Dolfin import error

[mwathen@…]

Hi,

I updated my macport packages and when I now try and import dolfin i get the following error

import dolfin
---------------------------------------------------------------------------
Exception                                 Traceback (most recent call last)
<ipython-input-1-7d9b2153bc0b> in <module>()
----> 1 import dolfin

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/__init__.py in <module>()
      2 
      3 # Special module to handle import issues
----> 4 import dolfin.importhandler
      5 
      6 # Import UFL form language

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/importhandler/__init__.py in <module>()
     37 for dep in runtime_dependencies:
     38     try:
---> 39         __import__(dep)
     40     except ImportError, e:
     41         import sys

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ffc/__init__.py in <module>()
     16 
     17 # Import compiler functions
---> 18 from ffc.compiler import compile_form, compile_element
     19 
     20 # Import JIT compiler

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ffc/compiler.py in <module>()
    125 
    126 # FFC modules
--> 127 from ffc.analysis import analyze_forms, analyze_elements
    128 from ffc.representation import compute_ir
    129 from ffc.optimization import optimize_ir

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ffc/analysis.py in <module>()
     40 from ffc.log import log, info, begin, end, warning, debug, error, ffc_assert, warning_blue
     41 from ffc.utils import all_equal
---> 42 from ffc.quadratureelement import default_quadrature_degree
     43 from ffc.utils import all_equal
     44 from ffc.tensor import estimate_cost

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ffc/quadratureelement.py in <module>()
     25 
     26 # FIAT modules.
---> 27 from FIAT.functional import PointEvaluation
     28 
     29 # FFC modules.

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/FIAT/__init__.py in <module>()
      9 
     10 # Import finite element classes
---> 11 from FIAT.finite_element import FiniteElement
     12 from FIAT.argyris import Argyris
     13 from FIAT.argyris import QuinticArgyris

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/FIAT/finite_element.py in <module>()
     17 
     18 import numpy
---> 19 from .polynomial_set import PolynomialSet
     20 
     21 class FiniteElement:

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/FIAT/polynomial_set.py in <module>()
     27 # an entire set of polynomials)
     28 
---> 29 from . import expansions
     30 import numpy
     31 from .functional import index_iterator

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/FIAT/expansions.py in <module>()
     32 Unable to import the Python Scientific module required by FIAT.
     33 Consider installing the package python-scientific.
---> 34 """)
     35 
     36 def xi_triangle( eta ):

Exception: Unable to import the Python Scientific module required by FIAT.
Consider installing the package python-scientific.

I checked that the Python Scientific module is installed

--->  Computing dependencies for py-scientific
--->  Fetching archive for py-scientific
--->  Attempting to fetch py-scientific-2.9.3_0.darwin_13.noarch.tbz2 from http://packages.macports.org/py-scientific
--->  Attempting to fetch py-scientific-2.9.3_0.darwin_13.noarch.tbz2.rmd160 from http://packages.macports.org/py-scientific
--->  Installing py-scientific @2.9.3_0
--->  Activating py-scientific @2.9.3_0
--->  Cleaning py-scientific
--->  Updating database of binaries
--->  Scanning binaries for linking errors
--->  No broken files found.

but I still get the same error....

[krishnamurthy.vijaykumar@…]

Cc Me!

[krishnamurthy.vijaykumar@…]

Cc Me!

[krishnamurthy.vijaykumar@…]

I can confirm this. Same problem.

Today I tried to reinstall dolfin and and it fails at the configuring stage with the same error. Relevant portion of the main.log file

