Merge pull request #165 from FreeFem/develop

Version 4.8

Author: prj-

3rdparty/ff-petsc/Makefile

@@ -146,8 +146,8 @@ all-local:
 	@echo "	make petsc-slepc "
 
 DIRPKG=../pkg
-VERSION=3.14.0
-VERSION_SLEPC=3.013.4
+VERSION=3.14.2
+VERSION_SLEPC=3.14.0
 PACKAGE=../pkg/petsc-lite-$(VERSION).tar.gz
 SRCDIR=petsc-$(VERSION)
 MPI_DIR:=$(shell dirname $(MPI_INC_DIR))

3rdparty/getall

@@ -174,18 +174,18 @@ 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/f353d07ea55da617965806a39de8a6d76f3e020f.zip',
+download('mmg','https://github.com/MmgTools/mmg/archive/a90b665e909a3921490d3e281f7afa2d243a5ba0.zip',
         'https://github.com/MmgTools',
         'mmg.zip',
-        '031e09d35c433e1a5b2900c207cba344');
+        'd824d08dac0544caff20a915194da0fe');
 download('parmmg','https://github.com/MmgTools/ParMmg/archive/f78f4e3e1019137787588aab7a8052fbc60dada2.zip',
         'https://github.com/MmgTools',
         'parmmg.zip',
         '9a76fef6be1ab66af3a813409a0388c9');
-download('PETSc','https://www.mcs.anl.gov/petsc/mirror/release-snapshots/petsc-lite-3.14.0.tar.gz',
+download('PETSc','https://www.mcs.anl.gov/petsc/mirror/release-snapshots/petsc-lite-3.14.2.tar.gz',
 	'https://www.mcs.anl.gov/petsc/mirror/release-snapshots/',
-	'petsc-lite-3.14.0.tar.gz',
-	'fb9f43e559e317160cb88265a3975bb5');
+	'petsc-lite-3.14.2.tar.gz',
+	'c3433f6f5f4ad8d5823ca69dd0c2f3e6');
 
 download('htool','https://github.com/htool-ddm/htool/archive/e008e87bded5626d73fa7655487aee48268e2149.zip',
 		'https://github.com/htool-ddm/',

3rdparty/ipopt/Makefile

@@ -49,7 +49,7 @@ $(SRCDIR)/FAIT: $(SRCDIR)/tag-tar
 	  CC='$(CC)' CFLAGS='$(CFLAGS) -I$(INCMUMPS)' \
 	  F77='$(FC)' FFLAGS='$(FCFLAGS)' \
 	  FLIBS='$(FLIBS)' \
-	  CXXCPP='$(CXXCPP)'  CPP='$(CXXCPP)' \
+	  CXXCPP='$(CXXCPP)'  CPP='$(CXXCPP)' MPICC='' MPICXX='' MPIFC='' \
 	 --with-blas-lib='$(LIBBLAS)' --with-lapack='$(LIBLAPACK)' --prefix='$(DOWNLOADFF)'
 	 -rm -rf ../include/coin
 	touch $(SRCDIR)/FAIT	

3rdparty/mmg/Makefile

@@ -38,8 +38,6 @@ install.done:FAIT.done
 	cp -r build/include/mmg ../include/mmg
 	cp build/lib/libmmg.a ../lib
 	touch $@
-clean::
-	-rm install.done FAIT.done
 
 mmg:$(PACKAGE)
 
@@ -67,14 +65,16 @@ $(PACKAGE): FORCE
 FORCE:
 
 clean::
-	-rm ff-flags
+	-rm ff-flags *.done 
 	-rm FAIT* 
 	-rm -rf mmg-* build
 	-rm flags-* tag-tar*
 	-rm -rf ../include/mmg
 	-rm ../lib/libmmg.a
 
-ff-flags: ../Makefile Makefile
+ff-flags: ../Makefile Makefile ../getall
+	../getall -o mmg -a
+	-cp -f ff-flags ff-flags.old
 	grep 'abs_top_builddir *=' ../Makefile > ff-flags
 	grep 'CC *=' ../Makefile >> ff-flags
 	grep 'CFLAGS *=' ../Makefile >> ff-flags
@@ -92,5 +92,7 @@ ff-flags: ../Makefile Makefile
 	grep 'FF_prefix_petsc_real *=' ../Makefile >> ff-flags
 	-awk '/^scotch LD /&&/petsc/ {print "scotch_dir=$$(FF_prefix_petsc_real)" }' ../../plugin/seq/WHERE_LIBRARY-config >> ff-flags
 	-awk '/^scotch LD /{print "scotch_dir=../../../3rdparty/" }' ../lib/WHERE.scotch >> ff-flags
+	../../bin/ff-md5 $(PACKAGE) >> ff-flags	
+	if diff -q ff-flags ff-flags.old ; then echo No Modif skip compile of mmg ; else touch -c tag-tar; fi
 
