<div dir="ltr">Makes sense, and definitely seems to be a more natural way to go now that I see it.<br><br><div>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):<br><br><div><font color="#999999">running build</font></div><div><font color="#999999">running config_cc</font></div><div><font color="#999999">unifing config_cc, config, build_clib, build_ext, build commands --compiler options</font></div><div><font color="#999999">running config_fc</font></div><div><font color="#999999">unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options</font></div><div><font color="#999999">running build_src</font></div><div><font color="#999999">build_src</font></div><div><font color="#999999">building extension "iga_blade_py" sources</font></div><div><font color="#999999">f2py options: []</font></div><div><font color="#999999">f2py:> /tmp/tmpIH70ZJ/src.macosx-10.10-x86_64-2.7/iga_blade_pymodule.c</font></div><div><font color="#999999">creating /tmp/tmpIH70ZJ/src.macosx-10.10-x86_64-2.7</font></div><div><font color="#999999">Reading fortran codes...</font></div><div><font color="#999999"><span class="gmail-Apple-tab-span" style="white-space:pre"> </span>Reading file 'run_analysis.f90' (format:free)</font></div><div><font color="#999999">Post-processing...</font></div><div><font color="#999999"><span class="gmail-Apple-tab-span" style="white-space:pre"> </span>Block: iga_blade_py</font></div><div><font color="#999999"><span class="gmail-Apple-tab-span" style="white-space:pre"> </span>Block: run_analysis</font></div><div><font color="#999999">Post-processing (stage 2)...</font></div><div><font color="#999999">Building modules...</font></div><div><font color="#999999"><span class="gmail-Apple-tab-span" style="white-space:pre"> </span>Building module "iga_blade_py"...</font></div><div><font color="#999999"><span class="gmail-Apple-tab-span" style="white-space:pre"> </span>Constructing wrapper function "run_analysis"...</font></div><div><font color="#999999"><span class="gmail-Apple-tab-span" style="white-space:pre"> </span> run_analysis()</font></div><div><font color="#999999"><span class="gmail-Apple-tab-span" style="white-space:pre"> </span>Wrote C/API module "iga_blade_py" to file "/tmp/tmpIH70ZJ/src.macosx-10.10-x86_64-2.7/iga_blade_pymodule.c"</font></div><div><font color="#999999"> adding '/tmp/tmpIH70ZJ/src.macosx-10.10-x86_64-2.7/fortranobject.c' to sources.</font></div><div><font color="#999999"> adding '/tmp/tmpIH70ZJ/src.macosx-10.10-x86_64-2.7' to include_dirs.</font></div><div><font color="#999999">copying /usr/local/lib/python2.7/site-packages/numpy/f2py/src/fortranobject.c -> /tmp/tmpIH70ZJ/src.macosx-10.10-x86_64-2.7</font></div><div><font color="#999999">copying /usr/local/lib/python2.7/site-packages/numpy/f2py/src/fortranobject.h -> /tmp/tmpIH70ZJ/src.macosx-10.10-x86_64-2.7</font></div><div><font color="#999999">build_src: building npy-pkg config files</font></div><div><font color="#999999">running build_ext</font></div><div><font color="#999999">customize UnixCCompiler</font></div><div><font color="#999999">customize UnixCCompiler using build_ext</font></div><div><font color="#999999">customize Gnu95FCompiler</font></div><div><font color="#999999">Found executable /usr/local/bin/gfortran</font></div><div><font color="#999999">customize Gnu95FCompiler</font></div><div><font color="#999999">customize Gnu95FCompiler using build_ext</font></div><div><font color="#999999">building 'iga_blade_py' extension</font></div><div><font color="#999999">compiling C sources</font></div><div><font color="#999999">C compiler: clang -fno-strict-aliasing -fno-common -dynamic -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes</font></div><div><font color="#999999"><br></font></div><div><font color="#999999">error: unknown file type '' (from '-Wl,-rpath,/usr/local/Cellar/slepc/3.7.3_4/real/lib')</font></div><div><font color="#999999">make: *** [iga_blade_py.so] Error 1</font></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Mar 22, 2017 at 1:39 PM, Jose E. Roman <span dir="ltr"><<a href="mailto:jroman@dsic.upv.es" target="_blank">jroman@dsic.upv.es</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class=""><br>
