[petsc-users] Calling MATLAB code within a parallel C/C++ code
Sanjay Govindjee
s_g at berkeley.edu
Tue Jun 9 16:55:24 CDT 2020
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
>
> 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
>
> exportDYLD_FALLBACK_LIBRARY_PATH=/Applications/MATLAB_R2019b.app/bin/maci64:/Applications/MATLAB_R2019b.app/sys/os/maci64:$DYLD_FALLBACK_LIBRARY_PATH
>
>
> exportDYLD_LIBRARY_PATH=/Applications/MATLAB_R2019b.app/bin/maci64:/Applications/MATLAB_R2019b.app/sys/os/maci64:$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
>>
>> 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
>>
>> 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
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20200609/df272182/attachment-0001.html>
More information about the petsc-users
mailing list