[firedrake] FD on mac

Mon Nov 30 16:05:14 GMT 2015

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<mailto: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<mailto: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 <<mailto:lawrence.mitchell at imperial.ac.uk>lawrence.mitchell at imperial.ac.uk<mailto:lawrence.mitchell at imperial.ac.uk>> wrote:

> On 27 Nov 2015, at 15:44, Onno Bokhove <O.Bokhove at leeds.ac.uk<mailto: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<mailto:firedrake-bounces at imperial.ac.uk> <firedrake-bounces at imperial.ac.uk<mailto:firedrake-bounces at imperial.ac.uk>> on behalf of Wingate, Beth <<mailto:B.Wingate at exeter.ac.uk>B.Wingate at exeter.ac.uk<mailto:B.Wingate at exeter.ac.uk>>
> Sent: Friday, November 27, 2015 3:41 PM
> To: firedrake at imperial.ac.uk<mailto: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

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