> El 22 mar 2017, a las 19:23, Barry Smith <<a href="mailto:bsmith@mcs.anl.gov">bsmith@mcs.anl.gov</a>> escribió:<br>
><br>
><br>
>> On Mar 22, 2017, at 1:08 PM, Austin Herrema <<a href="mailto:aherrema@iastate.edu">aherrema@iastate.edu</a>> wrote:<br>
>><br>
>> 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...<br>
><br>
> 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.<br>
<br>
<br>
</span>What Barry may be suggesting is: instead of using a script to invoke f2py, add a rule to your makefile<br>
<br>
modname.so: outer_driver.f90<br>
f2py -c -m modname outer_driver.f90 file1.o file2.o file3.o ${SLEPC_EPS_LIB}<br>
<br>
Then 'make modname.so' will pick the libraries from SLEPc makefiles.<br>
<span class="HOEnZb"><font color="#888888"><br>
Jose<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
><br>
>><br>
>> Thanks,<br>
>> Austin<br>
>><br>
>> On Wed, Mar 22, 2017 at 11:20 AM Jose E. Roman <<a href="mailto:jroman@dsic.upv.es">jroman@dsic.upv.es</a>> wrote:<br>
>> Try the following:<br>
>> $ cd $SLEPC_DIR<br>
>> $ make getlinklibs_slepc<br>
>> Then copy the output and paste it at the end of your f2py command.<br>
>><br>
>> Jose<br>
>><br>
>><br>
>>> El 22 mar 2017, a las 16:38, Austin Herrema <<a href="mailto:aherrema@iastate.edu">aherrema@iastate.edu</a>> escribió:<br>
>>><br>
>>> Hello all,<br>
>>><br>
>>> 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.<br>
>>><br>
>>> 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?).<br>
>>><br>
>>> 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...<br>
>>><br>
>>> Using a python script, I set up and run the f2py command. Right now it has the form...<br>
>>> "f2py -c -m modname outer_driver.f90 file1.o file2.o file3.o..." etc.<br>
>>><br>
>>> This appears to work, but upon attempting to import, it cannot find the SLEPc (and, I presume, PETSc) objects/functions:<br>
>>><br>
>>>>>> import mod_name<br>
>>> Traceback (most recent call last):<br>
>>> File "<stdin>", line 1, in <module><br>
>>> ImportError: dlopen(./mod_name.so, 2): Symbol not found: _epscreate_<br>
>>> Referenced from: ./mod_name.so<br>
>>> Expected in: flat namespace<br>
>>> in ./mod_name.so<br>
>>><br>
>>> 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.<br>
>>><br>
>>> Thank you for any help or suggestions!<br>
>>> Austin<br>
>>><br>
>>><br>
>>> --<br>
>>> Austin Herrema<br>
>>> PhD Student | Graduate Research Assistant | Iowa State University<br>
>>> Wind Energy Science, Engineering, and Policy | Mechanical Engineering<br>
>><br>
>> --<br>
>> Austin Herrema<br>
>> PhD Student | Graduate Research Assistant | Iowa State University<br>
>> Wind Energy Science, Engineering, and Policy | Mechanical Engineering<br>
><br>
<br>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div dir="ltr" style="color:rgb(136,136,136);font-size:12.8px"><b style="font-size:12.8px"><font color="#666666">Austin Herrema</font></b><br></div><div dir="ltr" style="color:rgb(136,136,136);font-size:12.8px"><div><font color="#999999">PhD Student | Graduate Research Assistant | Iowa State University</font></div><div><font color="#999999">Wind Energy Science, Engineering, and Policy | Mechanical Engineering</font></div></div></div></div>
</div>