> On Oct 23, 2017, at 6:01 PM, Adrian Croucher <[email protected]>
> wrote:
>
> hi Barry,
>
>
> On 23/10/17 15:04, Barry Smith wrote:
>> Adrian,
>>
>> Sorry for the delay in generating the bindings for you. I have put them
>> in the branch
>>
>> barry/fortran-PetscSFBcastBegin
>>
>> the example src/vec/sf/examples/tutorials/ex1f.F90 attempts to test them.
>> Please let us know if this works for you and if you need anything else. They
>> will only work for MPIU_INT and MPIU_REAL and MPIU_SCALAR because that is
>> the only Fortran pointer arrays we support currently.
>
> Oh, thanks very much for that. I really only need support for integers in my
> application at present, so what you've done should be fine for now.
>
> I checked out your new branch but it is giving a bunch of warnings and errors
> when I try to make it.
>
These warnings should be gone in the latest version of the branch. Do a git
pull on that branch.
> The warnings are:
>
> In file included from
> /home/acro018/software/PETSc/code/include/petscsys.h:1631:0,
> from
> /home/acro018/software/PETSc/code/include/petsc/private/petscimpl.h:8,
> from
> /home/acro018/software/PETSc/code/include/petsc/private/fortranimpl.h:6,
> from
> /home/acro018/software/PETSc/code/include/petsc/private/f90impl.h:4,
> from
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c:1:
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c: In function
> ‘F90Array1dCreate’:
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c:60:80: warning:
> cast from pointer to integer of different size [-Wpointer-to-int-cast]
> } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsupported MPI_Datatype:
> %d",(PetscInt)type);
> ^
> /home/acro018/software/PETSc/code/include/petscerror.h:126:122: note: in
> definition of macro ‘SETERRQ1’
> #define SETERRQ1(comm,ierr,s,a1) return
> PetscError(comm,__LINE__,PETSC_FUNCTION_NAME,__FILE__,ierr,PETSC_ERROR_INITIAL,s,a1)
> ^
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c: In function
> ‘F90Array1dAccess’:
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c:78:80: warning:
> cast from pointer to integer of different size [-Wpointer-to-int-cast]
> } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsupported MPI_Datatype:
> %d",(PetscInt)type);
> ^
> /home/acro018/software/PETSc/code/include/petscerror.h:126:122: note: in
> definition of macro ‘SETERRQ1’
> #define SETERRQ1(comm,ierr,s,a1) return
> PetscError(comm,__LINE__,PETSC_FUNCTION_NAME,__FILE__,ierr,PETSC_ERROR_INITIAL,s,a1)
> ^
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c: In function
> ‘F90Array1dDestroy’:
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c:93:80: warning:
> cast from pointer to integer of different size [-Wpointer-to-int-cast]
> } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsupported MPI_Datatype:
> %d",(PetscInt)type);
> ^
> /home/acro018/software/PETSc/code/include/petscerror.h:126:122: note: in
> definition of macro ‘SETERRQ1’
> #define SETERRQ1(comm,ierr,s,a1) return
> PetscError(comm,__LINE__,PETSC_FUNCTION_NAME,__FILE__,ierr,PETSC_ERROR_INITIAL,s,a1)
> ^
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c: In function
> ‘F90Array2dCreate’:
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c:151:80:
> warning: cast from pointer to integer of different size
> [-Wpointer-to-int-cast]
> } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsupported MPI_Datatype:
> %d",(PetscInt)type);
> ^
> /home/acro018/software/PETSc/code/include/petscerror.h:126:122: note: in
> definition of macro ‘SETERRQ1’
> #define SETERRQ1(comm,ierr,s,a1) return
> PetscError(comm,__LINE__,PETSC_FUNCTION_NAME,__FILE__,ierr,PETSC_ERROR_INITIAL,s,a1)
> ^
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c: In function
> ‘F90Array2dAccess’:
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c:166:80:
> warning: cast from pointer to integer of different size
> [-Wpointer-to-int-cast]
> } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsupported MPI_Datatype:
> %d",(PetscInt)type);
> ^
> /home/acro018/software/PETSc/code/include/petscerror.h:126:122: note: in
> definition of macro ‘SETERRQ1’
> #define SETERRQ1(comm,ierr,s,a1) return
> PetscError(comm,__LINE__,PETSC_FUNCTION_NAME,__FILE__,ierr,PETSC_ERROR_INITIAL,s,a1)
> ^
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c: In function
> ‘F90Array2dDestroy’:
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c:181:80:
