Merge pull request #158 from FreeFem/develop

Version 4.7-1
FreeFem · Oct 17, 2020 · 0804136 · 0804136
2 parents eca8ba5 + 8ae3266
commit 0804136
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Showing 72 changed files with 3,823 additions and 3,471 deletions.
diff --git a/3rdparty/ff-petsc/Makefile b/3rdparty/ff-petsc/Makefile
@@ -68,15 +68,13 @@ PETSC_DOWNLOAD := --download-metis --download-ptscotch \
 		--download-hypre --download-parmetis \
 		--download-superlu --download-suitesparse --download-tetgen \
 		--download-slepc
-# --download-slepc-commit=d3f7cd4a
 ifeq ($(FFCMAKE),no)
 PETSC_DOWNLOAD := $(PETSC_DOWNLOAD) --download-cmake
 endif
 PETSC_DOWNLOAD_C := $(PETSC_DOWNLOAD_C) --download-slepc
-# --download-slepc-commit=d3f7cd4a
 ifeq ($(WIN32DLLTARGET),)
-PETSC_DOWNLOAD := $(PETSC_DOWNLOAD) --download-hpddm --download-hpddm-commit=ce6ce80
-PETSC_DOWNLOAD_C := $(PETSC_DOWNLOAD_C) --download-hpddm --download-hpddm-commit=ce6ce80
+PETSC_DOWNLOAD := $(PETSC_DOWNLOAD) --download-hpddm
+PETSC_DOWNLOAD_C := $(PETSC_DOWNLOAD_C) --download-hpddm
 endif
 endif
 ifeq ($(FF_generic_petsc), yes)
@@ -91,17 +89,17 @@ ifeq ($(MPICC)$(MPICXX)$(MPIFC),)
 PETSC_DOWNLOAD += --with-cc='$(CC)' --with-cxx='$(CXX)' --download-mpich
 PETSC_DOWNLOAD_C += --with-mpi-dir=$(DIR_INSTALL_REAL)
 ifneq ($(FC),)
-PETSC_DOWNLOAD += --with-fc='$(FC)' --download-scalapack --download-mumps
-PETSC_DOWNLOAD_C += --with-scalapack-dir=$(DIR_INSTALL_REAL) --with-mumps-dir=$(DIR_INSTALL_REAL)
+PETSC_DOWNLOAD += --with-fc='$(FC)' --download-scalapack --download-mumps --download-slepc-configure-arguments="--download-arpack=https://github.com/prj-/arpack-ng/archive/6d11c37b2dc9110f3f6a434029353ae1c5112227.tar.gz"
+PETSC_DOWNLOAD_C += --with-scalapack-dir=$(DIR_INSTALL_REAL) --with-mumps-dir=$(DIR_INSTALL_REAL) # --download-slepc-configure-arguments="--with-arpack-dir=$(DIR_INSTALL_REAL)"
 else
 COMMON_FLAGS += --with-fc=0
 endif
 else
 COMMON_FLAGS += --with-cc='$(MPICC)' --with-cxx='$(MPICXX)'
 ifneq ($(MPIFC),)
 COMMON_FLAGS += --with-fc='$(MPIFC)'
-PETSC_DOWNLOAD += --download-scalapack --download-mumps
-PETSC_DOWNLOAD_C += --with-scalapack-dir=$(DIR_INSTALL_REAL) --with-mumps-dir=$(DIR_INSTALL_REAL)
+PETSC_DOWNLOAD += --download-scalapack --download-mumps --download-slepc-configure-arguments="--download-arpack=https://github.com/prj-/arpack-ng/archive/6d11c37b2dc9110f3f6a434029353ae1c5112227.tar.gz"
+PETSC_DOWNLOAD_C += --with-scalapack-dir=$(DIR_INSTALL_REAL) --with-mumps-dir=$(DIR_INSTALL_REAL) # --download-slepc-configure-arguments="--with-arpack-dir=$(DIR_INSTALL_REAL)"
 else
 COMMON_FLAGS += --with-fc=0
 PETSC_DOWNLOAD += --download-superlu_dist
@@ -114,6 +112,7 @@ COMMON_FLAGS += --with-shared-libraries=0 \
 	--with-cc='$(CC)' --with-cxx='$(CXX)' \
 	CXXFLAGS='-fno-stack-protector' \
 	CFLAGS='-fno-stack-protector' \
+	FFLAGS='$(FCFLAGS)' \
 	--with-mpi-lib='$(MPI_LIB)' \
 	--with-mpi-include='$(MPI_INC_DIR)' \
 	--with-mpiexec='/C/Program\ Files/Microsoft\ MPI/Bin/mpiexec'
@@ -123,8 +122,8 @@ PETSC_DOWNLOAD += '--download-metis-cmake-arguments=-G "MSYS Makefiles"' \
 	'--download-hypre-configure-arguments=--build=x86_64-linux-gnu --host=x86_64-linux-gnu'
 ifneq ($(FC),)
 COMMON_FLAGS += --with-fc='$(FC)'
-PETSC_DOWNLOAD += --download-scalapack --download-mumps
-PETSC_DOWNLOAD_C += --with-scalapack-dir=$(DIR_INSTALL_REAL) --with-mumps-dir=$(DIR_INSTALL_REAL)
+PETSC_DOWNLOAD += --download-scalapack --download-mumps --download-slepc-configure-arguments="--download-arpack=https://github.com/prj-/arpack-ng/archive/6d11c37b2dc9110f3f6a434029353ae1c5112227.tar.gz"
+PETSC_DOWNLOAD_C += --with-scalapack-dir=$(DIR_INSTALL_REAL) --with-mumps-dir=$(DIR_INSTALL_REAL) # --download-slepc-configure-arguments="--with-arpack-dir=$(DIR_INSTALL_REAL)"
 else
 COMMON_FLAGS += --with-fc=0
 endif
@@ -147,8 +146,8 @@ all-local:
 	@echo "	make petsc-slepc "
 
