On Mon, 30 Nov 2015 at 17:34 Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> wrote:
> I don't think Onno is using the installation script but the old
> step-by-step instructions. I am right, Onno?
>
> The installation script does not work on my Mac either; I reported it
> some time ago but did not get any update from you. It seems that it
> might not work on Mavericks OS (?)
>
This is quite possible. Unfortunately we have no access to Mavericks
machines which makes it difficult to work fix this problem.
The script does currently work for me on El Capitan!
Regards,
David
>
> Best, Anna.
>
>
> On 30/11/15 17:27, Onno Bokhove wrote:
> > with me but florin has it working now she forgot to remove the prompt I
> think
> > I have the same os as Floriane, installed anaconda, reinstalled
> > home-brew but that did not work.
> >
> > ________________________________________
> > From: firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk>
> on behalf of Lawrence Mitchell <lawrence.mitchell(a)imperial.ac.uk>
> > Sent: Monday, November 30, 2015 5:25 PM
> > To: firedrake(a)imperial.ac.uk
> > Subject: Re: [firedrake] FD on mac
> >
> >> On 30 Nov 2015, at 17:04, Onno Bokhove <O.Bokhove(a)leeds.ac.uk> wrote:
> >>
> >> -------------------------------------
> >> No underlying compiler was specified in the wrapper compiler data file
> >> (e.g., mpicc-wrapper-data
> > Ok, so there is no fortran compiler available. I thought our install
> script installed one, but plausibly that failed to work.
> >
> > Lawrence
> > _______________________________________________
> > firedrake mailing list
> > firedrake(a)imperial.ac.uk
> > https://mailman.ic.ac.uk/mailman/listinfo/firedrake
> > _______________________________________________
> > firedrake mailing list
> > firedrake(a)imperial.ac.uk
> > https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>
> --
>
> Dr Anna Kalogirou
> Research Fellow
> School of Mathematics
> University of Leeds
>
> http://www1.maths.leeds.ac.uk/~matak/
>
>
> _______________________________________________
> firedrake mailing list
> firedrake(a)imperial.ac.uk
> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>
Well El Capitan at least has the advantage that you're on the same platform
as us, which (a) increases the chance of things working, and (b) increases
the chance us being able to reproduce any issues you encounter.
On Mon, 30 Nov 2015 at 18:10 Onno Bokhove <O.Bokhove(a)leeds.ac.uk> wrote:
> Worthwhile switching all 3 to el-capitan then?
>
>
> ------------------------------
> *From:* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk>
> on behalf of David Ham <David.Ham(a)imperial.ac.uk>
> *Sent:* Monday, November 30, 2015 6:01 PM
> *To:* firedrake
>
> *Subject:* Re: [firedrake] FD on mac
> On Mon, 30 Nov 2015 at 17:34 Anna Kalogirou <a.kalogirou(a)leeds.ac.uk>
> wrote:
>
>> I don't think Onno is using the installation script but the old
>> step-by-step instructions. I am right, Onno?
>>
>> The installation script does not work on my Mac either; I reported it
>> some time ago but did not get any update from you. It seems that it
>> might not work on Mavericks OS (?)
>>
>
> This is quite possible. Unfortunately we have no access to Mavericks
> machines which makes it difficult to work fix this problem.
>
> The script does currently work for me on El Capitan!
>
> Regards,
>
> David
>
>
>
>>
>> Best, Anna.
>>
>>
>> On 30/11/15 17:27, Onno Bokhove wrote:
>> > with me but florin has it working now she forgot to remove the prompt I
>> think
>> > I have the same os as Floriane, installed anaconda, reinstalled
>> > home-brew but that did not work.
>> >
>> > ________________________________________
>> > From: firedrake-bounces(a)imperial.ac.uk <
>> firedrake-bounces(a)imperial.ac.uk> on behalf of Lawrence Mitchell <
>> lawrence.mitchell(a)imperial.ac.uk>
>> > Sent: Monday, November 30, 2015 5:25 PM
>> > To: firedrake(a)imperial.ac.uk
>> > Subject: Re: [firedrake] FD on mac
>> >
>> >> On 30 Nov 2015, at 17:04, Onno Bokhove <O.Bokhove(a)leeds.ac.uk> wrote:
>> >>
>> >> -------------------------------------
>> >> No underlying compiler was specified in the wrapper compiler data file
>> >> (e.g., mpicc-wrapper-data
>> > Ok, so there is no fortran compiler available. I thought our install
>> script installed one, but plausibly that failed to work.
