Users and developers of the "FiPy" package for solving partial differential equations in Python

Requesting help with a problem installing PySparse

I'm trying to set up fipy to run on a 64 bit red hat linux machine 
(specifically Rocks v5.2).   We have gcc v4.1.2  We also have the 
Enthought python distribution with python 2.7.

I'm having trouble installing pysparse v1.1.1.  When I use the command

python setup.py install

I receive this error message:

running install
running build
running build_py
running build_ext
building 'pysparse.spmatrix' extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -O2 -fPIC -DNUMPY=1 
-DLENFUNC_OK=1 -IInclude 
-I/share/apps/Python2.7/epd-7.1-2-rh5-x86/lib/python2.7/site-packages/numpy/core/include 
-I/share/apps/Python2.7/epd-7.1-2-rh5-x86/include/python2.7 -c 
Src/spmatrixmodule.c -o build/temp.linux-x86_64-2.7/Src/spmatrixmodule.o
In file included from 
/share/apps/Python2.7/epd-7.1-2-rh5-x86/include/python2.7/Python.h:58,
                  from Src/spmatrixmodule.c:1:
/share/apps/Python2.7/epd-7.1-2-rh5-x86/include/python2.7/pyport.h:849:2: error: 
#error "LONG_BIT definition appears wrong for platform (bad gcc/glibc 
config?)."
error: command 'gcc' failed with exit status 1

I also tried pysparse v1.2 with the same result (in addition to some 
library linking errors that I'll also probably have to fix).

(Continue reading)

headers

Fausto Arinos de A. Barbuto | 2 Feb 18:02

Re: Requesting help with a problem installing PySparse

Hi,

Ain't sure if this will be of help, but I installed pysparse on my 64-bit Ubuntu

machine without any glitches. Yet, quite a bit of dependencies must be

satisfied so that one can successfully install pysparse. A list of required

packages that a Ubuntu box must have installed prior to building pysparse

can be found here:

http://packages.ubuntu.com/source/natty/pysparse

Incidentally, "Natty Narwhal" is the Ubuntu version (11.04) I'm currently

running on my machine.

Cheers,

Fausto

From: Leland M Barnard <lmbarnard-63mtpxcE9Cs@public.gmane.org>
To: fipy-R3+/ord2DXQ@public.gmane.org
Sent: Wednesday, February 1, 2012 7:40:22 PM
Subject: Requesting help with a problem installing PySparse

I'm trying to set up fipy to run on a 64 bit red hat linux machine
(specifically Rocks v5.2). We have gcc v4.1.2 We also have the
Enthought python distribution with python 2.7.

I'm having trouble installing pysparse v1.1.1. When I use the command

python setup.py install

I receive this error message:

running install
running build
running build_py
running build_ext
building 'pysparse.spmatrix' extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -O2 -fPIC -DNUMPY=1
-DLENFUNC_OK=1 -IInclude
-I/share/apps/Python2.7/epd-7.1-2-rh5-x86/lib/python2.7/site-packages/numpy/core/include
-I/share/apps/Python2.7/epd-7.1-2-rh5-x86/include/python2.7 -c
Src/spmatrixmodule.c -o build/temp.linux-x86_64-2.7/Src/spmatrixmodule.o
In file included from
/share/apps/Python2.7/epd-7.1-2-rh5-x86/include/python2.7/Python.h:58,
from Src/spmatrixmodule.c:1:
/share/apps/Python2.7/epd-7.1-2-rh5-x86/include/python2.7/pyport.h:849:2: error:
#error "LONG_BIT definition appears wrong for platform (bad gcc/glibc
config?)."
error: command 'gcc' failed with exit status 1

I also tried pysparse v1.2 with the same result (in addition to some
library linking errors that I'll also probably have to fix).

I was hoping there might be someone else on the mailing list that
encountered this and might have a solution. Please let me know if there
is any more information I can supply that might be helpful in diagnosing
the trouble. Thanks!

