[firedrake] FD on mac

Colin Cotter colin.cotter at imperial.ac.uk
Mon Nov 30 16:10:09 GMT 2015 

Oh, you did this, sorry.

On 30 November 2015 at 16:09, Colin Cotter <colin.cotter at imperial.ac.uk>
wrote:

> Can you try Lawrence's suggestion of trying to compile a simple Fortran
> code using mpif90:
>
> $ cat > hello.f90 << EOF
> program main
> use mph
> implicit none
> write(*, *)'Hello world'
> end program
> EOF
> $ mpif90 hello.f90 -o hello
> $ ./hello
>
> (The $s indicate a shell prompt).
>
> all the best
> --cjc
>
> On 30 November 2015 at 16:05, Onno Bokhove <O.Bokhove at leeds.ac.uk> wrote:
>
>> Tried:
>>
>>
>> 1) Updating .profile as suggested by Justin
>>
>> 2) Reinstalled home-brew after uninstalling it.
>>
>> 3) But the hello.world fortran code still crashes.
>>
>> 4) Hence, same error message holds.
>>
>>
>>  *******************************************************************************
>>
>>              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.
>>
>>
>> *******************************************************************************
>>
>>
>>
>> ...
>>
>>
>>
>>     ----------------------------------------
>>
>> Command "//anaconda/bin/python -c "import setuptools,
>> tokenize;__file__='/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-TL5bgv-build/setup.py';exec(compile(getattr(tokenize,
>> 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))"
>> install --record
>> /var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-YcsuFy-record/install-record.txt
>> --single-version-externally-managed --compile" failed with error code 1 in
>> /var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-TL5bgv-build
>>
>> Any suggestions?
>>
>> ------------------------------
>> *From:* firedrake-bounces at imperial.ac.uk <
>> firedrake-bounces at imperial.ac.uk> on behalf of Justin Chang <
>> jychang48 at gmail.com>
>> *Sent:* Monday, November 30, 2015 3:53 PM
>> *To:* Firedrake Project
>>
>> *Subject:* Re: [firedrake] FD on mac
>>
>> 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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>>>>
>>>>
>>>>
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>>>>
>>>
>>>
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>>
>
>
> --
> http://www.imperial.ac.uk/people/colin.cotter
>
> www.cambridge.org/9781107663916
>
>
>


-- 
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