>> >
>> > Lawrence
>> > _______________________________________________
>> > firedrake mailing list
>> > firedrake(a)imperial.ac.uk
>> > https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>> > _______________________________________________
>> > firedrake mailing list
>> > firedrake(a)imperial.ac.uk
>> > https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>>
>> --
>>
>> Dr Anna Kalogirou
>> Research Fellow
>> School of Mathematics
>> University of Leeds
>>
>> http://www1.maths.leeds.ac.uk/~matak/
>>
>>
>> _______________________________________________
>> firedrake mailing list
>> firedrake(a)imperial.ac.uk
>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>>
>
Hi Onno,
What goes wrong?
all the best
--cjc
On 30 November 2015 at 17:57, Onno Bokhove <O.Bokhove(a)leeds.ac.uk> wrote:
> Yes, the script does not work either.
>
> ________________________________________
> From: firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk>
> on behalf of Anna Kalogirou <a.kalogirou(a)leeds.ac.uk>
> Sent: Monday, November 30, 2015 5:34 PM
> To: firedrake(a)imperial.ac.uk
> Subject: Re: [firedrake] FD on mac
>
> I don't think Onno is using the installation script but the old
> step-by-step instructions. I am right, Onno?
>
> The installation script does not work on my Mac either; I reported it
> some time ago but did not get any update from you. It seems that it
> might not work on Mavericks OS (?)
>
> Best, Anna.
>
>
> On 30/11/15 17:27, Onno Bokhove wrote:
> > with me but florin has it working now she forgot to remove the prompt I
> think
> > I have the same os as Floriane, installed anaconda, reinstalled
> > home-brew but that did not work.
> >
> > ________________________________________
> > From: firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk>
> on behalf of Lawrence Mitchell <lawrence.mitchell(a)imperial.ac.uk>
> > Sent: Monday, November 30, 2015 5:25 PM
> > To: firedrake(a)imperial.ac.uk
> > Subject: Re: [firedrake] FD on mac
> >
> >> On 30 Nov 2015, at 17:04, Onno Bokhove <O.Bokhove(a)leeds.ac.uk> wrote:
> >>
> >> -------------------------------------
> >> No underlying compiler was specified in the wrapper compiler data file
> >> (e.g., mpicc-wrapper-data
> > Ok, so there is no fortran compiler available. I thought our install
> script installed one, but plausibly that failed to work.
> >
> > Lawrence
> > _______________________________________________
> > firedrake mailing list
> > firedrake(a)imperial.ac.uk
> > https://mailman.ic.ac.uk/mailman/listinfo/firedrake
> > _______________________________________________
> > firedrake mailing list
> > firedrake(a)imperial.ac.uk
> > https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>
> --
>
> Dr Anna Kalogirou
> Research Fellow
> School of Mathematics
> University of Leeds
>
> http://www1.maths.leeds.ac.uk/~matak/
>
>
> _______________________________________________
> firedrake mailing list
> firedrake(a)imperial.ac.uk
> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>
> _______________________________________________
> firedrake mailing list
> firedrake(a)imperial.ac.uk
> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>
--
http://www.imperial.ac.uk/people/colin.cotterwww.cambridge.org/9781107663916
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(a)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(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk>
> on behalf of Justin Chang <jychang48(a)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(a)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(a)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(a)imperial.ac.uk>lawrence.mitchell(a)imperial.ac.uk>
>>> wrote:
>>>
>>>>
>>>> > On 27 Nov 2015, at 15:44, Onno Bokhove <O.Bokhove(a)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(a)imperial.ac.uk <
>>>> firedrake-bounces(a)imperial.ac.uk> on behalf of Wingate, Beth <
>>>> <B.Wingate(a)exeter.ac.uk>B.Wingate(a)exeter.ac.uk>
>>>> > Sent: Friday, November 27, 2015 3:41 PM
>>>> > To: firedrake(a)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(a)imperial.ac.uk
>>>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake
>>>
>>>
>>>
>>> _______________________________________________
>>> firedrake mailing list
>>> firedrake(a)imperial.ac.uk
>>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>>>
>>>
>>
>>
>> _______________________________________________
>> firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake
>>
>>
>>
>> _______________________________________________
>> firedrake mailing list
>> firedrake(a)imperial.ac.uk
>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>>
>>
>
--
http://www.imperial.ac.uk/people/colin.cotterwww.cambridge.org/9781107663916
The dollar is just a symbol for your bash prompt.