 DIRPKG=../pkg
-VERSION=3.13.5
-VERSION_SLEPC=3.13.3
+VERSION=3.14.0
+VERSION_SLEPC=3.013.4
 PACKAGE=../pkg/petsc-lite-$(VERSION).tar.gz
 SRCDIR=petsc-$(VERSION)
 MPI_DIR:=$(shell dirname $(MPI_INC_DIR))
@@ -296,9 +295,8 @@ WHERE-all:Makefile Make-petsc-download.mk
 endif
 $(SRCDIR)/tag-tar:$(PACKAGE)
 	-tar xzf $(PACKAGE)
-	patch -p1 < petsc-hpddm.patch
 ifeq ($(WIN32DLLTARGET),)
-	patch -p1 < petsc-metis.patch
+	cd petsc-$(VERSION) && patch -p1 < ../petsc-metis.patch && cd -
 endif
 	touch $@
 $(PACKAGE):

diff --git a/3rdparty/ff-petsc/petsc-hpddm.patch b/3rdparty/ff-petsc/petsc-hpddm.patch
diff --git a/3rdparty/ff-petsc/petsc-metis.patch b/3rdparty/ff-petsc/petsc-metis.patch
@@ -1,7 +1,7 @@
-diff --git a/petsc-3.13.5/config/BuildSystem/config/packages/metis.py b/petsc-3.13.5/config/BuildSystem/config/packages/metis.py
+diff --git a/config/BuildSystem/config/packages/metis.py b/config/BuildSystem/config/packages/metis.py
 index 136526da05..2d1c4d3271 100644
---- a/petsc-3.13.5/config/BuildSystem/config/packages/metis.py
-+++ b/petsc-3.13.5/config/BuildSystem/config/packages/metis.py
+--- a/config/BuildSystem/config/packages/metis.py
++++ b/config/BuildSystem/config/packages/metis.py
 @@ -44,6 +44,12 @@ class Configure(config.package.CMakePackage):
      if self.framework.argDB['download-metis-use-doubleprecision']:
        args.append('-DMETIS_USE_DOUBLEPRECISION=1')

