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|
#!/usr/bin/make -f
#
# build script for GROMACS
PACKAGE := gromacs
DEB_HOST_ARCH ?= $(shell dpkg-architecture -qDEB_HOST_ARCH)
DEB_HOST_ARCH_CPU ?= $(shell dpkg-architecture -qDEB_HOST_ARCH_CPU)
DEB_HOST_ARCH_OS ?= $(shell dpkg-architecture -qDEB_HOST_ARCH_OS)
DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
DEB_DISTRO ?= $(shell lsb_release -si)
DEB_VERSION ?= $(shell dpkg-parsechangelog -S version)
# add hardening flags, using dpkg-buildflags
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
DPKG_EXPORT_BUILDFLAGS = 1
include /usr/share/dpkg/buildflags.mk
#653916 and http://www.cmake.org/Bug/view.php?id=12928
CFLAGS += $(CPPFLAGS)
CXXFLAGS += $(CPPFLAGS)
ifneq (,$(findstring debug,$(DEB_BUILD_OPTIONS)))
CFLAGS += -g -Wall
endif
ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
CFLAGS += -O0
endif
COMMON_CONFIG_PARAMS = \
$(CURDIR) \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DCMAKE_RULE_MESSAGES=OFF \
-DCMAKE_INSTALL_PREFIX="/usr" \
-DCMAKE_EXE_LINKER_FLAGS="$(LDFLAGS)" \
-DCMAKE_SKIP_RPATH=ON \
-DGMX_EXTERNAL_ZLIB=ON \
-DGMX_VERSION_STRING_OF_FORK="$(DEB_DISTRO)-$(DEB_VERSION)" \
-DGMX_GIT_VERSION_INFO=OFF
# For compatibility reasons, disable SIMD CPU optimizations EXCEPT
# for SSE2 on x86, SSE4.1 on amd64/x32, and NEON on armhf/arm64.
# For local compilations, set DEB_BUILD_OPTIONS=cpuopt for automatic
# detection of the best available option.
# See http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Acceleration
# and http://manual.gromacs.org/documentation/2016.3/install-guide/index.html#simd-support
ifeq (,$(findstring cpuopt,$(DEB_BUILD_OPTIONS)))
ifeq ($(DEB_HOST_ARCH_CPU), i386)
COMMON_CONFIG_PARAMS += -DGMX_SIMD=SSE2
else ifeq ($(DEB_HOST_ARCH_CPU), amd64)
COMMON_CONFIG_PARAMS += -DGMX_SIMD=SSE4.1
else ifeq ($(DEB_HOST_ARCH_CPU), x32)
COMMON_CONFIG_PARAMS += -DGMX_SIMD=SSE4.1
else ifeq ($(DEB_HOST_ARCH_CPU), armhf)
COMMON_CONFIG_PARAMS += -DGMX_SIMD=ARM_NEON
else ifeq ($(DEB_HOST_ARCH_CPU), arm64)
