Merge branch 'develop' of https://github.com/FreeFem/FreeFem-sources …

…into develop

3rdparty/ff-petsc/Makefile

@@ -27,7 +27,7 @@ PYTHON2?=python2.7
 include Makefile.inc
 mkfile_path := $(abspath $(lastword $(MAKEFILE_LIST)))
 dir3rdparty := $(abspath $(dir $(mkfile_path))/..)
- 
+
 W_SUDO:=$(SHELL mkdir -p "$(DESTDIR)$(FF_prefix_petsc)" && test -w "$(DESTDIR)$(FF_prefix_petsc) || echo sudo)
 W_SUDO1=$(SHELL ls	)
 ifeq ($(FF_generic_petsc), yes)
@@ -39,22 +39,22 @@ ifeq ($(WIN32DLLTARGET),)
 ##   Not on  windows ....
   FFWINDOWS=false
   WITH_SLEPC=yes
-  FLAGS_CONF_PETSC_REAL= 		--with-debugging=no \
+  FLAGS_CONF_PETSC_REAL= --with-debugging=no \
 		--with-cc='$(MPICC)' --with-cxx='$(MPICXX)' --with-fc='$(MPIFC)' \
 		COPTFLAGS='-O3  $(FLAGS_MTUNE)' \
 		CXXOPTFLAGS='-O3  $(FLAGS_MTUNE)' \
 		FOPTFLAGS='-O3  $(FLAGS_MTUNE)' \
 		CFLAGS=' $(FLAGS_MTUNE)' \
 		CXXFLAGS='$(FLAGS_MTUNE)' \
 		FFLAGS='$(FLAGS_MTUNE)' \
-        --with-ssl=0 --with-x=0 --with-fortran-bindings=0 \
+		--with-ssl=0 --with-x=0 --with-fortran-bindings=0 \
 		--with-scalar-type=real $(WITH_MPI_DIR) $(PETSC_ADDCONF) \
 		--with-blas-lapack-lib='$(BLAS_LAPACK_LIBS)' \
 		--download-scalapack --download-metis --download-ptscotch \
 		--download-mumps --download-ml --download-hypre --download-parmetis \
 		--download-superlu --download-suitesparse --download-fftw --download-slepc 
 
-FLAGS_CONF_PETSC_COMPLEX= 	--with-debugging=no \
+FLAGS_CONF_PETSC_COMPLEX= --with-debugging=no \
 		--with-cc='$(MPICC)' --with-cxx='$(MPICXX)' --with-fc='$(MPIFC)' \
 		COPTFLAGS='-O3  $(FLAGS_MTUNE)' \
 		CXXOPTFLAGS='-O3  $(FLAGS_MTUNE)' \
@@ -93,34 +93,33 @@ else
 	--with-ssl=0 --with-x=0 --with-debugging=0 \
 	--with-mpiexec='/C/Program\ Files/Microsoft\ MPI/Bin/mpiexec' \
 	--download-f2cblaslapack
-  #--download-slepc 
-  #	--with-blas-lapack-lib='/mingw64/lib/libopenblas.a' \
+  #--download-slepc
+  #--with-blas-lapack-lib='/mingw64/lib/libopenblas.a' \
+
 
-
  FLAGS_CONF_PETSC_COMPLEX= --with-python-exec=/usr/bin/python2 	--with-shared-libraries=0	--with-debugging=no \
 	--with-cc='$(CC)' --with-cxx='$(CXX)' --with-fc=0 \
 	COPTFLAGS='-O3  $(FLAGS_MTUNE) -D__int64=long\ long' \
 	CXXOPTFLAGS='-O3  $(FLAGS_MTUNE) -D__int64=long\ long' \
 	CFLAGS=' $(FLAGS_MTUNE) -D__int64=long\ long' \
 	CXXFLAGS='$(FLAGS_MTUNE) -D__int64=long\ long' \
 	--with-scalar-type=complex \
-    --with-mpi-lib='$(MPI_LIB)' \
+	--with-mpi-lib='$(MPI_LIB)' \
 	--with-mpi-include='$(MPI_INC_DIR)' \
 	--with-metis-lib=$(dir3rdparty)/lib/parmetis/libmetis.a \
 	--with-metis-include=$(dir3rdparty)/include/parmetis \
 	--download-suitesparse \
-	--with-ssl=0 --with-x=0 --with-debugging=0  \
+	--with-ssl=0 --with-x=0 --with-debugging=0 \
 	--with-mpiexec='/C/Program\ Files/Microsoft\ MPI/Bin/mpiexec' \
 	--download-f2cblaslapack
-#	--download-slepc 
-
+#	--download-slepc
 #	--with-suitesparse-include=$(dir3rdparty)/include \
 #	--with-suitesparse-lib='[$(dir3rdparty)/lib/libumfpack.a,$(dir3rdparty)/lib/libcholmod.a,$(dir3rdparty)/lib/libcolamd.a,$(dir3rdparty)/lib/libamd.a,$(dir3rdparty)/lib/libsuitesparseconfig.a]' \	--with-suitesparse-lib='[$(dir3rdparty)/lib/libumfpack.a,$(dir3rdparty)/lib/libcolmod.a,$(dir3rdparty)/lib/libcholamd.a,$(dir3rdparty)/lib/libamd.a,$(dir3rdparty)/lib/libsuitesparseconfig.a]' \
 
