Re: [petsc-dev] calling petsc from a mex file

[Vaclav Hapla]

I confirm the same problem. But I also don't know how to fix this 
systematically in the buildsystem. I found hard-coded -L options here
  
https://bitbucket.org/petsc/petsc/src/9e21ac129fc054b3abeb584f186c61369f6d442a/config/BuildSystem/config/packages/MatlabEngine.py#lines-39
but I'm in doubts I can do the same with -Wl,-rpath.

Vaclav

> 9. 5. 2018 v 18:49, Munson, Todd :
> 
> 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.

Re: [petsc-dev] calling petsc from a mex file

[Munson, Todd]

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.  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  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.  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  wrote:
 
 
 
> On May 8, 2018, at 1:02 PM, Smith, Barry F.  wrote:
> 
> 
> 
>> On May 8, 2018, at 12:30 PM, Munson, Todd  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
 

Re: [petsc-dev] calling petsc from a mex file

[Smith, Barry F.]

  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  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.  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  wrote:
>>> 
>>> 
>>> 
 On May 8, 2018, at 1:02 PM, Smith, Barry F.  wrote:
 
 
 
> On May 8, 2018, at 12:30 PM, Munson, Todd  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
>> 
> 

Re: [petsc-dev] calling petsc from a mex file

[Munson, Todd]

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.  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  wrote:
>> 
>> 
>> 
>>> On May 8, 2018, at 1:02 PM, Smith, Barry F.  wrote:
>>> 
>>> 
>>> 
 On May 8, 2018, at 12:30 PM, Munson, Todd  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
> 

Re: [petsc-dev] calling petsc from a mex file

[Smith, Barry F.]

  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  wrote:
> 
> 
> 
>> On May 8, 2018, at 1:02 PM, Smith, Barry F.  wrote:
>> 
>> 
>> 
>>> On May 8, 2018, at 12:30 PM, Munson, Todd  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

Re: [petsc-dev] calling petsc from a mex file

[Munson, Todd]

> On May 8, 2018, at 1:02 PM, Smith, Barry F.  wrote:
> 
> 
> 
>> On May 8, 2018, at 12:30 PM, Munson, Todd  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

Re: [petsc-dev] calling petsc from a mex file

[Smith, Barry F.]

> On May 8, 2018, at 12:30 PM, Munson, Todd  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.

> 
> I have tried compiling both with --download-mpich and --with-mpi=0 with the
> same outcome.
> 
> Maybe I am missing something flags I need to set when configuring petsc?
> 
> Any help would be appreciated.
> 
> My backup plan is to rewrite the matlab code that wants to invoke a petsc 
> solver so 
> that I can make it work using a PetscMatlabEngine instead.
> 
> Thanks, Todd.
> 

[petsc-dev] calling petsc from a mex file

[Munson, Todd]

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.

I have tried compiling both with --download-mpich and --with-mpi=0 with the
same outcome.

Maybe I am missing something flags I need to set when configuring petsc?

Any help would be appreciated.

My backup plan is to rewrite the matlab code that wants to invoke a petsc 
solver so 
that I can make it work using a PetscMatlabEngine instead.

Thanks, Todd.