VTY,
Leland Barnard

_______________________________________________
fipy mailing list
fipy-R3+/ord2DXQ@public.gmane.org
http://www.ctcms.nist.gov/fipy
[ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

_______________________________________________
fipy mailing list
fipy@...
http://www.ctcms.nist.gov/fipy
  [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

headers

Daniel Wheeler | 3 Feb 16:09

Fwd: [Pysparse-users] Requesting help with PySparse installation

---------- Forwarded message ----------
From: Daniel Wheeler <daniel.wheeler2-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
Date: Fri, Feb 3, 2012 at 10:04 AM
Subject: Re: [Pysparse-users] Requesting help with PySparse installation
To: Leland M Barnard <lmbarnard-63mtpxcE9Cs@public.gmane.org>
Cc: pysparse-users-5NWGOfrQmneRv+LV9MX5uuRhgaa4a2kL@public.gmane.orgnet

I am not sure what the issue is, but it might be better to build pysparse against a version of python and numpy that is distributed and installed by the package manager for your system. Is there a numpy rpm available?

If for some reason that doesn't work or isn't available, maybe try installing numpy by hand using the system python. You can try different options in a virtualenv if you use that rather than installing into your system directories. Certainly with enthought, it is better to install in a virtualenv rather than messing with the system directories while prototyping.

Googling the actual issue, this may be a 32 versus 64 bit issue.

<http://stackoverflow.com/questions/648482/a-trivial-python-swig-error-question>

Maybe using a 32 bit distribution on a 64 bit platform is not the way to go (speculation). Is there not a 64 bit dist? Like it says in the link maybe try passing some of the 32 bit flags to gcc.

Hope this helps in some way.

On Thu, Feb 2, 2012 at 11:12 AM, Leland M Barnard <lmbarnard-63mtpxcE9Cs@public.gmane.org> wrote:

I'm trying to set up pysparse to run on a 64 bit red hat linux machine
(specifically Rocks v5.2). We have gcc v4.1.2. We also have the
Enthought python distribution v7.1-2 (32 bit). with python 2.7.

I'm having trouble installing pysparse v1.1.1. When I use the command

python setup.py install

I receive this error message:

running install
running build
running build_py
running build_ext
building 'pysparse.spmatrix' extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -O2 -fPIC -DNUMPY=1
-DLENFUNC_OK=1 -IInclude
-I/share/apps/Python2.7/epd-7.1-2-rh5-x86/lib/python2.7/site-packages/numpy/core/include
-I/share/apps/Python2.7/epd-7.1-2-rh5-x86/include/python2.7 -c
Src/spmatrixmodule.c -o build/temp.linux-x86_64-2.7/Src/spmatrixmodule.o
In file included from
/share/apps/Python2.7/epd-7.1-2-rh5-x86/include/python2.7/Python.h:58,
from Src/spmatrixmodule.c:1:
/share/apps/Python2.7/epd-7.1-2-rh5-x86/include/python2.7/pyport.h:849:2: error:
#error "LONG_BIT definition appears wrong for platform (bad gcc/glibc
config?)."
error: command 'gcc' failed with exit status 1

I was hoping there might be someone else on the mailing list that
encountered this and might have a solution. Please let me know if there
is any more information I can supply that might be helpful in diagnosing
the trouble. Thanks!

VTY,
Leland Barnard

------------------------------------------------------------------------------
Keep Your Developer Skills Current with LearnDevNow!
The most comprehensive online learning library for Microsoft developers
is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
Metro Style Apps, more. Free future releases when you subscribe now!
http://p.sf.net/sfu/learndevnow-d2d
_______________________________________________
Pysparse-users mailing list
Pysparse-users-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
https://lists.sourceforge.net/lists/listinfo/pysparse-users

--
Daniel Wheeler

_______________________________________________
fipy mailing list
fipy@...
http://www.ctcms.nist.gov/fipy
  [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

headers

Fausto Arinos de A. Barbuto | 4 Feb 02:51

Re: Requesting help with a problem installing PySparse

A question: do you have liblapack-dev and libblas-dev installed? They seemingly are essential

to compiling pysparse (you may still have other unresolved dependencies, though). You might

also try to compile the package as "root". Also, run "python setup.py build" first, and then

"python setup.py install". That worked on my 64-bit architecture.

