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

Wed Mar 29 17:12:19 CDT 2017

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? 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
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