Jon
Here is the error message I get when I try to run the Anaconda
installation of FiPy using Trilinos on OsX. I'm using El Capitan:
Traceback (most recent call last):
File "CH_SqMesh.py", line 8, in <module>
import fipy as fp
File
"/Users/ajacobo/anaconda/envs/MYFIPYENV/lib/python2.7/site-packages/fipy/__init__.py",
line 45, in <module>
from fipy.boundaryConditions import *
File
"/Users/ajacobo/anaconda/envs/MYFIPYENV/lib/python2.7/site-packages/fipy/boundaryConditions/__init__.py",
line 2, in <module>
from fipy.boundaryConditions.fixedFlux import *
File
"/Users/ajacobo/anaconda/envs/MYFIPYENV/lib/python2.7/site-packages/fipy/boundaryConditions/fixedFlux.py",
line 38, in <module>
from fipy.tools import numerix
File
"/Users/ajacobo/anaconda/envs/MYFIPYENV/lib/python2.7/site-packages/fipy/tools/__init__.py",
line 85, in <module>
serial, parallel = serialComm, parallelComm = _getComms()
File
"/Users/ajacobo/anaconda/envs/MYFIPYENV/lib/python2.7/site-packages/fipy/tools/__init__.py",
line 72, in _getComms
serialComm, parallelComm = _parallelImport()
File
"/Users/ajacobo/anaconda/envs/MYFIPYENV/lib/python2.7/site-packages/fipy/tools/__init__.py",
line 43, in _parallelImport
from PyTrilinos import Epetra
File
"/Users/ajacobo/anaconda/envs/MYFIPYENV/lib/python2.7/site-packages/PyTrilinos/Epetra.py",
line 78, in <module>
_Epetra = swig_import_helper()
File
"/Users/ajacobo/anaconda/envs/MYFIPYENV/lib/python2.7/site-packages/PyTrilinos/Epetra.py",
line 74, in swig_import_helper
_mod = imp.load_module('_Epetra', fp, pathname, description)
ImportError:
dlopen(/Users/ajacobo/anaconda/envs/MYFIPYENV/lib/python2.7/site-packages/PyTrilinos/_Epetra.so,
258): Symbol not found: _cgesv_
Referenced from:
/Users/ajacobo/anaconda/envs/MYFIPYENV/lib/python2.7/site-packages/PyTrilinos/../../..//libteuchosnumerics.11.dylib
Expected in:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
in
/Users/ajacobo/anaconda/envs/MYFIPYENV/lib/python2.7/site-packages/PyTrilinos/../../..//libteuchosnumerics.11.dylib
Adrian.
Adrian -
You're running examples.cahnHilliard.mesh2DCoupled? There are a couple of
issues with the example as posted:
- There is a sign error in this example. It was fixed over a year ago, but never merged to master or
released as a tarball. You can run our develop branch, or manually apply the changes at
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_usnistgov_fipy_commit_8a1f81da5a3af6774c7803aed98aa38398904492&d=DwICAg&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=L6ffpm32hXcrNVgPrCUpE1ETAP0ihkpRJw_LGmJrntY&m=b5PUXJNUOd4hCWOREzB7y5TD3kgcq4MbScDfT6RJCqM&s=m-lETtFeGzLLIvB2bk9ZYJYqPBX5LlUMbcEvFKvYxmE&e=
- The system domain in that example is very small. Parallelizing it will result
in lots of overlapping cells, so won't scale well.
- If you make the system bigger, you'll quickly find that the default Trilinos
solver/preconditioner for this problem (GMRES with
dynamic-domain-decomposition) doesn't converge. No errors get generated, but
the solver runs to maximum iterations and the solution doesn't change. If you
instantiate a GMRES solver with a Jacobi preconditioner, this problem should be
resolved.
Hopefully this combination of changes will show some parallel speedup.
I'm presently (haphazardly) doing some solver benchmarking and am working my
way toward both parallel and coupled-CH benchmarking, which I'll then
incorporate in the documentation and/or in the default settings. It's taking me
awhile to get there, though.
As far as anaconda, when did you try the Mac OS X installation? Those
instructions were updated about three weeks ago and work for me (Mac is my
primary machine) and worked for a couple of people I was at a workshop with. If
you've done this since then, I'd appreciate knowing what doesn't work.
- Jon
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