-   
+
 endif
 all-local:
-	@echo make .. 
+	@echo make ..
 	@echo " # To build petsc and slepc do $ make petsc-slepc"
 	@echo " # warning you have no write acces in $(DESTDIR)$(FF_prefix_petsc)"
 	@echo " # need sudo if '$(W_SUDO)' == 'sudo'  .." $(W_SUDO1)
@@ -134,7 +133,7 @@ all-local:
 # -------------------------------
 
 DIRPKG=../pkg
-VERSION=3.11.2
+VERSION=3.11.3
 VERSION_SLEPC=3.11.0
 PACKAGE=../pkg/petsc-lite-$(VERSION).tar.gz
 SRCDIR=petsc-$(VERSION)
@@ -269,28 +268,28 @@ endif
 ##  need include include Make-petsc-download.mk
 WHERE-all:Makefile WHERE WHERE-complex
 	echo >$@
-	test -z  '$(SCALAPACK_LIB)'  ||   echo scalapack LD $(SCALAPACK_LIB)  >>$@ 
-	test -z  '$(SCALAPACK_INCLUDE)'  ||    echo scalapack INCLUDE -I$(SCALAPACK_INCLUDE)  >>$@ 
-	test -z  '$(METIS_LIB)'  ||   echo metis LD $(METIS_LIB)  >>$@ 
-	test -z  '$(METIS_INCLUDE)'  ||   echo metis INCLUDE -I$(METIS_INCLUDE)  >>$@ 
-	test -z  '$(MUMPS_LIB)'  ||   echo mumps LD $(MUMPS_LIB)  >>$@ 
-	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)  >>$@ 
-	test -z  '$(FFTW_LIB)'  ||   echo fftw LD $(FFTW_LIB)  >>$@ 
-	test -z  '$(FFTW_INCLUDE)'  ||   echo fftw INCLUDE -I$(FFTW_INCLUDE)   >>$@ 
-	test -z  '$(PTSCOTCH_LIB)'  ||   echo ptscotch LD $(PTSCOTCH_LIB)  >>$@ 
-	test -z  '$(PTSCOTCH_INCLUDE)'  ||   echo ptscotch INCLUDE -I$(PTSCOTCH_INCLUDE)  >>$@ 
-	test -z  '$(PARMETIS_LIB)'  ||   echo parmetis LD $(PARMETIS_LIB) >>$@ 
-	test -z  '$(PARMETIS_INCLUDE)'  ||   echo parmetis INCLUDE -I$(PARMETIS_INCLUDE) >>$@ 
+	test -z  '$(SCALAPACK_LIB)'  ||   echo scalapack LD $(SCALAPACK_LIB)  >>$@
+	test -z  '$(SCALAPACK_INCLUDE)'  ||    echo scalapack INCLUDE -I$(SCALAPACK_INCLUDE)  >>$@
+	test -z  '$(METIS_LIB)'  ||   echo metis LD $(METIS_LIB)  >>$@
+	test -z  '$(METIS_INCLUDE)'  ||   echo metis INCLUDE -I$(METIS_INCLUDE)  >>$@
+	test -z  '$(MUMPS_LIB)'  ||   echo mumps LD $(MUMPS_LIB)  >>$@
+	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)  >>$@
+	test -z  '$(FFTW_LIB)'  ||   echo fftw LD $(FFTW_LIB)  >>$@
+	test -z  '$(FFTW_INCLUDE)'  ||   echo fftw INCLUDE -I$(FFTW_INCLUDE)   >>$@
+	test -z  '$(PTSCOTCH_LIB)'  ||   echo ptscotch LD $(PTSCOTCH_LIB)  >>$@
+	test -z  '$(PTSCOTCH_INCLUDE)'  ||   echo ptscotch INCLUDE -I$(PTSCOTCH_INCLUDE)  >>$@
+	test -z  '$(PARMETIS_LIB)'  ||   echo parmetis LD $(PARMETIS_LIB) >>$@
+	test -z  '$(PARMETIS_INCLUDE)'  ||   echo parmetis INCLUDE -I$(PARMETIS_INCLUDE) >>$@
 	echo 'petsc LD -Wl,-rpath,"$(DIR_INSTALL_REAL)/lib" -L"$(DIR_INSTALL_REAL)/lib" -lpetsc' >>$@
 	echo 'petsc INCLUDE -I"$(DIR_INSTALL_REAL)/include"'  >>$@
 	echo 'petsccomplex LD -Wl,-rpath,"$(DIR_INSTALL_COMPLEX)/lib" -L"$(DIR_INSTALL_COMPLEX)/lib" -lpetsc' >>$@
 	echo 'petsccomplex INCLUDE -I"$(DIR_INSTALL_COMPLEX)/include"'  >> $@
-	test  '$(WITH_SLEPC)' = yes ||  echo 'slepc LD -Wl,-rpath,"$(DIR_INSTALL_REAL)/lib" -L"$(DIR_INSTALL_REAL)/lib" -lslepc'  >>$@ 
-	test  '$(WITH_SLEPC)' = yes ||   echo 'slepc INCLUDE -I"$(DIR_INSTALL_REAL)/include"'   >>$@ 
-	test  '$(WITH_SLEPC)' = yes ||  echo 'slepccomplex LD -Wl,-rpath,"$(DIR_INSTALL_COMPLEX)/lib" -L"$(DIR_INSTALL_COMPLEX)/lib" -lslepc'  >>$@ 
-	test  '$(WITH_SLEPC)' = yes ||   echo 'slepccomplex INCLUDE -I"$(DIR_INSTALL_COMPLEX)/include"'  >>$@ 
+	test  '$(WITH_SLEPC)' = yes ||  echo 'slepc LD -Wl,-rpath,"$(DIR_INSTALL_REAL)/lib" -L"$(DIR_INSTALL_REAL)/lib" -lslepc'  >>$@
+	test  '$(WITH_SLEPC)' = yes ||   echo 'slepc INCLUDE -I"$(DIR_INSTALL_REAL)/include"'   >>$@
+	test  '$(WITH_SLEPC)' = yes ||  echo 'slepccomplex LD -Wl,-rpath,"$(DIR_INSTALL_COMPLEX)/lib" -L"$(DIR_INSTALL_COMPLEX)/lib" -lslepc'  >>$@
+	test  '$(WITH_SLEPC)' = yes ||   echo 'slepccomplex INCLUDE -I"$(DIR_INSTALL_COMPLEX)/include"'  >>$@
 
