Fix reproducibility issues

3rdparty/ff-petsc/Makefile

@@ -148,8 +148,8 @@ all-local:
 	@echo "	make petsc-slepc "
 
 DIRPKG=../pkg
-VERSION=3.15.0
-VERSION_SLEPC=3.014.2
+VERSION=3.15.1
+VERSION_SLEPC=3.15.1
 PACKAGE=../pkg/petsc-$(VERSION).tar.gz
 SRCDIR=petsc-$(VERSION)
 MPI_DIR:=$(shell dirname $(MPI_INC_DIR))
@@ -302,7 +302,7 @@ endif
 $(SRCDIR)/tag-tar:$(PACKAGE)
 	-tar xzf $(PACKAGE)
 ifeq ($(WIN32DLLTARGET),)
-	cd petsc-$(VERSION) && patch -p1 < ../petsc-metis.patch && cd -
+	cd petsc-$(VERSION) && patch -p1 < ../petsc-cmake-seq.patch && cd -
 endif
 	cd petsc-$(VERSION) && patch -p1 < ../petsc-suitesparse.patch && cd -
 	touch $@

3rdparty/ff-petsc/petsc-metis.patch → 3rdparty/ff-petsc/petsc-cmake-seq.patch

@@ -15,3 +15,20 @@ index 136526da05..2d1c4d3271 100644
      return args
 
    def configureLibrary(self):
+diff --git a/config/BuildSystem/config/packages/mmg.py b/config/BuildSystem/config/packages/mmg.py
+index 1cc9122f41..4affbce3b3 100644
+--- a/config/BuildSystem/config/packages/mmg.py
++++ b/config/BuildSystem/config/packages/mmg.py
+@@ -27,6 +27,12 @@ class Configure(config.package.CMakePackage):
+     args.append('-DUSE_ELAS=OFF')
+     args.append('-DUSE_VTK=OFF')
+     args.append('-DSCOTCH_DIR:STRING="'+self.ptscotch.directory+'"')
++    mpicc = self.framework.getMakeMacro('MPICC_SHOW')
++    mpicxx = self.framework.getMakeMacro('MPICXX_SHOW')
++    if mpicc and mpicxx:
++        args = self.rmArgsStartsWith(args,['-DCMAKE_CXX_COMPILER','-DCMAKE_C_COMPILER'])
++        args.append('-DCMAKE_C_COMPILER="'+mpicc.split(None, 1)[0]+'"')
++        args.append('-DCMAKE_CXX_COMPILER="'+mpicxx.split(None, 1)[0]+'"')
+     return args
+
+   def configureLibrary(self):

3rdparty/getall

@@ -171,21 +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-3.15.0.tar.gz',
+download('PETSc','https://www.mcs.anl.gov/petsc/mirror/release-snapshots/petsc-3.15.1.tar.gz',
 	'https://www.mcs.anl.gov/petsc/mirror/release-snapshots/',
-	'petsc-3.15.0.tar.gz',
-	'32cdb2a2aed1be52059f6221a41d2b18');
+	'petsc-3.15.1.tar.gz',
+	'af0d1b5c5a01a5f35636773661a025dd');
 
 download('htool','https://github.com/htool-ddm/htool/archive/e008e87bded5626d73fa7655487aee48268e2149.zip',
 		'https://github.com/htool-ddm/',
 		'htool.zip',
 		'7ee614df188cf501c03c5f27d1569b1c');
 
 
-download('hpddm','https://codeload.github.com/hpddm/hpddm/zip/e58205623814f59bf2aec2e2bab8eafcfbd22466',
+download('hpddm','https://codeload.github.com/hpddm/hpddm/zip/01bd3df5a5dcb657a257ee118af98ef15a78b816',
 	'https://codeload.github.com/hpddm',
 	'hpddm.zip',
-	'b7a4f9be6de2df302485c4689a6c8078');
+	'48dac6ddbcad86ba62a29d71e3460846');
 
 download('bemtool','https://github.com/PierreMarchand20/BemTool/archive/d327ef63c5abe88b13197c433a019e0db10eb426.zip',
 	'https://github.com/PierreMarchand20/BemTool',