F.

From: Leland M Barnard <lmbarnard-63mtpxcE9Cs@public.gmane.org>
To: fipy-R3+/ord2DXQ@public.gmane.org
Sent: Wednesday, February 1, 2012 7:40:22 PM
Subject: Requesting help with a problem installing PySparse

I'm trying to set up fipy to run on a 64 bit red hat linux machine
(specifically Rocks v5.2). We have gcc v4.1.2 We also have the
Enthought python distribution with python 2.7.

I'm having trouble installing pysparse v1.1.1. When I use the command

python setup.py install

I receive this error message:

running install
running build
running build_py
running build_ext
building 'pysparse.spmatrix' extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -O2 -fPIC -DNUMPY=1
-DLENFUNC_OK=1 -IInclude
-I/share/apps/Python2.7/epd-7.1-2-rh5-x86/lib/python2.7/site-packages/numpy/core/include
-I/share/apps/Python2.7/epd-7.1-2-rh5-x86/include/python2.7 -c
Src/spmatrixmodule.c -o build/temp.linux-x86_64-2.7/Src/spmatrixmodule.o
In file included from
/share/apps/Python2.7/epd-7.1-2-rh5-x86/include/python2.7/Python.h:58,
from Src/spmatrixmodule.c:1:
/share/apps/Python2.7/epd-7.1-2-rh5-x86/include/python2.7/pyport.h:849:2: error:
#error "LONG_BIT definition appears wrong for platform (bad gcc/glibc
config?)."
error: command 'gcc' failed with exit status 1

I also tried pysparse v1.2 with the same result (in addition to some
library linking errors that I'll also probably have to fix).

I was hoping there might be someone else on the mailing list that
encountered this and might have a solution. Please let me know if there
is any more information I can supply that might be helpful in diagnosing
the trouble. Thanks!

VTY,
Leland Barnard

_______________________________________________
fipy mailing list
fipy-R3+/ord2DXQ@public.gmane.org
http://www.ctcms.nist.gov/fipy
[ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

_______________________________________________
fipy mailing list
fipy@...
http://www.ctcms.nist.gov/fipy
  [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

headers

wang yunbo | 6 Feb 18:41

Re: Curvature calculation

Hi,

Followed up the previous question, now I calculated the curvature everywhere for the mesh and found the accuracy was not that within second order. Is my mesh not stable?

Here is my mesh:

mesh = Grid2D(dx=1.0, dy=1.0, nx=100, ny=100)

var = DistanceVariable(name='Test',

mesh=mesh,

value=-1.0,

hasOld=1)

For initial value,

var.setValue(1.0, where = ((x-50.0)**2+(y-50.0)**2>625.0))

var.calcDistanceFunction()

For this case, what is the best way to calculate the curvature?

Thanks,

Regards,

Yunbo

On Jan 20, 2012, at 10:47 AM, Daniel Wheeler wrote:

On Thu, Jan 19, 2012 at 6:34 PM, wang yunbo <wang1320-olO2ZdjDehc3uPMLIKxrzw@public.gmane.org> wrote:

I'm trying to calculate the curvature of a circle in 2D.

Sounds reasonable.

Firstly I set up a distance variable "var" to represent the circular shape. To calculate the curvature, I took the gradient of "var" and then the divergence as shown below:
(var.getFaceGrad()).getDivergence()

Should work with second order accuracy on a well structured mesh.

My trouble is :

My expectation is to obtain a matrix of curvature and
at the boundary of circle (where var=0). However, the obtained result from my program showed
at the boundary.