On 30 November 2015 at 17:04, Onno Bokhove <O.Bokhove(a)leeds.ac.uk> wrote:
>
> On Onno's macbook:
> cat > hello.f90 << EOF
> > program main
> > use mpi
> > implicit none
> > write(*, *)'Hello world'
> > end program
> > EOF
> math-mc1097:werk amtob$ mpif90 hello.f90 -o hello
> --------------------------------------------------------------------------
> No underlying compiler was specified in the wrapper compiler data file
> (e.g., mpicc-wrapper-data.txt)
> --------------------------------------------------------------------------
> math-mc1097:werk amtob$
>
> On Floriane's:
> With mpi I don't have an error at 'EOF', but the next command ('$ mpif90
> hello.f90 -o hello') does not work. Error: " -bash: $: command not found"
>
> ________________________________________
> From: firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk>
> on behalf of Lawrence Mitchell <lawrence.mitchell(a)imperial.ac.uk>
> Sent: Monday, November 30, 2015 4:11 PM
> To: firedrake(a)imperial.ac.uk
> Subject: Re: [firedrake] FD on mac
>
> On 30/11/15 16:09, Colin Cotter wrote:
> > use mph
>
> use mpi
>
>
> _______________________________________________
> firedrake mailing list
> firedrake(a)imperial.ac.uk
> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>
--
http://www.imperial.ac.uk/people/colin.cotterwww.cambridge.org/9781107663916
OK. I'm doing a scratch rebuild to see if I can reproduce this.
David
On Tue, 24 Nov 2015 at 21:33 Justin Chang <jychang48(a)gmail.com> wrote:
> Hi all,
>
> Just wanted to say that I am also now having these exact same issues as
> others after updating Firedrake on my mac.
>
> Thanks,
> Justin
>
> On Tue, Nov 24, 2015 at 6:11 AM, Lawrence Mitchell <
> lawrence.mitchell(a)imperial.ac.uk> wrote:
>
>>
>> On 23/11/15 16:52, Wingate, Beth wrote:
>> > module = imp.load_module(fullname, fo, fn, stuff)
>> > ImportError:
>> >
>> dlopen(/Users/wingate/firedrake/lib/python2.7/site-packages/petsc4py/lib/PETSc.so,
>> > 2): Library not loaded:
>> >
>> /private/var/folders/rw/1wgmdvd50sv7bb1dksy4y_l00000gq/T/pip-DOH6bI-build/arch-python-macosx-10.11-x86_64/lib/libpetsc.3.06.dylib
>> > Referenced from:
>> >
>> /Users/wingate/firedrake/lib/python2.7/site-packages/petsc4py/lib/PETSc.so
>> > Reason: image not found
>>
>>
>> Hmph, petsc4py has linked against the temporary location of libpetsc
>> (which appeared via pip presumably), rather than its final location.
>>
>> It is not immediately obvious to me why this would be the case. I do
>> not think it is likely anything wrong with your build setup though.
>>
>> Lawrence
>>
>>
>> _______________________________________________
>> firedrake mailing list
>> firedrake(a)imperial.ac.uk
>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>>
>>
>
Hi Onno,
I copied in the mailing list. There was a big merge last week which
Lawrence says is mostly fixed now. You might have tried to download at an
unfortunate moment. Please can you try again and report errors into this
mailing list?
all the best
--cjc
On 23 November 2015 at 11:52, Onno Bokhove <O.Bokhove(a)leeds.ac.uk> wrote:
> Hi David and Colin,
>
>
> Sorry to use the email, but what is the status of firedrake downloads for
> the mac, please?
