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memmettmemmett
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Merge pull request #80 from torbjoernk/feature/cleanup
LGTM.
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‎CHANGELOG.md‎

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# Changelog {#page_changelog}
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## v0.2.0 -- MPI PFASST (2014/XX/XX)
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## v0.2.0 -- MPI PFASST (2014/08/XX)
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XXX: DOI: [10.5281/zenodo.11047](http://dx.doi.org/10.5281/zenodo.11047)
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### Details
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* Addition of MPI based PFASST algorithm using the standard predictor
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stage in a block mode with fixed iterations.
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* Addition of MPI based PFASST algorithm using the standard predictor stage in a block mode with
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fixed iterations.
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([#46][], [#57][], [#59][])
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* Addition of a simple scalar example and appropriate tests.
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([#61][], [#76][])
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([#61][], [#63][], [#76][])
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* Further tests on proper calculation of quadrature nodes and weights
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([#74][])
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* Better handling of 3rd-party dependencies
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([#53][], [#55][])
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* Various tidying
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()
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([#56][], [#60][], [#77][])
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* Basic Profiling support and test coverage report
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([#78][])
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[#46]: https://github.com/Parallel-in-Time/PFASST/pull/46
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[#57]: https://github.com/Parallel-in-Time/PFASST/pull/56
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[#59]: https://github.com/Parallel-in-Time/PFASST/pull/59
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[#53]: https://github.com/Parallel-in-Time/PFASST/pull/53
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[#55]: https://github.com/Parallel-in-Time/PFASST/pull/55
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[#56]: https://github.com/Parallel-in-Time/PFASST/pull/56
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[#60]: https://github.com/Parallel-in-Time/PFASST/pull/60
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[#61]: https://github.com/Parallel-in-Time/PFASST/pull/61
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[#63]: https://github.com/Parallel-in-Time/PFASST/pull/63
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[#74]: https://github.com/Parallel-in-Time/PFASST/pull/74
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[#76]: https://github.com/Parallel-in-Time/PFASST/pull/76
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[#77]: https://github.com/Parallel-in-Time/PFASST/pull/77
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[#78]: https://github.com/Parallel-in-Time/PFASST/pull/78
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### Contributors
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[danielru]: https://github.com/danielru
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[pancetta]: https://github.com/pancetta
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## v0.1.0 -- First Release (2014/07/25)
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DOI: [10.5281/zenodo.11047](http://dx.doi.org/10.5281/zenodo.11047)

‎README.md‎

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* \subpage #page_examples
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* \subpage #page_contributing
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* \subpage #page_style_guide
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* \subpage #page_troubleshooting
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Releases
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For details see [Travis][pfasst-travis].
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A test coverage report is generated and published by [Jenkins][coverage-report].
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[documentation]: https://pint.fz-juelich.de/ci/view/PFASST/job/PFASST%20%28Docu%29/doxygen/
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[pfasst-travis]: https://travis-ci.org/Parallel-in-Time/PFASST
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[master-status]: https://travis-ci.org/Parallel-in-Time/PFASST.svg?branch=master
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[dev-status]: https://travis-ci.org/Parallel-in-Time/PFASST.svg?branch=development
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[documentation]: https://pint.fz-juelich.de/ci/view/PFASST/job/PFASST%20%28Docu%29/doxygen/
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[pfasst-travis]: https://travis-ci.org/Parallel-in-Time/PFASST
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[master-status]: https://travis-ci.org/Parallel-in-Time/PFASST.svg?branch=master
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[dev-status]: https://travis-ci.org/Parallel-in-Time/PFASST.svg?branch=development
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[coverage-report]: https://pint.fz-juelich.de/ci/job/PFASST_GCC_4-8_Coverage/Test_Coverage

‎doc/source/examples.md‎

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## Simple Advection Diffusion
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See \subpage page_examples_advection_diffusion.
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## Scalar
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See \subpage page_examples_scalar.

‎doc/source/installing.md‎

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* By default everything gets built, i.e. tests and examples.
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* To deactivate the tests, pass `-Dpfasst_BUILD_TESTS=OFF` to the
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_CMake_ command line.
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* To deactivate the tests, pass `-Dpfasst_BUILD_TESTS=OFF` to the _CMake_ command line.
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* To deactivate the examples, pass `-Dpfasst_BUILD_EXAMPLES=OFF` to
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the _CMake_ command line.
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* To deactivate the examples, pass `-Dpfasst_BUILD_EXAMPLES=OFF` to the _CMake_ command line.
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* If you are not on a _Darvin_ system (i.e. MacOS, OSX, ...) and
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you are using _Clang_ as the compiler, you want to deactivate the
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use of LLVM's libc++ by passing `-Dpfasst_DISABLE_LIBCXX=ON` to
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the _CMake_ command line.
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* To enable profiling support, you need to specify `-Dpfasst_WITH_GCC_PROF` and have the GNU
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compiler selected.
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* For example, to build with _Clang_ on a Linux system without the
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examples, the call to _CMake_ looks like:
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* If you are not on a _Darvin_ system (i.e. MacOS, OSX, ...) and you are using _Clang_ as the
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compiler, you want to deactivate the use of LLVM's libc++ by passing
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`-Dpfasst_DISABLE_LIBCXX=ON` to the _CMake_ command line. (this is the default)
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cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -Dpfasst_DISABLE_LIBCXX=ON -Dpfasst_BUILD_EXAMPLES=OFF ..
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* For example, to build with _Clang_ on a Linux system without the examples, the call to
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_CMake_ looks like:
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The [Google Testing] and [Mocking Framework] are required for the
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unit tests, and are automatically downloaded and built.
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cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ [-Dpfasst_DISABLE_LIBCXX=ON] -Dpfasst_BUILD_EXAMPLES=OFF ..
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The [FFTW3] library is required for (some) of the examples, and it
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automatically downloaded and built as well.
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The [Google Testing] and [Mocking Framework] are required for the unit tests, and are
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automatically downloaded and built.
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The [FFTW3] library is required for (some) of the examples. It will be automatically downloaded
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and built as well if it is not found on the system.
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3. Run the unit tests (if unit tests have been built):
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make test
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4. Run the examples (if they have been built):
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./examples/advection
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make run_example_all
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Or go to `./dist/examples` and look for the exetuable you want to run.
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[Google Testing]: https://code.google.com/p/googletest/
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[Mocking Framework]: https://code.google.com/p/googlemock/