The boundary of the domain assumes a zero gradient. It doesn't use any other information about the field. In version 2.1 there is nothing to be done other than ignore the cells close to the boundary. However, In FiPy 3.0 (not yet released) this will work:

from fipy import *
m = Grid2D(nx=4, ny=4)
v = CellVariable(mesh=m, value=m.x**2 + m.y**2)
X, Y = m.faceCenters
v.faceGrad.constrain((2 * X, 2 * Y), where=m.exteriorFaces)
print v.faceGrad.divergence

[ 4. 4. 4. 4. 4. 4. 4. 4. 4. 4. 4. 4. 4. 4. 4. 4.]

Cheers.

--
Daniel Wheeler
_______________________________________________
fipy mailing list
fipy-R3+/ord2DXQ@public.gmane.org
http://www.ctcms.nist.gov/fipy
[ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

_______________________________________________
fipy mailing list
fipy@...
http://www.ctcms.nist.gov/fipy
  [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

headers

Lucia AvOlocc | 6 Feb 19:11

fipy installation problems on ubuntu

Hi,
I am having problems when installing fipy in my notebook (ubuntu 11.10)

I got the following errors:

home:~/FiPy-2.1.2$ sudo python setup.py install
running install
Checking .pth file support in /usr/local/lib/python2.7/dist-packages/
/usr/bin/python -E -c pass
TEST PASSED: /usr/local/lib/python2.7/dist-packages/ appears to
support .pth files
running bdist_egg
running egg_info
writing FiPy.egg-info/PKG-INFO
writing top-level names to FiPy.egg-info/top_level.txt
writing dependency_links to FiPy.egg-info/dependency_links.txt
writing entry points to FiPy.egg-info/entry_points.txt
writing FiPy.egg-info/PKG-INFO
writing top-level names to FiPy.egg-info/top_level.txt
writing dependency_links to FiPy.egg-info/dependency_links.txt
writing entry points to FiPy.egg-info/entry_points.txt
reading manifest file 'FiPy.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*.png' found under
directory 'examples'
warning: no previously-included files matching '*.pdf' found under
directory 'examples'
warning: no previously-included files matching '*.png' found under
directory 'fipy'
warning: no previously-included files matching '*.pdf' found under
directory 'fipy'
writing manifest file 'FiPy.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/fipy
creating build/bdist.linux-x86_64/egg/fipy/steppers
................
..................
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing FiPy-2.1.2-py2.7.egg
removing '/usr/local/lib/python2.7/dist-packages/FiPy-2.1.2-py2.7.egg'
(and everything under it)
creating /usr/local/lib/python2.7/dist-packages/FiPy-2.1.2-py2.7.egg
Extracting FiPy-2.1.2-py2.7.egg to /usr/local/lib/python2.7/dist-packages
FiPy 2.1.2 is already the active version in easy-install.pth

Installed /usr/local/lib/python2.7/dist-packages/FiPy-2.1.2-py2.7.egg
Processing dependencies for FiPy==2.1.2
Finished processing dependencies for FiPy==2.1.2
Traceback (most recent call last):
  File "setup.py", line 594, in <module>
    __import__(pkg)
  File "/usr/local/lib/python2.7/dist-packages/pysparse-1.2_dev224-py2.7-linux-x86_64.egg/pysparse/__init__.py",
line 6, in <module>
    from numpy._import_tools import PackageLoader
  File "/usr/local/lib/python2.7/dist-packages/numpy/__init__.py",
line 137, in <module>
    import add_newdocs
  File "/usr/local/lib/python2.7/dist-packages/numpy/add_newdocs.py",
line 9, in <module>
    from numpy.lib import add_newdoc
  File "/usr/local/lib/python2.7/dist-packages/numpy/lib/__init__.py",
line 13, in <module>
    from polynomial import *
  File "/usr/local/lib/python2.7/dist-packages/numpy/lib/polynomial.py",
line 11, in <module>
    import numpy.core.numeric as NX
AttributeError: 'module' object has no attribute 'core'

So, I try to run fipy from python:

home:~/FiPy-2.1.2$ python
Python 2.7.2+ (default, Oct  4 2011, 20:06:09)
[GCC 4.6.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.