> warning: cast from pointer to integer of different size
> [-Wpointer-to-int-cast]
> } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsupported MPI_Datatype:
> %d",(PetscInt)type);
> ^
> /home/acro018/software/PETSc/code/include/petscerror.h:126:122: note: in
> definition of macro ‘SETERRQ1’
> #define SETERRQ1(comm,ierr,s,a1) return
> PetscError(comm,__LINE__,PETSC_FUNCTION_NAME,__FILE__,ierr,PETSC_ERROR_INITIAL,s,a1)
> ^
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c: In function
> ‘F90Array3dCreate’:
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c:239:80:
> warning: cast from pointer to integer of different size
> [-Wpointer-to-int-cast]
> } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsupported MPI_Datatype:
> %d",(PetscInt)type);
> ^
> /home/acro018/software/PETSc/code/include/petscerror.h:126:122: note: in
> definition of macro ‘SETERRQ1’
> #define SETERRQ1(comm,ierr,s,a1) return
> PetscError(comm,__LINE__,PETSC_FUNCTION_NAME,__FILE__,ierr,PETSC_ERROR_INITIAL,s,a1)
> ^
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c: In function
> ‘F90Array3dAccess’:
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c:254:80:
> warning: cast from pointer to integer of different size
> [-Wpointer-to-int-cast]
> } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsupported MPI_Datatype:
> %d",(PetscInt)type);
> ^
> /home/acro018/software/PETSc/code/include/petscerror.h:126:122: note: in
> definition of macro ‘SETERRQ1’
> #define SETERRQ1(comm,ierr,s,a1) return
> PetscError(comm,__LINE__,PETSC_FUNCTION_NAME,__FILE__,ierr,PETSC_ERROR_INITIAL,s,a1)
> ^
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c: In function
> ‘F90Array3dDestroy’:
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c:269:80:
> warning: cast from pointer to integer of different size
> [-Wpointer-to-int-cast]
> } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsupported MPI_Datatype:
> %d",(PetscInt)type);
> ^
> /home/acro018/software/PETSc/code/include/petscerror.h:126:122: note: in
> definition of macro ‘SETERRQ1’
> #define SETERRQ1(comm,ierr,s,a1) return
> PetscError(comm,__LINE__,PETSC_FUNCTION_NAME,__FILE__,ierr,PETSC_ERROR_INITIAL,s,a1)
> ^
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c: In function
> ‘F90Array4dCreate’:
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c:320:80:
> warning: cast from pointer to integer of different size
> [-Wpointer-to-int-cast]
> } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsupported MPI_Datatype:
> %d",(PetscInt)type);
> ^
> /home/acro018/software/PETSc/code/include/petscerror.h:126:122: note: in
> definition of macro ‘SETERRQ1’
> #define SETERRQ1(comm,ierr,s,a1) return
> PetscError(comm,__LINE__,PETSC_FUNCTION_NAME,__FILE__,ierr,PETSC_ERROR_INITIAL,s,a1)
> ^
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c: In function
> ‘F90Array4dAccess’:
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c:335:80:
> warning: cast from pointer to integer of different size
> [-Wpointer-to-int-cast]
> } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsupported MPI_Datatype:
> %d",(PetscInt)type);
> ^
> /home/acro018/software/PETSc/code/include/petscerror.h:126:122: note: in
> definition of macro ‘SETERRQ1’
> #define SETERRQ1(comm,ierr,s,a1) return
> PetscError(comm,__LINE__,PETSC_FUNCTION_NAME,__FILE__,ierr,PETSC_ERROR_INITIAL,s,a1)
> ^
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c: In function
> ‘F90Array4dDestroy’:
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c:344:80:
> warning: cast from pointer to integer of different size
> [-Wpointer-to-int-cast]
> } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsupported MPI_Datatype:
> %d",(PetscInt)type);
> ^
> /home/acro018/software/PETSc/code/include/petscerror.h:126:122: note: in
> definition of macro ‘SETERRQ1’
> #define SETERRQ1(comm,ierr,s,a1) return
> PetscError(comm,__LINE__,PETSC_FUNCTION_NAME,__FILE__,ierr,PETSC_ERROR_INITIAL,s,a1)
>
>
I don't know where these come from. In the branch you need to do a make
allfortranstubs, this may fix the problem
>
> The errors look like they're from some unrelated DMPlex box mesh changes:
>
> /home/acro018/software/PETSc/code/src/dm/impls/plex/ftn-auto/plexcreatef.c:
> In function ‘dmplexcreateboxmesh_’:
> /home/acro018/software/PETSc/code/src/dm/impls/plex/ftn-auto/plexcreatef.c:105:11:
> error: incompatible type for argument 4 of ‘DMPlexCreateBoxMesh’
> *__ierr = DMPlexCreateBoxMesh(
> ^
