Commit 9d9a8b47 authored by Nicholas Breen's avatar Nicholas Breen

* Update list of OpenMPI architectures to include mips*, arm64.

* patches/21_hurd.patch: Cherry-pick upstream commit 2c81d3ab to build shared libraries on GNU/Hurd.
* watch: Extend regex to detect -beta, -pre, _pre, *and* -rc suffixes.
* Remove chrpath workaround, no longer needed as of mpich 3.0.4-6.
parent 2034dae7
gromacs (4.6.5-2) unstable; urgency=medium
* Update list of OpenMPI architectures to include mips*, arm64.
* patches/21_hurd.patch: Cherry-pick upstream commit 2c81d3ab to build
shared libraries on GNU/Hurd.
* watch: Extend regex to detect -beta, -pre, _pre, *and* -rc suffixes.
* Remove chrpath workaround, no longer needed as of mpich 3.0.4-6.
-- Nicholas Breen <nbreen@debian.org> Mon, 16 Jun 2014 18:48:37 -0700
gromacs (4.6.5-1) unstable; urgency=low
* New upstream release.
......
......@@ -3,7 +3,7 @@ Section: science
Priority: extra
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Uploaders: Nicholas Breen <nbreen@debian.org>
Build-Depends: debhelper (>= 7.0.0), libfftw3-dev, libmpich-dev (>= 3), libopenmpi-dev (>= 1.2.4-5) [alpha amd64 armel armhf i386 ia64 powerpc powerpcspe ppc64 sparc sparc64 kfreebsd-i386 kfreebsd-amd64 hurd-i386], libx11-dev, zlib1g-dev, libgsl0-dev, libxml2-dev, libblas-dev, liblapack-dev, cmake, hardening-wrapper, chrpath
Build-Depends: debhelper (>= 7.0.0), libfftw3-dev, libmpich-dev (>= 3), libopenmpi-dev (>= 1.2.4-5) [alpha amd64 arm64 armel armhf hurd-i386 i386 ia64 kfreebsd-amd64 kfreebsd-i386 mips mips64 mips64el mipsel powerpc powerpcspe ppc64 ppc64el sparc sparc64], libx11-dev, zlib1g-dev, libgsl0-dev, libxml2-dev, libblas-dev, liblapack-dev, cmake, hardening-wrapper
Standards-Version: 3.9.5
Homepage: http://www.gromacs.org/
Vcs-Browser: http://anonscm.debian.org/viewvc/debichem/
......@@ -55,7 +55,7 @@ Architecture: any
Section: devel
Depends: ${shlibs:Depends}, gromacs (= ${binary:Version}), fftw3-dev, ${misc:Depends}
Recommends: gromacs-data
Suggests: gromacs-mpich (= ${binary:Version}) | gromacs-openmpi (= ${binary:Version}) [alpha amd64 armel armhf i386 ia64 powerpc powerpcspe sparc sparc64 kfreebsd-i386 kfreebsd-amd64 hurd-i386], libmpich-dev, libx11-dev, zlib1g-dev
Suggests: gromacs-mpich (= ${binary:Version}) | gromacs-openmpi (= ${binary:Version}) [alpha amd64 arm64 armel armhf hurd-i386 i386 ia64 kfreebsd-amd64 kfreebsd-i386 mips mips64 mips64el mipsel powerpc powerpcspe ppc64 ppc64el sparc sparc64], libmpich-dev, libx11-dev, zlib1g-dev
Description: GROMACS molecular dynamics sim, development kit
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate
the Newtonian equations of motion for systems with hundreds to millions of
......@@ -94,7 +94,7 @@ Description: Molecular dynamics sim, binaries for MPICH parallelization
processing cluster, or for multiprocessor machines.
