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

Wed Mar 29 11:27:10 CDT 2017

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
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