 #
 else
@@ -304,7 +303,7 @@ WHERE-all:Makefile  Make-petsc-download.mk
 endif
 $(SRCDIR)/tag-tar:$(PACKAGE)
 	tar xvzf $(PACKAGE)
-	patch -p1 < petsc-3.11.2.patch
+	patch -p1 < petsc-metis.patch
 	touch $@
 $(PACKAGE):
 	../getall -o PETSc -a
@@ -335,7 +334,7 @@ ifeq ($(WITH_SLEPC),yes)
 	echo 'slepc LD -Wl,-rpath,"$(DIR_INSTALL_REAL)/lib" -L"$(DIR_INSTALL_REAL)/lib" -lslepc' > $@
 	echo 'slepc INCLUDE -I"$(DIR_INSTALL_REAL)/include"' >> $@
 else
-	echo "sorry no SLEPC" 
+	echo "sorry no SLEPC"
 endif
 
 clean:clean-local

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

@@ -0,0 +1,12 @@
+diff --git a/petsc-3.11.3/config/BuildSystem/config/packages/metis.py b/petsc-3.11.3/config/BuildSystem/config/packages/metis.py
+index 136526da05..2d1c4d3271 100644
+--- a/petsc-3.11.3/config/BuildSystem/config/packages/metis.py
++++ b/petsc-3.11.3/config/BuildSystem/config/packages/metis.py
+@@ -42,6 +42,7 @@ class Configure(config.package.CMakePackage):
+     if self.framework.argDB['download-metis-use-doubleprecision']:
+       args.append('-DMETIS_USE_DOUBLEPRECISION=1')
+     args.append('-DMATH_LIB="'+self.libraries.toStringNoDupes(self.mathlib.lib)+'"')
++    args = self.rmArgsStartsWith(args,['-DCMAKE_CXX_COMPILER','-DCMAKE_C_COMPILER'])
+     return args
+
+   def configureLibrary(self):

3rdparty/getall

@@ -175,10 +175,10 @@ download('TetGen','http://www.tetgen.org/1.5/src/tetgen1.5.1-beta1.tar.gz',
 	'tetgen1.5.1-beta1.tar.gz',
 	'3d55c197bcbfc611b7ced6f343643756');
 
