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

[Barry Smith]

  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


   
> On Mar 22, 2017, at 11:20 AM, Jose E. Roman <jroman at dsic.upv.es> wrote:
> 
> Try the following:
> $ cd $SLEPC_DIR
> $ make getlinklibs_slepc
> Then copy the output and paste it at the end of your f2py command.
> 
> Jose
> 
> 
>> El 22 mar 2017, a las 16:38, Austin Herrema <aherrema at iastate.edu> escribió:
>> 
>> Hello all,
>> 
>> I am trying to do as the subject line describes--use f2py to run a large PETSc/SLEPc fortran finite element code through python. I really only need to wrap the outermost function of the fortran code--don't need any access to subroutines. I'll describe what I'm doing, some of which I'm not 100% confident is correct (not much experience with f2py)--feel free to correct/redirect any of it.
>> 
>> First, I'm editing the fortran code so that the top-level function is a subroutine rather than a main program (it's my understanding that this is required for f2py?).
>> 
>> I use my regular makefile (modeled after a standard SLEPc makefile from the user guide) to compile all of the .f90/.F90 files (many of them) to .o files using SLEPc/PETSc rules. The final linking phase fails since there isn't a main program, but I'm just ignoring that for now since that's not what I ultimately need...
>> 
>> Using a python script, I set up and run the f2py command. Right now it has the form...
>> "f2py -c -m modname outer_driver.f90 file1.o file2.o file3.o..." etc.
>> 
>> This appears to work, but upon attempting to import, it cannot find the SLEPc (and, I presume, PETSc) objects/functions:
>> 
>>>>> import mod_name
>> Traceback (most recent call last):
>>  File "<stdin>", line 1, in <module>
>> ImportError: dlopen(./mod_name.so, 2): Symbol not found: _epscreate_
>>  Referenced from: ./mod_name.so
>>  Expected in: flat namespace
>> in ./mod_name.so
>> 
>> Based on this discussion, I believe I need to somehow include PETSc/SLEPc info when linking with f2py. Is that correct? Any direction on how to do that? I don't quite understand what the OP of that question ultimately ended up doing to get it to work. I tried using the -I flag pointing to the slepc_common file (like the SLEPc makefile does). The problem is that that is a file, not a directory, which contains a number of other makefile-style variables--so it works to include it in a makefile, but doesn't work in python. Maybe there are only a few directories I really need to include? Or is it possible to somehow run f2py through a makefile? I'm a bit ignorant in that realm as well.
>> 
>> Thank you for any help or suggestions!
>> Austin
>> 
>> 
>> -- 
>> Austin Herrema
>> PhD Student | Graduate Research Assistant | Iowa State University
>> Wind Energy Science, Engineering, and Policy | Mechanical Engineering
>