[petsc-users] TS tutorial ex11 in Fortran
Thibault Bridel-Bertomeu
thibault.bridelbertomeu at gmail.com
Tue Dec 22 05:49:40 CST 2020
Dear all,
I have hit two snags while implementing the missing wrappers necessary to
transcribe ex11 to Fortran.
First is about the PetscDSAddBoundary wrapper, that I have done so :
static PetscErrorCode ourbocofunc(PetscReal time, const PetscReal *c, const
PetscReal *n, const PetscScalar *a_xI, const PetscScalar *a_xG, void *ctx)
{
PetscObjectUseFortranCallback((PetscDS)ctx, bocofunc,
(PetscReal*,const PetscReal*,const
PetscReal*,const PetscScalar*,const PetscScalar*,void*,PetscErrorCode*),
(&time,c,n,a_xI,a_xG,ctx,&ierr));
}
static PetscErrorCode ourbocofunc_time(PetscReal time, const PetscReal *c,
const PetscReal *n, const PetscScalar *a_xI, const PetscScalar *a_xG, void
*ctx)
{
PetscObjectUseFortranCallback((PetscDS)ctx, bocofunc_time,
(PetscReal*,const PetscReal*,const
PetscReal*,const PetscScalar*,const PetscScalar*,void*,PetscErrorCode*),
(&time,c,n,a_xI,a_xG,ctx,&ierr));
}
PETSC_EXTERN void petscdsaddboundary_(PetscDS *prob,
DMBoundaryConditionType *type, char *name, char *labelname, PetscInt
*field, PetscInt *numcomps, PetscInt *comps,
void (*bcFunc)(void),
void (*bcFunc_t)(void),
PetscInt *numids, const PetscInt
*ids, void *ctx, PetscErrorCode *ierr,
PETSC_FORTRAN_CHARLEN_T namelen,
PETSC_FORTRAN_CHARLEN_T labelnamelen)
{
char *newname, *newlabelname;
FIXCHAR(name, namelen, newname);
FIXCHAR(labelname, labelnamelen, newlabelname);
*ierr = PetscObjectSetFortranCallback((PetscObject)*prob,
PETSC_FORTRAN_CALLBACK_CLASS, &bocofunc, (PetscVoidFunction)bcFunc,
ctx);
*ierr = PetscObjectSetFortranCallback((PetscObject)*prob,
PETSC_FORTRAN_CALLBACK_CLASS, &bocofunc_time, (PetscVoidFunction)bcFunc_t,
ctx);
*ierr = PetscDSAddBoundary(*prob, *type, newname, newlabelname, *field,
*numcomps, comps,
(void (*)(void))ourbocofunc,
(void (*)(void))ourbocofunc_time,
*numids, ids, *prob);
FREECHAR(name, newname);
FREECHAR(labelname, newlabelname);
}
but when I call it in the program, with adequate routines, I obtain the
following error :
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------[0]PETSC
ERROR: Corrupt argument:
https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC
ERROR: Fortran callback not set on this object[0]PETSC ERROR: See
https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
shooting.[0]PETSC ERROR: Petsc Development GIT revision:
v3.14.2-297-gf36a7edeb8 GIT Date: 2020-12-18 04:42:53 +0000[0]PETSC
ERROR: ../../../bin/eulerian3D on a named
macbook-pro-de-thibault.home by tbridel Sun Dec 20 15:05:15
2020[0]PETSC ERROR: Configure options --with-clean=0
--prefix=/Users/tbridel/Documents/1-CODES/04-PETSC/build
--with-make-np=2 --with-windows-graphics=0 --with-debugging=0
--download-fblaslapack --download-mpich-shared=0 --with-x=0
--with-pthread=0 --with-valgrind=0 --PETSC_ARCH=macosx
--with-fc=/usr/local/Cellar/open-mpi/4.0.1_2/bin/mpifort
--with-cc=/usr/local/Cellar/open-mpi/4.0.1_2/bin/mpicc
--with-cxx=/usr/local/Cellar/open-mpi/4.0.1_2/bin/mpic++
--with-openmp=0 --download-hypre=yes --download-sowing=yes
--download-metis=yes --download-parmetis=yes --download-triangle=yes