:info:configure -- Generating SWIG interface.
:info:configure -- --------------------------
:info:configure -- 
:info:configure -- Generating form files in demo, test, bench and dolfin directories. May take some time...
:info:configure -- ----------------------------------------------------------------------------------------
:info:configure CMake Error at CMakeLists.txt:825 (message):
:info:configure   Generation of form files failed:
:info:configure 
:info:configure   Traceback (most recent call last):
:info:configure 
:info:configure     File "/opt/local/bin/ffc", line 45, in <module>
:info:configure       from ffc.log import info
:info:configure     File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ffc/__init__.py", line 18, in <module>
:info:configure       from ffc.compiler import compile_form, compile_element
:info:configure     File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ffc/compiler.py", line 127, in <module>
:info:configure       from ffc.analysis import analyze_forms, analyze_elements
:info:configure     File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ffc/analysis.py", line 42, in <module>
:info:configure       from ffc.quadratureelement import default_quadrature_degree
:info:configure     File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ffc/quadratureelement.py", line 27, in <module>
:info:configure       from FIAT.functional import PointEvaluation
:info:configure     File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/FIAT/__init__.py", line 11, in <module>
:info:configure       from FIAT.finite_element import FiniteElement
:info:configure     File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/FIAT/finite_element.py", line 19, in <module>
:info:configure       from .polynomial_set import PolynomialSet
:info:configure     File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/FIAT/polynomial_set.py", line 29, in <module>
:info:configure       from . import expansions
:info:configure     File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/FIAT/expansions.py", line 34, in <module>
:info:configure       """)
:info:configure 
:info:configure   Exception: Unable to import the Python Scientific module required by FIAT.
:info:configure 
:info:configure   Consider installing the package python-scientific.
:info:configure 
:info:configure   
:info:configure 
:info:configure   Traceback (most recent call last):
:info:configure 
:info:configure     File "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.4.0/cmake/scripts/generate-form-files", line 80, in <module>
:info:configure       raise RuntimeError, "Unable to compile form: %s/%s" % (root, f)
:info:configure 
:info:configure   RuntimeError: Unable to compile form: dolfin/ale/Poisson1D.ufl
:info:configure 
:info:configure 
:info:configure 
:info:configure -- Configuring incomplete, errors occurred!

[seanfarley (Sean Farley)]

I finally got around to reproducing this. Looking into it now.

[seanfarley (Sean Farley)]

It appears this is a problem with the new ​numpy 1.9:

• The oldnumeric and numarray modules have been removed.

Scientific Python needs this module, so I've created an issue ​here.

[krishnamurthy.vijaykumar@…]

Cc Me!

[krishnamurthy.vijaykumar@…]

Hi Sean,

It looks like the dev version of fiat does not have this problem. Would it be possible to make use of this and fix the dolfin port?

See this thread ​http://fenicsproject.org/pipermail/fenics-support/2014-October/000909.html

-Vijay

Replying to sean@…:

It appears this is a problem with the new ​numpy 1.9:

• The oldnumeric and numarray modules have been removed.

Scientific Python needs this module, so I've created an issue ​here.

[seanfarley (Sean Farley)]

Yeah, looks like that is what I'll have to do. I'm a little busy with work but will try to get around to this later this week. If you feel encouraged to write a patch, please don't hesitate to upload it here :-)

[krishnamurthy.vijaykumar@…]

I would be happy to help. But I have never written a patch and don't know how to do that either. If there are some guidelines, let me know and I'll do what I can.

[Schamschula (Marius Schamschula)]

Cc Me!

[seanfarley (Sean Farley)]

I tried to update this but it seems that all the dolfin ports need to be updated for changes in FIAT. I'll try to ping them on the mailing list.

[jacobsonclas@…]

Replying to sean@…:

I tried to update this but it seems that all the dolfin ports need to be updated for changes in FIAT. I'll try to ping them on the mailing list.

Now with the New Year...any progress from the Fenics camp on this?

[seanfarley (Sean Farley)]

Replying to jacobsonclas@…:

Replying to sean@…:

I tried to update this but it seems that all the dolfin ports need to be updated for changes in FIAT. I'll try to ping them on the mailing list.

Now with the New Year...any progress from the Fenics camp on this?

Waiting on the 1.5 release: ​http://fenicsproject.org/pipermail/fenics/2015-January/002323.html

[seanfarley (Sean Farley)]

Sounds like that will be around Jan. 12 or so.

[seanfarley (Sean Farley)]

Looks like dolfin has been updated. I'll try to get around to fixing this soon :-)

[seanfarley (Sean Farley)]

Should be fixed in r131540.

[jacobsonclas@…]

Replying to sean@…:

Should be fixed in r131540.

Thanks! Works fine...