[firedrake] error installing PyOP2

[Fabio Luporini]

If everything is up-to-date, you might have to clean the caches (run
firedrake/scripts/firedrake-clean)

-- Fabio

2015-08-06 2:19 GMT+01:00 Justin Chang <jychang48 at gmail.com>:

> Lawrence,
>
> Upgrading "six" resolved that issue. However, when I attempt to run my
> mixed-poisson.py I get this error:
>
> Traceback (most recent call last):
>
>   File "mixed-poisson.py", line 79, in <module>
>
>     solver_parameters=selfp_parameters)
>
>   File
> "/Users/justin/Software/firedrake-deps/firedrake/firedrake/variational_solver.py",
> line 231, in __init__
>
>     super(LinearVariationalSolver, self).__init__(*args, **kwargs)
>
>   File
> "/Users/justin/Software/firedrake-deps/firedrake/firedrake/variational_solver.py",
> line 110, in __init__
>
>     ctx = solving_utils._SNESContext(problem)
>
>   File
> "/Users/justin/Software/firedrake-deps/firedrake/firedrake/solving_utils.py",
> line 105, in __init__
>
>     for problem in problems)
>
>   File
> "/Users/justin/Software/firedrake-deps/firedrake/firedrake/solving_utils.py",
> line 105, in <genexpr>
>
>     for problem in problems)
>
>   File
> "/Users/justin/Software/firedrake-deps/firedrake/firedrake/assemble.py",
> line 67, in assemble
>
>     inverse=inverse, nest=nest)
>
>   File
> "/Users/justin/Software/firedrake-deps/firedrake/firedrake/assemble.py",
> line 100, in _assemble
>
>     inverse=inverse)
>
>   File
> "/Users/justin/Software/firedrake-deps/firedrake/firedrake/ffc_interface.py",
> line 285, in compile_form
>
>     ffc_kernel = FFCKernel(f, name + str(i) + str(j), parameters)
>
>   File
> "/usr/local/lib/python2.7/site-packages/PyOP2-0.11.0_368_g6ee644d-py2.7-macosx-10.10-x86_64.egg/pyop2/caching.py",
> line 201, in __new__
>
>     return cls._cache_lookup(key)
>
>   File
> "/usr/local/lib/python2.7/site-packages/PyOP2-0.11.0_368_g6ee644d-py2.7-macosx-10.10-x86_64.egg/pyop2/caching.py",
> line 253, in _cache_lookup
>
>     return cls._cache.get(key) or cls._read_from_disk(key)
>
>   File
> "/usr/local/lib/python2.7/site-packages/PyOP2-0.11.0_368_g6ee644d-py2.7-macosx-10.10-x86_64.egg/pyop2/caching.py",
> line 279, in _read_from_disk
>
>     val = cPickle.loads(val)
> AttributeError: 'module' object has no attribute 'ColSparseArrayInit'
>
> This was after pulling the latest PyOP2 and firedrake repositories.
>
> Thanks,
> Justin
>
> On Wed, Aug 5, 2015 at 3:50 AM, Lawrence Mitchell <
> lawrence.mitchell at imperial.ac.uk> wrote:
>
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>> Hi Justin,
>>
>> On 04/08/15 23:05, Justin Chang wrote:
>> > Coming back to this.
>> >
>> > I believe I have puled the latest petsc, petsc4py, and PyOP2
>> > repositories onto my laptop. Following through with all the
>> > (re)installation, I come across this error when I run 'make test'
>> > in PyOP2:
>> >
>> > Error in atexit._run_exitfuncs:
>>
>> Sorry for these continued pains!
>>
>> So PyOP2 imports cPickle elsewhere, so I think this module most exist.
>>  Plausibly the "six" module on your system is not sufficiently up-to-date.
>>
>> Does the following fail:
>>
>> python -c "from six.moves.cPickle import dumps"
>>
>> If that works, I'm very confused, but I suspect it won't.
>>
>> If it doesn't work, can you try installing an updated "six" module:
>>
>> pip install --user six
>>
>> and then go again.
>>
>> Lawrence
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>>
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>
>
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