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

[Austin Herrema]

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
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