COMMON_CONFIG_PARAMS += -DGMX_SIMD=ARM_NEON_ASIMD
else
COMMON_CONFIG_PARAMS += -DGMX_SIMD=None
endif
endif
# Include "gpu" in DEB_BUILD_OPTIONS to build GPU-accelerated binaries as well.
# This build option is not always well tested, please send comments.
# You must have the pacakges "nvidia-cuda-toolkit" and "nvidia-cuda-dev"
# installed. Those are not official build dependencies to keep the package in
# Debian main!
#
# If you use this option, it is strongly recommended that you also set
# DEB_BUILD_OPTIONS=cpuopt, assuming you are compiling and running on the same
# machine.
#
# Further details at http://www.gromacs.org/GPU_acceleration
GPU_CONFIG_PARAMS =
ifneq (,$(findstring gpu,$(DEB_BUILD_OPTIONS)))
GPU_CONFIG_PARAMS += -DGMX_GPU=ON
endif
MPICH_CONFIG_PARAMS = \
-DGMX_MPI=ON \
-DGMX_X11=OFF \
-DGMX_DEFAULT_SUFFIX=OFF \
-DMPIEXEC="/usr/bin/mpiexec.mpich" \
-DGMX_BUILD_MDRUN_ONLY=ON
OPENMPI_CONFIG_PARAMS = \
-DGMX_MPI=ON \
-DGMX_X11=OFF \
-DGMX_DEFAULT_SUFFIX=OFF \
-DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib $(LDFLAGS)" \
-DMPIEXEC="/usr/bin/mpiexec.openmpi" \
-DGMX_BUILD_MDRUN_ONLY=ON
# optional parallel build
ifneq (,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
NUMJOBS = $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
MAKE += -j$(NUMJOBS)
endif
export GTEST_COLOR=no
export CTEST_OUTPUT_ON_FAILURE=1
configure: configure-stamp
configure-stamp:
dh_testdir
(mkdir -p build/basic; cd build/basic; cmake $(COMMON_CONFIG_PARAMS) $(GPU_CONFIG_PARAMS) -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_INSTALL_LEGACY_API=ON)
(mkdir -p build/basic-dp; cd build/basic-dp; cmake $(COMMON_CONFIG_PARAMS) -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_DOUBLE=ON)
(mkdir -p build/mpich; cd build/mpich; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \
$(COMMON_CONFIG_PARAMS) $(MPICH_CONFIG_PARAMS) $(GPU_CONFIG_PARAMS) -DGMX_BINARY_SUFFIX="_mpi.mpich" -DGMX_LIBS_SUFFIX="_mpi.mpich")
(mkdir -p build/mpich-dp; cd build/mpich-dp; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \
$(COMMON_CONFIG_PARAMS) $(MPICH_CONFIG_PARAMS) -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.mpich" -DGMX_LIBS_SUFFIX="_mpi_d.mpich")
(mkdir -p build/openmpi; cd build/openmpi; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \
$(COMMON_CONFIG_PARAMS) $(OPENMPI_CONFIG_PARAMS) $(GPU_CONFIG_PARAMS) -DGMX_BINARY_SUFFIX="_mpi.openmpi" -DGMX_LIBS_SUFFIX="_mpi.openmpi")
(mkdir -p build/openmpi-dp; cd build/openmpi-dp; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \
$(COMMON_CONFIG_PARAMS) $(OPENMPI_CONFIG_PARAMS) -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.openmpi" -DGMX_LIBS_SUFFIX="_mpi_d.openmpi")
touch $@
build: build-arch build-indep
build-arch: configure-stamp build-basic build-mpich build-openmpi
build-indep: build-manual
build-basic: configure-stamp
dh_testdir
$(MAKE) -C build/basic
$(MAKE) -C build/basic-dp
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
$(MAKE) -C build/basic tests
(cd build/basic; LD_LIBRARY_PATH=$(CURDIR)/build/basic/lib ctest -V || dpkg-architecture -i hurd-i386 )
$(MAKE) -C build/basic-dp tests
(cd build/basic-dp; LD_LIBRARY_PATH=$(CURDIR)/build/basic-dp/lib ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i i386 )
endif
touch $@
build-manual:
dh_testdir
# Build speedy, stripped-down version just for documentation generation.
# Derived from admin/build-docs.sh
(mkdir -p build/documentation ; cd build/documentation; LD_LIBRARY_PATH=$(CURDIR)/build/documentation/lib \
cmake $(CURDIR) -DCMAKE_BUILD_TYPE=Debug -DGMX_OPENMP=OFF -DGMX_SIMD=None \
-DGMX_GPU=OFF -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DGMX_BUILD_MANUAL=ON \
-DGMX_BUILD_HELP=ON -DGMX_VERSION_STRING_OF_FORK="$(DEB_DISTRO)-$(DEB_VERSION)")
$(MAKE) gmx -C build/documentation
# Generate PDF
$(MAKE) manual -C build/documentation
