Merge pull request #173 from FreeFem/develop

Version 4.9

3rdparty/Makefile.am

@@ -41,6 +41,7 @@ EXTRA_DIST= \
 ./scotch/Makefile-scotch.inc \
 ./scotch/scotch_6.0.4.patch \
 ./superlu/Makefile \
+./superlu/patch-superlu-5.2.2 \
 ./superlu/make.inc \
 ./tetgen/Makefile \
 ./mmg/Makefile \

3rdparty/ff-petsc/Makefile

@@ -39,7 +39,10 @@ PETSC_OPENBLAS_C = $(PETSC_OPENBLAS)
 endif
 PETSC_DOWNLOAD_C := --with-metis-dir=$(DIR_INSTALL_REAL) \
 		--with-ptscotch-dir=$(DIR_INSTALL_REAL) \
-		--with-suitesparse-include='$(SUITESPARSE_INCLUDE)' --with-suitesparse-lib='$(SUITESPARSE_LIB)' \
+		--with-mmg-dir=$(DIR_INSTALL_REAL) \
+		--with-parmmg-dir=$(DIR_INSTALL_REAL) \
+		--with-superlu-dir=$(DIR_INSTALL_REAL) \
+		--with-suitesparse-dir=$(DIR_INSTALL_REAL) \
 		--with-parmetis-dir=$(DIR_INSTALL_REAL) \
 		--with-tetgen-dir=$(DIR_INSTALL_REAL)
 ifeq ($(PETSC_PKG),yes)
@@ -66,16 +69,13 @@ endif
 else
 PETSC_DOWNLOAD := --download-metis --download-ptscotch \
 		--download-hypre --download-parmetis \
+		--download-mmg --download-parmmg \
 		--download-superlu --download-suitesparse --download-tetgen \
-		--download-slepc
+		--download-slepc --download-hpddm
 ifeq ($(FFCMAKE),no)
 PETSC_DOWNLOAD := $(PETSC_DOWNLOAD) --download-cmake
 endif
-PETSC_DOWNLOAD_C := $(PETSC_DOWNLOAD_C) --download-slepc
-ifeq ($(WIN32DLLTARGET),)
-PETSC_DOWNLOAD := $(PETSC_DOWNLOAD) --download-hpddm
-PETSC_DOWNLOAD_C := $(PETSC_DOWNLOAD_C) --download-hpddm
-endif
+PETSC_DOWNLOAD_C := $(PETSC_DOWNLOAD_C) --download-slepc --download-hpddm
 endif
 ifeq ($(FF_generic_petsc), yes)
 FLAGS_MTUNE := -mtune=generic
@@ -89,7 +89,7 @@ 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 --download-slepc-configure-arguments="--download-arpack=https://github.com/prj-/arpack-ng/archive/6d11c37b2dc9110f3f6a434029353ae1c5112227.tar.gz"
+PETSC_DOWNLOAD += --with-fc='$(FC)' --download-scalapack --download-mumps --download-slepc-configure-arguments="--download-arpack=https://github.com/prj-/arpack-ng/archive/b64dccb.tar.gz"
 PETSC_DOWNLOAD_C += --with-scalapack-dir=$(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
@@ -98,7 +98,7 @@ else
 COMMON_FLAGS += --with-cc='$(MPICC)' --with-cxx='$(MPICXX)'
 ifneq ($(MPIFC),)
 COMMON_FLAGS += --with-fc='$(MPIFC)'
-PETSC_DOWNLOAD += --download-scalapack --download-mumps --download-slepc-configure-arguments="--download-arpack=https://github.com/prj-/arpack-ng/archive/6d11c37b2dc9110f3f6a434029353ae1c5112227.tar.gz"
+PETSC_DOWNLOAD += --download-scalapack --download-mumps --download-slepc-configure-arguments="--download-arpack=https://github.com/prj-/arpack-ng/archive/b64dccb.tar.gz"
 PETSC_DOWNLOAD_C += --with-scalapack-dir=$(DIR_INSTALL_REAL) --with-mumps-dir=$(DIR_INSTALL_REAL) # --download-slepc-configure-arguments="--with-arpack-dir=$(DIR_INSTALL_REAL)"
 else
 COMMON_FLAGS += --with-fc=0
@@ -118,6 +118,8 @@ COMMON_FLAGS += --with-shared-libraries=0 \
 	--with-mpiexec='/C/Program\ Files/Microsoft\ MPI/Bin/mpiexec'
 PETSC_DOWNLOAD += '--download-metis-cmake-arguments=-G "MSYS Makefiles"' \
 	'--download-parmetis-cmake-arguments=-G "MSYS Makefiles"' \
+	'--download-mmg-cmake-arguments=-G "MSYS Makefiles"' \
+	'--download-parmmg-cmake-arguments=-DMPI_GUESS_LIBRARY_NAME=MSMPI -G "MSYS Makefiles"' \
 	'--download-superlu-cmake-arguments=-G "MSYS Makefiles"' \
 	'--download-hypre-configure-arguments=--build=x86_64-linux-gnu --host=x86_64-linux-gnu'
 ifneq ($(FC),)
@@ -146,9 +148,9 @@ all-local:
 	@echo "	make petsc-slepc "
 
