
+              coreutils \
+              curl \
+              environment-modules \
+	            file \
+              gfortran \
+              git \
+              openssh-server \
+              python \
+              unzip \
+              vim \
+              wget \
+           && rm -rf /var/lib/apt/lists/*
+
+# load spack environment on login
+RUN echo "source $SPACK_ROOT/share/spack/setup-env.sh" \
+           > /etc/profile.d/spack.sh
+
+RUN adduser user
+USER user
+WORKDIR /home/user
+
+# install spack
+RUN git clone https://github.com/spack/spack.git
+# default branch is develop
+RUN cd spack && git checkout $SPACK_VERSION
+
+# # show which version we use
+RUN $SPACK --version
+
+# copy our package.py into the spack tree (and also example files)
+COPY spack/package.py $SPACK_ROOT/var/spack/repos/builtin/packages/octopus/package.py
+RUN ls -l $SPACK_ROOT/var/spack/repos/builtin/packages/octopus
+COPY spack/test/ $SPACK_ROOT/var/spack/repos/builtin/packages/octopus/test
+RUN ls -l $SPACK_ROOT/var/spack/repos/builtin/packages/octopus/test
+COPY check_buildlog.py /home/user 
+
+# Install and test serial and MPI versions of ocoptus via spack
+# # serial version
+
+RUN . $SPACK_ROOT/share/spack/setup-env.sh && \
+      # create a new environment for the serial version and activate it:
+      spack env create octopus-serial && \
+      spack env activate octopus-serial && \
+      # make a dev-build direcotry for the serial version:
+      mkdir ~/dev-build-serial && cd ~/dev-build-serial && \
+
+      wget https://octopus-code.org/down.php?file=12.1/octopus-12.1.tar.gz -O octopus-12.1.tar.gz &&\
+      tar --strip-components=1 -xf octopus-12.1.tar.gz -C ./&& \
+      # install the serial version of octopus:
+      # display specs of upcoming spack installation:
+      spack spec octopus@${OCT_VERSION} ~mpi+netcdf+parmetis+arpack+cgal+pfft+python+likwid+libyaml+elpa+nlopt~debug~cuda~metis~scalapack && \
+      # run the spack installation (adding it to the environment):
+      spack dev-build octopus@${OCT_VERSION} ~mpi+netcdf+parmetis+arpack+cgal+pfft+python+likwid+libyaml+elpa+nlopt~debug~cuda~metis~scalapack && \
+      # run spack smoke tests for octopus. We get an error if any of the fails:
+      spack test run --alias test_serial octopus && \
+      # display output from smoke tests (just for information):
+      spack test results -l test_serial && \
+      # show which octopus version we use (for convenience):
+      spack load octopus && octopus --version && \
+      # Run make checks
+      cd ~/dev-build-serial ; \
+      echo "-+-+-+-+ Running make check-short" ; \
+      make check-short | tee serial_check-short.log || /bin/true ; \
+      echo "-+-+-+-+ Running make check-long" ; \
+      make check-long  | tee serial_check-long.log || /bin/true ; \
+      echo "-+-+-+-+ Parsing serial_check-short.log" ; \
+      python3 /home/user/check_buildlog.py serial_check-short.log foss2021a-serial || /bin/true; \
+      echo "-+-+-+-+ Parsing serial_check-long.log" ; \
+      python3 /home/user/check_buildlog.py serial_check-long.log foss2021a-serial || /bin/true; \
+      # deactivate the environment.
+      spack env deactivate
+
+# # MPI version
+
+RUN . $SPACK_ROOT/share/spack/setup-env.sh && \
+      # create a new environment for the MPI version and activate it:
+      spack env create octopus-mpi && \
+      spack env activate octopus-mpi && \
+      # make a dev-build direcotry for the parallel version:
+      mkdir ~/dev-build-parallel && cd ~/dev-build-parallel && \
+      wget https://octopus-code.org/down.php?file=12.1/octopus-12.1.tar.gz -O octopus-12.1.tar.gz &&\
+      tar --strip-components=1 -xf octopus-12.1.tar.gz -C ./&& \
+      # display specs of upcoming spack installation:
+      spack spec octopus@${OCT_VERSION} +mpi +netcdf+parmetis+arpack+cgal+pfft+python+likwid+libyaml+elpa+nlopt~debug~cuda~metis~scalapack  && \
+      # run the spack installation (adding it to the environment):
+      spack dev-build octopus@${OCT_VERSION} +mpi +netcdf+parmetis+arpack+cgal+pfft+python+likwid+libyaml+elpa+nlopt~debug~cuda~metis~scalapack  && \
+      # run spack smoke tests for octopus. We get an error if any of the fails:
+      spack test run --alias test_MPI octopus && \
+      # display output from smoke tests (just for information):
+      spack test results -l test_MPI && \
+      # show which octopus version we use (for convenience):
+      spack load octopus && octopus --version && \
+      # Run make checks
+      cd ~/dev-build-parallel ; \
+      echo "+|+|+|+ Running make check-short" ; \
+      make check-short | tee mpi_check-short.log || /bin/true ; \
+      echo "+|+|+|+ Running make check-long" ; \
+      make check-long  | tee mpi_check-long.log || /bin/true ; \
+      echo "+|+|+|+ Parsing mpi_check-short.log" ; \
+      python3 /home/user/check_buildlog.py mpi_check-short.log foss2021a-mpi || /bin/true; \
+      echo "+|+|+|+ Parsing mpi_check-long.log" ; \
+      python3 /home/user/check_buildlog.py mpi_check-long.log foss2021a-mpi || /bin/true; \
+      spack env deactivate
+
+# Provide bash in case the image is meant to be used interactively
+CMD /bin/bash -l
+