 .PHONY:$(SRCDIR)/$(INSTALL)

3rdparty/parmmg/Makefile

@@ -82,7 +82,9 @@ clean::
 	-rm -rf ../include/parmmg
 	-rm ../lib/libparmmg.a
 
-ff-flags: ../Makefile Makefile
+ff-flags: ../Makefile Makefile ../getall
+	../getall -o parmmg -a
+	-cp -f ff-flags ff-flags.old
 	grep 'abs_top_builddir *=' ../Makefile > ff-flags
 	grep 'CC *=' ../Makefile >> ff-flags
 	grep 'FC *=' ../Makefile >> ff-flags
@@ -107,5 +109,7 @@ ff-flags: ../Makefile Makefile
 	-awk '/^scotch LD /{print "scotch_dir=../../../3rdparty/" }' ../lib/WHERE.scotch >> ff-flags
 	-awk '/^metis LD /&&/petsc/ {print "metis_dir=$$(FF_prefix_petsc_real)" }' ../../plugin/seq/WHERE_LIBRARY-config >> ff-flags
 	-awk '/^metis LD /{print "metis_dir=../../../3rdparty/" }' ../lib/WHERE.metis >> ff-flags
+	../../bin/ff-md5 $(PACKAGE) >> ff-flags	
+	if diff -q ff-flags ff-flags.old ; then echo No Modif skip compile of parmmg ; else touch -c tag-tar; fi
 
 .PHONY:$(SRCDIR)/$(INSTALL)

3rdparty/tetgen/Makefile

@@ -21,28 +21,28 @@ INSTALL=../..
 tetgen: FAIRE 
 
 
-FAIRE:install.done $(SRCDIR)/FAIT cxxflags WHERE.done
+FAIRE:install.done WHERE.done
 	touch FAIRE
 
 
 # ALH - FFCS - 18/12/8 - need '-fPIC' on Linux64 because the .a will be used in a .so (by examples++-load/tetgen.cpp).
 
 # FFCS - 30/11/10 - need ranlib on Win64. The PATH is setup so that mingw/ranlib is called
 
-$(SRCDIR)/FAIT: $(SRCDIR)/tags  cxxflags 
+fait-tags.done:tar-tags.done cxxflags 
 	cd $(SRCDIR);$(CXX) $(CXXFLAGS) -O3 -fPIC -DSELF_CHECK  -DNDEBUG -DTETLIBRARY -c tetgen.cxx
 	cd $(SRCDIR);$(CXX) $(CXXFLAGS) -O0 -fPIC -DSELF_CHECK  -DNDEBUG -DTETLIBRARY -c predicates.cxx
-	touch $(SRCDIR)/FAIT
+	touch fait-tags.done
 WHERE:WHERE.done
-WHERE.done: $(SRCDIR)/FAIT
+WHERE.done: fait-tags.done
 	echo tetgen LD -L@DIR@/lib -ltet  >$(SRCDIR)/$(INSTALL)/lib/WHERE.tetgen
 	echo tetgen  INCLUDE -I@DIR@/include >> $(SRCDIR)/$(INSTALL)/lib/WHERE.tetgen
 	touch $@
 clean-local::
 	-rm WHERE.done
 
 # FFCS - avoid remaking install every time
-install.done:$(SRCDIR)/FAIT
+install.done:fait-tags.done
 	cd $(SRCDIR);$(AR) $(ARFLAGS)  $(INSTALL)/lib/libtet.a tetgen.o predicates.o
 	ranlib $(SRCDIR)/$(INSTALL)/lib/libtet.a
 	cp $(SRCDIR)/tetgen.h $(SRCDIR)/$(INSTALL)/include 
@@ -51,23 +51,24 @@ clean-local::
 	-rm install.done
 
