[petsc-users] How to use f2py on a PETSc/SLEPc-based fortran code

Austin Herrema aherrema at iastate.edu
Thu Mar 30 09:12:28 CDT 2017 

Indeed it did seem to be an issue with the integer of value 500 in that
function call (8 byte/4 byte? Don't know...). Upon explicitly using a
PetscInt variable, everything works just fine.

Thank you, everyone, for your patient help!

Best,
Austin



On Wed, Mar 29, 2017 at 6:48 PM, Matthew Knepley <knepley at gmail.com> wrote:

> On Wed, Mar 29, 2017 at 5:12 PM, Austin Herrema <aherrema at iastate.edu>
> wrote:
>
>> Quick update on this issue in case it brings any other thoughts/ideas to
>> light. For a very simple, small problem, I am successfully able to use
>> MatSeqAIJSetPreallocation in a fortran-based code compiled for python via
>> f2py. I am still unsure why, in a larger code, this particular function
>> call fails when the code is executed in python (on a setup that runs fine
>> under pure Fortran). Does the error " nnz cannot be greater than row
>> length: local row 2 value 1330400321 rowlength 37065" imply that the
>> program thinks I am trying to allocate 1330400321 nonzeros in a row of
>> max length 37065?
>>
>
> Yes.
>
>   Thanks,
>
>     Matt
>
>
>> That is obviously not my intent nor what I think I have coded. I am
>> trying to skip preallocation and use merely MatSetUp but, as we would
>> expect, the dynamic allocation is ridiculously slow...
>>
>> On Wed, Mar 29, 2017 at 11:27 AM, Austin Herrema <aherrema at iastate.edu>
>> wrote:
>>
>>> Got it--just had to link against other compiled source, as you said.
>>> I've attached my makefile for doing everything (including variable
>>> definitions, compiling source, and running requisite f2py commands) in case
>>> that's helpful for anyone else trying to do something similar. But
>>> obviously the meat of it is in what Gaetan provided.
>>>
>>> I am now able to successfully run simple PETSc-based fortran codes in
>>> python. For a larger, more complex code, I am getting some PETSc errors
>>> when running in python that I don't normally get. In particular,
>>> preallocation is failing--the relevant fortran code block and PETSc error
>>> is below.
>>>
>>>
>>>     call MatCreate(PETSC_COMM_WORLD, LHS_pc, pc_ier)
>>>     call MatSetSizes(LHS_pc, PETSC_DECIDE, PETSC_DECIDE, NSD*FUN%NNODE,
>>> NSD*FUN%NNODE, pc_ier)
>>>     call MatSetFromOptions(LHS_pc, pc_ier)
>>>     call MatSeqAIJSetPreallocation(LHS_pc, 500, PETSC_NULL_INTEGER,
>>> pc_ier)
>>>
>>>
>>> [0]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>> [0]PETSC ERROR: Argument out of range
>>> [0]PETSC ERROR: nnz cannot be greater than row length: local row 2 value
>>> 1330400321 rowlength 37065
>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>>> for trouble shooting.
>>> [0]PETSC ERROR: Petsc Release Version 3.7.5, Jan, 01, 2017
>>> [0]PETSC ERROR: Unknown Name on a real named
>>> austin-ethernet.student.iastate.edu by Austin Wed Mar 29 10:59:33 2017
>>> [0]PETSC ERROR: Configure options CC=/usr/local/bin/mpicc
>>> CXX=/usr/local/bin/mpicxx F77=/usr/local/bin/mpif77
>>> FC=/usr/local/bin/mpif90 --with-shared-libraries=1 --with-pthread=0
>>> --with-openmp=0 --with-debugging=1 --with-ssl=0
>>> --with-superlu_dist-include=/usr/local/opt/superlu_dist/include
>>> --with-superlu_dist-lib="-L/usr/local/opt/superlu_dist/lib
>>> -lsuperlu_dist" --with-fftw-dir=/usr/local/opt/fftw
>>> --with-netcdf-dir=/usr/local/opt/netcdf --with-suitesparse-dir=/usr/local/opt/suite-sparse
>>> --with-hdf5-dir=/usr/local/opt/hdf5 --with-metis-dir=/usr/local/opt/metis
>>> --with-parmetis-dir=/usr/local/opt/parmetis
>>> --with-scalapack-dir=/usr/local/opt/scalapack
>>> --with-mumps-dir=/usr/local/opt/mumps/libexec --with-x=0