CHANGELOG.md

@@ -22,34 +22,65 @@
 
 # Changelog
 All notable changes to this project will be documented in this file.
+## [Unreleased]
+### Added
+- ridgeangle named parameter in ExtractMeshL in msh3 plugin
+- DG formulation in 1d :
+  add integral of all border of element : `intallBE(ThL)` and unified the notation by adding
+   `intallBE(ThS)` , `intallBE(Th2)`, `intallBE(Th3)`
+
+  `nuVertex` of now the vertex number of element in intallBE0d integral
+  `BoundaryBE`, `InternalBE` to know if border element (BE) is on true boundary of not.
+  update `nElementonB` in case on no manifold data (value greater > 2) in meshL, MeshS case ..
+  add code to use jump, mean of test functuon on MeshL case. ( not in mesh3 ) to compute RHS. 
+
+- add getcwd() function in shell plugin to ghet the current working dir 
+- add nuVertex to get the vextex on element in some int?
+
+### Changed
+-
+
+### Deprecated
+- SLEPc and SLEPc-complex have been part of PETSc and PETSc-complex for multiple releases and are now deprecated
+
+### Removed
+-
+
+### Fixed
+- examples/potential.edp correct problem in times loops and BC
+- tutorial/mortar-DN-4.edp correct problem of region number in meshL
+- fixe problem in Curve mesh and intallBE , vertex number is wrong 
+
+### Security
+-
 
 ## [4.9]
 ### Added
-- add P3 lagrange finite element on meshS and meshS 
+- add P3 lagrange finite element on meshS and meshS
 - add new plugin `meshtool`to add tool to compute the number of connected components of a all kind of mesh
   (mesh,mesh3,meshS,meshL) with 2 kind of connected components ones on interior part of the mesh (default) ans
   secondly on the closure of the mesh (see `examples/hpddm/bConnectedComponents.edp` )
   add functions  int[int] In=iminP1K(Th,u) or int[int] Ix=imaxP1K(Th,u)  get the array min/max of value u[i]  
-  where i is vertex number on  each element k, so we have  u[Im[k]] = min u[i]/ i in k; 
+  where i is vertex number on  each element k, so we have  u[Im[k]] = min u[i]/ i in k;
 - add in plugin `bfstream` to to read binary int (4 bytes) to read fortran file and try to pull tools to share the endiannes
   in progress
 - add gluemesh of array of MeshL and MeshS type
 - interface to `PC_MG_GALERKIN_BOTH`
 - Kronecker product of two sparse matrices `matrix C = kron(A, B)`
 - add lot of finite element on Mesh3, MeshS, MeshL of Discontinous Galerling Element
-  in 3d       : P1dc3d, P2dc3d, P3dc3d, P4dc3d , P0edge3d ,P0edgedc3d ,  P0face3d ,P0facedc3d , P0VF3d ,P0VFdc3d , 
-  on Surface  : P1dcS, P2dcS, P3dcS, P4dcS , P0edgeS ,P0edgedcS , P0VFS ,P0VFdcS, 
+  in 3d       : P1dc3d, P2dc3d, P3dc3d, P4dc3d , P0edge3d ,P0edgedc3d ,  P0face3d ,P0facedc3d , P0VF3d ,P0VFdc3d ,
+  on Surface  : P1dcS, P2dcS, P3dcS, P4dcS , P0edgeS ,P0edgedcS , P0VFS ,P0VFdcS,
   on Curve   : P1dcL, P2dcL, P3dcL, P4dcL ,  P0VFL ,P0VFdcL
   remark; the associated generic name existe of P1dc, P2dc, P0edge, P0VF and all  dc finite element corresponding to
-  no continuity across element. 
-- add code of intallfaces to  do Discontinous Galerkin  formulation in 3d (in test FH.) 
+  no continuity across element.
+- add code of intallfaces to  do Discontinous Galerkin  formulation in 3d (in test FH.)
 ### Changed
 - Now the order to find MPI in configure is first if you have PETSC then take MPI from PETSc
   otherwise use previous method
 - on MeshL defined with buildmeshL now the default label are 2*k-1  (resp. 2*k)  for the begin (resp. end) of curve
   where k is the order of curve use in buildmeshL. So if you have one curve the  labels are 1  and 2.
   And new  the element label are te region number not the label.
-  This element are not really test so be carfull. 
+  This element are not really test so be carfull.
 - PETSc 3.15.0
 
 ### Deprecated
@@ -59,9 +90,9 @@ All notable changes to this project will be documented in this file.
 -
 
 ### Fixed
-- bug in Find triangle contening point in 2d (border case), 
+- bug in Find triangle contening point in 2d (border case),
    `int Mesh::DataFindBoundary::Find(R2 PP,R *l,int & outside) const`
-   the parameter l not correclty return due to local variable. 
+   the parameter l not correclty return due to local variable.
 - set CFLAGS=-Wno-implicit-function-declaration to complie with Apple clang version 12.0.0 (clang-1200.0.32.29)
   to remove following error: implicit declaration of function
   correct `3dCurve/basicGlue.edp`and add missing test

configure.ac

@@ -185,7 +185,9 @@ m4_define([TOOL_DISABLE_NO],
     TOOL_PARAMETERS($1,$2,$3)
 ])
 