>
> All of us mac users are crashing while downloading the new version of
> firedrake.
>
>
> We are meeting Thu in Leeds from 12-1 to tackle this issue with the
>
> laptops around one table in our meeting room. Is there any chance someone
> of the firedrake team
>
> is available on Skype or team view, or email, to help us along?
>
>
> Or any other tips regarding the mac firedrake update?
>
>
> Best wishes,
>
>
> Onno
>
>
>
>
--
http://www.imperial.ac.uk/people/colin.cotterwww.cambridge.org/9781107663916
On Thu, 26 Nov 2015 at 13:12 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> wrote:
>
> Dear all,
>
>
> Onno and I still have problem when trying to update/install Firedrake on
> our mac, at different stages. Here are the errors we get:
>
>
> I first tried to update FD, but the command to update petsc4py (pip
> install -U --no-deps git+
> https://bitbucket.org/mapdes/petsc4py.git@firedrake#egg=petsc4py) was
> taking all the application memory of the computer, and the computer just
> crashed in the end.
>
>
> So I tried to re-install Firedrake from scratch, but I still have an issue
> when trying to install petsc4py:
>
>
> - when installing Petsc, it installs version 3.7.0; I get the following
> message :
>
>
> Installing collected packages: petsc
>
> Found existing installation: petsc 3.6.2
>
> Uninstalling petsc-3.6.2:
>
> Successfully uninstalled petsc-3.6.2
>
> Running setup.py install for petsc
>
> Successfully installed petsc-3.7.0.dev0
>
> - when I then try to install petsc4py, I've got an error saying that the
> version of petsc needed must be lower than 3.7.0 :
>
> Collecting petsc<3.7,>=3.6 (from petsc4py)
>
> Could not find a version that satisfies the requirement petsc<3.7,>=3.6
> (from petsc4py) (from versions: )
>
> Some externally hosted files were ignored as access to them may be
> unreliable (use --allow-external petsc to allow).
>
> No matching distribution found for petsc<3.7,>=3.6 (from petsc4py)
>
>
This error is usually a symptom of failing to pass --no-deps to the
petsc4py build (it's a bug in upstream petsc4py really but --no-deps is
usually an adequate work around).
Regards,
David
> I tried to allow external petsc by adding the option '--allow-external
> petsc', but I then have a fatal error :
>
> fatal error: too many errors emitted, stopping now [-ferror-limit=]
>
> 1 warning and 20 errors generated.
>
> error: command '/usr/local/bin/mpicc' failed with exit status 1
>
> and this comment:
>
> Command "/Users/mmfg/anaconda/bin/python -c "import setuptools,
> tokenize;__file__='/private/tmp/pip-build-8fgPi3/petsc4py/setup.py';exec(compile(getattr(tokenize,
> 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))"
> install --record /tmp/pip-u2WItt-record/install-record.txt
> --single-version-externally-managed --compile" failed with error code 1 in
> /private/tmp/pip-build-8fgPi3/petsc4py
>
> I have also tried to install FD using your script, but I get error as well
> :
>
> Creating firedrake virtualenv.