 
-$(SRCDIR)/tags: $(PACKAGE)
+tar-tags.done: $(PACKAGE)
 	gunzip -c  $(PACKAGE)|tar zxf - 
 #       FFCS: needs to patch tetgen because mingw64 has 4-byte longs
-	touch $(SRCDIR)/tags
+	touch tar-tags.done
 #	cd tetgen1.4.2;patch -p1 <../tetgen1.4.2.patch 
 
 $(PACKAGE):
 	../getall -o TetGen -a
 
 clean-local::
-	-rm -rf tetgen1.?.*  FAIT FAIRE 
+	-rm -rf tetgen1.?.*  *.done
 clean:
-	-rm $(SRCDIR)/$(INSTALL)/lib/libtet.a
-	-rm $(SRCDIR)/$(INSTALL)/include/tetgen.h
-	-rm FAIT *.done
-	-rm -rf tetgen1.4.?
-cxxflags: ../Makefile  Makefile
+	-rm $(SRCDIR)
+	-rm *.done
+	-rm -rf tetgen1.?.* cxxflags
+cxxflags: ../Makefile  Makefile ../getall 
+	../getall -o TetGen -a
+	-mv -f cxxflags cxxflags.old
 	grep 'CXX *=' ../Makefile >cxxflags
 	grep 'CC *=' ../Makefile >>cxxflags
 #	FFCS - 10/5/12 - bug under Windows if -O3 is specified tetgen never returns. It could also be the case under
@@ -76,4 +77,7 @@ cxxflags: ../Makefile  Makefile
 	grep 'WGET *=' ../Makefile >>cxxflags
 	grep 'AR *=' ../Makefile >>cxxflags
 	grep 'ARFLAGS *=' ../Makefile >>cxxflags
+	../../bin/ff-md5 $(PACKAGE) >> cxxflags	
+	if diff -q cxxflags cxxflags.old ; then echo No Modif skip compile of tetgen ; mv -f cxxflags.old cxxflags; else touch -c tar-tags.done; fi
+	
 .PHONY:$(SRCDIR)/$(INSTALL)

AutoGeneratedFile.tar.gz

@@ -1,6 +1,6 @@
 <!--USE THIS TEMPLATE TO COMPLETE THE CHANGELOG-->
 <!--
-## [Version number] - YYYY-MM-DD
+## [Version number]
 ### Added
 -
 
@@ -23,6 +23,30 @@
 # Changelog
 All notable changes to this project will be documented in this file.
 
+## [4.8]
+### Added
+- Bilaplacian example using Morley FE with PETSc, see `examples/hpddm/bilaplacian-2d-PETSc.edp`
+- Oseen problem preconditioned by PCD, see `examples/hpddm/oseen-2d-PETSc.edp`
+- SLEPc polynomial eigenvalue solver `PEPSolve()`
+- add trivail example to check periodic boundary condition on meshS , meshL  , mesh3 
+    examples/3d/periodic3.edp	examples/3dSurf/periodicS.edp
+    examples/3dCurve/periodicL.edp	
+
+### Changed
+- PETSc version 3.14.2
+- Mmg version 5.5.2
+- link of ffglut so change in configure.ac and Makefile.am  LIBS -> FF_LIBS and LIBS become empty 
+    to remove default libs 
+- change number of save plot in ffglut from 10 to 20 for O. Pironneau
+
+### Fixed
+- some memory leaks
+- the periodic boundary condition have wrong before first a sementic level of MeshS and MeshL case.
+     the new syntexe is for example: 
+     meshL Tl=segment(10);   fespace Vl(Tl,P1,periodic=[[1],[2]]); 
+     meshS Th=square3(10,10,[x*2*pi,y*2*pi]); fespace Vh2(Th,P1,periodic=[[1,x],[3,x],[2,y],[4,y]]);
+- fixed '*' keyboard trick,  to keep  the viewpoint in ffglut or not. 
+
 ## [4.7-1]
 ### Changed
 - change the language definition to use type as a construction function with named arguments for bem plugin
@@ -69,7 +93,7 @@ All notable changes to this project will be documented in this file.
 