-echo "#  Build with FreeFEM with ./configure " `date`  >$ff_where_lib_conf
+BUILD_DATE="$(date --utc --date="@${SOURCE_DATE_EPOCH:-$(date +%s)}" +%Y-%m-%d)"
+
+echo "#  Build with FreeFEM with ./configure $BUILD_DATE" >$ff_where_lib_conf
 # To allow anonymous CVS version to contain a "./configure" and
 # Makefiles
 
@@ -667,7 +669,7 @@ ff_prefix_dir="${prefix}/lib/ff++/$VERSION"
 AC_MSG_CHECKING(prefix dir freefem++  )
 AC_MSG_RESULT($ff_prefix_dir)
 
-FF_DATE=`date`
+FF_DATE="$BUILD_DATE"
 AC_DEFINE_UNQUOTED(VersionFreeFemDate,"$FF_DATE",FreeFEM build date)
 AC_DEFINE_UNQUOTED(FF_PREFIX_DIR,"${ff_prefix_dir}",FreeFem prefix  dir)
 AC_SUBST(ff_prefix_dir,$ff_prefix_dir)

etc/config/m4/acmpi.m4

@@ -296,7 +296,7 @@ fi
            test -n "$MPICC" && ff_mpicshow=`$MPICC -show` 2>/dev/null
            test -n "$MPIFC" && ff_mpifcshow=`$MPIFC -show` 2>/dev/null
 	    if test "$with_mpilibs" = no -o -z "$with_mpilibs" ; then
-		[ff_MPI_INCLUDE=`echo $ff_mpishow|tr ' ' '\n'| grep -E '^[-/][^WLlOgpf]|^-Wp,'|tr '\n' ' '`]
+		[ff_MPI_INCLUDE=`echo $ff_mpishow|tr ' ' '\n' | sed '1 d'| grep -E '^[-/][^WLlOgpf]|^-Wp,'|tr '\n' ' '`]
 		ff_MPI_LIB_DIRS=""
 		[ff_MPI_LIB=`echo $ff_mpishow|tr ' ' '\n'| grep -E '^-[Llp]|^-Wl,'|tr '\n' ' '`]
 		[ff_MPI_LIBC=`echo $ff_mpicshow|tr ' ' '\n'| grep -E '^-[Llp]|^-Wl,'|tr '\n' ' '`]

