[petsc-dev] calling petsc from a mex file

Wed May 9 11:49:23 CDT 2018

There is some issue with my matlab installation.  I also tried it on linux and the 
simple Petsc initialize and finalize work fine.  When I start setting up
and using TaoSolve, I get a segmentation violation.

I am going to switch to using the PetscMatlabEngine, which is what I should
have done from the beginning; that seems to be the safer option.

Note: I compiled the latest Petsc using --with-matlab and changed to the
src/snes/examples/tutorials directory and did a "make ex5".  The
compilation works fine, but the "-Wl,-rpath" for the matlab
libraries is missing and I have to set my DYLD_LIBRARY_PATH
manually.  I don't know where to fix this in the build
system.

Thanks, Todd.

> On May 9, 2018, at 1:55 AM, Smith, Barry F. <bsmith at mcs.anl.gov> wrote:
> 
> 
>  Huh
> 
> $ matlab -nodisplay
> 
>                                              < M A T L A B (R) >
>                                    Copyright 1984-2018 The MathWorks, Inc.
>                                     R2018a (9.4.0.813654) 64-bit (maci64)
>                                               February 23, 2018
> 
> Warning: Name is nonexistent or not a directory: /Users/barrysmith/Src/nodal-dg/Codes1.1 
> Warning: Name is nonexistent or not a directory: /Users/barrysmith/Src/nodal-dg/Codes1.1/CFD2D 
> Warning: Name is nonexistent or not a directory: /Users/barrysmith/Src/nodal-dg/Codes1.1 
> 
> To get started, type one of these: helpwin, helpdesk, or demo.
> For product information, visit www.mathworks.com.
> 
>>> taopounders()
>>> exit
> ~/Src/petsc/src/tao/leastsquares/examples/matlab (tmunson/tao-pounders-matlab-interface=) arch-matlab
> 
> 
>> On May 8, 2018, at 2:30 PM, Munson, Todd <tmunson at mcs.anl.gov> wrote:
>> 
>> 
>> Its in tmunson/tao-pounders-matlab-interface
>> 
>> Most of the code is commented out or otherwise inactive.  There is a hacked
>> command in src/tao/leastsquares/examples/matlab that I use to compile the
>> mex file.
>> 
>> To test, you should be able to start matlab and say "taopounders(); exit".
>> 
>> Todd.
>> 
>>> On May 8, 2018, at 2:21 PM, Smith, Barry F. <bsmith at mcs.anl.gov> wrote:
>>> 
>>> 
>>> Push the branch that does this or send me the code and I'll debug it. I now have some vague memory about this behavior.
>>> 
>>>  Barry
>>> 
>>> 
>>>> On May 8, 2018, at 1:53 PM, Munson, Todd <tmunson at mcs.anl.gov> wrote:
>>>> 
>>>> 
>>>> 
>>>>> On May 8, 2018, at 1:02 PM, Smith, Barry F. <bsmith at mcs.anl.gov> wrote:
>>>>> 
>>>>> 
>>>>> 
>>>>>> On May 8, 2018, at 12:30 PM, Munson, Todd <tmunson at mcs.anl.gov> wrote:
>>>>>> 
>>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> I wonder if anyone has experience calling petsc from matlab using mex.  I have the 
>>>>>> simplest possible mexFunction that just calls PetscInitialize() and 
>>>>>> PetscFinalize().  That part seems to work fine, but when I exit 
>>>>>> from matlab I get a segmentation violation and a petsc error
>>>>>> message.
>>>>> 
>>>>> What are all the error messages? Cut and paste. I've done this in the past but not for years.
>>>> 
>>>> Below is the matlab session and error message.  I do note that if I issue PetscFinalize() and 
>>>> that command completes, the Petsc signal handlers remain installed/active.  If I do a
>>>> PetscPopSignalHandler() immediately after PetscInitialize(), I do not get the error
>>>> message, but a "Segmentation fault: 11" output at the end.
>>>> 
>>>> Because petsc is being loaded as a dynamic library, are there possibly uninitialized global
>>>> variables or state?
>>>> 
>>>> Thanks, Todd.
>>>> 
>>>> [0]PETSC ERROR: ------------------------------------------------------------------------
>>>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
>>>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>>>> [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>>>> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
>>>> [0]PETSC ERROR: likely location of problem given in stack below
>>>> [0]PETSC ERROR: ---------------------  Stack Frames ------------------------------------
>>>> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
>>>> [0]PETSC ERROR:       INSTEAD the line number of the start of the function
>>>> [0]PETSC ERROR:       is given.
>>>> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
>>>> [0]PETSC ERROR: Signal received
>>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>>>> [0]PETSC ERROR: Petsc Development GIT revision: v3.9.1-409-gf553c6556e  GIT Date: 2018-05-07 17:17:17 -0500
>>>> [0]PETSC ERROR: Unknown Name on a arch-darwin-c-debug named eduroam062-089.wl.anl-external.org by tmunson Tue May  8 12:04:45 2018
>>>> [0]PETSC ERROR: Configure options --download-mpich CC=/usr/bin/clang CXX=/usr/bin/clang++ FC=/opt/local/bin/gfortran
>>>> [0]PETSC ERROR: #1 User provided function() line 0 in  unknown file
>>>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>>>> [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=59
>>>> :
>>>> system msg for write_line failure : Bad file descriptor
>>> 
>> 
> 