 DIRPKG=../pkg
-VERSION=3.14.2
-VERSION_SLEPC=3.14.0
-PACKAGE=../pkg/petsc-lite-$(VERSION).tar.gz
+VERSION=3.15.0
+VERSION_SLEPC=3.014.2
+PACKAGE=../pkg/petsc-$(VERSION).tar.gz
 SRCDIR=petsc-$(VERSION)
 MPI_DIR:=$(shell dirname $(MPI_INC_DIR))
 W_MPICC:=$(strip $(shell which mpicc))
@@ -223,7 +225,7 @@ $(SRCDIR)/tag-conf-real:$(SRCDIR)/tag-tar
 	touch $@
 Make-petsc-download.mk:$(SRCDIR)/tag-install-real 
 	test -e $(DIR_INSTALL_REAL)/lib/petsc/conf/petscvariables
-	egrep 'PETSC_LIB_BASIC|SCALAPACK_|METIS_|MUMPS_|HPDDM_|TETGEN_|SUPERLU_|PTSCOTCH_|SUITESPARSE_' $(DIR_INSTALL_REAL)/lib/petsc/conf/petscvariables | sed 's/-I/ /g'|sort >$@
+	egrep 'PETSC_LIB_BASIC|SCALAPACK_|METIS_|MUMPS_|HPDDM_|TETGEN_|SUPERLU_|MMG_|PTSCOTCH_|SUITESPARSE_' $(DIR_INSTALL_REAL)/lib/petsc/conf/petscvariables | sed 's/-I/ /g'|sort >$@
 ifdef 	COMPLEX_CASE
 #  version COMPLEX.....
 $(SRCDIR)/tag-conf-complex:$(SRCDIR)/tag-tar Make-petsc-download.mk
@@ -266,6 +268,10 @@ WHERE-all:Makefile WHERE WHERE-complex
 	test -z '$(MUMPS_INCLUDE)' || echo mumps INCLUDE -I$(MUMPS_INCLUDE) >>$@
 	test -z '$(SUPERLU_LIB)' || echo superlu LD $(SUPERLU_LIB) >>$@
 	test -z '$(SUPERLU_INCLUDE)' || echo superlu INCLUDE -I$(SUPERLU_INCLUDE) >>$@
+	test -z '$(MMG_LIB)' || echo mmg LD $(MMG_LIB) >>$@
+	test -z '$(MMG_INCLUDE)' || echo mmg INCLUDE -I$(MMG_INCLUDE) >>$@
+	test -z '$(PARMMG_LIB)' || echo parmmg LD $(PARMMG_LIB) >>$@
+	test -z '$(PARMMG_INCLUDE)' || echo parmmg INCLUDE -I$(PARMMG_INCLUDE) >>$@
 	test -z '$(PTSCOTCH_LIB)' || echo ptscotch LD $(PTSCOTCH_LIB) >>$@
 	test -z '$(PTSCOTCH_INCLUDE)' || echo ptscotch INCLUDE -I$(PTSCOTCH_INCLUDE) >>$@
 	test -z '$(TETGEN_LIB)' || echo tetgen LD $(TETGEN_LIB) >>$@
@@ -298,6 +304,7 @@ $(SRCDIR)/tag-tar:$(PACKAGE)
 ifeq ($(WIN32DLLTARGET),)
 	cd petsc-$(VERSION) && patch -p1 < ../petsc-metis.patch && cd -
 endif
+	cd petsc-$(VERSION) && patch -p1 < ../petsc-suitesparse.patch && cd -
 	touch $@
 $(PACKAGE):
 	../getall -o PETSc -a

