Commit 44dc8ae3 authored by Nicholas Breen's avatar Nicholas Breen

Merge experimental branch for 2016-rcX uploads back into unstable

parent 96b46f8c
gromacs (5.1.3-1) unstable; urgency=medium
gromacs (2016-1) unstable; urgency=low
* New upstream maintenance release.
- Remove patches/spelling.patch and empty-man7-directory.patch,
incorporated upstream.
* control: Update Standards-Version to 3.9.8, no changes required.
* rules: Apply dh_shlibdeps workaround for #831442.
* New upstream release, upload to unstable.
- Remove patches/gmxManageSimd.patch, incorporated upstream.
-- Nicholas Breen <> Sat, 23 Jul 2016 17:19:36 -0700
-- Nicholas Breen <> Tue, 09 Aug 2016 06:06:12 -0700
gromacs (2016~rc1-3) experimental; urgency=medium
* Workaround for #831442: manually prepend /usr/lib/<TRIPLET> to search
path for dh_shlibdeps -pgromacs-mpich.
* Set SIMD extensions to VSX on ppc64el, already the minimum requirement
for that architecture. Disable SIMD on ppc64 due to lower CPU baseline
requirements and the lack of double-precision support in basic VMX.
-- Nicholas Breen <> Sat, 16 Jul 2016 10:17:07 -0700
gromacs (2016~rc1-2) experimental; urgency=medium
* OpenMPI now supported on all relevant architectures, so gromacs-openmpi
changed to "Architecture: any" and arch-specific handling removed.
* Revive part of the test patch from beta2-2 as disable-cpuinfotest.patch,
as the issue is not fully resolved upstream.
* For SSE settings, use DEB_HOST_ARCH_CPU instead of DEB_HOST_ARCH.
* patches/gmxManageSimd.patch: Correctly pass -msse2 to compiler flags.
-- Nicholas Breen <> Fri, 15 Jul 2016 17:44:18 -0700
gromacs (2016~rc1-1) experimental; urgency=medium
* First upstream release candidate.
- Drop patches from beta2-2, incorporated or fixed upstream.
* Switch from building with libxml2 to libtinyxml.
* rules: Convert deprecated debhelper -s flags to -a.
-- Nicholas Breen <> Mon, 11 Jul 2016 18:28:25 -0700
gromacs (2016~beta2-2) experimental; urgency=medium
* Two patches to address test suits failures:
- numerically-unstable-gaussian-test.patch: Backport a fix from git
master branch to address Gaussian test failures on all i386
platforms. (
- disable-hardware-topology-tests.patch: Two CPU info tests cause hard
failures that should probably just be warnings, so disable those tests
for now. (
-- Nicholas Breen <> Fri, 17 Jun 2016 06:40:18 -0700
gromacs (2016~beta2-1) experimental; urgency=low
* Beta for major new upstream release. New date-based versioning system.
- SONAME bump: package rename, libgromacs1 -> libgromacs2
- spelling and empty-man7-directory patches incorporated upstream.
- Refresh other patches.
- Versioned Depends: on python-sphinx (>= 1.4) for new imgmath
* Update Standards-Version to 3.9.8, no changes required.
-- Nicholas Breen <> Tue, 07 Jun 2016 14:20:10 -0700
gromacs (5.1.2-3) experimental; urgency=medium
* Add LD_LIBRARY_PATH overrides to unit tests.
-- Nicholas Breen <> Thu, 21 Apr 2016 17:35:41 -0700
gromacs (5.1.2-2) experimental; urgency=medium
* Run upstream unit tests. Supports DEB_BUILD_OPTIONS=nocheck bypass.
* Use rdfind/symlinks to reduce internal duplication in doxygen output.
* Only build process changes in this upload - uploading to
experimental as a safety.
-- Nicholas Breen <> Mon, 18 Apr 2016 21:04:31 -0700
gromacs (5.1.2-1) unstable; urgency=medium
......@@ -10,7 +10,7 @@ Build-Depends: cmake,
libmpich-dev (>= 3.0.4-6),
libopenmpi-dev (>= 1.10.2-7) [alpha amd64 arm64 armel armhf hppa hurd-i386 i386 ia64 kfreebsd-amd64 kfreebsd-i386 mips mips64 mips64el mipsel powerpc powerpcspe ppc64 ppc64el s390x sparc sparc64 x32],
libopenmpi-dev (>= 1.10.2-7),
......@@ -144,7 +144,7 @@ Description: Molecular dynamics sim, binaries for MPICH parallelization
processing cluster, or for multiprocessor machines.
Package: gromacs-openmpi
Architecture: alpha amd64 arm64 armel armhf hppa hurd-i386 i386 ia64 kfreebsd-amd64 kfreebsd-i386 mips mips64 mips64el mipsel powerpc powerpcspe ppc64 ppc64el s390x sparc sparc64 x32
Architecture: any
Depends: openmpi-bin (>= 1.2.3), ${misc:Depends}, ${shlibs:Depends}
Recommends: gromacs
Suggests: gromacs-data
Description: Disable CpuInfoTest.SupportLevel test
This test is still a hard failure on less common architectures instead of
a warning. Disable for now, as it should not fail the build.