# Generate man pages
$(MAKE) man -C build/documentation
# Generate HTML
$(MAKE) webpage -C build/documentation
build-mpich: configure-stamp
dh_testdir
$(MAKE) -C build/mpich
$(MAKE) -C build/mpich-dp
sed -e 's/#MPIABBR#/mpich/g' -e 's/#MPIPROG#/MPICH/g' \
< debian/gromacs-parallel.README.Debian.in \
> debian/gromacs-mpich.README.Debian
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
$(MAKE) -C build/mpich tests
(cd build/mpich; LD_LIBRARY_PATH=$(CURDIR)/build/mpich/lib \
ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i s390x )
endif
touch $@
build-openmpi: configure-stamp
dh_testdir
$(MAKE) -C build/openmpi
$(MAKE) -C build/openmpi-dp
sed -e 's/#MPIABBR#/openmpi/g' -e 's/#MPIPROG#/OpenMPI/g' \
< debian/gromacs-parallel.README.Debian.in \
> debian/gromacs-openmpi.README.Debian
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
# rsh_agent: https://bugs.debian.org/494046
# oversubscribe: https://bugs.debian.org/850229#51
$(MAKE) -C build/openmpi tests
(cd build/openmpi ; LD_LIBRARY_PATH=$(CURDIR)/build/openmpi/lib \
OMPI_MCA_plm_rsh_agent=/bin/false \
OMPI_MCA_rmaps_base_oversubscribe=1 \
ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i x32 )
endif
touch $@
clean:
dh_testdir
dh_testroot
rm -rf build docs/doxygen/*.pyc
dh_clean build-basic build-mpich build-openmpi build-manual configure-stamp \
debian/gromacs-mpich.README.Debian debian/gromacs-openmpi.README.Debian
install: build-arch install-basic install-mpich install-openmpi
dh_testdir
dh_testroot
dh_prep -pgromacs-data -plibgromacs-dev
dh_installdirs -pgromacs-data
mv $(CURDIR)/debian/gromacs/usr/share/gromacs/top \
$(CURDIR)/debian/gromacs-data/usr/share/gromacs
mv $(CURDIR)/debian/gromacs/usr/share/man \
$(CURDIR)/debian/gromacs-data/usr/share/man
# some of the default installation directories for documentation and
# example shell scripts are not FHS-friendly; move them appropriately
perl -lne 'print' $(CURDIR)/debian/gromacs/usr/bin/gmx*.bash > \
$(CURDIR)/debian/gromacs-data/usr/share/bash-completion/completions/gmx
rm -f $(CURDIR)/debian/gromacs/usr/bin/GMXRC* $(CURDIR)/debian/gromacs/usr/bin/gmx*.bash
# symlinks, primarily for /usr/share/doc/{gromacs,libgromacs*} -> gromacs-data
dh_link -pgromacs-data
# rename a pair of Perl scripts to drop the .pl extension (Policy 10.4)
mv $(CURDIR)/debian/gromacs/usr/bin/demux.pl $(CURDIR)/debian/gromacs/usr/bin/demux
mv $(CURDIR)/debian/gromacs/usr/bin/xplor2gmx.pl $(CURDIR)/debian/gromacs/usr/bin/xplor2gmx
mkdir -p $(CURDIR)/debian/libgromacs5/usr/lib/$(DEB_HOST_MULTIARCH)
mv $(CURDIR)/debian/gromacs/usr/lib/*/*.so.* $(CURDIR)/debian/libgromacs5/usr/lib/$(DEB_HOST_MULTIARCH)/
dh_installdirs -plibgromacs-dev
mv $(CURDIR)/debian/gromacs/usr/include $(CURDIR)/debian/libgromacs-dev/usr/include
# catch normal libraries plus all applicable MPI variants
mkdir -p $(CURDIR)/debian/libgromacs-dev/usr/lib/$(DEB_HOST_MULTIARCH)
mv $(CURDIR)/debian/gromacs/usr/lib/$(DEB_HOST_MULTIARCH)/*.so \
$(CURDIR)/debian/gromacs/usr/lib/$(DEB_HOST_MULTIARCH)/pkgconfig \
$(CURDIR)/debian/libgromacs-dev/usr/lib/$(DEB_HOST_MULTIARCH)/
rmdir $(CURDIR)/debian/gromacs/usr/lib/$(DEB_HOST_MULTIARCH) $(CURDIR)/debian/gromacs/usr/lib
mv $(CURDIR)/debian/gromacs/usr/share/gromacs/template $(CURDIR)/debian/libgromacs-dev/usr/share/gromacs/template
# remaining documentation catch-all
mv $(CURDIR)/debian/gromacs/usr/share/gromacs/* $(CURDIR)/debian/gromacs-data/usr/share/doc/gromacs
-rmdir $(CURDIR)/debian/gromacs/usr/share/gromacs
# what are you doing here?
mv $(CURDIR)/debian/gromacs/usr/share/cmake $(CURDIR)/debian/libgromacs-dev/usr/share/gromacs/
dh_lintian -pgromacs -pgromacs-data -plibgromacs5
install-manual: build-manual install
dh_testdir
dh_testroot
dh_install -pgromacs-data
dh_installman -pgromacs-data $(CURDIR)/build/documentation/docs/man/*.[1-9]