>>> --prefix=/usr/local/Cellar/petsc/3.7.5/real --with-scalar-type=real
>>> --with-hypre-dir=/usr/local/opt/hypre --with-sundials-dir=/usr/local/opt/sundials
>>> --with-hwloc-dir=/usr/local/opt/hwloc
>>> [0]PETSC ERROR: #1 MatSeqAIJSetPreallocation_SeqAIJ() line 3598 in
>>> /private/tmp/petsc-20170223-508-1xeniyc/petsc-3.7.5/src/mat/
>>> impls/aij/seq/aij.c
>>> [0]PETSC ERROR: #2 MatSeqAIJSetPreallocation() line 3570 in
>>> /private/tmp/petsc-20170223-508-1xeniyc/petsc-3.7.5/src/mat/
>>> impls/aij/seq/aij.c
>>>
>>>
>>> Is there anything about the MatSeqAIJSetPreallocation function that
>>> would make it not work correctly in Python even though everything else
>>> seems to work properly? If anyone has thoughts on this that would be great.
>>> But, again, I do realize I'm venturing into potentially unsupported
>>> territory.
>>>
>>>
>>> On Tue, Mar 28, 2017 at 4:53 PM, Gaetan Kenway <gaetank at gmail.com>
>>> wrote:
>>>
>>>> Looks like it isn't finding your source from run_analysis.f90. You
>>>> still need to compile that yourself and include in the final link. In my
>>>> example, all the "original" source code was precompiled into a library from
>>>> a different makefile and then this was run after-the-fact.
>>>>
>>>> Gaetan
>>>>
>>>> On Tue, Mar 28, 2017 at 2:38 PM, Austin Herrema <aherrema at iastate.edu>
>>>> wrote:
>>>>
>>>>> Gotcha. In that case, it seems I should be good without that line.
>>>>> I've gotten the compile to succeed, but upon attempting to import the
>>>>> module I get the following:
>>>>>
>>>>> >>> import run_analysis_final
>>>>> Traceback (most recent call last):
>>>>>   File "<stdin>", line 1, in <module>
>>>>> ImportError: dlopen(./run_analysis_final.so, 2): Symbol not found:
>>>>> _run_analysis_
>>>>>   Referenced from: ./run_analysis_final.so
>>>>>   Expected in: flat namespace
>>>>>  in ./run_analysis_final.so
>>>>>
>>>>> Seems I may have gotten the linking wrong somehow. Will keep
>>>>> searching, but the simplified makefile that I used is attached in case
>>>>> anyone thinks they might be able to spot the issue in it. That said, I do
>>>>> realize that this may be starting to reach beyond the scope of this mailing
>>>>> list so feel free to ignore...
>>>>>
>>>>> On Tue, Mar 28, 2017 at 2:31 PM, Gaetan Kenway <gaetank at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> You only get that file if you have wrapped a module explicitly in the
>>>>>> .pyf file. If you haven't wrapped a module, that doesn't get created.
>>>>>>
>>>>>> Gaetan
>>>>>>
>>>>>> On Tue, Mar 28, 2017 at 12:28 PM, Austin Herrema <
>>>>>> aherrema at iastate.edu> wrote:
>>>>>>
>>>>>>> Gaetan,
>>>>>>>
>>>>>>> Thank you for this. With your help, I think I am getting close to
>>>>>>> getting this to work for my case. At the moment, I am hung up on the line
>>>>>>> of your makefile which reads "$(FF90) $(FF90_ALL_FLAGS) -I$(MAIN_DIR)/mod
>>>>>>> -c warpustruct-f2pywrappers2.f90". Am I correct that
>>>>>>> warpustruct-f2pywrappers2.f90 should be generated by f2py? If so, do you
>>>>>>> (or does anyone else) know the command for telling f2py to do so? At the
>>>>>>> moment I am using:
>>>>>>>
>>>>>>> f2py run_analysis.f90 -m run_analysis -h run_analysis.pyf
>>>>>>>
>>>>>>> to get the requisite .pyf and .c files, but no .f90 file. If I am
>>>>>>> wrong about the origin of this file, please do tell me!
>>>>>>>
>>>>>>> Thank you,
>>>>>>> Austin
>>>>>>>
>>>>>>> On Mon, Mar 27, 2017 at 5:13 PM, Gaetan Kenway <gaetank at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Austin
>>>>>>>>
>>>>>>>> Here is the full makefile for a code we use. The variables defined
>>>>>>>> externally in a separate config file are:
