[petsc-users] Calling MATLAB code within a parallel C/C++ code

Amneet Bhalla mail2amneet at gmail.com
Tue Jun 9 16:26:15 CDT 2020 

Forgot to mention that configure found the following about MATLAB

Matlab:

  Includes: -I/Applications/MATLAB_R2019b.app/extern/include

  /Applications/MATLAB_R2019b.app

MatlabEngine:

  Library:  -L/Applications/MATLAB_R2019b.app/bin/maci64
-L/Applications/MATLAB_R2019b.app/extern/lib/maci64 -leng -lmex -lmx -lmat
-lut -licudata -licui18n -licuuc

On Tue, Jun 9, 2020 at 2:20 PM Amneet Bhalla <mail2amneet at gmail.com> wrote:

> Do these additional configure flags for MATLAB look OK?
>
> --with-matlab=1 --with-matlab-dir=/Applications/MATLAB_R2019b.app
> --with-matlab-engine=1
> --with-matlab-engine-dir=/Applications/MATLAB_R2019b.app/extern/engines/
>
>
>
>
> With this configuration make compiled files like:
>
>
>           CC darwin-dbg/obj/sys/classes/viewer/impls/matlab/vmatlab.o
>
>           CC
> darwin-dbg/obj/sys/classes/viewer/impls/matlab/ftn-custom/zvmatlabf.o
>
>           CC darwin-dbg/obj/sys/classes/matlabengine/matlab.o
>
>           CC darwin-dbg/obj/sys/classes/matlabengine/ftn-auto/matlabf.o
>
>           CC darwin-dbg/obj/sys/classes/matlabengine/ftn-custom/zmatlabf.o
>
>           CC darwin-dbg/obj/vec/pf/impls/matlab/cmatlab.o
>
>           CC darwin-dbg/obj/vec/vec/utils/matlab/gcreatev.o
>
>
> make[2]: Leaving directory `/Users/amneetb/Softwares/PETSc-Gitlab/PETSc'
>
> BEGINNING TO COMPILE MATLAB INTERFACE
>
> Building with 'Xcode with Clang'.
>
> ld: warning: cannot export hidden symbol _mexfilerequiredapiversion from
> c_mexapi_version.o
>
>
> ld: warning: cannot export hidden symbol _mexfilerequiredapiversion from
> c_mexapi_version.o
>
>
> MEX completed successfully.
>
> Building with 'Xcode with Clang'.
>
> ld: warning: cannot export hidden symbol _mexfilerequiredapiversion from
> c_mexapi_version.o
>
>
> ld: warning: cannot export hidden symbol _mexfilerequiredapiversion from
> c_mexapi_version.o
>
>
> MEX completed successfully.
>
> Building with 'Xcode with Clang'.
>
> ld: warning: cannot export hidden symbol _mexfilerequiredapiversion from
> c_mexapi_version.o
>
>
> MEX completed successfully.
>
> Building with 'Xcode with Clang'.
>
> ld: warning: cannot export hidden symbol _mexfilerequiredapiversion from
> c_mexapi_version.o
>
>
> ld: warning: cannot export hidden symbol _mexfilerequiredapiversion from
> c_mexapi_version.o
>
>
> MEX completed successfully.
>
>
> However, make check gives error
>
>
> amneetb at Amneets-MBP:~/Softwares/PETSc-Gitlab/PETSc$ make
> PETSC_DIR=/Users/amneetb/Softwares/PETSc-Gitlab/PETSc PETSC_ARCH=darwin-dbg
> check
>
> Running test examples to verify correct installation
>
> Using PETSC_DIR=/Users/amneetb/Softwares/PETSc-Gitlab/PETSc and
> PETSC_ARCH=darwin-dbg
>
> Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI
> process
>
> See http://www.mcs.anl.gov/petsc/documentation/faq.html
>
> dyld: Library not loaded: @rpath/libeng.dylib
>
>   Referenced from:
> /Users/amneetb/Softwares/PETSc-Gitlab/PETSc/src/snes/examples/tutorials/./ex19
>
>   Reason: image not found
>
>
>
> ===================================================================================
>
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>
> =   PID 14057 RUNNING AT Amneets-MBP
>
> =   EXIT CODE: 6
>
> =   CLEANING UP REMAINING PROCESSES
>
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>
>
> ===================================================================================
>
> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Abort trap: 6 (signal 6)
>
> This typically refers to a problem with your application.
>
> Please see the FAQ page for debugging suggestions
>
> Possible error running C/C++ src/snes/examples/tutorials/ex19 with 2 MPI
> processes
>
> See http://www.mcs.anl.gov/petsc/documentation/faq.html
>
> dyld: Library not loaded: @rpath/libeng.dylib
>
>   Referenced from:
> /Users/amneetb/Softwares/PETSc-Gitlab/PETSc/src/snes/examples/tutorials/./ex19
