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
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 <[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
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
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
