[petsc-users] Calling MATLAB code within a parallel C/C++ code
Amneet Bhalla
mail2amneet at gmail.com
Tue Jun 9 16:58:59 CDT 2020
It is under
amneetb at Amneets-MBP:/Applications/MATLAB_R2019b.app/bin/maci64$ ls
*eng.dylib
libeng.dylib*
On Tue, Jun 9, 2020 at 2:51 PM Junchao Zhang <junchao.zhang at gmail.com>
wrote:
> 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
>>
>>
>>
>>
--
--Amneet
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20200609/5bdda307/attachment-0001.html>
More information about the petsc-users
mailing list