>>> import fipy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "fipy/__init__.py", line 41, in <module>
    from solvers import *
  File "fipy/solvers/__init__.py", line 68, in <module>
    raise ImportError, "Could not import any solver package. If you
are using Trilinos, make sure you have all of the necessary Trilinos
packages installed - Epetra, EpetraExt, AztecOO, Amesos, ML, and
IFPACK."
ImportError: Could not import any solver package. If you are using
Trilinos, make sure you have all of the necessary Trilinos packages
installed - Epetra, EpetraExt, AztecOO, Amesos, ML, and IFPACK.
>>>

I don't know how to fix this problem. Thanks in advance for your help
Regards,
Lucia
_______________________________________________
fipy mailing list
fipy@...
http://www.ctcms.nist.gov/fipy
  [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

headers

Leland M Barnard | 6 Feb 19:31

Re: Requesting help with a problem installing PySparse

Thanks for your help. It turned out I was working with a 32-bit installation of python, that was the source of my trouble.

-Leland

On 2/3/2012 7:51 PM, Fausto Arinos de A. Barbuto wrote:

A question: do you have liblapack-dev and libblas-dev installed? They seemingly are essential

to compiling pysparse (you may still have other unresolved dependencies, though). You might

also try to compile the package as "root". Also, run "python setup.py build" first, and then

"python setup.py install". That worked on my 64-bit architecture.

F.

From: Leland M Barnard <lmbarnard-63mtpxcE9Cs@public.gmane.org>
To: fipy-R3+/ord2DXQ@public.gmane.org
Sent: Wednesday, February 1, 2012 7:40:22 PM
Subject: Requesting help with a problem installing PySparse

I'm trying to set up fipy to run on a 64 bit red hat linux machine
(specifically Rocks v5.2). We have gcc v4.1.2 We also have the
Enthought python distribution with python 2.7.

I'm having trouble installing pysparse v1.1.1. When I use the command

python setup.py install

I receive this error message:

running install
running build
running build_py
running build_ext
building 'pysparse.spmatrix' extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -O2 -fPIC -DNUMPY=1
-DLENFUNC_OK=1 -IInclude
-I/share/apps/Python2.7/epd-7.1-2-rh5-x86/lib/python2.7/site-packages/numpy/core/include
-I/share/apps/Python2.7/epd-7.1-2-rh5-x86/include/python2.7 -c
Src/spmatrixmodule.c -o build/temp.linux-x86_64-2.7/Src/spmatrixmodule.o
In file included from
/share/apps/Python2.7/epd-7.1-2-rh5-x86/include/python2.7/Python.h:58,
from Src/spmatrixmodule.c:1:
/share/apps/Python2.7/epd-7.1-2-rh5-x86/include/python2.7/pyport.h:849:2: error:
#error "LONG_BIT definition appears wrong for platform (bad gcc/glibc
config?)."
error: command 'gcc' failed with exit status 1

I also tried pysparse v1.2 with the same result (in addition to some
library linking errors that I'll also probably have to fix).

I was hoping there might be someone else on the mailing list that
encountered this and might have a solution. Please let me know if there
is any more information I can supply that might be helpful in diagnosing
the trouble. Thanks!

VTY,
Leland Barnard

_______________________________________________
fipy mailing list
fipy-R3+/ord2DXQ@public.gmane.org
http://www.ctcms.nist.gov/fipy
[ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

_______________________________________________ fipy mailing list fipy-R3+/ord2DXQ@public.gmane.org http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

_______________________________________________
fipy mailing list
fipy@...
http://www.ctcms.nist.gov/fipy
  [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

headers

Fausto Arinos de A. Barbuto | 7 Feb 15:02

Re: fipy installation problems on ubuntu

Hi,

I'm confused about your problem, but the "import" command immediately below:

import numpy.core.numeric as NX
AttributeError: 'module' object has no attribute 'core'

should have worked. I assume you have numpy installed on your Ubuntu box.

How did you install it? From Synaptic or building from the tarball (or any other

source)? I too run a Ubuntu 11.04 home.

