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

Thu Mar 23 12:14:19 CDT 2017

Sorry to self-bump this. Sounds like there are no quick and easy answers to
get this solved, which I understand. I just wanted to say that if anybody
has any suggestions about what I should be looking into specifically (C
compiler? f2py? etc...) then even that would be helpful as I'm pretty stuck
on this. And I have also posted a discussion on StackOverflow (
http://stackoverflow.com/questions/42978049/unable-to-use-f2py-to-link-large-petsc-slepc-fortran-code?noredirect=1#comment73055943_42978049)
in case anything there might be useful (it's mostly all the same).

Thank you regardless!
Austin

On Wed, Mar 22, 2017 at 2:08 PM, Austin Herrema <aherrema at iastate.edu>
wrote:

> Makes sense, and definitely seems to be a more natural way to go now that
> I see it.
>
> When compiling using this rule it seems to get close but doesn't compile
> all the way. Here is the output (in reality, what I was referring to as
> "modname.so" is "iga_blade_py.so" and the "outer_driver.f90" is called
> merely "run_analysis.f90"--sorry for the confusion):
>
> running build
> running config_cc
> unifing config_cc, config, build_clib, build_ext, build commands
> --compiler options
> running config_fc
> unifing config_fc, config, build_clib, build_ext, build commands
> --fcompiler options
> running build_src
> build_src
> building extension "iga_blade_py" sources
> f2py options: []
> f2py:> /tmp/tmpIH70ZJ/src.macosx-10.10-x86_64-2.7/iga_blade_pymodule.c
> creating /tmp/tmpIH70ZJ/src.macosx-10.10-x86_64-2.7
> Reading fortran codes...
> Reading file 'run_analysis.f90' (format:free)
> Post-processing...
> Block: iga_blade_py
> Block: run_analysis
> Post-processing (stage 2)...
> Building modules...
> Building module "iga_blade_py"...
> Constructing wrapper function "run_analysis"...
>  run_analysis()
> Wrote C/API module "iga_blade_py" to file "/tmp/tmpIH70ZJ/src.macosx-10.
> 10-x86_64-2.7/iga_blade_pymodule.c"
>   adding '/tmp/tmpIH70ZJ/src.macosx-10.10-x86_64-2.7/fortranobject.c' to
> sources.
>   adding '/tmp/tmpIH70ZJ/src.macosx-10.10-x86_64-2.7' to include_dirs.
> copying /usr/local/lib/python2.7/site-packages/numpy/f2py/src/fortranobject.c
> -> /tmp/tmpIH70ZJ/src.macosx-10.10-x86_64-2.7
> copying /usr/local/lib/python2.7/site-packages/numpy/f2py/src/fortranobject.h
> -> /tmp/tmpIH70ZJ/src.macosx-10.10-x86_64-2.7
> build_src: building npy-pkg config files
> running build_ext
> customize UnixCCompiler
> customize UnixCCompiler using build_ext
> customize Gnu95FCompiler
> Found executable /usr/local/bin/gfortran
> customize Gnu95FCompiler
> customize Gnu95FCompiler using build_ext
> building 'iga_blade_py' extension
> compiling C sources
> C compiler: clang -fno-strict-aliasing -fno-common -dynamic -g -O2
> -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
>
> error: unknown file type '' (from '-Wl,-rpath,/usr/local/Cellar/
> slepc/3.7.3_4/real/lib')
> make: *** [iga_blade_py.so] Error 1
>
> On Wed, Mar 22, 2017 at 1:39 PM, Jose E. Roman <jroman at dsic.upv.es> wrote:
>
>>
>> > 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
>> >
>>
>>
>
>
> --
> *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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