diff --git a/3rdparty/getall b/3rdparty/getall
@@ -174,34 +174,34 @@ download('TetGen','http://www.tetgen.org/1.5/src/tetgen1.5.1-beta1.tar.gz',
 	'http://www.tetgen.org/1.5/src/',
 	'tetgen1.5.1-beta1.tar.gz',
 	'3d55c197bcbfc611b7ced6f343643756');
-download('mmg','https://github.com/MmgTools/mmg/archive/90371befa5271afd427d7bdbdec0a68284730805.zip',
+download('mmg','https://github.com/MmgTools/mmg/archive/f353d07ea55da617965806a39de8a6d76f3e020f.zip',
         'https://github.com/MmgTools',
         'mmg.zip',
-        'ee8e6592dc206af065c4fdfa28fd0d39');
-download('parmmg','https://github.com/MmgTools/ParMmg/archive/771743b153aba05f690ca7ee920d6fa2380dbb10.zip',
+        '031e09d35c433e1a5b2900c207cba344');
+download('parmmg','https://github.com/MmgTools/ParMmg/archive/f78f4e3e1019137787588aab7a8052fbc60dada2.zip',
         'https://github.com/MmgTools',
         'parmmg.zip',
-        'd085aaabf1c976a4ec7b7bc0c9191a6e');
-download('PETSc','https://www.mcs.anl.gov/petsc/mirror/release-snapshots/petsc-lite-3.13.5.tar.gz',
-	'https://www.mcs.anl.gov/petsc/mirror/release-snapshots',
-	'petsc-lite-3.13.5.tar.gz',
-	'41ef2cfbf21a755105ab81cacd0f7124');
+        '9a76fef6be1ab66af3a813409a0388c9');
+download('PETSc','https://www.mcs.anl.gov/petsc/mirror/release-snapshots/petsc-lite-3.14.0.tar.gz',
+	'https://www.mcs.anl.gov/petsc/mirror/release-snapshots/',
+	'petsc-lite-3.14.0.tar.gz',
+	'fb9f43e559e317160cb88265a3975bb5');
 
-download('htool','https://github.com/htool-ddm/htool/archive/71818cbf11b109c0c5a9bd3cdbcde76225a2e0b7.zip',
+download('htool','https://github.com/htool-ddm/htool/archive/e008e87bded5626d73fa7655487aee48268e2149.zip',
 		'https://github.com/htool-ddm/',
 		'htool.zip',
-		'9b349a67632d6110143ce174bd18d8b4');
+		'7ee614df188cf501c03c5f27d1569b1c');
 
 
-download('hpddm','https://github.com/hpddm/hpddm/archive/ce6ce80b62e9bc71efedf8b9cb6ffb00dfd6e44e.zip',
+download('hpddm','https://github.com/hpddm/hpddm/archive/882ec1041ed3e112237ceb6986ea0e79d335ade5.zip',
 	'https://github.com/hpddm',
 	'hpddm.zip',
-	'340f81270d5e16faa86a0372d10ce417');
+	'490275da4e47760a86e4747abd0306e7');
 
