diff --git a/.gitignore b/.gitignore index 04f1846..e74d3bc 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,2 @@ /BOUT++-v4.3.0.tar.gz +/BOUT++-v4.3.1.tar.gz diff --git a/arm-deref.patch b/arm-deref.patch deleted file mode 100644 index d10064b..0000000 --- a/arm-deref.patch +++ /dev/null @@ -1,27 +0,0 @@ -commit 97418106eb7cf1f6dd660b494939af83b88beda6 -Author: David Schwörer -Date: Mon Nov 25 13:18:33 2019 +0000 - - Address needs to be aligned - - This value gets dereferenced by python, but without knowing it's true - type. Thus a SIGBUS is thrown on some architectures, namely arm. This - can be avoided by copying it to a larger type first, e.g. long, that - is sufficiently aligned, and thus can be safely dereferenced by - python. - -diff --git a/tools/pylib/_boutcore_build/helper.h.in b/tools/pylib/_boutcore_build/helper.h.in -index 24c26bdf0..21f264d4c 100644 ---- a/tools/pylib/_boutcore_build/helper.h.in -+++ b/tools/pylib/_boutcore_build/helper.h.in -@@ -77,8 +77,9 @@ class PythonModelCallback{ - class PythonModel: public PhysicsModel{ - protected: - int init(bool restarting) override{ -+ long aligned_restarting = restarting; - if (_init){ -- _init->cy_execute(&restarting); -+ _init->cy_execute(&aligned_restarting); - } - return 0; - }; diff --git a/bout++.spec b/bout++.spec index 8a9108a..8b2f7c3 100644 --- a/bout++.spec +++ b/bout++.spec @@ -1,6 +1,6 @@ Name: bout++ -Version: 4.3.0 -Release: 3%{?dist} +Version: 4.3.1 +Release: 1%{?dist} Summary: Library for the BOUndary Turbulence simulation framework # BOUT++ itself is LGPL, but we are linking with GPLed code, so the distributed library is GPL @@ -10,18 +10,6 @@ Source0: https://github.com/boutproject/BOUT-dev/releases/download/v%{ver # Do not install mpark Patch0: remove-mpark.patch -# PR 1851 -Patch1: test-mpi.patch -# PR 1853 -Patch2: test-metric-precision.patch -# PR 1855 -Patch3: arm-deref.patch -# PR 1856 -Patch4: parallel-race.patch -# install make.config to header -Patch5: bout-conf.patch -# PR 1871 -Patch6: typo-released.patch # Disable tests and manual on epel < 8 %if 0%{?rhel} && 0%{?rhel} < 8 @@ -288,13 +276,6 @@ mkdir -p externalpackages/mpark.variant/include/ %patch0 -p 1 %endif -%patch1 -p 1 -%patch2 -p 1 -%patch3 -p 1 -%patch4 -p 1 -%patch5 -p 1 -%patch6 -p 1 - # Remove shebang for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build ) do @@ -455,7 +436,7 @@ done %if %{with mpich} %files mpich -%{_libdir}/mpich/lib/libbout++.so.4.3.0 +%{_libdir}/mpich/lib/libbout++.so.4.3.1 %{_libdir}/mpich/lib/*.so.1.0.0 %{_libdir}/mpich/bin/* %doc README.md @@ -477,7 +458,7 @@ done %if %{with openmpi} %files openmpi -%{_libdir}/openmpi/lib/libbout++.so.4.3.0 +%{_libdir}/openmpi/lib/libbout++.so.4.3.1 %{_libdir}/openmpi/lib/*.so.1.0.0 %{_libdir}/openmpi/bin/* %doc README.md @@ -520,6 +501,9 @@ done # %changelog +* Fri Mar 27 2020 David Schwörer - 4.3.1-1 +- Update to 4.3.1 + * Tue Jan 28 2020 Fedora Release Engineering - 4.3.0-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild diff --git a/bout-conf.patch b/bout-conf.patch deleted file mode 100644 index 6f671d3..0000000 --- a/bout-conf.patch +++ /dev/null @@ -1,31 +0,0 @@ -diff --git a/make.config.in b/make.config.in -index a1e75fdc0..aab91a972 100644 ---- a/make.config.in -+++ b/make.config.in -@@ -178,21 +178,21 @@ install: libfast - $(INSTALL_DATA) tools/idllib/README $(DESTDIR)@datadir@/bout++/idllib/ - $(INSTALL_DATA) tools/pylib/boutdata/*.py $(DESTDIR)@datadir@/bout++/pylib/boutdata/ - $(INSTALL_DATA) tools/pylib/boututils/*.py $(DESTDIR)@datadir@/bout++/pylib/boututils/ -- $(INSTALL_DATA) make.config $(DESTDIR)@datadir@/bout++/ -+ $(INSTALL_DATA) make.config $(INSTALL_INCLUDE_PATH)/ - for mo in $(MO_FILES); do $(MKDIR) $(DESTDIR)@localedir@/`dirname $$mo`; $(INSTALL_DATA) locale/$$mo $(DESTDIR)@localedir@/$$mo; done - $(POST_INSTALL) # Post-install commands follow. - - @# Modify paths in the bout-config script - sed -i "s|^BOUT_INCLUDE_PATH=.*|BOUT_INCLUDE_PATH=@includedir@/bout++|" $(DESTDIR)@bindir@/bout-config - sed -i "s|^BOUT_LIB_PATH=.*|BOUT_LIB_PATH=@libdir@|" $(DESTDIR)@bindir@/bout-config -- sed -i "s|^BOUT_CONFIG_FILE=.*|BOUT_CONFIG_FILE=@datadir@/bout++/make.config|" $(DESTDIR)@bindir@/bout-config -+ sed -i "s|^BOUT_CONFIG_FILE=.*|BOUT_CONFIG_FILE=@includedir@/bout++/make.config|" $(DESTDIR)@bindir@/bout-config - sed -i "s|^idlpath=.*|idlpath=@datadir@/bout++/idllib/|" $(DESTDIR)@bindir@/bout-config - sed -i "s|^pythonpath=.*|pythonpath=@datadir@/bout++/pylib/|" $(DESTDIR)@bindir@/bout-config - - @# Modify paths in the make.config file -- sed -i "s|^BOUT_INCLUDE_PATH=.*|BOUT_INCLUDE_PATH=@includedir@/bout++|" $(DESTDIR)@datadir@/bout++/make.config -- sed -i "s|^BOUT_LIB_PATH=.*|BOUT_LIB_PATH=@libdir@|" $(DESTDIR)@datadir@/bout++/make.config -- sed -i "s|^BOUT_CONFIG_FILE=.*|BOUT_CONFIG_FILE=@datadir@/bout++/make.config|" $(DESTDIR)@datadir@/bout++/make.config -+ sed -i "s|^BOUT_INCLUDE_PATH=.*|BOUT_INCLUDE_PATH=@includedir@/bout++|" $(INSTALL_INCLUDE_PATH)/make.config -+ sed -i "s|^BOUT_LIB_PATH=.*|BOUT_LIB_PATH=@libdir@|" $(INSTALL_INCLUDE_PATH)/make.config -+ sed -i "s|^BOUT_CONFIG_FILE=.