[petsc-users] Calling MATLAB code within a parallel C/C++ code
Junchao Zhang
junchao.zhang at gmail.com
Tue Jun 9 16:51:05 CDT 2020
Find recursively where is libeng.dylib under
/Applications/MATLAB_R2019b.app/extern/engines/
--Junchao Zhang
On Tue, Jun 9, 2020 at 4:27 PM Amneet Bhalla <mail2amneet at gmail.com> wrote:
> 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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