-download('bemtool','https://github.com/PierreMarchand20/BemTool/archive/c608875aca175b3bb424c50a9c13131aa7e2b257.zip',
+download('bemtool','https://github.com/PierreMarchand20/BemTool/archive/d327ef63c5abe88b13197c433a019e0db10eb426.zip',
 	'https://github.com/PierreMarchand20/BemTool',
 	'bemtool.zip',
-	'55b1890ce0d688c8694550857f2670da');
+	'70fcbea1f1bd2e8c8d9c44f59626f934');
 
 download('Boost','https://www.ljll.math.upmc.fr/~tournier/boost_for_bemtool.tar.gz',
 	'https://www.boost.org',

diff --git a/3rdparty/parmmg/Makefile b/3rdparty/parmmg/Makefile
@@ -29,6 +29,7 @@ FAIT.done:tag-tar
 	-DCMAKE_C_FLAGS="$(CFLAGS) -fPIC" \
 	-DCMAKE_CXX_COMPILER="$(CXX)" \
 	-DCMAKE_CXX_FLAGS="$(CXXFLAGS) $(CXX11FLAGS) -fPIC" \
+	-DCMAKE_Fortran_COMPILER="$(FC)" \
 	-DMPI_C_COMPILER="$(MPICC)" \
 	-DMPI_CXX_COMPILER="$(MPICXX)" \
 	-DMPI_Fortran_COMPILER="$(MPIFC)" \

diff --git a/AutoGeneratedFile.tar.gz b/AutoGeneratedFile.tar.gz
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -23,21 +23,24 @@
 # Changelog
 All notable changes to this project will be documented in this file.
 
-## [Unreleased]
-### Added
-
+## [4.7-1]
 ### Changed
-
-### Deprecated
+- change the language definition to use type as a construction function with named arguments for bem plugin
+- PETSc version 3.14.0
+- ARPACK compiled by SLEPc
+- Mmg version 5.5.0
+- -std=c++14 instead of -std=c++11 when possible
 
 ### Removed
-
+- plugins thresholdings, symmetrizeCSR, and fflapack and associed example
 
 ### Fixed
-
+- problem compilation with gfortran-10 of arpack and mumps (add -fallow-argument-mismatch flags)
 
 ## [4.7]
 ### Added
+
+- new way to build matrix beetween 2d Finite element 2d and Curve finite element to do mortar (Thank to Axel ) , see first example `examples/tutorial/mortar-DN-4-v4.5.edp`
 - add `Ns` normal vector  in R^3 on meshS (normal of the surface) of current point (to day Ns of [x,y,0] plan  is [0,0,-1])  no be compatibe to exterior normal. 
 - add `Tl` tangent vector in R^3 on meshL (tangent vector of the line/curve) of current point 
 - compile ffmaster / ffslave example under windows (thanks to johann@ifado.de)
@@ -337,14 +340,15 @@ All notable changes to this project will be documented in this file.
 ### Changed
 - The main distribution is now on Github
 
-[Unreleased]: https://github.com/FreeFem/FreeFem-sources/compare/v4.7..develop
+[Unreleased]: https://github.com/FreeFem/FreeFem-sources/compare/v4.7-1..develop
+[4.7-1]: https://github.com/FreeFem/FreeFem-sources/compare/v4.7...v4.7-1
 [4.7]: https://github.com/FreeFem/FreeFem-sources/compare/v4.6...v4.7
 [4.6]: https://github.com/FreeFem/FreeFem-sources/compare/v4.5...v4.6
 [4.5]: https://github.com/FreeFem/FreeFem-sources/compare/v4.4-3...v4.5
 [4.4-3]: https://github.com/FreeFem/FreeFem-sources/compare/v4.4-2...v4.4-3
 [4.4-2]: https://github.com/FreeFem/FreeFem-sources/compare/v4.4...v4.4-2
 [4.4]: https://github.com/FreeFem/FreeFem-sources/compare/v4.2.1...v4.4
-[4.2.1]: https://github.com/FreeFem/FreeFem-sources/compare/v4.0...v4.2.1
+[4.2.1]: https://github.com/FreeFem/FreeFem-sources/compare/v4.1...v4.2.1
 [4.1]: https://github.com/FreeFem/FreeFem-sources/compare/v4.0...v4.1
 [4.0]: https://github.com/FreeFem/FreeFem-sources/compare/3.62...v4.0
 [3.62]: https://github.com/FreeFem/FreeFem-sources/compare/3.61...3.62