I had the same "Could not import any solver package" message in the past, but

as far as I can remember the error history you got and mine were different.

32- versus 64- bit packages have given trouble to some people (and not only with

regard to FiPy). Is your system a 64-bit one?

Good luck,

Fausto

From: Lucia AvOlocc <avallelucia-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
To: fipy <fipy-R3+/ord2DXQ@public.gmane.org>
Sent: Monday, February 6, 2012 4:11:51 PM
Subject: fipy installation problems on ubuntu

Hi,
I am having problems when installing fipy in my notebook (ubuntu 11.10)

I got the following errors:

home:~/FiPy-2.1.2$ sudo python setup.py install
running install
Checking .pth file support in /usr/local/lib/python2.7/dist-packages/
/usr/bin/python -E -c pass
TEST PASSED: /usr/local/lib/python2.7/dist-packages/ appears to
support .pth files
running bdist_egg
running egg_info
writing FiPy.egg-info/PKG-INFO
writing top-level names to FiPy.egg-info/top_level.txt
writing dependency_links to FiPy.egg-info/dependency_links.txt
writing entry points to FiPy.egg-info/entry_points.txt
writing FiPy.egg-info/PKG-INFO
writing top-level names to FiPy.egg-info/top_level.txt
writing dependency_links to FiPy.egg-info/dependency_links.txt
writing entry points to FiPy.egg-info/entry_points.txt
reading manifest file 'FiPy.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*.png' found under
directory 'examples'
warning: no previously-included files matching '*.pdf' found under
directory 'examples'
warning: no previously-included files matching '*.png' found under
directory 'fipy'
warning: no previously-included files matching '*.pdf' found under
directory 'fipy'
writing manifest file 'FiPy.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/fipy
creating build/bdist.linux-x86_64/egg/fipy/steppers
................
..................
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing FiPy-2.1.2-py2.7.egg
removing '/usr/local/lib/python2.7/dist-packages/FiPy-2.1.2-py2.7.egg'
(and everything under it)
creating /usr/local/lib/python2.7/dist-packages/FiPy-2.1.2-py2.7.egg
Extracting FiPy-2.1.2-py2.7.egg to /usr/local/lib/python2.7/dist-packages
FiPy 2.1.2 is already the active version in easy-install.pth

Installed /usr/local/lib/python2.7/dist-packages/FiPy-2.1.2-py2.7.egg
Processing dependencies for FiPy==2.1.2
Finished processing dependencies for FiPy==2.1.2
Traceback (most recent call last):
File "setup.py", line 594, in <module>
__import__(pkg)
File "/usr/local/lib/python2.7/dist-packages/pysparse-1.2_dev224-py2.7-linux-x86_64.egg/pysparse/__init__.py",
line 6, in <module>
from numpy._import_tools import PackageLoader
File "/usr/local/lib/python2.7/dist-packages/numpy/__init__.py",
line 137, in <module>
import add_newdocs
File "/usr/local/lib/python2.7/dist-packages/numpy/add_newdocs.py",
line 9, in <module>
from numpy.lib import add_newdoc
File "/usr/local/lib/python2.7/dist-packages/numpy/lib/__init__.py",
line 13, in <module>
from polynomial import *
File "/usr/local/lib/python2.7/dist-packages/numpy/lib/polynomial.py",
line 11, in <module>
import numpy.core.numeric as NX
AttributeError: 'module' object has no attribute 'core'

So, I try to run fipy from python:

home:~/FiPy-2.1.2$ python
Python 2.7.2+ (default, Oct 4 2011, 20:06:09)
[GCC 4.6.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.

