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Commits (4)
gromacs (2019~rc1-1) experimental; urgency=medium
* New upstream release candidate.
* Set debhelper compat 11.
* Re-enable several previously disabled OpenMPI tests that now work again,
but set hurd-i386 tests to non-fatal as their failures all seem to be
from outside sources.
* control: Point Vcs-Git URL at debian-experimental branch specifically.
-- Nicholas Breen <nbreen@debian.org> Sun, 16 Dec 2018 09:56:11 -0800
gromacs (2019~beta3-1) experimental; urgency=medium
* New upstream beta release.
......@@ -38,7 +49,7 @@ gromacs (2018.2-1) unstable; urgency=medium
* Updated RRID in debian/upstream/metadata.
[ Nicholas Breen ]
* New upstream release.
* New upstream release.
-- Nicholas Breen <nbreen@debian.org> Sat, 16 Jun 2018 10:24:50 -0700
......@@ -1056,4 +1067,3 @@ gromacs (3.3-1) unstable; urgency=low
* Initial Debian release. (Closes: #228319, #252101)
-- Nicholas Breen <nbreen@ofb.net> Thu, 16 Mar 2006 23:00:13 -0800
......@@ -5,7 +5,7 @@ Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Uploaders: Nicholas Breen <nbreen@debian.org>
Build-Depends: chrpath,
cmake,
debhelper (>= 10),
debhelper (>= 11),
libblas-dev,
libboost-dev,
libfftw3-dev,
......@@ -31,7 +31,7 @@ Build-Depends-Indep: doxygen,
Rules-Requires-Root: no
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/debichem-team/gromacs
Vcs-Git: https://salsa.debian.org/debichem-team/gromacs.git
Vcs-Git: https://salsa.debian.org/debichem-team/gromacs.git -b debian-experimental
Homepage: http://www.gromacs.org/
Package: gromacs
......
Description: [hurd-i386] Disable HardwareTopologyTest.NumaCacheSelfconsistency
On Hurd only, this test reports zero memory. lstopo(1) looks normal,
so this is probably just a hwloc limitation; disable until solved properly
either here or in hwloc.
Author: Nicholas Breen
Last-Update: 2016-08-19
Index: gromacs-2016/src/gromacs/hardware/tests/hardwaretopology.cpp
===================================================================
--- gromacs-2016.orig/src/gromacs/hardware/tests/hardwaretopology.cpp
+++ gromacs-2016/src/gromacs/hardware/tests/hardwaretopology.cpp
@@ -164,10 +164,13 @@ TEST(HardwareTopologyTest, NumaCacheSelf
EXPECT_EQ(uniqueProcessorsinNumaNudes, hwTop.machine().logicalProcessorCount);
// We must have some memory in a numa node
+ // Doesn't detect memory on Hurd at the moment, it seems
+ #ifndef __GNU__
for (auto &n : hwTop.machine().numa.nodes)
{
EXPECT_GT(n.memory, 0);
}
+ #endif // __GNU__
// Check latency matrix size and contents
EXPECT_GT(hwTop.machine().numa.baseLatency, 0);
......@@ -9,7 +9,7 @@ Index: gromacs/docs/conf.py
===================================================================
--- gromacs.orig/docs/conf.py
+++ gromacs/docs/conf.py
@@ -374,3 +374,7 @@ texinfo_documents = [
@@ -377,3 +377,7 @@ texinfo_documents = [
# Make it possible to use numbered labels for figures and tables
numfig = True
......
......@@ -2,6 +2,5 @@ readme.patch
copyright-file.patch
doxygen.patch
disable-cpuinfotest.patch
hurd-disable-numa-test.patch
mdrun-test-timeout.patch
local-mathjax.patch
......@@ -123,9 +123,9 @@ build-basic: configure-stamp
$(MAKE) -C build/basic-dp
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
$(MAKE) -C build/basic tests
(cd build/basic; LD_LIBRARY_PATH=$(CURDIR)/build/basic/lib ctest -V)
(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)
(cd build/basic-dp; LD_LIBRARY_PATH=$(CURDIR)/build/basic-dp/lib ctest -V || dpkg-architecture -i hurd-i386 )
endif
touch $@
......@@ -153,9 +153,9 @@ build-mpich: configure-stamp
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
ifneq ($(DEB_HOST_ARCH), armhf)
$(MAKE) -C build/mpich tests
(cd build/mpich; LD_LIBRARY_PATH=$(CURDIR)/build/mpich/lib ctest -V)
(cd build/mpich; LD_LIBRARY_PATH=$(CURDIR)/build/mpich/lib ctest -V || dpkg-architecture -i hurd-i386 )
$(MAKE) -C build/mpich-dp tests
(cd build/mpich-dp ; LD_LIBRARY_PATH=$(CURDIR)/build/mpich-dp/lib ctest -V)
(cd build/mpich-dp ; LD_LIBRARY_PATH=$(CURDIR)/build/mpich-dp/lib ctest -V || dpkg-architecture -i hurd-i386 )
endif
endif
touch $@
......@@ -168,24 +168,18 @@ build-openmpi: configure-stamp
< debian/gromacs-parallel.README.Debian.in \
> debian/gromacs-openmpi.README.Debian
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
ifeq ($(DEB_HOST_ARCH_OS), linux)
# above ifeq..linux: See https://bugs.debian.org/839387 for background,
# seems to have a specific non-fakeroot failure on hurd/kfreebsd as well?
# 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 \
GTEST_FILTER="-*ChangingPinningPolicyRequiresCuda" \
ctest -V -E MdrunUtilityMpiUnitTests)
ctest -V || dpkg-architecture -i hurd-i386 )
$(MAKE) -C build/openmpi-dp tests
(cd build/openmpi-dp ; LD_LIBRARY_PATH=$(CURDIR)/build/openmpi-dp/lib \
OMPI_MCA_plm_rsh_agent=/bin/false \
OMPI_MCA_rmaps_base_oversubscribe=1 \
GTEST_FILTER="-*ChangingPinningPolicyRequiresCuda" \
ctest -V -E MdrunUtilityMpiUnitTests)
endif
ctest -V || dpkg-architecture -i hurd-i386 )
endif
touch $@
......