‎doc/source/troubleshooting.md‎

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# Trouble shooting {#page_trouble}
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# Trouble Shooting {#page_troubleshooting}
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## I'm getting SEGFAULTs, how do I track them down?
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‎examples/scalar/README.md‎

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# Scalar {#page_examples_scalar}
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This directory contains a simple implementations of scalar ODE solver using the PFASST framework.
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The SDC sweeper is defined in `scalar_sweeper.hpp`.
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As this simple equation does not require any special handling, all the SDC magic is derived and
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taken from pfasst::encap::IMEXSweeper::sweep().

‎generate_coverage.sh‎

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#!/bin/sh
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basepath=`pwd`
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basepath="`pwd`"
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function print_help {
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echo "#######################################################################"
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exit -1
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fi
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builddir=${1}
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cd ${builddir}
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builddir="${basepath}/${1}"
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if [[ ! -d "${builddir}" ]]
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then
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echo "ERROR: Given build directory '${bilddir}' does not exist."
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exit -1
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fi
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cd "${builddir}"
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rm -rf ${basepath}/coverage
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mkdir -p ${basepath}/coverage
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coveragedir="${basepath}/coverage"
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rm -rf "${coveragedir}"
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mkdir -p "${coveragedir}"
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for testdir in `find ${basepath}/${builddir} -type d | grep -o 'tests/.*/.*\dir'`
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for testdir in `find ${builddir} -type d | grep -o 'tests/.*/.*\dir'`
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do
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testname=`expr "$testdir" : '.*\(test_[a-zA-Z\-_]*\)\.dir'`
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echo "Gathering Coverage for ${testname}"
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cd $testdir
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lcov --zerocounters --directory .
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cd ${basepath}/${builddir}
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ctest -R $testname
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cd $testdir
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lcov --directory . --capture --output-file ${testname}.info.tmp
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lcov --extract ${testname}.info.tmp "*${basepath}/include/**/*" --output-file ${testname}.info
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rm ${testname}.info.tmp
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cd ${basepath}/${builddir}
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if [[ -e all_tests.info ]]
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testname=`expr "${testdir}" : '.*\(test_[a-zA-Z\-_]*\)\.dir'`
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echo "# ${testname}"
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cd "${testdir}"
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echo " Deleting old tracing data"
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lcov --zerocounters --directory . \
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> "${coveragedir}/log_${testname}_zero.log" 2&>1
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cd "${builddir}"
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echo " Running test and generating tracing data"
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ctest -R ${testname} \
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> "${coveragedir}/log_${testname}_test.log"
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if [[ $? -ne 0 ]]
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then
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echo "ERROR: test '${testname}' failed."
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echo " See '${coveragedir}/log_${testname}_test.log' for details."
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cd ${basepath}
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exit -1
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fi
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cd "${testdir}"
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echo " Capturing all tracing data"
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lcov --directory . --capture --output-file "${testname}.info.tmp" \
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> "${coveragedir}/log_${testname}_capture.log"
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echo " Extracting interesting tracing data"
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lcov --extract "${testname}.info.tmp" "*${basepath}/include/**/*" \
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--output-file "${testname}.info" \
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> "${coveragedir}/log_${testname}_extract.log"
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rm "${testname}.info.tmp"
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cd "${builddir}"
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echo " Aggegrating coverage data"
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if [[ -e "${coveragedir}/all_tests.info" ]]
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then
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lcov --add-tracefile all_tests.info --add-tracefile ${testdir}/${testname}.info --output-file all_tests.info
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lcov --add-tracefile "${coveragedir}/all_tests.info" \
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--add-tracefile "${testdir}/${testname}.info" \
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--output-file "${coveragedir}/all_tests.info" \
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> "${coveragedir}/log_${testname}_aggregate.log"
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else
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lcov --add-tracefile ${testdir}/${testname}.info --output-file all_tests.info
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lcov --add-tracefile "${testdir}/${testname}.info" \
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--output-file "${coveragedir}/all_tests.info" \
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> "${coveragedir}/log_${testname}_aggregate.log"
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fi
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done
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cd ${basepath}
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genhtml --output-directory ./coverage \
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--demangle-cpp --num-spaces 2 --sort \
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--title "PFASST++ Test Coverage" --prefix ${basepath}/include \
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--function-coverage --branch-coverage --legend ${basepath}/${builddir}/all_tests.info
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echo "# Generating HTML report"
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genhtml --output-directory "${coveragedir}" \
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--demangle-cpp --num-spaces 2 --sort \
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--title "PFASST++ Test Coverage" --prefix "${basepath}/include" \
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--function-coverage --branch-coverage --legend \
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"${coveragedir}/all_tests.info" \
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> "${coveragedir}/log_generate.log"
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echo "# Coverage report can be found in ${coveragedir}/index.html"
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echo "# Everything done."

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