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

[Jose E. Roman]

> El 22 mar 2017, a las 19:23, Barry Smith <bsmith at mcs.anl.gov> escribió:
> 
> 
>> On Mar 22, 2017, at 1:08 PM, Austin Herrema <aherrema at iastate.edu> wrote:
>> 
>> Thank you for the suggestion! Seems like a reasonable way to go. Not working for me, however, I suspect because I'm using homebrew installations of PETSc and SLEPc (I don't think all the makefiles are kept). Any other way to do the same thing by chance? Worst case I could use a non-homebrew installation but I'd prefer not to mess with that if I can help it...
> 
>   How do you link a "regular" SLEPc C program using the home-brew libraries? You need basically the same link line for f2py as you need for C programs.


What Barry may be suggesting is: instead of using a script to invoke f2py, add a rule to your makefile

modname.so: outer_driver.f90
	f2py -c -m modname outer_driver.f90 file1.o file2.o file3.o ${SLEPC_EPS_LIB}

Then 'make modname.so' will pick the libraries from SLEPc makefiles.

Jose

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