>
> Traceback (most recent call last):
>
> File "firedrake-install", line 527, in <module>
>
> virtualenv.create_environment("firedrake", site_packages=True)
>
> File "/Users/mmfg/.local/lib/python2.7/site-packages/virtualenv.py",
> line 1004, in create_environment
>
> install_wheel(to_install, py_executable, search_dirs)
>
> File "/Users/mmfg/.local/lib/python2.7/site-packages/virtualenv.py",
> line 969, in install_wheel
>
> 'PIP_NO_INDEX': '1'
>
> File "/Users/mmfg/.local/lib/python2.7/site-packages/virtualenv.py",
> line 910, in call_subprocess
>
> % (cmd_desc, proc.returncode))
>
> OSError: Command /Users/mmfg/anaconda/bin/firedrake/bin/python -c "import
> sys, pip; sys...d\"] + sys.argv[1:]))" setuptools pip wheel failed with
> error code 1
>
> Moreover, Onno gets stalled as well at his macbook pro at:
>
>
> campus-10-41-94-68:werk amtob$ PETSC_CONFIGURE_OPTIONS="--download-ctetgen
> --download-triangle --download-chaco --download-hdf5" \
>
> > pip install https://bitbucket.org/mapdes/petsc/get/firedrake.tar.bz2
>
> Collecting https://bitbucket.org/mapdes/petsc/get/firedrake.tar.bz2
>
> Downloading https://bitbucket.org/mapdes/petsc/get/firedrake.tar.bz2
> (12.1MB)
>
> 100% |████████████████████████████████| 12.1MB 40kB/s
>
> Installing collected packages: petsc
>
> Running setup.py install for petsc
>
> Complete output from command /usr/local/opt/python/bin/python2.7 -c
> "import setuptools,
> tokenize;__file__='/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-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-I6eRXQ-record/install-record.txt
> --single-version-externally-managed --compile:
>
> running install
>
> PETSc: configure
>
> configure options:
>
> --prefix=/usr/local/lib/python2.7/site-packages/petsc
>
> PETSC_ARCH=arch-python-macosx-10.9-x86_64
>
> --with-shared-libraries=1
>
> --with-debugging=0
>
> --with-c2html=0
>
> --with-cc=/usr/local/bin/mpicc
>
> --with-cxx=/usr/local/bin/mpicxx
>
> --with-fc=/usr/local/bin/mpif90
>
> --download-ctetgen
>
> --download-triangle
>
> --download-chaco
>
> --download-hdf5
>
>
> ===============================================================================
>
> Configuring PETSc to compile on your system
>
>
> ===============================================================================
>
> TESTING: configureExternalPackagesDir from
> config.framework(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/framework.py:833)
>
> TESTING: configureDebuggers from
> config.utilities.debuggers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/utilities/debuggers.py:22)
>
> TESTING: configureGit from
> config.sourceControl(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/sourceControl.py:24)
>
> TESTING: configureCLanguage from
> PETSc.options.languages(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/languages.py:27)
>
> TESTING: configureDirectories from
> PETSc.options.petscdir(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/petscdir.py:23)
>
> TESTING: configureInstallationMethod from
> PETSc.options.petscclone(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/petscclone.py:20)
>
> TESTING: getDatafilespath from
> PETSc.options.dataFilesPath(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/dataFilesPath.py:29)
>
> TESTING: configureArchitecture from
> PETSc.options.arch(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/arch.py:25)
>
> TESTING: setInstallDir from
> PETSc.options.installDir(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/installDir.py:35)
>
> TESTING: saveReconfigure from
> PETSc.options.installDir(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/installDir.py:74)
>
> TESTING: cleanInstallDir from
> PETSc.options.installDir(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/installDir.py:67)
>
> TESTING: configureInstallDir from
> PETSc.options.installDir(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/installDir.py:51)
>
> TESTING: restoreReconfigure from
> PETSc.options.installDir(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/installDir.py:87)
>
> TESTING: setExternalPackagesDir from
> PETSc.options.externalpackagesdir(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/externalpackagesdir.py:15)
>
> TESTING: cleanExternalpackagesDir from
> PETSc.options.externalpackagesdir(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/externalpackagesdir.py:22)
>
> TESTING: printEnvVariables from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:1572)
>
> TESTING: resetEnvCompilers from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:1579)
>
> TESTING: checkEnvCompilers from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:1609)
>
> TESTING: checkMPICompilerOverride from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:1544)
>
> TESTING: requireMpiLdPath from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:1563)
>
> TESTING: checkVendor from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:402)
>
> TESTING: checkInitialFlags from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:412)
>
> TESTING: checkCCompiler from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:538)
>
> TESTING: checkCPreprocessor from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:571)
>
> TESTING: checkCUDACompiler from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:612)
>
> TESTING: checkCUDAPreprocessor from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:652)
>
> TESTING: checkCxxCompiler from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:764)
>
> TESTING: checkCxxPreprocessor from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:802)
>
> TESTING: checkFortranCompiler from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:919)
>
>
> *******************************************************************************
>
> UNABLE to EXECUTE BINARIES for ./configure
>
>
> -------------------------------------------------------------------------------
>
> Cannot run executables created with FC. If this machine uses a batch
> system
>
> to submit jobs you will need to configure using ./configure with the
> additional option --with-batch.