>>> import fipy
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "fipy/__init__.py", line 41, in <module>
from solvers import *
File "fipy/solvers/__init__.py", line 68, in <module>
raise ImportError, "Could not import any solver package. If you
are using Trilinos, make sure you have all of the necessary Trilinos
packages installed - Epetra, EpetraExt, AztecOO, Amesos, ML, and
IFPACK."
ImportError: Could not import any solver package. If you are using
Trilinos, make sure you have all of the necessary Trilinos packages
installed - Epetra, EpetraExt, AztecOO, Amesos, ML, and IFPACK.
>>>

I don't know how to fix this problem. Thanks in advance for your help
Regards,
Lucia
_______________________________________________
fipy mailing list
fipy <at> nist.gov
http://www.ctcms.nist.gov/fipy
[ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

_______________________________________________
fipy mailing list
fipy@...
http://www.ctcms.nist.gov/fipy
  [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

headers

Daniel Wheeler | 7 Feb 15:54

Re: Curvature calculation

On Mon, Feb 6, 2012 at 12:41 PM, wang yunbo <wang1320-olO2ZdjDehc3uPMLIKxrzw@public.gmane.org> wrote:

Hi,

Followed up the previous question, now I calculated the curvature everywhere for the mesh and found the accuracy was not that within second order.

How do you know? How did you check the order of accuracy? Is the curvature calculation not second order accurate or the calculation of the distance function?

Is my mesh not stable?

I don't think stability is an issue here.

Here is my mesh:

mesh = Grid2D(dx=1.0, dy=1.0, nx=100, ny=100)

var = DistanceVariable(name='Test',

mesh=mesh,

value=-1.0,

hasOld=1)

For initial value,

var.setValue(1.0, where = ((x-50.0)**2+(y-50.0)**2>625.0))

var.calcDistanceFunction()

For this case, what is the best way to calculate the curvature?

var.getFaceGrad().getDivergence()

should be second order accurate.

--
Daniel Wheeler

_______________________________________________
fipy mailing list
fipy@...
http://www.ctcms.nist.gov/fipy
  [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

headers

Daniel Wheeler | 7 Feb 16:02

Re: fipy installation problems on ubuntu

Hi Lucia,

What happens when you do each of

$ python -c "import numpy; print numpy.__version__"
$ python -c "import pysparse; print pysparse.__version__"
$ python -c "import PyTrilinos; print PyTrilinos.version()"

Just want to check that they import properly independent of fipy.

Cheers

On Mon, Feb 6, 2012 at 1:11 PM, Lucia AvOlocc <avallelucia-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:

Hi,
I am having problems when installing fipy in my notebook (ubuntu 11.10)

I got the following errors:

home:~/FiPy-2.1.2$ sudo python setup.py install
running install
Checking .pth file support in /usr/local/lib/python2.7/dist-packages/
/usr/bin/python -E -c pass
TEST PASSED: /usr/local/lib/python2.7/dist-packages/ appears to
support .pth files
running bdist_egg
running egg_info
writing FiPy.egg-info/PKG-INFO
writing top-level names to FiPy.egg-info/top_level.txt
writing dependency_links to FiPy.egg-info/dependency_links.txt
writing entry points to FiPy.egg-info/entry_points.txt
writing FiPy.egg-info/PKG-INFO
writing top-level names to FiPy.egg-info/top_level.txt
writing dependency_links to FiPy.egg-info/dependency_links.txt
writing entry points to FiPy.egg-info/entry_points.txt
reading manifest file 'FiPy.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*.png' found under
directory 'examples'
warning: no previously-included files matching '*.pdf' found under
directory 'examples'
warning: no previously-included files matching '*.png' found under
directory 'fipy'
warning: no previously-included files matching '*.pdf' found under
directory 'fipy'
writing manifest file 'FiPy.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/fipy
creating build/bdist.linux-x86_64/egg/fipy/steppers
................
..................
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing FiPy-2.1.2-py2.7.egg
removing '/usr/local/lib/python2.7/dist-packages/FiPy-2.1.2-py2.7.egg'
(and everything under it)
creating /usr/local/lib/python2.7/dist-packages/FiPy-2.1.2-py2.7.egg
Extracting FiPy-2.1.2-py2.7.egg to /usr/local/lib/python2.7/dist-packages
FiPy 2.1.2 is already the active version in easy-install.pth