--download-tetgen=yes --download-ctetgen=yes --download-p4est=yes
--download-zlib=yes --download-c2html=yes --download-eigen=yes
--download-pragmatic=yes
--with-hdf5-dir=/usr/local/Cellar/hdf5/1.10.5_1
--with-cmake-dir=/usr/local/Cellar/cmake/3.15.3[0]PETSC ERROR: #1
PetscObjectGetFortranCallback() line 258 in
/Users/tbridel/Documents/1-CODES/04-PETSC/src/sys/objects/inherit.c[0]PETSC
ERROR: #2 ourbocofunc() line 141 in
/Users/tbridel/Documents/1-CODES/59-EULERIAN3D/sources/petsc_wrapping/wrapper_petsc.c[0]PETSC
ERROR: #3 DMPlexInsertBoundaryValuesRiemann() line 989 in
/Users/tbridel/Documents/1-CODES/04-PETSC/src/dm/impls/plex/plexfem.c[0]PETSC
ERROR: #4 DMPlexInsertBoundaryValues_Plex() line 1052 in
/Users/tbridel/Documents/1-CODES/04-PETSC/src/dm/impls/plex/plexfem.c[0]PETSC
ERROR: #5 DMPlexInsertBoundaryValues() line 1142 in
/Users/tbridel/Documents/1-CODES/04-PETSC/src/dm/impls/plex/plexfem.c[0]PETSC
ERROR: #6 DMPlexComputeResidual_Internal() line 4524 in
/Users/tbridel/Documents/1-CODES/04-PETSC/src/dm/impls/plex/plexfem.c[0]PETSC
ERROR: #7 DMPlexTSComputeRHSFunctionFVM() line 74 in
/Users/tbridel/Documents/1-CODES/04-PETSC/src/ts/utils/dmplexts.c[0]PETSC
ERROR: #8 ourdmtsrhsfunc() line 186 in
/Users/tbridel/Documents/1-CODES/59-EULERIAN3D/sources/petsc_wrapping/wrapper_petsc.c[0]PETSC
ERROR: #9 TSComputeRHSFunction_DMLocal() line 105 in
/Users/tbridel/Documents/1-CODES/04-PETSC/src/ts/utils/dmlocalts.c[0]PETSC
ERROR: #10 TSComputeRHSFunction() line 653 in
/Users/tbridel/Documents/1-CODES/04-PETSC/src/ts/interface/ts.c[0]PETSC
ERROR: #11 TSSSPStep_RK_3() line 120 in
/Users/tbridel/Documents/1-CODES/04-PETSC/src/ts/impls/explicit/ssp/ssp.c[0]PETSC
ERROR: #12 TSStep_SSP() line 208 in
/Users/tbridel/Documents/1-CODES/04-PETSC/src/ts/impls/explicit/ssp/ssp.c[0]PETSC
ERROR: #13 TSStep() line 3757 in
/Users/tbridel/Documents/1-CODES/04-PETSC/src/ts/interface/ts.c[0]PETSC
ERROR: #14 TSSolve() line 4154 in
/Users/tbridel/Documents/1-CODES/04-PETSC/src/ts/interface/ts.c[0]PETSC
ERROR: #15 User provided function() line 0 in User file
Second is about the DMProjectFunction wrapper, that I have done so :
static PetscErrorCode ourdmprojfunc(PetscInt dim, PetscReal time, PetscReal
x[], PetscInt Nf, PetscScalar u[], void *ctx)
{
PetscObjectUseFortranCallback((DM)ctx, dmprojfunc,
(PetscInt*,PetscReal*,PetscReal*,PetscInt*,PetscScalar*,void*,PetscErrorCode*),
(&dim,&time,x,&Nf,u,_ctx,&ierr))
}
PETSC_EXTERN void dmprojectfunction_(DM *dm, PetscReal *time,
void
(*func)(PetscInt*,PetscReal*,PetscReal*,PetscInt*,PetscScalar*,void*,PetscErrorCode*),
void *ctx, InsertMode *mode, Vec X,
PetscErrorCode *ierr)
{
PetscErrorCode (*funcarr[1]) (PetscInt dim, PetscReal time, PetscReal
x[], PetscInt Nf, PetscScalar *u, void *ctx);
*ierr = PetscObjectSetFortranCallback((PetscObject)*dm,
PETSC_FORTRAN_CALLBACK_CLASS, &dmprojfunc, (PetscVoidFunction)func, ctx);
funcarr[0] = ourdmprojfunc;
*ierr = DMProjectFunction(*dm, *time, funcarr, &ctx, *mode, X);
}
This time there is no error because I cannot reach this point in the
program, but I am not sure anyways how to write this wrapper, especially
because of the double pointers that DMProjectFunction takes as arguments.