Author: Nicholas Breen
Last-Update: 2016-07-15
Index: gromacs-2016~rc1/src/gromacs/hardware/tests/CMakeLists.txt
--- gromacs-2016~rc1.orig/src/gromacs/hardware/tests/CMakeLists.txt
+++ gromacs-2016~rc1/src/gromacs/hardware/tests/CMakeLists.txt
@@ -33,5 +33,7 @@
# the research papers on the package. Check out
gmx_add_unit_test(HardwareUnitTests hardware-test
- cpuinfo.cpp
+# cpuinfo.cpp disabled in Debian patch pending resolution of
......@@ -2,3 +2,4 @@ readme.patch
......@@ -2,16 +2,10 @@
# build script for GROMACS
# export DH_VERBOSE=1
PACKAGE := gromacs
# OpenMPI is only supported on a subset of architectures at this time.
# This list should remain synced with the Build-Depends and the Architecture
# line of gromacs-openmpi in debian/control.
OPENMPI_ARCH = alpha amd64 arm64 armel armhf hppa hurd-i386 i386 ia64 kfreebsd-amd64 kfreebsd-i386 mips mips64 mips64el mipsel powerpc powerpcspe ppc64 ppc64el s390x sparc sparc64 x32
DEB_HOST_ARCH ?= $(shell dpkg-architecture -qDEB_HOST_ARCH)
DEB_HOST_ARCH_CPU ?= $(shell dpkg-architecture -qDEB_HOST_ARCH_CPU)
DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
# add hardening flags, using dpkg-buildflags
......@@ -39,16 +33,24 @@ COMMON_CONFIG_PARAMS = \
# Force compiler to use no more than SSE2 CPU optimizations, for broadest
# compatibility. For local compilations, pass DEB_BUILD_OPTIONS=cpuopt
# for automatic detection of the best available option. kfreebsd-* doesn't
# yet support the higher extensions anyhow, no special casing needed.
# Force compiler to use no more than SSE2 CPU optimizations on x86/amd64,
# and VSX on ppc64el, for broadest compatibility.
# For local compilations, pass DEB_BUILD_OPTIONS=cpuopt for automatic
# detection of the best available option.
# See
ifeq (,$(findstring cpuopt,$(DEB_BUILD_OPTIONS)))
ifneq (,$(findstring $(DEB_HOST_ARCH),i386 amd64))
ifneq (,$(findstring $(DEB_HOST_ARCH_CPU),i386 amd64))
# ppc64*
ifneq (,$(findstring $(DEB_HOST_ARCH_CPU),ppc64))
ifneq (,$(findstring $(DEB_HOST_ARCH_CPU),ppc64el))
endif # ifneq .. ppc64el
endif # ifneq .. ppc64
# Include "gpu" in DEB_BUILD_OPTIONS to build GPU-accelerated binaries as well.
# This build option is not always well tested, please send comments.
......@@ -94,12 +96,10 @@ configure-stamp:
(mkdir -p build/mpich-dp; cd build/mpich-dp; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \
ifneq (,$(findstring $(DEB_HOST_ARCH),$(OPENMPI_ARCH)))
(mkdir -p build/openmpi; cd build/openmpi; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \
(mkdir -p build/openmpi-dp; cd build/openmpi-dp; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \
touch $@
......@@ -112,6 +112,10 @@ build-basic: configure-stamp
$(MAKE) -C build/basic
$(MAKE) -C build/basic-dp
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
LD_LIBRARY_PATH=$(CURDIR)/build/basic/lib $(MAKE) -C build/basic check
LD_LIBRARY_PATH=$(CURDIR)/build/basic-dp/lib $(MAKE) -C build/basic-dp check
touch $@
......@@ -124,7 +128,9 @@ build-manual:
