[firedrake] FD on mac

Colin Cotter colin.cotter at imperial.ac.uk
Mon Nov 30 16:09:52 GMT 2015 

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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>


-- 
http://www.imperial.ac.uk/people/colin.cotter

www.cambridge.org/9781107663916
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