Installed /usr/local/lib/python2.7/dist-packages/FiPy-2.1.2-py2.7.egg
Processing dependencies for FiPy==2.1.2
Finished processing dependencies for FiPy==2.1.2
Traceback (most recent call last):
File "setup.py", line 594, in <module>
__import__(pkg)
File "/usr/local/lib/python2.7/dist-packages/pysparse-1.2_dev224-py2.7-linux-x86_64.egg/pysparse/__init__.py",
line 6, in <module>
from numpy._import_tools import PackageLoader
File "/usr/local/lib/python2.7/dist-packages/numpy/__init__.py",
line 137, in <module>
import add_newdocs
File "/usr/local/lib/python2.7/dist-packages/numpy/add_newdocs.py",
line 9, in <module>
from numpy.lib import add_newdoc
File "/usr/local/lib/python2.7/dist-packages/numpy/lib/__init__.py",
line 13, in <module>
from polynomial import *
File "/usr/local/lib/python2.7/dist-packages/numpy/lib/polynomial.py",
line 11, in <module>
import numpy.core.numeric as NX
AttributeError: 'module' object has no attribute 'core'

So, I try to run fipy from python:

home:~/FiPy-2.1.2$ python
Python 2.7.2+ (default, Oct 4 2011, 20:06:09)
[GCC 4.6.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.

>>> import fipy
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "fipy/__init__.py", line 41, in <module>
from solvers import *
File "fipy/solvers/__init__.py", line 68, in <module>
raise ImportError, "Could not import any solver package. If you
are using Trilinos, make sure you have all of the necessary Trilinos
packages installed - Epetra, EpetraExt, AztecOO, Amesos, ML, and
IFPACK."
ImportError: Could not import any solver package. If you are using
Trilinos, make sure you have all of the necessary Trilinos packages
installed - Epetra, EpetraExt, AztecOO, Amesos, ML, and IFPACK.
>>>

I don't know how to fix this problem. Thanks in advance for your help
Regards,
Lucia
_______________________________________________
fipy mailing list
fipy-R3+/ord2DXQ@public.gmane.org
http://www.ctcms.nist.gov/fipy
[ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

--
Daniel Wheeler

_______________________________________________
fipy mailing list
fipy@...
http://www.ctcms.nist.gov/fipy
  [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

32	May 2012
48	April 2012
50	March 2012
61	February 2012
56	January 2012
9	December 2011
16	November 2011
22	October 2011
17	September 2011
10	August 2011
22	July 2011
31	June 2011
43	May 2011
24	April 2011
50	March 2011
101	February 2011
17	January 2011
15	December 2010
20	November 2010
24	October 2010
10	September 2010
7	August 2010
36	July 2010
26	June 2010
121	May 2010
20	April 2010
9	March 2010
18	February 2010
18	January 2010
14	December 2009
49	November 2009
70	October 2009
41	September 2009
20	August 2009
24	July 2009
31	June 2009
24	May 2009
12	April 2009
44	February 2009
27	January 2009
39	December 2008
38	November 2008
18	October 2008
44	September 2008
102	August 2008
80	July 2008
40	June 2008
26	May 2008
8	April 2008
17	March 2008
16	February 2008
19	January 2008
20	December 2007
29	November 2007
10	October 2007
18	September 2007
10	August 2007
5	July 2007
9	June 2007
36	May 2007
18	April 2007
32	March 2007
1	February 2007
37	January 2007
12	December 2006
23	November 2006
64	October 2006
17	September 2006
15	August 2006
16	July 2006
29	June 2006
35	May 2006
39	April 2006
8	March 2006
54	February 2006
3	January 2006
19	November 2005
24	October 2005
18	September 2005
14	August 2005
9	July 2005
34	June 2005
25	May 2005
50	April 2005
34	March 2005
19	February 2005
22	January 2005
23	December 2004
15	November 2004
3	October 2004

Mon	Tue	Wed	Thu	Fri	Sat	Sun

		1	2	3	4	5
6	7	8	9	10	11	12
13	14	15	16	17	18	19
20	21	22	23	24	25	26
27	28	29