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 <[email protected]> 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 <[email protected] > <mailto:[email protected]>> 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 <[email protected] >> <mailto:[email protected]>> 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 <[email protected] >> <mailto:[email protected]>> 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@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 <[email protected] >> <mailto:[email protected]>> 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 <[email protected] >>> <mailto:[email protected]>> 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 <[email protected] >>> <mailto:[email protected]>> 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 <[email protected] >>>> <mailto:[email protected]>> 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 > > >