> In file included from
> /home/acro018/software/PETSc/code/src/dm/impls/plex/ftn-auto/plexcreatef.c:30:0:
> /home/acro018/software/PETSc/code/include/petscdmplex.h:124:29: note:
> expected ‘const PetscInt *’ but argument is of type ‘PetscBool’
> PETSC_EXTERN PetscErrorCode DMPlexCreateBoxMesh(MPI_Comm, PetscInt,
> PetscBool, const PetscInt[], const PetscReal[], const PetscReal[], const
> DMBoundaryType[], PetscBool, DM *);
> ^
> /home/acro018/software/PETSc/code/src/dm/impls/plex/ftn-auto/plexcreatef.c:106:52:
> warning: passing argument 5 of ‘DMPlexCreateBoxMesh’ from incompatible
> pointer type
> MPI_Comm_f2c(*(comm)),*dim,*numFaces,*interpolate,dm);
> ^
> In file included from
> /home/acro018/software/PETSc/code/src/dm/impls/plex/ftn-auto/plexcreatef.c:30:0:
> /home/acro018/software/PETSc/code/include/petscdmplex.h:124:29: note:
> expected ‘const PetscReal *’ but argument is of type ‘struct _p_DM **’
> PETSC_EXTERN PetscErrorCode DMPlexCreateBoxMesh(MPI_Comm, PetscInt,
> PetscBool, const PetscInt[], const PetscReal[], const PetscReal[], const
> DMBoundaryType[], PetscBool, DM *);
> ^
> /home/acro018/software/PETSc/code/src/dm/impls/plex/ftn-auto/plexcreatef.c:105:11:
> error: too few arguments to function ‘DMPlexCreateBoxMesh’
> *__ierr = DMPlexCreateBoxMesh(
> ^
> In file included from
> /home/acro018/software/PETSc/code/src/dm/impls/plex/ftn-auto/plexcreatef.c:30:0:
> /home/acro018/software/PETSc/code/include/petscdmplex.h:124:29: note:
> declared here
> PETSC_EXTERN PetscErrorCode DMPlexCreateBoxMesh(MPI_Comm, PetscInt,
> PetscBool, const PetscInt[], const PetscReal[], const PetscReal[], const
> DMBoundaryType[], PetscBool, DM *);
> ^
> /home/acro018/software/PETSc/code/src/dm/impls/plex/ftn-auto/plexcreatef.c:
> In function ‘dmplexcreatehexboxmesh_’:
> /home/acro018/software/PETSc/code/src/dm/impls/plex/ftn-auto/plexcreatef.c:109:1:
> warning: implicit declaration of function ‘DMPlexCreateHexBoxMesh’
> [-Wimplicit-function-declaration]
> *__ierr = DMPlexCreateHexBoxMesh(
> ^
> gmakefile:227: recipe for target
> 'linux-gnu-c-opt/obj/src/dm/impls/plex/ftn-auto/plexcreatef.o' failed
> make[2]: *** [linux-gnu-c-opt/obj/src/dm/impls/plex/ftn-auto/plexcreatef.o]
> Error 1
>
>
>> I was shocked, shocked to discover that it looks like PetscSF has
>> essentially no bindings for Fortran. We can add more relatively easily if
>> you need them. I don't understand how you could previously test your code
>> given that PetscSFCreate() didn't even have a Fortran stub generated?
>
> My tests are based on DMPlex and I was just using DMGetPointSF() and
> DMPlexDistribute() to get some SFs to test.
>
You shouldn't need to make any of these stubs. They can be automatically
generated. I turned on the automatic generation for them if
you do
make allfortranstubs
I think you should throw away the stubs you wrote.
Please let me know if what I suggested above doesn't resolve everything.
Barry
>
> I have also written some Fortran bindings for PetscSFGetGraph() and
> PetscSFSetGraph(). However it looks like you have made the PetscSFNode type
> accessible from Fortran in your branch? In which case my bindings could
> probably be modified to make use of that. Currently they look like this
> (using a 2-by-n array of int instead of an array of PetscSFNode for the root
> data array):
>
> + Interface
> + Subroutine PetscSFGetGraph(sf,nroots,nleaves,
> + & larray,rarray,ierr)
> + use petscisdef
> + PetscSF :: sf
> + PetscInt :: nroots, nleaves
> + PetscInt, pointer :: larray(:)
> + PetscInt, pointer :: rarray(:,:)
> + PetscErrorCode :: ierr
> + End Subroutine
> + End Interface
>
>
> +PETSC_EXTERN void PETSC_STDCALL petscsfgetgraph_(PetscSF *sf, PetscInt
> *nroots, PetscInt *nleaves, F90Array1d *lptr, F90Array2d *rptr, int *ierr
> PETSC_F90_2PTR_PROTO(lptrd) PETSC_F90_2PTR_PROTO(rptrd))
> +{
> + const PetscInt *ilocal;
> + const PetscSFNode *iremote;
> +
> + *ierr = PetscSFGetGraph(*sf, nroots, nleaves, &ilocal, &iremote); if
> (*ierr) return;
> +
> + *ierr = F90Array1dCreate((void*) ilocal, PETSC_INT, 1, *nleaves, lptr
> PETSC_F90_2PTR_PARAM(lptrd)); if (*ierr) return;
> + *ierr = F90Array2dCreate((void*) iremote, PETSC_INT, 1, 2, 1, *nleaves,
> rptr PETSC_F90_2PTR_PARAM(rptrd));
> +}
>
> - Adrian
>
> --
> Dr Adrian Croucher
> Senior Research Fellow
> Department of Engineering Science
> University of Auckland, New Zealand
> email: [email protected]
> tel: +64 (0)9 923 4611
>