3rdparty/ff-petsc/petsc-suitesparse.patch

@@ -0,0 +1,40 @@
+diff --git b/config/BuildSystem/config/packages/SuiteSparse.py a/config/BuildSystem/config/packages/SuiteSparse.py
+index e9c7c7d3b2..3de634af59 100644
+--- b/config/BuildSystem/config/packages/SuiteSparse.py
++++ a/config/BuildSystem/config/packages/SuiteSparse.py
+@@ -4,7 +4,7 @@ class Configure(config.package.Package):
+   def __init__(self, framework):
+     config.package.Package.__init__(self,framework)
+     self.minversion        = '5.6.0'
+-    self.version           = '5.8.1'
++    self.version           = '5.7.1'
+     self.versioninclude    = 'SuiteSparse_config.h'
+     self.versionname       = 'SUITESPARSE_MAIN_VERSION.SUITESPARSE_SUB_VERSION.SUITESPARSE_SUBSUB_VERSION'
+     self.gitcommit         = 'v'+self.version
+@@ -59,7 +59,7 @@ class Configure(config.package.Package):
+       ldflags=self.getDynamicLinkerFlags()
+     else:
+       ldflags=''
+-    ldflags += ' '+self.setCompilers.LDFLAGS
++    ldflags+=self.setCompilers.LDFLAGS
+     # SuiteSparse 5.6.0 makefile has a bug in how it treats LDFLAGS (not using the override directive)
+     ldflags+=" -L\$(INSTALL_LIB)"
+     self.popLanguage()
+@@ -81,9 +81,6 @@ class Configure(config.package.Package):
+     args.append('INSTALL_DOC='+self.installDir+'/share/doc/suitesparse')
+     args.append('BLAS="'+self.libraries.toString(self.blasLapack.dlib)+'"')
+     args.append('LAPACK="'+self.libraries.toString(self.blasLapack.dlib)+'"')
+-    # fix for bug in SuiteSparse
+-    if self.setCompilers.isDarwin(self.log):
+-      args.append('LDLIBS=""')
+     if self.blasLapack.mangling == 'underscore':
+       flg = ''
+     elif self.blasLapack.mangling == 'caps':
+@@ -129,7 +126,6 @@ class Configure(config.package.Package):
+       args.append('CF="'+cflags+'"')
+       args.append('CHOLMOD_CONFIG="'+flg+'"')
+       args.append('CUDA=no')
+-      args.append('CUDA_PATH=')
+
+     args = ' '.join(args)
+     conffile = os.path.join(self.packageDir,self.package+'.petscconf')

3rdparty/getall

@@ -99,20 +99,6 @@ download('OpenBLAS','https://github.com/xianyi/OpenBLAS/archive/v0.3.6.tar.gz',
 	'8a110a25b819a4b94e8a9580702b6495',
 	'BAD_CERT');
 
-# downloading the binary package is required for Windows because
-# compiling requires big amounts of RAM (more than 4GB). This is not a
-# big package so we download it in any situation just in case an
-# offline Windows compile follows.
-
-download('OpenBLAS-Win64','http://downloads.sourceforge.net/project/openblas/v0.2.14/OpenBLAS-v0.2.14-Win64-int64.zip',
-	'http://www.openblas.net/',
-	'OpenBLAS-v0.2.14-Win64-int64.zip',
-	'9f2d41076857a514b921bf0bf03b5d39');
-download('OpenBLAS-Win32','http://downloads.sourceforge.net/project/openblas/v0.2.14/OpenBLAS-v0.2.14-Win32.zip',
-	'http://www.openblas.net/',
-	'OpenBLAS-v0.2.14-Win32.zip',
-	'eefdf170439620d78fabb3139b7aeb2f');
-
 download('FFTW','http://www.fftw.org/fftw-3.3.8.tar.gz',
 	'http://www.fftw.org',
 	'fftw-3.3.8.tar.gz','8aac833c943d8e90d51b697b27d4384d');
@@ -153,23 +139,26 @@ download('NLopt','http://ab-initio.mit.edu/nlopt/nlopt-2.2.4.tar.gz',
 	'http://ab-initio.mit.edu/wiki/index.php/NLopt',
 	'nlopt-2.2.4.tar.gz',
 	'9c60c6380a10c6d2a06895f0e8756d4f');
-download('ScaLAPACK','http://www.netlib.org/scalapack/scalapack-2.0.2.tgz',
+download('ScaLAPACK','http://www.netlib.org/scalapack/scalapack-2.1.0.tgz',
 	'http://www.netlib.org/scalapack/',
-	'scalapack-2.0.2.tgz',
-	'2f75e600a2ba155ed9ce974a1c4b536f');
-download('Scotch','https://gforge.inria.fr/frs/download.php/file/34618/scotch_6.0.4.tar.gz',
-	'https://gforge.inria.fr/projects/scotch/',
-	'scotch_6.0.4.tar.gz',
-	'd58b825eb95e1db77efe8c6ff42d329f',
-	'BAD_CERT'); # web certificate from gforge.inria.fr is rejected
+	'scalapack-2.1.0.tgz',
+	'3b239ef80353c67354a0a62d54946fa8');
+download('Scotch','https://gitlab.inria.fr/scotch/scotch/-/archive/v6.1.0/scotch-v6.1.0.tar.gz',
+	'https://gitlab.inria.fr/scotch/',
+	'scotch-v6.1.0.tar.gz',
+	'7bfad4aaa851af6815b2160da7ebe36a'); # web certificate from gforge.inria.fr is rejected
 download('SuiteSparse','http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.4.4.tar.gz',
 	'http://faculty.cse.tamu.edu/davis/SuiteSparse/',
 	'SuiteSparse-4.4.4.tar.gz',
 	'e0af74476935c9ff6d971df8bb6b82fc') ;
-download('SuperLU','https://github.com/xiaoyeli/superlu/archive/4f2da83a24c52641c1f7ab06f57c00b8954cf215.zip',
-	'https://github.com/xiaoyeli/superlu',
-	'superlu.zip',
-	'596927f39d28a7d6eb396764f46455b2');
+#download('SuperLU','https://github.com/xiaoyeli/superlu/archive/4f2da83a24c52641c1f7ab06f57c00b8954cf215.zip',
+#	'https://github.com/xiaoyeli/superlu',
+#	'superlu.zip',
+#	'596927f39d28a7d6eb396764f46455b2');
+download('SuperLU','https://github.com/xiaoyeli/superlu/archive/v5.2.2.zip',
+		'https://github.com/xiaoyeli/superlu',
+		'superlu-5.2.2.zip',
+		'6e24842b0aa07f457d929b162e09ca6c');
 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',
@@ -182,21 +171,21 @@ download('parmmg','https://github.com/MmgTools/ParMmg/archive/f78f4e3e1019137787
         'https://github.com/MmgTools',
         'parmmg.zip',
         '9a76fef6be1ab66af3a813409a0388c9');
-download('PETSc','https://www.mcs.anl.gov/petsc/mirror/release-snapshots/petsc-lite-3.14.2.tar.gz',
+download('PETSc','https://www.mcs.anl.gov/petsc/mirror/release-snapshots/petsc-3.15.0.tar.gz',
 	'https://www.mcs.anl.gov/petsc/mirror/release-snapshots/',
-	'petsc-lite-3.14.2.tar.gz',
-	'c3433f6f5f4ad8d5823ca69dd0c2f3e6');
+	'petsc-3.15.0.tar.gz',
+	'32cdb2a2aed1be52059f6221a41d2b18');
 