*|BOUT_CONFIG_FILE=@includedir@/bout++/make.config|" $(INSTALL_INCLUDE_PATH)/make.config - - uninstall: - $(PRE_UNINSTALL) # Pre-uninstall commands follow. diff --git a/parallel-race.patch b/parallel-race.patch deleted file mode 100644 index ea9ca1b..0000000 --- a/parallel-race.patch +++ /dev/null @@ -1,44 +0,0 @@ -commit 6612b6ab8f07f10065cfc8ec0925addb910cecb8 -Author: David Schwörer -Date: Mon Nov 25 13:44:23 2019 +0000 - - Try to prevent race condition while building. - - This improves the current situation, as before it could happen that - building failed, because the .a was not yet created. Now it waits for - it to be created. Switching to atomic mv rather then to create it - inplace, ensures that if the file is seen, it is valid. - This does not address the case when the .a is recreated, and the - dependend file is checked before whether the .a has changed. - -diff --git a/make.config.in b/make.config.in -index df80ed2ad..a183cf2e8 100644 ---- a/make.config.in -+++ b/make.config.in -@@ -242,11 +242,15 @@ endif - - ifeq ("$(TARGET)", "sub") - LIB=$(MODULE_DIR)/$(SUB_NAME).a --sub: makefile $(BOUT_CONFIG_FILE) $(BOUT_TOP)/include $(BOUT_TOP)/lib $(OBJ) -+sub:$(LIB) -+ -+$(LIB): makefile $(BOUT_CONFIG_FILE) $(BOUT_TOP)/include $(BOUT_TOP)/lib $(OBJ) - ifneq ("$(OBJ)foo", "foo") - @echo " Adding $(OBJ) to $(LIB)" -- @$(AR) $(ARFLAGS) $(LIB) $(OBJ) -- @$(RANLIB) $(LIB) -+ @LIBT=$(LIB).$$$$.a && \ -+ $(AR) $(ARFLAGS) $${LIBT} $(OBJ) && \ -+ $(RANLIB) $${LIBT} && \ -+ mv $${LIBT} $(LIB) - endif - endif - -@@ -282,6 +286,7 @@ $(SUB_LIBS):$(DIRS__) - - $(SOURCEC): checklib - $(SOURCEC:%.cxx=%.o): $(LIB) -+$(TARGET): | $(DIRS) - $(TARGET): makefile $(BOUT_CONFIG_FILE) $(OBJ) $(SUB_LIBS) - @echo " Linking" $(TARGET) - @$(LD) $(LDFLAGS) -o $(TARGET) $(OBJ) $(SUB_LIBS) $(BOUT_LIBS) diff --git a/remove-mpark.patch b/remove-mpark.patch index 18f8a06..1000665 100644 --- a/remove-mpark.patch +++ b/remove-mpark.patch @@ -1,8 +1,6 @@ -diff --git a/make.config.in b/make.config.in -index df80ed2ad..a1e75fdc0 100644 --- a/make.config.in +++ b/make.config.in -@@ -88,8 +88,7 @@ LIB = $(BOUT_LIB_PATH)/libbout++.a +@@ -91,8 +91,7 @@ LIB = $(BOUT_LIB_PATH)/libbout++.a LIB_SO = $(BOUT_LIB_PATH)/libbout++.so endif @@ -12,7 +10,7 @@ index df80ed2ad..a1e75fdc0 100644 BOUT_LIBS = -lm -L$(BOUT_LIB_PATH) -lbout++ $(EXTRA_LIBS) CHANGED = $(shell find -f $(BOUT_TOP)/include $(BOUT_TOP)/src -type f \( -name \*.cxx -or -name \*.h \) -newer $(LIB) -print 2> /dev/null) -@@ -162,11 +161,10 @@ install: libfast +@@ -163,11 +162,10 @@ install: libfast $(PRE_INSTALL) # Pre-install commands follow. $(NORMAL_INSTALL) # Normal commands follow. @@ -25,28 +23,31 @@ index df80ed2ad..a1e75fdc0 100644 $(INSTALL_DATA) include/pvode/*.h $(INSTALL_INCLUDE_PATH)/pvode/ $(INSTALL_DATA) include/bout/*.hxx $(INSTALL_INCLUDE_PATH)/bout/ $(INSTALL_DATA) include/bout/sys/*.hxx $(INSTALL_INCLUDE_PATH)/bout/sys/ -@@ -190,13 +188,11 @@ install: libfast - sed -i "s|^BOUT_CONFIG_FILE=.