# Generate PDF
$(MAKE) manual -C build/documentation
# Generate HTML
$(MAKE) webpage -C build/documentation
# This sometimes seems to work the *second* time? Still trying to trace it down.
$(MAKE) webpage -C build/documentation || \
(echo "===== Failed to build documentation, retrying." ; $(MAKE) webpage -C build/documentation )
build-mpich: configure-stamp
......@@ -133,17 +139,21 @@ build-mpich: configure-stamp
sed -e 's/#MPIABBR#/mpich/g' -e 's/#MPIPROG#/MPICH2/g' \
< debian/ \
> debian/gromacs-mpich.README.Debian
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
LD_LIBRARY_PATH=$(CURDIR)/build/mpich/lib $(MAKE) -C build/mpich check
LD_LIBRARY_PATH=$(CURDIR)/build/mpich-dp/lib $(MAKE) -C build/mpich-dp check
touch $@
build-openmpi: configure-stamp
ifneq (,$(findstring $(DEB_HOST_ARCH),$(OPENMPI_ARCH)))
$(MAKE) -C build/openmpi
$(MAKE) -C build/openmpi-dp
sed -e 's/#MPIABBR#/openmpi/g' -e 's/#MPIPROG#/OpenMPI/g' \
< debian/ \
> debian/gromacs-openmpi.README.Debian
LD_LIBRARY_PATH=$(CURDIR)/build/openmpi/lib $(MAKE) -C build/openmpi check
LD_LIBRARY_PATH=$(CURDIR)/build/openmpi-dp/lib $(MAKE) -C build/openmpi-dp check
touch $@
......@@ -173,15 +183,15 @@ install: build-arch install-basic install-mpich install-openmpi
chmod 644 $(CURDIR)/debian/gromacs-data/usr/share/gromacs/shell-specific/*
dh_link -pgromacs-data usr/share/doc/gromacs/html usr/share/doc/gromacs-data/html
dh_link -pgromacs-data usr/share/doc/gromacs/html usr/share/doc/libgromacs-dev/html
dh_link -pgromacs-data usr/share/doc/gromacs/html usr/share/doc/libgromacs1/html
dh_link -pgromacs-data usr/share/doc/gromacs/html usr/share/doc/libgromacs2/html
# this name is also given in documentation
dh_link -pgromacs-data usr/share/doc/gromacs-data/copyright usr/share/doc/gromacs-data/COPYING
# rename a pair of Perl scripts to drop the .pl extension (Policy 10.4)
mv $(CURDIR)/debian/gromacs/usr/bin/ $(CURDIR)/debian/gromacs/usr/bin/demux
mv $(CURDIR)/debian/gromacs/usr/bin/ $(CURDIR)/debian/gromacs/usr/bin/xplor2gmx
mkdir -p $(CURDIR)/debian/libgromacs1/usr/lib/$(DEB_HOST_MULTIARCH)
mv $(CURDIR)/debian/gromacs/usr/lib/*/*.so.* $(CURDIR)/debian/libgromacs1/usr/lib/$(DEB_HOST_MULTIARCH)/
mkdir -p $(CURDIR)/debian/libgromacs2/usr/lib/$(DEB_HOST_MULTIARCH)
mv $(CURDIR)/debian/gromacs/usr/lib/*/*.so.* $(CURDIR)/debian/libgromacs2/usr/lib/$(DEB_HOST_MULTIARCH)/
dh_installdirs -plibgromacs-dev
mv $(CURDIR)/debian/gromacs/usr/include $(CURDIR)/debian/libgromacs-dev/usr/include
......@@ -197,12 +207,14 @@ install: build-arch install-basic install-mpich install-openmpi
-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 -plibgromacs1
dh_lintian -pgromacs -pgromacs-data -plibgromacs2
install-manual: build-manual install
dh_install -pgromacs-data
rdfind -outputname /dev/null -makesymlinks true $(CURDIR)/debian/gromacs-data/usr/share/doc/
symlinks -r -s -c $(CURDIR)/debian/gromacs-data/usr/share/doc/
install-basic: build-arch
......@@ -233,7 +245,6 @@ install-openmpi: build-openmpi
dh_prep -pgromacs-openmpi
ifneq (,$(findstring $(DEB_HOST_ARCH),$(OPENMPI_ARCH)))
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
......@@ -242,7 +253,6 @@ ifneq (,$(findstring $(DEB_HOST_ARCH),$(OPENMPI_ARCH)))
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
......@@ -257,25 +267,23 @@ binary-indep: build-arch build-indep install install-manual
dh_builddeb -i
binary-arch: build-arch install
dh_testdir -s
dh_testroot -s
dh_installchangelogs -s
dh_installdocs -s
dh_testdir -a
dh_testroot -a
dh_installchangelogs -a
dh_installdocs -a
dh_strip -A
dh_compress -s
dh_fixperms -s
dh_makeshlibs -s
dh_shlibdeps -plibgromacs1 -L libgromacs1 -l debian/libgromacs1/usr/lib
dh_shlibdeps -pgromacs -L libgromacs1 -l debian/libgromacs1/usr/lib:debian/gromacs/usr/lib
dh_compress -a
dh_fixperms -a
dh_makeshlibs -a
dh_shlibdeps -plibgromacs2 -L libgromacs2 -l debian/libgromacs2/usr/lib
dh_shlibdeps -pgromacs -L libgromacs2 -l debian/libgromacs2/usr/lib:debian/gromacs/usr/lib
# Prepend /usr/lib/TRIPLET to work around #831442
dh_shlibdeps -pgromacs-mpich -L gromacs-mpich -l /usr/lib/$(DEB_HOST_MULTIARCH):debian/gromacs-mpich/usr/lib
ifneq (,$(findstring $(DEB_HOST_ARCH),$(OPENMPI_ARCH)))
dh_shlibdeps -pgromacs-mpich -L gromacs-mpich -l /usr/lib/$(DEB_HOST_MULTIARCH):debian/gromacs-mpich/usr/lib
dh_shlibdeps -pgromacs-openmpi -L gromacs-openmpi -l debian/gromacs-openmpi/usr/lib
dh_gencontrol -s
dh_installdeb -s
dh_md5sums -s
dh_builddeb -s
dh_gencontrol -a
dh_installdeb -a
dh_md5sums -a
dh_builddeb -a
binary: binary-indep binary-arch
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