etc/jenkins/README.md

@@ -210,7 +210,7 @@ make -j4 install
 
 ```
 
-Jenkins projets are [here](https://ci.inria.fr/freefem-dev/) and [here](https://ci.inria.fr/freefem-dev-2/) 
+Jenkins projects are [here](https://ci.inria.fr/freefem-dev/) and [here](https://ci.inria.fr/freefem-dev-2/) 
 
 
 # Job 1

examples/3d/Makefile.am

@@ -132,7 +132,7 @@ EXTRA_DIST = *.edp \
 
 all.edp: Makefile
 	(echo "NoGraphicWindow=true;NoUseOfWait=true;int verbosityy=verbosity;int MEM1234=storageused();"; \
-	for i in *`ls *.edp|grep -v -E '^(all|regtests|makeref|ref)\.edp$$'` ; do \
+	for i in *`ls *.edp|grep -v -E '^(all|regtests|makeref|ref)\.edp$$' | LC_ALL=C sort` ; do \
 		echo ' cout << "--------- file : '$$i' --------------------------------------------------------" << endl;' ;\
 		echo "verbosity=verbosityy;searchMethod=0;" ; \
 		echo \{ include \"$$i\"\;\}\; ;\

examples/3dCurve/Makefile.am

@@ -55,7 +55,7 @@ EXTRA_DIST = *.edp all.edp
 
 all.edp: Makefile
 	(echo "NoGraphicWindow=true;NoUseOfWait=true;int verbosityy=verbosity;int MEM1234=storageused();"; \
-	for i in *`ls *.edp|grep -v -E '^(all|regtests|makeref|ref)\.edp$$'` ; do \
+	for i in *`ls *.edp|grep -v -E '^(all|regtests|makeref|ref)\.edp$$' | LC_ALL=C sort` ; do \
 		echo ' cout << "--------- file : '$$i' --------------------------------------------------------" << endl;' ;\
 		echo "verbosity=verbosityy;searchMethod=0;" ; \
 		echo \{ include \"$$i\"\;\}\; ;\

examples/3dCurve/periodicL.edp

@@ -2,8 +2,12 @@ load "msh3"
 
 meshL Th=segment(10,[x*pi*2]);
 fespace Vh(Th,P1,periodic=[[1],[2]]);
+meshL ThVh = Vh.Th; // check code ..
 func u1e =(sin(x+1));
 Vh u,v,uh=u1e;
+
+meshL Thu = u.Th; // check code ..
+u.n; // check code ..  
 func f1= 1*u1e;
 macro grad3(u) [dx(u),dy(u),dz(u)]//
 solve PP2(u,v) = int1d(Th)(grad3(u)'*grad3(v)+1e-6*u*v) - int1d(Th)(f1*v) ;

examples/3dSurf/Makefile.am

@@ -64,7 +64,7 @@ EXTRA_DIST = *.edp all.edp
 
 all.edp: Makefile
 	(echo "NoGraphicWindow=true;NoUseOfWait=true;int verbosityy=verbosity;int MEM1234=storageused();"; \
-	for i in *`ls *.edp|grep -v -E '^(all|regtests|makeref|ref)\.edp$$'` ; do \
+	for i in *`ls *.edp|grep -v -E '^(all|regtests|makeref|ref)\.edp$$' | LC_ALL=C sort` ; do \
 		echo ' cout << "--------- file : '$$i' --------------------------------------------------------" << endl;' ;\
 		echo "verbosity=verbosityy;searchMethod=0;" ; \
 		echo \{ include \"$$i\"\;\}\; ;\

examples/CMakeLists.txt

@@ -6,7 +6,6 @@ ADD_SUBDIRECTORY(examples)
 ADD_SUBDIRECTORY(eigen)
 #ADD_SUBDIRECTORY(plugin)
 ADD_SUBDIRECTORY(mpi)
-ADD_SUBDIRECTORY(other)
 ADD_SUBDIRECTORY(tutorial)
 ADD_SUBDIRECTORY(ffddm)
 

examples/CheckAll

@@ -8,7 +8,7 @@ rm CheckAll-out
 for i in */.; do
     cd $i;
     case $i in
-	*mpi/.|*hpddm/.)  ;;
+	*mpi/.|*hpddm/.|*ffddm/)  ;;
 	*)      echo  ----  $i  ---
      ../CheckAllEdp "$ff -nw" *.edp | tee -a ../CheckAll-out ;;
     esac;
@@ -19,7 +19,7 @@ if [ -n "$ffmpi" ] ; then
     for i in */.; do
 	cd $i;
 	case $i in
-	    *mpi/.|*hpddm/.)
+	    *mpi/.|*hpddm/.|*ffddm/.)
 		echo  MPI ----  $i  ---
 		../CheckAllEdp "$ffmpi -np 4" *.edp | tee -a ../CheckAll-out;;
 	esac;

examples/eigen/Makefile.am

@@ -57,7 +57,7 @@ EXTRA_DIST = *.edp all.edp
 
 all.edp:
 	(echo "NoUseOfWait=true;int verbosityy=verbosity;"; \
-	for i in *`ls *.edp|grep -v -E '^(all|regtests|makeref|ref)\.edp$$'` ; do \
+	for i in *`ls *.edp|grep -v -E '^(all|regtests|makeref|ref)\.edp$$' | LC_ALL=C sort` ; do \
 		echo ' cout << "--------- file : '$$i' --------------------------------------------------------" << endl;' ;\
 		echo "verbosity=verbosityy;" ; \
 		echo \{ include \"$$i\"\;\}\; ;\
@@ -66,4 +66,4 @@ all.edp:
 