*|BOUT_CONFIG_FILE=@datadir@/bout++/make.config|" $(DESTDIR)@bindir@/bout-config +@@ -191,13 +189,11 @@ install: libfast + sed -i "s|^BOUT_CONFIG_FILE=.*|BOUT_CONFIG_FILE=@includedir@/bout++/make.config|" $(DESTDIR)@bindir@/bout-config sed -i "s|^idlpath=.*|idlpath=@datadir@/bout++/idllib/|" $(DESTDIR)@bindir@/bout-config sed -i "s|^pythonpath=.*|pythonpath=@datadir@/bout++/pylib/|" $(DESTDIR)@bindir@/bout-config - sed -i "s|^MPARK_VARIANT_INCLUDE_PATH=.*|MPARK_VARIANT_INCLUDE_PATH=@includedir@/bout++|" $(DESTDIR)@bindir@/bout-config @# Modify paths in the make.config file - sed -i "s|^BOUT_INCLUDE_PATH=.*|BOUT_INCLUDE_PATH=@includedir@/bout++|" $(DESTDIR)@datadir@/bout++/make.config - sed -i "s|^BOUT_LIB_PATH=.*|BOUT_LIB_PATH=@libdir@|" $(DESTDIR)@datadir@/bout++/make.config - sed -i "s|^BOUT_CONFIG_FILE=.*|BOUT_CONFIG_FILE=@datadir@/bout++/make.config|" $(DESTDIR)@datadir@/bout++/make.config -- sed -i "s|^MPARK_VARIANT_INCLUDE_PATH=.*|MPARK_VARIANT_INCLUDE_PATH=@includedir@/bout++|" $(DESTDIR)@datadir@/bout++/make.config + sed -i "s|^BOUT_INCLUDE_PATH=.*|BOUT_INCLUDE_PATH=@includedir@/bout++|" $(INSTALL_INCLUDE_PATH)/make.config + sed -i "s|^BOUT_LIB_PATH=.*|BOUT_LIB_PATH=@libdir@|" $(INSTALL_INCLUDE_PATH)/make.config + sed -i "s|^BOUT_CONFIG_FILE=.*|BOUT_CONFIG_FILE=@includedir@/bout++/make.config|" $(INSTALL_INCLUDE_PATH)/make.config +- sed -i "s|^MPARK_VARIANT_INCLUDE_PATH=.*|MPARK_VARIANT_INCLUDE_PATH=@includedir@/bout++|" $(INSTALL_INCLUDE_PATH)/make.config - uninstall: - $(PRE_UNINSTALL) # Pre-uninstall commands follow. -@@ -220,13 +216,7 @@ uninstall: + # Set the make.config as released, so the library isn't rebuild. This way the .a file doesn't need to be preserved/installed + sed -i '26 i RELEASED = yes' $(INSTALL_INCLUDE_PATH)/make.config +@@ -223,16 +219,7 @@ uninstall: # Builds the library with $(OBJ) which is defined from the SOURCEC variable #################################################################### -MPARK_VARIANT_SENTINEL = $(MPARK_VARIANT_INCLUDE_PATH)/mpark/variant.hpp -$(MPARK_VARIANT_SENTINEL): - @echo "Downloading mpark.variant" -- git submodule update --init --recursive $(BOUT_TOP)/externalpackages/mpark.variant +- @lock=$(BOUT_TOP)/externalpackages/.get.mpark ;ex=0; mkdir $$lock && ( \ +- git submodule update --init --recursive $(BOUT_TOP)/externalpackages/mpark.variant \ +- ;ex=$$? ; rmdir $$lock ) || \ +- ( while test -d $$lock ; do sleep .1 ; done); exit $$ex - ifeq ("$(TARGET)", "libfast") -libfast: | $(MPARK_VARIANT_SENTINEL) diff --git a/sources b/sources index 8285297..28ced67 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (BOUT++-v4.3.0.tar.gz) = 41dbb1f3b07230daf30d7c6a6ec4014c67041df1a5146bd792a5991535a9426cff58f40dbd24f87cf79814bf0771ba4d74b5bc04f93dd70fc7602dd0bb2b340f +SHA512 (BOUT++-v4.3.1.tar.gz) = 6d78f48e1d26599868bcc371b3bd6920f32658ba042590bcc8b7d005d5e7f1bd9f8ed2b19dab0a97f81d949d9817201bb96652890836e8a77d85ff2acb2ad0a9 diff --git a/test-metric-precision.patch b/test-metric-precision.patch deleted file mode 100644 index 365f15e..0000000 --- a/test-metric-precision.patch +++ /dev/null @@ -1,20 +0,0 @@ -commit 9feb40fb4feb6d90456a45f8b09464307f1a1873 -Author: David Schwörer -Date: Sun Nov 24 13:56:49 2019 +0000 - - Loosen tolerance for other arches - -diff --git a/tests/unit/mesh/parallel/test_shiftedmetric.cxx b/tests/unit/mesh/parallel/test_shiftedmetric.cxx -index 9fb0c421f..b589af68d 100644 ---- a/tests/unit/mesh/parallel/test_shiftedmetric.cxx -+++ b/tests/unit/mesh/parallel/test_shiftedmetric.cxx -@@ -166,7 +166,8 @@ TEST_F(ShiftedMetricTest, FromFieldAligned) { - // Loosen tolerance a bit due to FFTs - EXPECT_TRUE(IsFieldEqual(result, expected, "RGN_ALL", - FFTTolerance)); -- EXPECT_TRUE(IsFieldEqual(toFieldAligned(result), input)); -+ EXPECT_TRUE(IsFieldEqual(toFieldAligned(result), input, -+ "RGN_ALL", FFTTolerance)); - EXPECT_TRUE(areFieldsCompatible(result, expected)); - EXPECT_FALSE(areFieldsCompatible(result, input)); - } diff --git a/test-mpi.patch b/test-mpi.patch deleted file mode 100644 index 25c40dd..0000000 --- a/test-mpi.patch +++ /dev/null @@ -1,22 +0,0 @@ -commit 5879823ab8b53b7f41ab62c1850d85294d68e28a -Author: David Schwörer -Date: Fri Nov 22 19:27:56 2019 +0000 - - Bugfix: $MPIRUN should include -np - -diff --git a/tests/integrated/test-coordinates-initialization/runtest b/tests/integrated/test-coordinates-initialization/runtest -index 0c5626896..f1bc16044 100755 ---- a/tests/integrated/test-coordinates-initialization/runtest -+++ b/tests/integrated/test-coordinates-initialization/runtest -@@ -2,9 +2,9 @@ - - make || exit - --test -z $MPIRUN && MPIRUN=mpirun -+test -z $MPIRUN && MPIRUN='mpirun -np' - # Kill the test after 3 seconds, if it hasn't already exited --OMP_NUM_THREADS=1 $MPIRUN -n 3 timeout 3s ./test-coordinates-initialization -+OMP_NUM_THREADS=1 $MPIRUN 3 timeout 3s ./test-coordinates-initialization - - e=$? - diff --git a/typo-released.patch b/typo-released.patch deleted file mode 100644 index 3e1e54a..0000000 --- a/typo-released.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/make.config.in b/make.config.in -index c5c4a2ef7..951fed1c6 100644 ---- a/make.config.in -+++ b/make.config.in -@@ -83,7 +83,7 @@ BOUT_VERSION = @PACKAGE_VERSION@ - # Files that are needed by configure and should be dependencies for 'all' - - OBJ = $(SOURCEC:%.cxx=%.o) --ifndef RELEASE -+ifndef RELEASED - LIB = $(BOUT_LIB_PATH)/libbout++.a - LIB_SO = $(BOUT_LIB_PATH)/libbout++.so - endif