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

Barry Smith bsmith at petsc.dev
Tue Jun 9 17:17:28 CDT 2020 

   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> 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 
> 
> 
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20200609/bdecd17f/attachment-0001.html>

More information about the petsc-users mailing list