Dockerfile

@@ -4,7 +4,7 @@ FROM debian:bullseye
 # # but other strings can be given to the docker build command
 # # (for example docker build --build-arg SPACK_VERSION=v0.16.2)
 ARG SPACK_VERSION=develop
-ARG OCT_VERSION=12.1
+ARG SPACK_OCT_VERSION=12.1
 RUN echo "Building with spack version ${SPACK_VERSION}"
 
 # Any extra packages to be installed in the host
@@ -68,9 +68,9 @@ RUN . $SPACK_ROOT/share/spack/setup-env.sh && \
       spack env create octopus-serial && \
       spack env activate octopus-serial && \
       # display specs of upcoming spack installation:
-      spack spec octopus@${OCT_VERSION} ~mpi+netcdf+parmetis+arpack+cgal+pfft+python+likwid+libyaml+elpa+nlopt~debug~cuda~metis~scalapack && \
+      spack spec octopus@${SPACK_OCT_VERSION} ~mpi+netcdf+parmetis+arpack+cgal+pfft+python+likwid+libyaml+elpa+nlopt~debug~cuda~metis~scalapack && \
       # run the spack installation (adding it to the environment):
-      spack add octopus@${OCT_VERSION} ~mpi+netcdf+parmetis+arpack+cgal+pfft+python+likwid+libyaml+elpa+nlopt~debug~cuda~metis~scalapack && \
+      spack add octopus@${SPACK_OCT_VERSION} ~mpi+netcdf+parmetis+arpack+cgal+pfft+python+likwid+libyaml+elpa+nlopt~debug~cuda~metis~scalapack && \
       spack install && \
       # run spack smoke tests for octopus. We get an error if any of the fails:
       spack test run --alias test_serial octopus && \
@@ -88,9 +88,9 @@ RUN . $SPACK_ROOT/share/spack/setup-env.sh && \
       spack env create octopus-mpi && \
       spack env activate octopus-mpi && \
       # display specs of upcoming spack installation:
-      spack spec octopus@${OCT_VERSION} +mpi +netcdf+parmetis+arpack+cgal+pfft+python+likwid+libyaml+elpa+nlopt~debug~cuda~metis~scalapack  && \
+      spack spec octopus@${SPACK_OCT_VERSION} +mpi +netcdf+parmetis+arpack+cgal+pfft+python+likwid+libyaml+elpa+nlopt~debug~cuda~metis~scalapack  && \
       # run the spack installation (adding it to the environment):
-      spack add octopus@${OCT_VERSION} +mpi +netcdf+parmetis+arpack+cgal+pfft+python+likwid+libyaml+elpa+nlopt~debug~cuda~metis~scalapack  && \
+      spack add octopus@${SPACK_OCT_VERSION} +mpi +netcdf+parmetis+arpack+cgal+pfft+python+likwid+libyaml+elpa+nlopt~debug~cuda~metis~scalapack  && \
       spack install && \
       # run spack smoke tests for octopus. We get an error if any of the fails:
       spack test run --alias test_MPI octopus && \