Package: gromacs-openmpi
Architecture: alpha amd64 armel armhf i386 ia64 powerpc powerpcspe ppc64 sparc sparc64 kfreebsd-i386 kfreebsd-amd64 hurd-i386
Architecture: alpha amd64 arm64 armel armhf hurd-i386 i386 ia64 kfreebsd-amd64 kfreebsd-i386 mips mips64 mips64el mipsel powerpc powerpcspe ppc64 ppc64el sparc sparc64
Depends: ${shlibs:Depends}, ${misc:Depends}, openmpi-bin (>= 1.2.3)
Recommends: gromacs
Suggests: gromacs-data
......
Description: Build shared libraries on hurd-i386
Author: Pino Toscano
Origin: upstream, https://gerrit.gromacs.org/3406
Bug: http://redmine.gromacs.org/issues/1495
Applied-Upstream: 2c81d3ab
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Index: gromacs-4.6.5/CMakeLists.txt
===================================================================
--- gromacs-4.6.5.orig/CMakeLists.txt
+++ gromacs-4.6.5/CMakeLists.txt
@@ -431,7 +431,7 @@ include(TestBigEndian)
test_big_endian(GMX_INTEGER_BIG_ENDIAN)
-if(APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD")
+if(APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD|GNU")
# Maybe Solaris should be here? Patch this if you know!
SET(SHARED_LIBS_DEFAULT ON)
elseif(WIN32 OR ${CMAKE_SYSTEM_NAME} MATCHES "BlueGene")
11_readme.patch
12_copyright-file.patch
20_manpages.patch
21_hurd.patch
......@@ -10,7 +10,7 @@ PACKAGE := gromacs
# This list should remain synced with the Build-Depends and the Architecture
# line of gromacs-openmpi in debian/control.
OPENMPI_ARCH = alpha amd64 armel armhf i386 ia64 powerpc powerpcspe ppc64 sparc sparc64 kfreebsd-i386 kfreebsd-amd64 hurd-i386
OPENMPI_ARCH = alpha amd64 arm64 armel armhf hurd-i386 i386 ia64 kfreebsd-amd64 kfreebsd-i386 mips mips64 mips64el mipsel powerpc powerpcspe ppc64 ppc64el sparc sparc64
DEB_HOST_ARCH ?= $(shell dpkg-architecture -qDEB_HOST_ARCH)
# add hardening flags, using hardening-wrapper
......@@ -43,9 +43,9 @@ endif
# for automatic detection of the best available option. Planned for an
# overhaul in GROMACS 5.0 with proper runtime detection. kfreebsd-* doesn't
# yet support the higher extensions anyhow, no special casing needed.
ifneq (,$(findstring cpuopt,$(DEB_BUILD_OPTIONS)))
ifeq (,$(findstring cpuopt,$(DEB_BUILD_OPTIONS)))
ifneq (,$(findstring $(DEB_HOST_ARCH),i386 amd64))
COMMON_CONFIG_PARAMS += -DGMX_CPU_ACCELERATION=SSE2
COMMON_CONFIG_PARAMS += -DGMX_CPU_ACCELERATION=SSE2
endif
endif
......@@ -212,8 +212,6 @@ install-mpich: build
dh_installdirs -pgromacs-mpich
$(MAKE) -C build/mpich install-mdrun DESTDIR=$(CURDIR)/debian/gromacs-mpich
$(MAKE) -C build/mpich-dp install-mdrun DESTDIR=$(CURDIR)/debian/gromacs-mpich
# temporary workaround for RPATH issue in mpich3
chrpath -d $(CURDIR)/debian/gromacs-mpich/usr/bin/* $(CURDIR)/debian/gromacs-mpich/usr/lib/*
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
......
# See uscan(1) for format
version=3
opts=pasv,uversionmangle=s/[-_]((pre|beta)[^.]+)/~$1/ \
ftp://ftp.gromacs.org/pub/gromacs/gromacs-([\d\.betapr_-]*)\.tar\.gz
opts=pasv,uversionmangle=s/[-_]((pre|beta|rc)[^.]+)/~$1/ \
ftp://ftp.gromacs.org/pub/gromacs/gromacs-([\d\.betaprc_-]*)\.tar\.gz
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