>
>   Reason: image not found
>
> dyld: Library not loaded: @rpath/libeng.dylib
>
>   Referenced from:
> /Users/amneetb/Softwares/PETSc-Gitlab/PETSc/src/snes/examples/tutorials/./ex19
>
>   Reason: image not found
>
>
>
> ===================================================================================
>
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>
> =   PID 14062 RUNNING AT Amneets-MBP
>
> =   EXIT CODE: 6
>
> =   CLEANING UP REMAINING PROCESSES
>
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>
>
> ===================================================================================
>
> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Abort trap: 6 (signal 6)
>
> This typically refers to a problem with your application.
>
> Please see the FAQ page for debugging suggestions
>
> 1,5c1,17
>
> < lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
>
> <   0 SNES Function norm 0.0406612
>
> <   1 SNES Function norm 4.12227e-06
>
> <   2 SNES Function norm 6.098e-11
>
> < Number of SNES iterations = 2
>
> ---
>
> > dyld: Library not loaded: @rpath/libeng.dylib
>
> >   Referenced from:
> /Users/amneetb/Softwares/PETSc-Gitlab/PETSc/src/snes/examples/tutorials/./ex19
>
> >   Reason: image not found
>
> > dyld: Library not loaded: @rpath/libeng.dylib
>
> >   Referenced from:
> /Users/amneetb/Softwares/PETSc-Gitlab/PETSc/src/snes/examples/tutorials/./ex19
>
> >   Reason: image not found
>
> >
>
> >
> ===================================================================================
>
> > =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>
> > =   PID 14072 RUNNING AT Amneets-MBP
>
> > =   EXIT CODE: 6
>
> > =   CLEANING UP REMAINING PROCESSES
>
> > =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>
> >
> ===================================================================================
>
> > YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Abort trap: 6 (signal
> 6)
>
> > This typically refers to a problem with your application.
>
> > Please see the FAQ page for debugging suggestions
>
> /Users/amneetb/Softwares/PETSc-Gitlab/PETSc/src/snes/examples/tutorials
>
> Possible problem with ex19 running with hypre, diffs above
>
> =========================================
>
> Possible error running Fortran example src/snes/examples/tutorials/ex5f
> with 1 MPI process
>
> See http://www.mcs.anl.gov/petsc/documentation/faq.html
>
> dyld: Library not loaded: @rpath/libeng.dylib
>
>   Referenced from:
> /Users/amneetb/Softwares/PETSc-Gitlab/PETSc/src/snes/examples/tutorials/./ex5f
>
>   Reason: image not found
>
>
>
> ===================================================================================
>
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>
> =   PID 14211 RUNNING AT Amneets-MBP
>
> =   EXIT CODE: 6
>
> =   CLEANING UP REMAINING PROCESSES
>
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>
>
> ===================================================================================
>
> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Abort trap: 6 (signal 6)
>
> This typically refers to a problem with your application.
>
> Please see the FAQ page for debugging suggestions
>
> Completed test examples
>
>
> I have added the following paths in my .profile and sourced it before make
> all and make check
>
> export DYLD_FALLBACK_LIBRARY_PATH=
> /Applications/MATLAB_R2019b.app/bin/maci64:/Applications/MATLAB_R2019b.app/sys/os/maci64:
> $DYLD_FALLBACK_LIBRARY_PATH
>
>
> export DYLD_LIBRARY_PATH=
> /Applications/MATLAB_R2019b.app/bin/maci64:/Applications/MATLAB_R2019b.app/sys/os/maci64:
> $DYLD_LIBRARY_PATH
>
>
>
>
> On Mon, Jun 8, 2020 at 6:39 PM Barry Smith <bsmith at petsc.dev> wrote:
>
>>
>>   Looks like the tool to list the examples in the manual pages is broken
>> since it didn't find these other examples, I'll take a look at it.
>>
>>   There is also a discussion in the users manual
>>
>> $ git grep MatlabEngine | grep ex
>> src/docs/tex/manual/part2.tex:PetscMatlabEngineCreate(MPI_Comm comm,char
