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

Barry Smith bsmith at petsc.dev
Tue Jun 9 18:26:51 CDT 2020 

  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 <mailto: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 <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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <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 <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 <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 <mailto: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 <mailto: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 <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 <mailto:bsmith at petsc.dev>> wrote:
>>>> 
>>>>   You should use the PetscMatlabEngine https://www.mcs.anl.gov/petsc/petsc-3.13/docs/manualpages/Sys/PetscMatlabEngine.html <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 <mailto: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 
> 
> 
> 

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