-download('PETSc','http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.11.2.tar.gz',
+download('PETSc','http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.11.3.tar.gz',
 	'http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/',
-	'petsc-lite-3.11.2.tar.gz',
-	'ccd4f1e07edc453a74b52fd9a0c52a1c');
+	'petsc-lite-3.11.3.tar.gz',
+	'e04cbb1aaccde4a33c8843e75a1fba15');
 
 download('htool','https://github.com/PierreMarchand20/htool/archive/4af73fa94bd9ac7c81aba8191cb5da31da5f767a.zip',
 		'https://github.com/PierreMarchand20/',

configure.ac

@@ -84,9 +84,6 @@ m4_define([AC_FF_PETSC_WHERELIB],
 	  [
 	    ff_$2=`AC_FF_PETSC_AWK($2,$4)`
 	    ff_$3=`AC_FF_PETSC_AWK($3,$4)`
-		if test -n "$5" ; then 
-		   ff_$2="[$]ff_$2 `AC_FF_PETSC_AWK($5,$4)`"
-		fi
 	   if test -n "[$]ff_$2"; then
 			    ff_$1_ok=yes;
 			    AC_FF_ADDWHERELIB($1,[$]ff_$2,[$]ff_$3)
@@ -989,8 +986,8 @@ if test "$with_petsc" != no -a  $ff_mpi = yes; then
 		    test  "$PETSC_SCALAR" = "real" && test "$ff_win32" = yes -o  "$PETSC_MPIRUN" = "$MPIRUN" ||  cmp -s "$WPETSC_MPIRUN" "$WMPIRUN"
 		    if test "$?"  -eq 0 ; then
 		        AC_FF_PETSC_WHERELIB_BASIC(petsc,$ffconfpetsc)
-		        AC_FF_PETSC_WHERELIB(parmetis,PARMETIS_LIB,PARMETIS_INCLUDE,$ffconfpetsc,METIS_LIB)
-dnl		        AC_FF_PETSC_WHERELIB(metis,METIS_LIB,METIS_INCLUDE,$ffconfpetsc)
+		        AC_FF_PETSC_WHERELIB(parmetis,PARMETIS_LIB,PARMETIS_INCLUDE,$ffconfpetsc)
+		        AC_FF_PETSC_WHERELIB(metis,METIS_LIB,METIS_INCLUDE,$ffconfpetsc)
 		        AC_FF_PETSC_WHERELIB(ptscotch,PTSCOTCH_LIB,PTSCOTCH_INCLUDE,$ffconfpetsc)
                 ff_SCOTCH_INCLUDE=$ff_PTSCOTCH_INCLUDE
                 ff_SCOTCH_LIB=`echo $ff_PTSCOTCH_LIB | sed -e 's/@<:@^ @:>@*ptscotch@<:@^ @:>@*//g' | sed -e 's/@<:@^ @:>@*ptes@<:@^ @:>@*//g'`
@@ -1047,8 +1044,8 @@ if test "$with_petsc_complex" != no -a  $ff_mpi = yes; then
 		    test  "$PETSC_COMPLEX_SCALAR" = "complex" &&  test  "$ff_win32" = yes -o  "$PETSC_COMPLEX_MPIRUN" = "$MPIRUN" ||  cmp -s `which "$PETSC_COMPLEX_MPIRUN"` `which "$MPIRUN"`
 		   	if test "$?"  -eq 0 ; then
 			AC_FF_PETSC_WHERELIB_BASIC(petsccomplex,$ffconfpetscc)
-            AC_FF_PETSC_WHERELIB(parmetis,PARMETIS_LIB,PARMETIS_INCLUDE,$ffconfpetscc,METIS_LIB)
-dnl            AC_FF_PETSC_WHERELIB(metis,METIS_LIB,METIS_INCLUDE,$ffconfpetscc)
+            AC_FF_PETSC_WHERELIB(parmetis,PARMETIS_LIB,PARMETIS_INCLUDE,$ffconfpetscc)
+            AC_FF_PETSC_WHERELIB(metis,METIS_LIB,METIS_INCLUDE,$ffconfpetscc)
             AC_FF_PETSC_WHERELIB(ptscotch,PTSCOTCH_LIB,PTSCOTCH_INCLUDE,$ffconfpetscc)
             ff_SCOTCH_INCLUDE=$ff_PTSCOTCH_INCLUDE
             ff_SCOTCH_LIB=`echo $ff_PTSCOTCH_LIB | sed -e 's/@<:@^ @:>@*ptscotch@<:@^ @:>@*//g' | sed -e 's/@<:@^ @:>@*ptes@<:@^ @:>@*//g'`

idp/ffddm.idp

@@ -32,8 +32,6 @@ IFMACRO(WITHHPDDM)
 load "hpddm"
 ENDIFMACRO
 
-load "thresholdings"
-
 include "ffddm_partitioning.idp"
 
 include "ffddm_coarsemeshCS.idp"

idp/macro_ddm.idp

@@ -1,4 +1,3 @@
-load "thresholdings"
 include "getARGV.idp"
 IFMACRO(!partitioner)
 macro partitioner()metis// EOM