# dh_doxygen expects a different location of index.html, so do its cleanup manually.
-find $(CURDIR)/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/ -type f -a \( -name '*.md5' -o -name '*.map' \) -delete
rdfind -outputname /dev/null -makesymlinks true $(CURDIR)/debian/gromacs-data/usr/share/doc/
symlinks -r -s -c $(CURDIR)/debian/gromacs-data/usr/share/doc/
install-basic: build-arch
dh_testdir
dh_testroot
dh_prep -pgromacs
dh_installdirs -pgromacs
$(MAKE) -C build/basic install DESTDIR=$(CURDIR)/debian/gromacs
$(MAKE) -C build/basic-dp install DESTDIR=$(CURDIR)/debian/gromacs
dh_installman -pgromacs debian/man/demux.1 debian/man/xplor2gmx.1
# gmx(1) -> gmx_d(1)
dh_link -pgromacs -pgromacs-data
install-mpich: build-mpich
dh_testdir
dh_testroot
dh_prep -pgromacs-mpich
dh_installdirs -pgromacs-mpich
$(MAKE) -C build/mpich install DESTDIR=$(CURDIR)/debian/gromacs-mpich
$(MAKE) -C build/mpich-dp install DESTDIR=$(CURDIR)/debian/gromacs-mpich
# overlapping include files with libgromacs-dev: temporary fix as of 2020-beta1
rm -rf $(CURDIR)/debian/gromacs-mpich/usr/include
chmod 644 $(CURDIR)/debian/gromacs-mpich/usr/bin/gmx-completion*
mv $(CURDIR)/debian/gromacs-mpich/usr/bin/gmx-completion-mdrun_mpi.mpich.bash $(CURDIR)/debian/gromacs-mpich/usr/share/bash-completion/completions/mdrun_mpi.mpich
mv $(CURDIR)/debian/gromacs-mpich/usr/bin/gmx-completion-mdrun_mpi_d.mpich.bash $(CURDIR)/debian/gromacs-mpich/usr/share/bash-completion/completions/mdrun_mpi_d.mpich
dh_installman -pgromacs-mpich debian/man/mdrun_mpi.mpich.1
dh_link -pgromacs-mpich usr/share/man/man1/mdrun_mpi.mpich.1.gz usr/share/man/man1/mdrun_mpi_d.mpich.1.gz
dh_lintian -pgromacs-mpich
install-openmpi: build-openmpi
dh_testdir
dh_testroot
dh_prep -pgromacs-openmpi
dh_installdirs -pgromacs-openmpi
$(MAKE) -C build/openmpi install DESTDIR=$(CURDIR)/debian/gromacs-openmpi
$(MAKE) -C build/openmpi-dp install DESTDIR=$(CURDIR)/debian/gromacs-openmpi
# overlapping include files with libgromacs-dev: temporary fix as of 2020-beta1
rm -rf $(CURDIR)/debian/gromacs-openmpi/usr/include
chmod 644 $(CURDIR)/debian/gromacs-openmpi/usr/bin/gmx-completion*
mv $(CURDIR)/debian/gromacs-openmpi/usr/bin/gmx-completion-mdrun_mpi.openmpi.bash $(CURDIR)/debian/gromacs-openmpi/usr/share/bash-completion/completions/mdrun_mpi.openmpi
mv $(CURDIR)/debian/gromacs-openmpi/usr/bin/gmx-completion-mdrun_mpi_d.openmpi.bash $(CURDIR)/debian/gromacs-openmpi/usr/share/bash-completion/completions/mdrun_mpi_d.openmpi
# Force-disable RUNPATH - see <https://github.com/open-mpi/ompi/issues/521>
# and lintian tag binary-or-shlib-defines-rpath in versions >= 2.5.50
chrpath -d $(CURDIR)/debian/gromacs-openmpi/usr/bin/mdrun_mpi*
dh_installman -pgromacs-openmpi debian/man/mdrun_mpi.openmpi.1
dh_link -pgromacs-openmpi usr/share/man/man1/mdrun_mpi.openmpi.1.gz usr/share/man/man1/mdrun_mpi_d.openmpi.1.gz
dh_lintian -pgromacs-openmpi
binary-indep: build-arch build-indep install install-manual
dh_testdir
dh_testroot
dh_installchangelogs -i
dh_installdocs -pgromacs-data
dh_strip_nondeterminism -i
dh_compress -i -X.pdf
dh_fixperms -i
dh_installdeb -i
dh_gencontrol -i
dh_md5sums -i
dh_builddeb -i
binary-arch: build-arch install
dh_testdir -a
dh_testroot -a
dh_installchangelogs -a
dh_installdocs -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_dwz -a
dh_strip -A
dh_makeshlibs -a
dh_shlibdeps -plibgromacs5 -L libgromacs5 -l debian/libgromacs5/usr/lib
dh_shlibdeps -pgromacs -L libgromacs5 -l debian/libgromacs5/usr/lib:debian/gromacs/usr/lib
dh_shlibdeps -pgromacs-mpich -L gromacs-mpich -l debian/gromacs-mpich/usr/lib
dh_shlibdeps -pgromacs-openmpi -L gromacs-openmpi -l debian/gromacs-openmpi/usr/lib
dh_gencontrol -a
dh_installdeb -a
dh_md5sums -a
dh_builddeb -a
binary: binary-indep binary-arch
.PHONY: binary binary-arch binary-indep build clean install install-basic install-mpich install-openmpi install-manual
|
