Dear group,

We are trying to adapt sfepy for mechanobiological tissue modeling at Yeditepe University, Istanbul.

We are primarily using the arch (linux-x64) platform for our work. Python 3.5 and 2.7.11 are already installed in our systems. Building and installing sfepy somehow worked, though without mayavi. I believe mayavi does not install as a result of version incompatibilities with vtk and python 2.7.

Is a virtual environment more suitable for sfepy, and what are the preferred versions of dependencies (python, vtk, and mayavi)?

Thanks,

Fethi

On Thursday, December 17, 2015 at 3:10:34 PM UTC+2, Robert Cimrman wrote:

Hi Nina,

could you try mayavi 4.3? The version 4.4 is not compatible with sfepy for the moment (cf. [1]).

r.

[1] https://github.com/sfepy/sfepy/issues/292

On 12/16/2015 03:09 PM, Nina Halabi wrote:

...

Dear Robert

I could overcome my previous problems of not having root privileges, so it all worked up till the command:

./postproc.py cylinder.vtk

This echoed the below message:

Exception In

/home/gmh/.local/lib/python2.7/site-packages/mayavi-4.4.4.dev0-py2.7-linux-x86_64.egg/mayavi/sources/vtk_xml_file_reader.py:86

...

AttributeError: 'AlgorithmOutput' object has no attribute 'point_data' (in get_all_attributes)

Traceback (most recent call last): File

"/home/gmh/.local/lib/python2.7/site-packages/traits-4.6.0.dev354-py2.7-linux-x86_64.egg/traits/trait_notifiers.py",

...

line 340, in __call__ self.handler( *args ) File "/home/gmh/sfepy/sfepy/postprocess/dataset_manager.py", line 177, in _dataset_changed self._assign_attribute.input = value File

"/home/gmh/.local/lib/python2.7/site-packages/traits-4.6.0.dev354-py2.7-linux-x86_64.egg/traits/trait_handlers.py",

...

line 104, in _read_only name, class_of( object ) ) TraitError: The 'input' trait of an AssignAttribute instance is 'read only'. sfepy: point scalars t at [-0.05 -0.02 0. ] sfepy: range: -2.00e+00 2.00e+00 l2 norm range: 1.06e-02 2.00e+00 No handlers could be found for logger "mayavi.core.common"

I'm using Python 2.7.8 if that's relevant to the current issue.

Thanks again Cheers

Hi Fethi,

You can also use paraview [1] instead of mayavi for postprocessing. Paraview is distributed in a self-containing package.

Regards, Vladimir

[1] http://www.paraview.org

On 2016-05-03 09:35, Fethi Okyar wrote:

Dear group,

We are trying to adapt sfepy for mechanobiological tissue modeling at Yeditepe University, Istanbul.

We are primarily using the arch (linux-x64) platform for our work. Python 3.5 and 2.7.11 are already installed in our systems. Building and installing sfepy somehow worked, though without mayavi. I believe mayavi does not install as a result of version incompatibilities with vtk and python 2.7.

Is a virtual environment more suitable for sfepy, and what are the preferred versions of dependencies (python, vtk, and mayavi)?

Thanks,

Fethi

On Thursday, December 17, 2015 at 3:10:34 PM UTC+2, Robert Cimrman wrote:

Hi Nina,

could you try mayavi 4.3? The version 4.4 is not compatible with
sfepy for the
moment (cf. [1]).

r.

[1] https://github.com/sfepy/sfepy/issues/292
<https://github.com/sfepy/sfepy/issues/292>

On 12/16/2015 03:09 PM, Nina Halabi wrote:
 > Dear Robert
 >
 > I could overcome my previous problems of not having root
privileges, so it
 > all worked up till the command:
 >
 > ./postproc.py cylinder.vtk
 >
 >
 > This echoed the below message:
 >
 > Exception
 > In
 >
/home/gmh/.local/lib/python2.7/site-packages/mayavi-4.4.4.dev0-py2.7-linux-x86_64.egg/mayavi/sources/vtk_xml_file_reader.py:86

 > AttributeError: 'AlgorithmOutput' object has no attribute
'point_data' (in
 > get_all_attributes)
 >
 > Traceback (most recent call last):
 >    File
 >
"/home/gmh/.local/lib/python2.7/site-packages/traits-4.6.0.dev354-py2.7-linux-x86_64.egg/traits/trait_notifiers.py",

 > line 340, in __call__
 >      self.handler( *args )
 >    File "/home/gmh/sfepy/sfepy/postprocess/dataset_manager.py",
line 177, in
 > _dataset_changed
 >      self._assign_attribute.input = value
 >    File
 >
"/home/gmh/.local/lib/python2.7/site-packages/traits-4.6.0.dev354-py2.7-linux-x86_64.egg/traits/trait_handlers.py",

 > line 104, in _read_only
 >      name, class_of( object ) )
 > TraitError: The 'input' trait of an AssignAttribute instance is
'read only'.
 > sfepy: point scalars t at [-0.05 -0.02  0.  ]
 > sfepy: range: -2.00e+00 2.00e+00 l2 norm range: 1.06e-02 2.00e+00
 > No handlers could be found for logger "mayavi.core.common"
 >
 >
 > I'm using Python 2.7.8 if that's relevant to the current issue.
 >
 > Thanks again
 > Cheers
 >

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