>
> Otherwise there is problem with the compilers. Can you compile and
> run code with your compiler '/usr/local/bin/mpif90'?
>
>
> *******************************************************************************
>
>
>
> Traceback (most recent call last):
>
> File "<string>", line 1, in <module>
>
> File
> "/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/setup.py",
> line 302, in <module>
>
> **metadata)
>
> File
> "/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py",
> line 151, in setup
>
> dist.run_commands()
>
> File
> "/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py",
> line 953, in run_commands
>
> self.run_command(cmd)
>
> File
> "/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py",
> line 972, in run_command
>
> cmd_obj.run()
>
> File
> "/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/setup.py",
> line 218, in run
>
> config(prefix, self.dry_run)
>
> File
> "/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/setup.py",
> line 148, in config
>
> if status != 0: raise RuntimeError(status)
>
> RuntimeError: 256
>
>
>
> ----------------------------------------
>
> Command "/usr/local/opt/python/bin/python2.7 -c "import setuptools,
> tokenize;__file__='/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-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-I6eRXQ-record/install-record.txt
> --single-version-externally-managed --compile" failed with error code 1 in
> /var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build
>
>
> Best regards,
> Floriane
>
> ------------------------------
> *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk>
> de la part de David Ham <David.Ham(a)imperial.ac.uk>
> *Envoyé :* mercredi 25 novembre 2015 12:03
> *À :* firedrake
> *Objet :* Re: [firedrake] FD on mac
>
> Hi all,
>
> It turns out that this is a problem in PETSc caused by a "fix" to a
> different OSX problem. We have reverted the offending commit on the
> firedrake/petsc fork so hopefully updating now should fix the issue. Please
> scream immediately if it does not.
>
> Regards,
>
> David
>
> On Tue, 24 Nov 2015 at 22:23 David Ham <David.Ham(a)imperial.ac.uk> wrote:
>
>> Reproduced. Very odd, it seems petsc4py is currently borked. I don't
>> understand where this library location is coming from. It certainly isn't
>> where the petsc python module reports the python being installed.
>>
>> On Tue, 24 Nov 2015 at 22:06 David Ham <David.Ham(a)imperial.ac.uk> wrote:
>>
>>> OK. I'm doing a scratch rebuild to see if I can reproduce this.
>>>
>>> David
>>>
>>> On Tue, 24 Nov 2015 at 21:33 Justin Chang <jychang48(a)gmail.com> wrote:
>>>
>>>> Hi all,
>>>>
>>>> Just wanted to say that I am also now having these exact same issues as
>>>> others after updating Firedrake on my mac.
>>>>
>>>> Thanks,
>>>> Justin
>>>>
>>>> On Tue, Nov 24, 2015 at 6:11 AM, Lawrence Mitchell <
>>>> lawrence.mitchell(a)imperial.ac.uk> wrote:
>>>>
>>>>>
>>>>> On 23/11/15 16:52, Wingate, Beth wrote:
>>>>> > module = imp.load_module(fullname, fo, fn, stuff)
>>>>> > ImportError:
>>>>> >
>>>>> dlopen(/Users/wingate/firedrake/lib/python2.7/site-packages/petsc4py/lib/PETSc.so,
>>>>> > 2): Library not loaded:
>>>>> >
>>>>> /private/var/folders/rw/1wgmdvd50sv7bb1dksy4y_l00000gq/T/pip-DOH6bI-build/arch-python-macosx-10.11-x86_64/lib/libpetsc.3.06.dylib
>>>>> > Referenced from:
>>>>> >
>>>>> /Users/wingate/firedrake/lib/python2.7/site-packages/petsc4py/lib/PETSc.so
>>>>> > Reason: image not found
>>>>>
>>>>>
>>>>> Hmph, petsc4py has linked against the temporary location of libpetsc
>>>>> (which appeared via pip presumably), rather than its final location.
