Commit 3cfb3bfc authored by Nicholas Breen's avatar Nicholas Breen

* New 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.
parent c99b4e75
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 <nbreen@debian.org> Mon, 11 Jul 2016 18:28:25 -0700
gromacs (2016~beta2-2) experimental; urgency=medium
* Two patches to address test suits failures:
......
......@@ -11,8 +11,8 @@ Build-Depends: cmake,
liblapack-dev,
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],
libtinyxml-dev,
libx11-dev,
libxml2-dev,
zlib1g-dev
Build-Depends-Indep: doxygen,
ghostscript,
......
......@@ -6,10 +6,10 @@ Origin: vendor
Forwarded: not-needed
Last-Update: 2015-09-26
---
Index: gromacs-2016~beta2/CMakeLists.txt
Index: gromacs-2016~rc1/CMakeLists.txt
===================================================================
--- gromacs-2016~beta2.orig/CMakeLists.txt
+++ gromacs-2016~beta2/CMakeLists.txt
--- gromacs-2016~rc1.orig/CMakeLists.txt
+++ gromacs-2016~rc1/CMakeLists.txt
@@ -90,6 +90,9 @@ set(build_types_with_explicit_flags RELE
set_property(GLOBAL PROPERTY FIND_LIBRARY_USE_LIB64_PATHS ON)
......@@ -20,7 +20,7 @@ Index: gromacs-2016~beta2/CMakeLists.txt
# Set a default valgrind suppression file.
# This unfortunately needs to duplicate information from CTest to work as
# expected...
@@ -844,7 +847,7 @@ endif()
@@ -868,7 +871,7 @@ endif()
#COPYING file: Only necessary for binary distributions.
#Simpler to always install.
......
Description: Disable hwloc CPU tests
Certain tests for hardwre topology fail on less-common architectures where
the expected values are not available. This should probably be a configure
time warning instead of a fatal test failure. Temporarily disable these
tests pending a fix acceptable upstream.
Author: Nicholas Breen
Bug: http://redmine.gromacs.org/issues/1987
Last-Update: 2016-06-17
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Index: gromacs-2016~beta2/src/gromacs/hardware/tests/hardwaretopology.cpp
===================================================================
--- gromacs-2016~beta2.orig/src/gromacs/hardware/tests/hardwaretopology.cpp
+++ gromacs-2016~beta2/src/gromacs/hardware/tests/hardwaretopology.cpp
@@ -76,7 +76,8 @@ TEST(HardwareTopologyTest, Execute)
<< "Please mail gmx-developers@gromacs.org so we can try to fix it.";
}
-#if GMX_HWLOC
+#if TEST_DISABLED_DEBIAN_PATCH____GMX_HWLOC
+// http://redmine.gromacs.org/issues/1987
TEST(HardwareTopologyTest, HwlocExecute)
{
#ifdef __linux__
Index: gromacs-2016~beta2/src/gromacs/hardware/tests/CMakeLists.txt
===================================================================
--- gromacs-2016~beta2.orig/src/gromacs/hardware/tests/CMakeLists.txt
+++ gromacs-2016~beta2/src/gromacs/hardware/tests/CMakeLists.txt
@@ -33,5 +33,8 @@
# the research papers on the package. Check out http://www.gromacs.org.
gmx_add_unit_test(HardwareUnitTests hardware-test
- cpuinfo.cpp
hardwaretopology.cpp)
+
+# cpuinfo.cpp disabled in Debian patch pending resolution of
+# http://redmine.gromacs.org/issues/1987
+
Description: Fix numerically unstable Gaussian test
Author: Roland Schulz
Bug: http://redmine.gromacs.org/issues/1986
Last-Update: 2016-06-13
diff --git a/src/gromacs/random/tests/tabulatednormaldistribution.cpp b/src/gromacs/random/tests/tabulatednormaldistribution.cpp
index a4e8fc6..6b48aa6 100644
--- a/src/gromacs/random/tests/tabulatednormaldistribution.cpp
+++ b/src/gromacs/random/tests/tabulatednormaldistribution.cpp
@@ -100,6 +100,7 @@
{
result.push_back(dist(rng));
}
+ checker.setDefaultTolerance(test::ulpTolerance(15)); //compiler usage of FMA in makeTable can cause higher difference
checker.checkSequence(result.begin(), result.end(), "TabulatedNormalDistributionDouble14");
}
......@@ -2,5 +2,3 @@ readme.patch
copyright-file.patch
reproducible-builds.patch
doxygen.patch
numerically-unstable-gaussian-test.patch
disable-hardware-topology-tests.patch
......@@ -128,7 +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." ; $(MAKE) webpage -C build/documentation )
build-mpich: configure-stamp
dh_testdir
......@@ -271,24 +273,24 @@ binary-indep: build-arch build-indep install install-manual
dh_builddeb -i
binary-arch: build-arch install
dh_testdir -s
dh_testroot -s
dh_installchangelogs -s
dh_installdocs -s
dh_testdir -a
dh_testroot -a
dh_installchangelogs -a
dh_installdocs -a
dh_strip -A
dh_compress -s
dh_fixperms -s
dh_makeshlibs -s
dh_compress -a
dh_fixperms -a
dh_makeshlibs -a
dh_shlibdeps -plibgromacs2 -L libgromacs2 -l debian/libgromacs2/usr/lib
dh_shlibdeps -pgromacs -L libgromacs2 -l debian/libgromacs2/usr/lib:debian/gromacs/usr/lib
dh_shlibdeps -pgromacs-mpich -L gromacs-mpich -l debian/gromacs-mpich/usr/lib
ifneq (,$(findstring $(DEB_HOST_ARCH),$(OPENMPI_ARCH)))
dh_shlibdeps -pgromacs-openmpi -L gromacs-openmpi -l debian/gromacs-openmpi/usr/lib
endif
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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