>>>>>>>> $(FF90)
>>>>>>>> $(FF90_FLAGS)
>>>>>>>> $(LIBDIR)
>>>>>>>> $(PETSC_LINKER_FLAGS)
>>>>>>>> $(LINKER_FLAGS)
>>>>>>>> $(CGNS_LINKER_FLAGS)
>>>>>>>>
>>>>>>>> $(PYTHON)
>>>>>>>> $(PYTHON-CONIFG)
>>>>>>>> $(F2PY)
>>>>>>>> (These are usually use python, python-config and f2py. You can
>>>>>>>> overwrite as necessary)
>>>>>>>>
>>>>>>>> $(CC)
>>>>>>>> $(CC_ALL_FLAGS)
>>>>>>>>
>>>>>>>> This essentially just mimics what f2py does automatically but we
>>>>>>>> found it easier to control exactly what is going on. Essentially you are
>>>>>>>> just compiling exactly as you normally an executable, but instead make a
>>>>>>>> .so (with the -shared option) and including the additional .o files
>>>>>>>> generated by compiling the f2py-generated wrappers.
>>>>>>>>
>>>>>>>> Hope this helps,
>>>>>>>> Gaetan
>>>>>>>>
>>>>>>>> On Sat, Mar 25, 2017 at 5:38 AM, Lisandro Dalcin <dalcinl at gmail.com
>>>>>>>> > wrote:
>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 22 March 2017 at 20:29, Barry Smith <bsmith at mcs.anl.gov> wrote:
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>   Lisandro,
>>>>>>>>>>
>>>>>>>>>>     We've had a couple questions similar to this with f2py; is
>>>>>>>>>> there a way we could add to the PETSc/SLEPc makefile rules something to
>>>>>>>>>> allow people to trivially use f2py without having to make their own (often
>>>>>>>>>> incorrect) manual command lines?
>>>>>>>>>>
>>>>>>>>>>    Thanks
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> Barry, it is quite hard and hacky to get f2py working in the
>>>>>>>>> general case. I think the email from Gaetan in this thread proves my point.
>>>>>>>>>
>>>>>>>>> IMHO, it is easier to write a small Fortran source exposing the
>>>>>>>>> API to call using ISO_C_BINDINGS, then wrap that code with the more
>>>>>>>>> traditional C-based "static" tools (SWIG, Cython) or even "dynamically"
>>>>>>>>> with ctypes or cffi (which use dlopen'ing).
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Lisandro Dalcin
>>>>>>>>> ============
>>>>>>>>> Research Scientist
>>>>>>>>> Computer, Electrical and Mathematical Sciences & Engineering
>>>>>>>>> (CEMSE)
>>>>>>>>> Extreme Computing Research Center (ECRC)
>>>>>>>>> King Abdullah University of Science and Technology (KAUST)
>>>>>>>>> http://ecrc.kaust.edu.sa/
>>>>>>>>>
>>>>>>>>> 4700 King Abdullah University of Science and Technology
>>>>>>>>> al-Khawarizmi Bldg (Bldg 1), Office # 0109
>>>>>>>>> Thuwal 23955-6900, Kingdom of Saudi Arabia
>>>>>>>>> http://www.kaust.edu.sa
>>>>>>>>>
>>>>>>>>> Office Phone: +966 12 808-0459 <+966%2012%20808%200459>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> *Austin Herrema*
>>>>>>> PhD Student | Graduate Research Assistant | Iowa State University
>>>>>>> Wind Energy Science, Engineering, and Policy | Mechanical Engineering
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> *Austin Herrema*
>>>>> PhD Student | Graduate Research Assistant | Iowa State University
>>>>> Wind Energy Science, Engineering, and Policy | Mechanical Engineering
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> *Austin Herrema*
>>> PhD Student | Graduate Research Assistant | Iowa State University
>>> Wind Energy Science, Engineering, and Policy | Mechanical Engineering
>>>
>>
>>
>>
>> --
>> *Austin Herrema*
>> PhD Student | Graduate Research Assistant | Iowa State University
>> Wind Energy Science, Engineering, and Policy | Mechanical Engineering
>>
>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>



-- 
*Austin Herrema*
PhD Student | Graduate Research Assistant | Iowa State University
Wind Energy Science, Engineering, and Policy | Mechanical Engineering
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