[petsc-users] Calling MATLAB code within a parallel C/C++ code
Amneet Bhalla
mail2amneet at gmail.com
Fri Jun 12 00:00:43 CDT 2020
This is so cool! Thank you for providing a gateway to MATLAB via PETSc.
On Thu, Jun 11, 2020 at 6:21 PM Barry Smith <bsmith at petsc.dev> wrote:
>
>
> On Jun 11, 2020, at 2:47 PM, Amneet Bhalla <mail2amneet at gmail.com> wrote:
>
> Ok, I'm able to call and use MATLAB functionality from PETSc. If I'm
> understanding correctly, when PetscMatlabEngineCreate() is called, a
> MATLAB workspace is created, that persists until PetscMatlabEngineDestroy()
> is called. PETSc can access/put/manipulate variables in this workspace, and
> can also call several MATLAB scripts and MATLAB functions, and subsequently
> access/manipulate new data created in the existing workspace. Is there
> something else that I should keep in mind to take advantage of Engine
> functionality or to avoid pitfalls. Also are there any limitations on
> MATLAB toolboxes that cannot be used via the Engine framework? I don't
> anticipate using any graphical interface functionality via MatlabEngine.
>
>
> Yes this is all correct. It seems the Matlab engine is Matlab so it
> provides all the functionality of standalone Matlab.
>
> You can use Matlab graphics as usual if you run your program with the
> additional option "-matlab_engine_graphics We just had it off by default
> because sometimes Matlab Engine may have trouble access the users
> graphics/window system but hopefully it won't be a problem
>
> Barry
>
>
>
>
>
> On Tue, Jun 9, 2020 at 4:26 PM Barry Smith <bsmith at petsc.dev> wrote:
>
>>
>> Great, yes you should not need the DYLIB paths
>>
>> The branch is off master but what you can do is copy the
>> config/BuildSystem/config/MatlabEngine.py to your PETSc 3.12.2 version and
>> the configure
>> should work (it won't automatically run the test case but you can test it
>> manually).
>>
>> Barry
>>
>>
>> On Jun 9, 2020, at 5:48 PM, Amneet Bhalla <mail2amneet at gmail.com> wrote:
>>
>> That worked!
>>
>> amneetb at Amneets-MBP:~/Softwares/PETSc-Gitlab/petsc-matlab$ make
>> PETSC_DIR=/Users/amneetb/Softwares/PETSc-Gitlab/petsc-matlab
>> PETSC_ARCH=darwin-dbg check
>> Running check examples to verify correct installation
>> Using PETSC_DIR=/Users/amneetb/Softwares/PETSc-Gitlab/petsc-matlab and
>> PETSC_ARCH=darwin-dbg
>> C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process
>> C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI
>> processes
>> C/C++ example src/snes/tutorials/ex19 run successfully with hypre
>> Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI
>> process
>> C/C++ example src/vec/vec/tutorials/ex31 run successfully with Matlab
>> engine
>> Completed test examples
>>
>> Should I remove DYLIB paths from .profile since these are now baked in
>> the linker?
>>
>> Also, Is this branch based-off of latest master? I'm currently using
>> PETSc v3.12.2 for IBAMR. Anything close to this version should work for
>> me.
>>
>>
>> On Tue, Jun 9, 2020 at 3:17 PM Barry Smith <bsmith at petsc.dev> wrote:
>>
>>>
>>> I tried including the directories into my DYLD environmental
>>> variables and it didn't work; I am not sure why. This might be why
>>> https://stackoverflow.com/questions/35568122/why-isnt-dyld-library-path-being-propagated-here
>>>
>>> Anyways try my branch and that should work.
>>>
>>> Barry
>>>
>>>
>>>
>>> On Jun 9, 2020, at 5:09 PM, Amneet Bhalla <mail2amneet at gmail.com> wrote:
>>>
>>>
>>> That's where I also found it. Thanks, Sanjay!
>>>
>>> (This path is included in my .profile file
>>>
>>> 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
>>>
>>>
>>>
>>> )
>>>
>>> Do I need to tell PETSc about this path as well? Something like:
>>>
>>>
>>> --with-matlab-engine-lib=/Applications/MATLAB_R2019b.app/bin/maci64/libeng.dylib
>>>
>>>
>>> On Tue, Jun 9, 2020 at 2:56 PM Sanjay Govindjee <s_g at berkeley.edu>
>>> wrote:
>>>
>>>> Try looking in:
>>>>
>>>> $(MLROOT)/bin/maci64
>>>>
>>>> where MLROOT = /Applications/MATLAB_R2019a.app or the like
>>>>
>>>>
>>>>
>>>> On 6/9/20 2:51 PM, Junchao Zhang 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
>>>
>>>
>>>
>>>
>>>
>>
>> --
>> --Amneet
>>
>>
>>
>>
>>
>
> --
> --Amneet
>
>
>
>
>
--
--Amneet
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