[firedrake] FD on mac

[Justin Chang]

Miklos,

Yes my error has been resolved by recompiling spatialindex with the same
homebrew compilers as was used for firedrake

Thanks
Justin

On Mon, Nov 30, 2015 at 3:29 AM, Miklós Homolya <m.homolya14 at imperial.ac.uk>
wrote:

> Please let me know if that fixes your problem.
>
>
> On 28/11/15 20:08, Justin Chang wrote:
>
> Ah right, didn't think about that. Got it, thanks!
>
> On Sat, Nov 28, 2015 at 3:35 AM, Miklós Homolya <
> m.homolya14 at imperial.ac.uk> wrote:
>
>> With respect to the libspatialindex problem:
>>
>> Yes, see https://github.com/firedrakeproject/firedrake/issues/640
>>
>> I suggest you to try rebuilding libspatialindex from source (you can do
>> that with homebrew) using the same compiler as you used to build firedrake.
>>
>>
>> On 28/11/15 07:11, Justin Chang wrote:
>>
>> Hi all,
>>
>> I also had the mpif90 error on my El Capitan Macbook, but worked around
>> it by rebuilding the openmpi with the latest brew gcc compilers (GCC
>> 5.2.0). It seems the default configuration provided by Homebrew is built
>> with Apple's compilers (and thus has no wrapper for the mpif90). I put
>> these in my ~/.profile:
>>
>> export HOMEBREW_CC=gcc-5
>> export HOMEBREW_CXX=g++-5
>> export FC=gfortran-5
>>
>> and rebuilt openmpi via:
>>
>>
>> brew reinstall openmpi --build-from-source
>>
>>
>> Firedrake installs successfully, but now I am running into a spatialindex
>> related problem whenever I try to import the firedrake module:
>>
>>
>> python -c 'from firedrake import *'
>>
>> Traceback (most recent call last):
>>
>>   File "<string>", line 1, in <module>
>>
>>   File
>> "/Users/justin/Software/firedrake/src/firedrake/firedrake/__init__.py",
>> line 31, in <module>
>>
>>     from firedrake.assemble import *
>>
>>   File
>> "/Users/justin/Software/firedrake/src/firedrake/firedrake/assemble.py",
>> line 10, in <module>
>>
>>     from firedrake import assemble_expressions
>>
>>   File
>> "/Users/justin/Software/firedrake/src/firedrake/firedrake/assemble_expressions.py",
>> line 17, in <module>
>>
>>     from firedrake import function
>>
>>   File
>> "/Users/justin/Software/firedrake/src/firedrake/firedrake/function.py",
>> line 14, in <module>
>>
>>     from firedrake import functionspace
>>
>>   File
>> "/Users/justin/Software/firedrake/src/firedrake/firedrake/functionspace.py",
>> line 17, in <module>
>>
>>     import firedrake.mesh as mesh_t
>>
>>   File
>> "/Users/justin/Software/firedrake/src/firedrake/firedrake/mesh.py", line
>> 16, in <module>
>>
>>     import firedrake.spatialindex as spatialindex
>>
>> ImportError:
>> dlopen(/Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so,
>> 2): Symbol not found:
>> __ZN5Tools11PropertySet11setPropertyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_7VariantE
>>
>>   Referenced from:
>> /Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so
>>
>>   Expected in: flat namespace
>>
>>  in
>> /Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so
>>
>> Looks like something went awry with spatialindex. Anyone else having this
>> problem?
>>
>> Thanks,
>> Justin
>>
>> On Fri, Nov 27, 2015 at 11:26 AM, Lawrence Mitchell <
>> <lawrence.mitchell at imperial.ac.uk>lawrence.mitchell at imperial.ac.uk>
>> wrote:
>>
>>>
>>> > On 27 Nov 2015, at 15:44, Onno Bokhove <O.Bokhove at leeds.ac.uk> wrote:
>>> >
>>> > That is what I got yesterday, but Floriane Gidel went past it on her
>>> mac laptop.
>>> > Computer IT staff and I could not figure out what it was.
>>> > We tried anaconda (worked with Floriane), but not with me.
>>> > He thought my mpif90 was probably slightly older: so reloading Xcode
>>> an option?
>>> > Updating the OS?
>>>
>>> Hopefully not!
>>>
>>> > From: firedrake-bounces at imperial.ac.uk <
>>> firedrake-bounces at imperial.ac.uk> on behalf of Wingate, Beth <
>>> <B.Wingate at exeter.ac.uk>B.Wingate at exeter.ac.uk>
>>> > Sent: Friday, November 27, 2015 3:41 PM
>>> > To: firedrake at imperial.ac.uk
>>> > Subject: Re: [firedrake] FD on mac
>>> >
>>> > I’m getting the same thing — firedrake now doesn’t install due to
>>> “mpif90” not working:
>>> >
>>> >     TESTING: checkFortranCompiler from
>>> config.setCompilers(/private/var/folders/zn/46_9pn0x2k32_z59z6fw5j2w0000gn/T/pip-AO07XK-build/config/BuildSystem/config/setCompilers.py:919)
>>> >
>>>  *******************************************************************************
>>> >              UNABLE to CONFIGURE with GIVEN OPTIONS    (see
>>> configure.log for details):
>>> >
>>>  -------------------------------------------------------------------------------
>>> >     Fortran compiler you provided with --with-fc=/usr/local/bin/mpif90
>>> does not work.
>>> >     Cannot compile FC with /usr/local/bin/mpif90.
>>> >
>>>  *******************************************************************************
>>>
>>>
>>> If you try to compile the following simple Fortran hello world code with
>>> mpif90, what happens?
>>>
>>> $ cat > hello.f90 << EOF
>>> program main
>>> use mph
>>> implicit none
>>> write(*, *)'Hello world'
>>> end program
>>> EOF
>>> $ mpif90 hello.f90 -o hello
>>> $ ./hello
>>>
>>> Cheers,
>>>
>>> Lawrence
>>>
>>>
>>> _______________________________________________
>>> firedrake mailing list
>>> firedrake at imperial.ac.uk
>>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>>>
>>>
>>
>>
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