>> *machine,PetscMatlabEngine *e);
>> src/docs/tex/manual/part2.tex:PetscMatlabEnginePut(PetscMatlabEngine
>> e,PetscObject obj);
>> src/docs/tex/manual/part2.tex:PetscMatlabEngineGet(PetscMatlabEngine
>> e,PetscObject obj);
>> src/docs/tex/manual/part2.tex:PetscMatlabEnginePutArray(PetscMatlabEngine
>> e,int m,int n,PetscScalar *array,char *name);
>> src/docs/tex/manual/part2.tex:PetscMatlabEngineGetArray(PetscMatlabEngine
>> e,int m,int n,PetscScalar *array,char *name);
>>
>> src/docs/tex/manual/part2.tex:PetscMatlabEngineEvaluate(PetscMatlabEngine,"format",...);
>> src/docs/tex/manual/part2.tex:PetscMatlabEngineEvaluate(PetscMatlabEngine,"x
>> = \%g *y + z;",avalue);
>> src/docs/tex/manual/part2.tex:PetscMatlabEngineGetOutput(PetscMatlabEngine,char
>> **);
>>
>> src/docs/tex/manual/part2.tex:PetscMatlabEnginedPrintOutput(PetscMatlabEngine,FILE*).
>> src/snes/tutorials/ex5.c:  ierr =
>> PetscMatlabEnginePut(PETSC_MATLAB_ENGINE_(comm),(PetscObject)localX);CHKERRQ(ierr);
>> src/snes/tutorials/ex5.c:  ierr =
>> PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_(comm),"localF=ex5m(localX,%18.16e,%18.16e,%18.16e)",hx,hy,lambda);CHKERRQ(ierr);
>> src/snes/tutorials/ex5.c:  ierr =
>> PetscMatlabEngineGet(PETSC_MATLAB_ENGINE_(comm),(PetscObject)localF);CHKERRQ(ierr);
>> src/sys/tests/ex16.c:static char help[] = "Demonstrates
>> PetscMatlabEngineXXX()\n";
>> src/sys/tests/ex16.c:  ierr =
>> PetscMatlabEngineGetOutput(PETSC_MATLAB_ENGINE_(PETSC_COMM_WORLD),&output);CHKERRQ(ierr);
>> src/sys/tests/ex16.c:  ierr =
>> PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_(PETSC_COMM_WORLD),"MPI_Comm_rank");CHKERRQ(ierr);
>> src/sys/tests/ex16.c:    ierr =
>> PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_(PETSC_COMM_WORLD),user);CHKERRQ(ierr);
>> src/vec/vec/tests/ex31.c:static const char help[] = "Demonstrates
>> PetscMatlabEngineXXX()\n";
>> src/vec/vec/tests/ex31.c:  ierr =
>> PetscMatlabEngineGetOutput(PETSC_MATLAB_ENGINE_WORLD,&output);
>> src/vec/vec/tests/ex31.c:  ierr =
>> PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_WORLD,"MPI_Comm_rank");
>> src/vec/vec/tests/ex31.c:  ierr =
>> PetscMatlabEnginePut(PETSC_MATLAB_ENGINE_WORLD,(PetscObject)x);CHKERRQ(ierr);
>> src/vec/vec/tests/ex31.c:  ierr =
>> PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_WORLD,"x = x +
>> MPI_Comm_rank;\n");
>> src/vec/vec/tests/ex31.c:  ierr =
>> PetscMatlabEngineGet(PETSC_MATLAB_ENGINE_WORLD,(PetscObject)x);CHKERRQ(ierr);
>> src/vec/vec/tests/ex31.c:  ierr =
>> PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_WORLD,"whos\n");CHKERRQ(ierr);
>>
>> On Jun 8, 2020, at 8:26 PM, Amneet Bhalla <mail2amneet at gmail.com> wrote:
>>
>> Great!
>>
>> Clicking on some of the functions pointed me to this example
>> https://www.mcs.anl.gov/petsc/petsc-3.13/src/snes/tutorials/ex5.c.html
>>
>> Are there more examples, which are perhaps simpler than the above, which
>> I can refer to?
>>
>> On Mon, Jun 8, 2020 at 5:51 PM Barry Smith <bsmith at petsc.dev> wrote:
>>
>>>
>>>   You should use the PetscMatlabEngine
>>> https://www.mcs.anl.gov/petsc/petsc-3.13/docs/manualpages/Sys/PetscMatlabEngine.html
>>>
>>>   Barry
>>>
>>>
>>> On Jun 8, 2020, at 7:09 PM, Amneet Bhalla <mail2amneet at gmail.com> wrote:
>>>
>>> Hi Folks,
>>>
>>> My parallel application written in C++ (which also uses PETSc library
>>> for linear solvers) requires calling control and optimization toolbox of
>>> MATLAB at every time step to get a small number of double values. Likewise
>>> the MATLAB function will need to know some values from the parallel C++
>>> application to return those doubles. I'm wondering if there is a
>>> recommended way of calling MATLAB from parallel C/C++/Fortran codes, and if
>>> PETSc has some interface that could be leveraged for this exchange.
>>>
>>> Thanks,
>>> --
>>> --Amneet
>>>
>>>
>>>
>>>
>>>
>>
>> --
>> --Amneet
>>
>>
>>
>>
>>
>
> --
> --Amneet
>
>
>
>

-- 
--Amneet
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