 freefem++.pref:Makefile
 	echo includepath = \"../../idp/\" > freefem++.pref
-	echo loadpath = \"../../plugin/seq/\" >> freefem++.pref
+	echo loadpath = \"../../plugin/seq/\" >> freefem++.pref

examples/eigen/condition-number.edp

@@ -1,4 +1,4 @@
-mesh Th=square(100,100,[x*pi,y*pi]);
+mesh Th=square(50,50,[x*pi,y*pi]);
 macro grad(u) [dx(u),dy(u)]//
 int[int] L=[1,2,3,4];
 varf vlapWithBC(u,v)= int2d(Th)(grad(u)'*grad(v))+ on(L,u=0);
@@ -8,7 +8,7 @@ fespace Vh(Th,P1);
 Vh u,v;
 u=1; 
 matrix Id=u[]; // vMass(Vh,Vh,solver=CG) ;
-set(Id,solver=CG);
+set(Id,solver=CG,verb=0);
 matrix Abc= vlapWithBC(Vh,Vh,solver=sparsesolver);
 matrix Ancl= vlapWithoutBC(Vh,Vh,solver=CG);
 real[int] aevmin(2),aevmax(2);

examples/examples/Makefile.am

@@ -66,7 +66,7 @@ EXTRA_DIST = *.edp all.edp regtests.edp regtests.m4 ref.edp
 
 all.edp:
 	(echo "NoUseOfWait=true;int verbosityy=verbosity;"; \
-	for i in *`ls *.edp|grep -v -E '^(all|regtests|makeref|ref)\.edp$$'` ; do \
+	for i in *`ls *.edp|grep -v -E '^(all|regtests|makeref|ref)\.edp$$' | LC_ALL=C sort` ; do \
 		echo ' cout << "--------- file : '$$i' --------------------------------------------------------" << endl;' ;\
 		echo "verbosity=verbosityy;" ; \
 		echo \{ include \"$$i\"\;\}\; ;\

examples/examples/potential.edp

@@ -14,57 +14,59 @@
 /* You should have received a copy of the GNU Lesser General Public License */
 /* along with FreeFEM. If not, see <http://www.gnu.org/licenses/>.          */
 /****************************************************************************/
-
+// Corrected by F. Hecht may 2021 
 // Parameters
 real S = 99;
 
-border C(t=0, 2*pi){x=3*cos(t); y=3*sin(t);}
-border Splus(t=0, 1){x=t; y=0.17735*sqrt(t) - 0.075597*t - 0.212836*(t^2) + 0.17363*(t^3) - 0.06254*(t^4); label=S;}
-border Sminus(t=1, 0){x=t; y=-(0.17735*sqrt(t) - 0.075597*t - 0.212836*(t^2) + 0.17363*(t^3) - 0.06254*(t^4)); label=S;}
+border C(t=0, 2*pi){x=3*cos(t); y=3*sin(t);} // Label 1,2 
+border Splus(t=0, 1){x=t-0.5; y=0.17735*sqrt(t) - 0.075597*t - 0.212836*(t^2) + 0.17363*(t^3) - 0.06254*(t^4); label=S;}
+border Sminus(t=1, 0){x=t-0.5; y=-(0.17735*sqrt(t) - 0.075597*t - 0.212836*(t^2) + 0.17363*(t^3) - 0.06254*(t^4)); label=S;}
 mesh Th = buildmesh(C(50) + Splus(70) + Sminus(70));
-
 // Fespace
 fespace Vh(Th, P2);
 Vh psi, w;
-
+real cost = cos(5.*pi/180.), sint=sin(5.*pi/180.);// incidence 5 degres
 // Problem
 solve potential(psi, w)
   = int2d(Th)(dx(psi)*dx(w)+dy(psi)*dy(w))
-  + on(C, psi = y)
+  + on(C, psi = cost*y-sint*x) 
   + on(S, psi=0);
 
 // Plot
 plot(psi, wait=1);
 
 /// Thermic
 // Parameters
-real dt = 0.05, nbT = 50;
+real dt = 0.005, nbT = 50;
 
 // Mesh
-border D(t=0, 2){x=1+t; y=0;}
+border D(t=0, 2.){x=0.5+t*cost; y=+t*sint;}
 mesh Sh = buildmesh(C(25) + Splus(-90) + Sminus(-90) + D(200));
 int steel = Sh(0.5, 0).region, air = Sh(-1, 0).region;
-
+// Change label to put BC on In flow 
 // Fespace
 fespace Wh(Sh, P1);
-Wh v, vv;
+Wh  vv;
 
 fespace W0(Sh, P0);
 W0 k = 0.01*(region == air) + 0.1*(region == steel);
 W0 u1 = dy(psi)*(region == air), u2 = -dx(psi)*(region == air);
-Wh vold = 120*(region == steel);
-
+Wh v = 120*(region == steel), vold;
+// pul label 10 on inflow boundary to inforce the temperature.
+Sh = change(Sh,flabel = (label == C &&  [u1,u2]'*N<0) ? 10 : label);
 int i;
 problem thermic(v, vv, init=i, solver=LU)
   = int2d(Sh)(
       v*vv/dt + k*(dx(v)*dx(vv) + dy(v)*dy(vv))
     + 10*(u1*dx(v) + u2*dy(v))*vv
   )
-  - int2d(Sh)(vold*vv/dt);
+  - int2d(Sh)(vold*vv/dt)
+  + on(10, v= 0);
+
 
 for(i = 0; i < nbT; i++) {
-    v = vold;
+    vold[]= v[];
     thermic;
     plot(v);
 }
-plot(v, wait=1);
+plot(v, wait=1,fill=1,value=1);