Makefile

@@ -8,8 +8,10 @@ spack-latest:
 	docker build -f Dockerfile --build-arg SPACK_VERSION=releases/latest -t octopus-spack .
 
 spack-latest-octopus-develop:
-	docker build -f Dockerfile --build-arg SPACK_VERSION=releases/latest --build-arg OCT_VERSION=develop -t octopus-spack .
+	docker build -f Dockerfile --build-arg SPACK_VERSION=releases/latest --build-arg SPACK_OCT_VERSION=develop -t octopus-spack .
 
+spack-dev-build:
+	docker build -f Docker-dev-build --build-arg SPACK_VERSION=releases/latest --build-arg SPACK_OCT_VERSION=12.1 -t octopus-spack-dev-build .
 
 run-spack:
 	docker run --rm -ti -v $PWD:/io octopus-spack 

check_buildlog.py

@@ -0,0 +1,87 @@
+# A simple script to check the log file of `make check or `make check-short`
+# and report the number of failed tests.
+# And if the failed tests  are ignorable.
+# (errors due to tight thresholds, for example) or needs attention.
+
+import sys
+import re
+
+ignored_test_list = {
+    "foss2021a-mpi": [
+        "finite_systems_2d/06-gdlib.test",
+        "finite_systems_3d/30-local_multipoles.test",
+        "periodic_systems/11-silicon_force.test",
+    ],
+    "foss2021a-serial": [
+        "components/07-cholesky serial.test",
+        "finite_systems_2d/06-gdlib.test",
+    ],
+}
+
+
+def check_log(log_file):
+    with open(log_file, "r") as f:
+        logs = f.readlines()
+    # extract the last lines that has the format
+
+    # |Status: 1 failures
+    # |    Passed:  139 / 142
+    # |    Skipped: 0 / 142
+    # |    Failed:  3 / 142
+    # |
+    # |    testfile                                                    # failed testcases
+    # |    ------------------------------------------------------------------------------
+    # |    finite_systems_2d/06-gdlib.test                             1
+    # |    finite_systems_3d/30-local_multipoles.test                  2
+    # |    periodic_systems/11-silicon_force.test                      1
+    # |
+    # |Total run-time of the testsuite: 03:27:12
+
+    # and extract the list of failed test files like
+    # finite_systems_2d/06-gdlib.test,
+    # finite_systems_3d/30-local_multipoles.test,
+    # periodic_systems/11-silicon_force.test
+    # from this example, by scanning from the end of the log file
+    # starting from the line that has the format
+    # `Total run-time of the testsuite:`
+    # and stop when the first line with the format
+    # `'    -------------------------------------`
+
+    test_lists = []
+    reversed_logs = reversed(logs)
+    while not next(reversed_logs).startswith(
+        "Total run-time of the testsuite:"
+    ):
+        pass
+    while not re.match(r" +-+", (line := next(reversed_logs))):
+        if not line == "\n":  # skip blank lines
+            test_lists.append(line.split()[0])
+
+    if not test_lists:
+        print("No failed tests")
+        sys.exit(0)
+    unexpected_failures = [
+        test
+        for test in test_lists
+        if test not in ignored_test_list[used_toolchain]
+    ]
+    if unexpected_failures:
+        print("Unexpected failures : \n" + ", ".join(unexpected_failures))
+        print("Built with tool chain : " + used_toolchain)
+        sys.exit(1)
+    print("All failed tests are ignored")
+
+
+if __name__ == "__main__":
+
+    try:
+        log_file = sys.argv[1]
+    except IndexError:
+        print("Usage: python3 check_buildlog.py log_file toolchain[optional]")
+        sys.exit(1)
+    try:
+        used_toolchain = sys.argv[2]
+    except IndexError:
+        print("No toolchain specified, assuming the default foss2021a-mpi")
+        used_toolchain = "foss2021a-mpi"
+    check_log(log_file)