[petsc-users] memory scalable AO

[Barry Smith]

> On Feb 17, 2016, at 8:58 PM, Randall Mackie <rlmackie862 at gmail.com> wrote:
> 
> If I remove lines 47-50 in daindexf.c (the PETSC_EXTERN …for dmdasetaotype_), then when I try to compile the test code, it complains of an undefined reference to dmdasetaotype_.
> 
> So I put the lines back in, and with your patch applied, and then run in the debugger, with a breakpoint at dmdasetaotype_, it stops at /src/dm/impls/da/ftn-auto/daindexf.c.
> 
> 3 steps later, at *__ierr = DMDASetAOType( 
> 
> is where it bombs out.
> 
> 
> So it seems to be ignoring the dmdasetaotype_ in /src/dm/impls/da/ftn-custom/zdaindexf.c in favor of ../ftn-auto/daindexf.c

   This makes no sense. Ok just try pasting the new definition in daindexf.c. instead of the old one, compile and run.

Barry

> 
> Randy
> 
> 
>> On Feb 17, 2016, at 6:31 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>> 
>> 
>> It is probably my fault. Edit src/dm/impls/da/ftn-auto/daindexf.c and remove the function function from that file and then run make on the library again. If that does not work then run in the debugger and put a break point in dmdasetaotype_ once it is there in the debugger you can make sure it is the right function and step until it crashes to see what I have done wrong.
>> 
>>  Baryr
>> 
>>> On Feb 17, 2016, at 7:29 PM, Randall Mackie <rlmackie862 at gmail.com> wrote:
>>> 
>>> Unfortunately I am getting exactly the same result.
>>> 
>>> I applied the patch (patch -p1 < fix-fortran-dmdasetaotype.patch)
>>> 
>>> Then I recompiled the library, and my code, but the error remains.
>>> 
>>> Perhaps there is something else I’m missing?
>>> 
>>> Randy
>>> 
>>> 
>>>> On Feb 17, 2016, at 3:15 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>>>> 
>>>> 
>>>> Here is  patch. <fix-fortran-dmdasetaotype.patch>
>>>> 
>>>> If it works for you I'll put it in maint and master tomorrow.
>>>> 
>>>> Barry
>>>> 
>>>>> On Feb 17, 2016, at 3:46 PM, Randall Mackie <rlmackie862 at gmail.com> wrote:
>>>>> 
>>>>> The attached test program demonstrates the problem. When I run it, I get the following output:
>>>>> 
>>>>> [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: [0] PetscStrlen line 150 /home/rmackie/PETSc/petsc-3.6.3/src/sys/utils/str.c
>>>>> [0]PETSC ERROR: [0] PetscStrallocpy line 185 /home/rmackie/PETSc/petsc-3.6.3/src/sys/utils/str.c
>>>>> [0]PETSC ERROR: [0] DMDASetAOType line 84 /home/rmackie/PETSc/petsc-3.6.3/src/dm/impls/da/daindex.c
>>>>> [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.
>>>>> 
>>>>> 
>>>>> Randy
>>>>> 
>>>>> 
>>>>>> On Feb 17, 2016, at 11:35 AM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>>>>>> 
>>>>>> 
>>>>>> Should be ok. Do you have implicit none and the correct include files so AOMEMORYSCALABLE is defined?
>>>>>> 
>>>>>> I think you need to run in the debugger next to track why this happens.
>>>>>> 
>>>>>> Barry
>>>>>> 
>>>>>>> On Feb 17, 2016, at 11:33 AM, Randall Mackie <rlmackie862 at gmail.com> wrote:
>>>>>>> 
>>>>>>> What is the correct way to set the AO for a DMDA to be the memory scalable version?
>>>>>>> 
>>>>>>> I have tried this:
>>>>>>> 
>>>>>>> call DMDASetAOType(da,AOMEMORYSCALABLE,ierr)
>>>>>>> call DMDAGetAO(da,ao,ierr)
>>>>>>> 
>>>>>>> The code compiles fine, but I simply get a Segmentation Violation when I run it:
>>>>>>> 
>>>>>>> [3]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>> [3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
>>>>>>> [3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>>>>>>> [3]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>>>>>>> [3]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
>>>>>>> [3]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
>>>>>>> [3]PETSC ERROR: to get more information on the crash.
>>>>>>> [3]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
>>>>>>> [3]PETSC ERROR: Signal received
>>>>>>> [3]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>>>>>>> [3]PETSC ERROR: Petsc Release Version 3.6.3, Dec, 03, 2015 
>>>>>>> [3]PETSC ERROR: Configure options PETSC_ARCH=linux-gfortran-opt --with-clean=1 --with-scalar-type=complex --with-debugging=0 --with-fortran=1 --download-mpich=./mpich-3.1.3.tar.gz --FOPTFLAGS=-O3 --COPTFLAGS=-O3
>>>>>>> [3]PETSC ERROR: #1 User provided function() line 0 in  unknown file
>>>>>>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3
>>>>>>> [cli_3]: aborting job:
>>>>>>> 
>>>>>>> 
>>>>>>> In fact, I get the same thing even if I set the AOType to AOBASIC, in other words
>>>>>>> 
>>>>>>> call DMDASetAOTYPE(da,AOBASIC,ierr)
>>>>>>> 
>>>>>>> 
>>>>>>> Previously, I did not set an AOType, and only called DMDAGetAO, which works fine, and from what I can tell sets the type to basic.
>>>>>>> 
>>>>>>> 
>>>>>>> Thanks, Randy M.
>>>>>> 
>>>>> <test.F90><makefile>
>>>> 
>>> 
>> 
>