 download('htool','https://github.com/htool-ddm/htool/archive/e008e87bded5626d73fa7655487aee48268e2149.zip',
 		'https://github.com/htool-ddm/',
 		'htool.zip',
 		'7ee614df188cf501c03c5f27d1569b1c');
 
 
-download('hpddm','https://github.com/hpddm/hpddm/archive/882ec1041ed3e112237ceb6986ea0e79d335ade5.zip',
-	'https://github.com/hpddm',
+download('hpddm','https://codeload.github.com/hpddm/hpddm/zip/e58205623814f59bf2aec2e2bab8eafcfbd22466',
+	'https://codeload.github.com/hpddm',
 	'hpddm.zip',
-	'490275da4e47760a86e4747abd0306e7');
+	'b7a4f9be6de2df302485c4689a6c8078');
 
 download('bemtool','https://github.com/PierreMarchand20/BemTool/archive/d327ef63c5abe88b13197c433a019e0db10eb426.zip',
 	'https://github.com/PierreMarchand20/BemTool',

3rdparty/scalapack/Makefile

@@ -12,8 +12,8 @@ all-local: scalapack
 # http://www.netlib.org/scalapack/
 # Hips information
 DIRPKG=../pkg
-SRCDIR=scalapack-2.0.2
-PACKAGE1=$(DIRPKG)/scalapack-2.0.2.tgz
+SRCDIR=scalapack-2.1.0
+PACKAGE1=$(DIRPKG)/scalapack-2.1.0.tgz
 SERVER=http://www.netlib.org/scalapack/
 INSTALL=../..
 
@@ -62,8 +62,6 @@ SLmake.inc: ../../config.status	Makefile SLmake-scalapack.inc
 
 $(SRCDIR)/tag-tar: $(PACKAGE1)
 	gunzip -c $(PACKAGE1) | tar xf -
-	#  fto pach 
-	patch -p0 <scalapack.patch
 	touch $(SRCDIR)/tag-tar
 
 $(PACKAGE1):

3rdparty/scalapack/SLmake-scalapack.inc

@@ -33,7 +33,7 @@ NOOPT         = -O0 @CNOFLAGS@
 # FFCS - some return statements without value cause trouble on MacOS
 # FFCS - add path to mpi.h (required for MacOS 10.8 + MacPorts OpenMPI)
 # FFCS - added @CNOFLAGS@ according to upstream changes
-CCFLAGS       = -O3 -Wreturn-type @CFLAGS@ -I'@MPI_INC_DIR@' @CNOFLAGS@
+CCFLAGS       = -O3 -Wreturn-type @CFLAGS@ -I'@MPI_INC_DIR@' @CNOFLAGS@ -Wno-implicit-function-declaration
 FCFLAGS       = -O3 @CNOFLAGS@
 FCLOADER      = $(FC)
 CCLOADER      = $(CC)