Does anyone have any idea what could be going wrong with those two wrappers
?
Thank you very much in advance !!
Thibault
Le ven. 18 déc. 2020 à 11:02, Thibault Bridel-Bertomeu <
thibault.bridelbertomeu at gmail.com> a écrit :
> Aah that is a nice trick, I was getting ready to fork, clone the fork and
> redo the work, but that worked fine ! Thank you Barry !
>
> The MR will appear in a little while !
>
> Thibault
>
>
> Le ven. 18 déc. 2020 à 10:16, Barry Smith <bsmith at petsc.dev> a écrit :
>
>>
>> Good question. There is a trick to limit the amount of work you need
>> to do with a new fork after you have already made changes with a PETSc
>> clone, but it looks like we do not document this clearly in the webpages.
>> (I couldn't find it).
>>
>> Yes, you do need to make a fork, but after you have made the fork on
>> the GitLab website (and have done nothing on your machine) edit the file
>> $PETSC_DIR/.git/config for your clone on your machine
>>
>> Locate the line that has url = git at gitlab.com:petsc/petsc.git (this
>> may have an https at the beginning of the line)
>>
>> Change this line to point to the fork url instead with git@ not https,
>> which will be pretty much the same URL but with your user id instead of
>> petsc in the address. Then git push and it will push to your fork.
>>
>> Now you changes will be in your fork and you can make the MR from your
>> fork URL on Gitlab. (In other words this editing trick converts your PETSc
>> clone on your machine to a PETSc fork).
>>
>> I hope I have explained this clearly enough it goes smoothly.
>>
>> Barry
>>
>>
>>
>> On Dec 18, 2020, at 3:00 AM, Thibault Bridel-Bertomeu <
>> thibault.bridelbertomeu at gmail.com> wrote:
>>
>> Hello Barry,
>>
>> I'll start the MR as soon as possible then so that specialists can indeed
>> have a look. Do I have to fork PETSc to start a MR or are PETSc repo
>> settings such that can I push a branch from the PETSc clone I got ?
>>
>> Thibault
>>
>>
>> Le mer. 16 déc. 2020 à 07:47, Barry Smith <bsmith at petsc.dev> a écrit :
>>
>>>
>>> Thibault,
>>>
>>> A subdirectory for the example is fine; we have other examples that
>>> use subdirectories and multiple files.
>>>
>>> Note: even if you don't have something completely working you can
>>> still make MR and list it as DRAFT request for comments, some other PETSc
>>> members who understand the packages you are using and Fortran better than I
>>> may be able to help as you develop the code.
>>>
>>> Barry
>>>
>>>
>>>
>>>
>>> On Dec 16, 2020, at 12:35 AM, Thibault Bridel-Bertomeu <
>>> thibault.bridelbertomeu at gmail.com> wrote:
>>>
>>> Hello everyone,
>>>
>>> Thank you Barry for the feedback.
>>> OK, yes I'll work up an MR as soon as I have got something working. By
>>> the way, does the fortran-version of the example have to be a single file ?
>>> If my push contains a directory with several files (different modules and
>>> the main), and the Makefile that goes with it, is that ok ?
>>>
>>> Thibault Bridel-Bertomeu
>>>
>>>
>>> Le mer. 16 déc. 2020 à 04:46, Barry Smith <bsmith at petsc.dev> a écrit :
>>>
>>>>
>>>> This is great. If you make a branch off of the PETSc git repository
>>>> with these additions and work on ex11 you can make a merge request and we
>>>> can run the code easily on all our test systems (for security reasons one
>>>> of use needs to launch the tests from your MR).
>>>> https://docs.petsc.org/en/latest/developers/integration/
>>>>
>>>> Barry
>>>>
>>>>
>>>> On Dec 15, 2020, at 5:35 AM, Thibault Bridel-Bertomeu <
>>>> thibault.bridelbertomeu at gmail.com> wrote:
>>>>
>>>> Hello everyone,
>>>>
>>>> So far, I have the wrappers in the files attached to this e-mail. I
>>>> still do not know if they work properly - at least the code compiles and
>>>> the calls to the wrapped-subroutine do not fail - but I wanted to put this
>>>> here in case someone sees something really wrong with it already.
>>>>
>>>> Thank you again for your help, I'll try to post updates of the F90
>>>> version of ex11 regularly in this thread.