 ### Deprecated
 - rename `changeNumbering`, `globalNumbering`, `originalNumbering`, `changeOperator`, `destroyRecycling`, and `attachCoarseOperator` to respectively `ChangeNumbering`, `GlobalNumbering`, `OriginalNumbering`, `ChangeOperator`, `DestroyRecycling`, and `AttachCoarseOperator`
-- `Nt` the normal vector of the current (wrong on meshL) use `Ns` pr `Tl` 
+- `Nt` the normal vector of the current (wrong on meshL) use `Ns` or `Tl` 
 ### Removed
 - `augmentation` routine from the PETSc plugin
 - `MPIF77` variable
@@ -340,7 +364,8 @@ 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/v4.7-1..develop
+[Unreleased]: https://github.com/FreeFem/FreeFem-sources/compare/v4.8..develop
+[4.8]: https://github.com/FreeFem/FreeFem-sources/compare/v4.7-1..v4.8
 [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

CHANGELOG.md

@@ -1,4 +1,4 @@
-#/bin/bash
+#/usr/bin/env bash
 
 DESTDIR=no
 while [ $# -ne 0 ]  ; do

bin/Build-MacOS-Distribution

@@ -1,4 +1,4 @@
-#!/bin/bash 
+#!/usr/bin/env bash
 # -xe
 
 ############################################################################

bin/build/download

@@ -0,0 +1,17 @@
+#!/usr/bin/perl
+use Digest::MD5 qw(md5_hex);
+$num_args = $#ARGV + 1;
+if ($num_args != 1) {
+    print "Usage: ff-md5  filename\n";
+    exit 1;
+}
+$filename = $ARGV[0];
+
+if (-e $filename) {
+print "# md5  $filename : ", md5_hex($filename), "\n";
+}
+else
+{
+	print " ff-md5 Error : $filename do not exist \n";
+	 exit 1;
+}

bin/ff-md5

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 ##  fist tentavie to create un mac installer 
 #  first 
 #  create dir for install

bin/pkgbuild-macos

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 # Runs all regression tests on all compiled FreeFem++ versions
 # ------------------------------------------------------------
 MPIRUN=`awk  '$1 =="MPIRUN" {print $3}' Makefile`

bin/regtests.sh

@@ -9,7 +9,7 @@
 # number in debian/changelog.
 
 
-AC_INIT(FreeFEM,4.7-1,frederic.hecht@sorbonne-universite.fr,FreeFEM)
+AC_INIT(FreeFEM,4.8,frederic.hecht@sorbonne-universite.fr,FreeFEM)
 dnl : ${CFLAGS=""}
 dnl : ${CXXFLAGS=""}
 dnl : ${FCFLAGS=""}
@@ -333,7 +333,8 @@ then
 	    AC_MSG_WARN([  get dir of -lg2c  FLIBS :  $FLIBS ])
 	    ;;
 # add FH sep 2006 / modif  2009
-        *gfortran)
+#  remove FH jan 2021 (Idea of P. Jolivet)
+        *gfortran-obsolete)
 	    ff_okkk=0
             for i in $FLIBS; do
 		case $i in
@@ -1115,10 +1116,12 @@ if test "$with_petsc_complex" != no; then
             AC_FF_PETSC_WHERELIB(superlu,SUPERLU_LIB,SUPERLU_INCLUDE,$ffconfpetscc)
             AC_FF_PETSC_WHERELIB(scalapack,SCALAPACK_LIB,SCALAPACK_INCLUDE,$ffconfpetscc)
             AC_FF_PETSC_WHERELIB(suitesparse,SUITESPARSE_LIB,SUITESPARSE_INCLUDE,$ffconfpetscc)
+            if test -z "$ff_BLASLAPACK_LIB"; then
             AC_FF_PETSC_WHERELIB(blaslapack,BLASLAPACK_LIB,BLASLAPACK_INCLUDE,$ffconfpetscc)
             if test -n "$ff_BLASLAPACK_LIB"; then
                 ff_where_lib_blaslapack="`echo $ff_BLASLAPACK_LIB | sed -e 's/@<:@^ @:>@*scalapack@<:@^ @:>@*//g' | sed -e 's/@<:@^ @:>@*blacs@<:@^ @:>@*//g'`"
             fi
+            fi
             if test -f $d/libslepc.$ff_suffix_dylib -o -f $d/libslepc.a ; then
 				   ff_slepccomplex_ok=yes
                    ff_SLEPCCOMPLEX_LIB="-Wl,-rpath,$d -L$d -lslepc"
@@ -1548,6 +1551,11 @@ then
     ff_cblas_libs=yes
 fi
 
+if test -n "$ff_BLASLAPACK_LIB"; then
+    AC_SUBST(BLACSLIBS,"$ff_SCALAPACK_LIB $ff_BLASLAPACK_LIB")
+else
+    AC_SUBST(BLACSLIBS,$ff_blas_libs)
+fi
 AC_SUBST(BLASLIBS,$ff_blas_libs)
 AC_SUBST(BLASINC,$ff_blas_inc)
 