>>>>>
>>>>> It is not immediately obvious to me why this would be the case. I do
>>>>> not think it is likely anything wrong with your build setup though.
>>>>>
>>>>> Lawrence
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> firedrake mailing list
>>>>> firedrake(a)imperial.ac.uk
>>>>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>>>>>
>>>>>
>>>>
Dear David,
Thanks for downloading Firedrake. Firedrake is a python package, not an
executable, so one would not expect to type "firedrake" on the Python
command line.
First, you need to ensure that python will see your installed Firedrake. If
you installed using the install script, then you have to source the
activate script for the Python virtualenv in which the script lives. If
your shell is in the top directory of your firedrake install, the command
to do this is:
. ./bin/activate
note the first . which is important.
Once you have done this, then from the python (preferably ipython) shell,
you can "from firedrake import *" and you are good to go. You probably want
to start by trying some of the tutorials at
http://firedrakeproject.org/documentation.html
For future support requests, please use the firedrake mailing list, to
which I have copied this answer. You'll need to subscribe at
https://mailman.ic.ac.uk/mailman/listinfo/firedrake
Regards,
David
On Tue, 24 Nov 2015 at 13:52 Angwenyi David <kipkoej(a)gmail.com> wrote:
> Dear sir,
>
> I am doctoral student of Prof. Dr. Sebastian Reich, Universität Potsdam.
> We have been trying to install and run firedrake. It has been installed
> successfully but I seemingly cannot start it off by typing ‘firedrake’ at
> the Python command line; or rather, when I do try it this way, I get a
> feedback: command not found. Could you please advise.
>
> Thanks in advance.
>
> Angwenyi David
Hi Stephan. Thanks, I will look into this first thing next week and will
get back to you.
Cheers
-- Fabio
2015-11-19 14:59 GMT+00:00 Kramer, Stephan <s.kramer(a)imperial.ac.uk>:
> Hey guys
>
> More weirdness related to facet integrals from IP viscosity that only
> appears with COFFEE optimisations. This time both on the bendy branches
> and on master (of last week). In the code below, the matrices M, Ms and
> M1+M2 should all be the same.
>
> For DG1 they are not equal on a recent (last week, before any sprint
> merges) install of firedrake/ffc/ufl/coffee on master. It is also
> incorrect on an older install I had, so it's not a recent thing. DG1
> does however produce the right answer on the bendy branches: firedrake
> (bendy_changes) + ffc/ufl (fd_bendy) + coffee (master).
>
> For RT1 on the other hand it's the opposite: the matrices are correct
> and equal on master, but with bendy some of them are different from the
> correct answer.
>
> All of this only if use COFFEE optimisation, i.e. with
> parameters['coffee']={} the matrices are correct and all equal.
>
> I realize at this point the best thing to do is probably to wait if this
> all gets magically fixed when the sprint is over - will report back if
> not - but just thought to let you guys know already
>
> Cheers
> Stephan
>
> from firedrake import *
> mesh2d = UnitSquareMesh(1,1)
> U = VectorFunctionSpace(mesh2d, "DG", 1)
> v = TestFunction(U)
> u = Function(U)
>
> #parameters['coffee']={}
> n = FacetNormal(mesh2d)
>
> def outer_jump(v, n):
> return outer(v('+'), n('+'))+outer(v('-'), n('-'))
>
> F1 = inner(outer_jump(v, n), outer_jump(u,n))*dS
> F2 = inner(outer_jump(v, n), outer_jump(n,u))*dS
> F = inner(outer_jump(v, n), outer_jump(u,n)+outer_jump(n,u))*dS
>
> M1 = assemble(derivative(F1, u)).M.values
> M2 = assemble(derivative(F2, u)).M.values
> Ms = assemble(derivative(F1+F2, u)).M.values
> M = assemble(derivative(F, u)).M.values
> print abs(M-(M1+M2)).max()
> print abs(M-Ms).max()
>
>
> _______________________________________________
> firedrake mailing list
> firedrake(a)imperial.ac.uk
> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>