>>>>
>>>> Stay safe,
>>>>
>>>> Thibault Bridel-Bertomeu
>>>>
>>>> Le dim. 13 déc. 2020 à 16:39, Jed Brown <jed at jedbrown.org> a écrit :
>>>>
>>>>> Thibault Bridel-Bertomeu <thibault.bridelbertomeu at gmail.com> writes:
>>>>>
>>>>> > Thank you Mark for your answer.
>>>>> >
>>>>> > I am not sure what you think could be in the setBC1 routine ? How to
>>>>> make
>>>>> > the connection with the PetscDS ?
>>>>> >
>>>>> > On the other hand, I actually found after a while TSMonitorSet has a
>>>>> > fortran wrapper, and it does take as arguments two function
>>>>> pointers, so I
>>>>> > guess it is possible ? Although I am not sure exactly how to play
>>>>> with the
>>>>> > PetscObjectSetFortranCallback & PetscObjectUseFortranCallback macros
>>>>> -
>>>>> > could anybody advise please ?
>>>>>
>>>>> tsmonitorset_ is a good example to follow. In your file, create one of
>>>>> these static structs with a member for each callback. These are IDs that
>>>>> will be used as keys for Fortran callbacks and their contexts. The salient
>>>>> parts of the file are below.
>>>>>
>>>>> static struct {
>>>>> PetscFortranCallbackId prestep;
>>>>> PetscFortranCallbackId poststep;
>>>>> PetscFortranCallbackId rhsfunction;
>>>>> PetscFortranCallbackId rhsjacobian;
>>>>> PetscFortranCallbackId ifunction;
>>>>> PetscFortranCallbackId ijacobian;
>>>>> PetscFortranCallbackId monitor;
>>>>> PetscFortranCallbackId mondestroy;
>>>>> PetscFortranCallbackId transform;
>>>>> #if defined(PETSC_HAVE_F90_2PTR_ARG)
>>>>> PetscFortranCallbackId function_pgiptr;
>>>>> #endif
>>>>> } _cb;
>>>>>
>>>>> /*
>>>>> Note ctx is the same as ts so we need to get the Fortran context
>>>>> out of the TS; this gets put in _ctx using the callback ID
>>>>> */
>>>>> static PetscErrorCode ourmonitor(TS ts,PetscInt i,PetscReal d,Vec
>>>>> v,void *ctx)
>>>>> {
>>>>>
>>>>> PetscObjectUseFortranCallback(ts,_cb.monitor,(TS*,PetscInt*,PetscReal*,Vec
>>>>> *,void*,PetscErrorCode*),(&ts,&i,&d,&v,_ctx,&ierr));
>>>>> }
>>>>>
>>>>> Then follow as in tsmonitorset_, which sets two callbacks.
>>>>>
>>>>> PETSC_EXTERN void tsmonitorset_(TS *ts,void
>>>>> (*func)(TS*,PetscInt*,PetscReal*,Vec*,void*,PetscErrorCode*),void
>>>>> *mctx,void (*d)(void*,PetscErrorCode*),PetscErrorCode *ierr)
>>>>> {
>>>>> CHKFORTRANNULLFUNCTION(d);
>>>>> if ((PetscVoidFunction)func == (PetscVoidFunction)
>>>>> tsmonitordefault_) {
>>>>> *ierr = TSMonitorSet(*ts,(PetscErrorCode
>>>>> (*)(TS,PetscInt,PetscReal,Vec,void*))TSMonitorDefault,*(PetscViewerAndFormat**)mctx,(PetscErrorCode
>>>>> (*)(void **))PetscViewerAndFormatDestroy);
>>>>> } else {
>>>>> *ierr =
>>>>> PetscObjectSetFortranCallback((PetscObject)*ts,PETSC_FORTRAN_CALLBACK_CLASS,&_cb.monitor,(PetscVoidFunction)func,mctx);
>>>>> *ierr =
>>>>> PetscObjectSetFortranCallback((PetscObject)*ts,PETSC_FORTRAN_CALLBACK_CLASS,&_cb.mondestroy,(PetscVoidFunction)d,mctx);
>>>>> *ierr = TSMonitorSet(*ts,ourmonitor,*ts,ourmonitordestroy);
>>>>> }
>>>>> }
>>>>>
>>>> <wrapper_petsc.h90><wrapper_petsc.c>
>>>>
>>>>
>>>>
>>>
>>
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