@@ -2292,17 +2300,17 @@ AX_LIB_HDF5()
 if test "$with_hdf5" = "yes"; then
   ff_save_cppflags="$CPPFLAGS";
   CPPFLAGS="$CPPFLAGS $HDF5_CPPFLAGS"
-  AC_CHECK_HEADER([H5Cpp.h],[],[with_hdf=no])
+  AC_CHECK_HEADER([H5Cpp.h],[],[with_hdf5=no])
   CPPFLAGS="$ff_save_cppflags"
-  #if test "$with_hdf5" = "yes"; then
+  if test "$with_hdf5" = "yes"; then
   AC_FF_ADDWHERELIB(hdf5,$HDF5_LDFLAGS  $HDF5_LIBS,$HDF5_CPPFLAGS)
   LIBS="$LIBS $HDF5_LDFLAGS  $HDF5_LIBS"
   # hack, if enable_download=no
   AC_SUBST([TOOL_COMPILE_iohdf5],ifelse(,,iohdf5,))
   AC_SUBST([TOOL_DYLIB_iohdf5],iohdf5.$DYLIB_SUFFIX)
   ifelse(nodownload,,[ff_download_lib="iohdf5 $ff_download_lib"])
   ifelse(nodownload,,[enable_iohdf5_download=yes])
-  #fi
+  fi
 else
   enable_iohdf5=no
 fi
@@ -2332,6 +2340,8 @@ fi
 TOOL_DISABLE(NewSolver,"NewSolver.$DYLIB_SUFFIX",,nodownload)
 TOOL_DISABLE(mkl,"PARDISO.$DYLIB_SUFFIX",,nodownload)
 
+AC_SUBST([FF_LIBS],$LIBS)
+LIBS=
 # echo "debug cxxx11: $ff_cxx11 mpi: $ff_mpi petsc: $ff_petsc_ok "
 test "$enable_download" != "yes" -a "$enable_download_hpddm" != "yes" -a \( "$enable_hpddm" != "yes" -o "$ff_hpddm_ok" != "yes" \) && enable_hpddm=no
 test "$enable_download" != "yes" -a "$enable_htool" != yes && enable_htool=no
@@ -2428,6 +2438,7 @@ AM_CONDITIONAL([SUPERLU], [test "$ff_superlu_ok" = yes])
 AM_CONDITIONAL([TETGEN], [test "$ff_tetgen_" = yes])
 AM_CONDITIONAL([UMFPACK], [test "$ff_umfpack_" = yes])
 
+
 ##
 # All makefiles
 AC_OUTPUT(

configure.ac

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 #
 # This script configures, compiles and package FreeFem into AppImage
 #

etc/AppImage/build-appimage.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 #
 # The purpose of this custom AppRun script is
 # to allow symlinking the AppImage and invoking

etc/AppImage/freefem-apprun.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 #
 # You need to prepare this docker container if you want to buitd AppImage locally.
 # Normally it should be built with TravisCI (see .travis.yml)

etc/AppImage/rebuild-and-run-appimage-builder.sh

@@ -48,7 +48,7 @@ on freefem(edpfile)
 		if not (exists window 1) then reopen
 		activate
 		try
-			do shell script "/bin/bash -c 'export PATH=\"$PATH:$(cat /etc/paths.d/FreeFem++)\";cd \"" & edpdir & "\";FreeFem++-CoCoa  \"" & edppath & "\"'"
+			do shell script "/usr/bin/env bash -c 'export PATH=\"$PATH:$(cat /etc/paths.d/FreeFem++)\";cd \"" & edpdir & "\";FreeFem++-CoCoa  \"" & edppath & "\"'"
 		end try
 	end tell
 end freefem

etc/config/FreeFem++.scrpt-txt.in

@@ -175,8 +175,10 @@ CXXFLAGS="`echo $CXXFLAGS | sed 's/-O2//g'`"
 	    ff_fast="-O3 $ff_fast";;
 	  x86_64*)
 	  ff_fast="-O3 $ff_fast";;
+	  arm64*)
+	  ff_fast="-O3 $ff_fast";;
 	  *)
-	    AC_MSG_ERROR(cannot determine apple cpu type )
+	    AC_MSG_WARN(cannot determine apple cpu type )
 	    ff_fast="-O3";;
 	 esac