Installation problem with openpnm

[debanik1]

Hello. I followed the installation guideline [here](url) using Anaconda but I haven't been able to install yet.

Can somebody please help?

This is the error I am getting.

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\deban\anaconda3\lib\site-packages\openpnm\__init__.py", line 64, in <module>
    from . import algorithms
  File "C:\Users\deban\anaconda3\lib\site-packages\openpnm\algorithms\__init__.py", line 13, in <module>
    from .GenericTransport import GenericTransport
  File "C:\Users\deban\anaconda3\lib\site-packages\openpnm\algorithms\GenericTransport.py", line 3, in <module>
    import scipy.sparse.linalg
  File "C:\Users\deban\anaconda3\lib\site-packages\scipy\sparse\linalg\__init__.py", line 114, in <module>
    from .eigen import *
  File "C:\Users\deban\anaconda3\lib\site-packages\scipy\sparse\linalg\eigen\__init__.py", line 9, in <module>
    from .arpack import *
  File "C:\Users\deban\anaconda3\lib\site-packages\scipy\sparse\linalg\eigen\arpack\__init__.py", line 20, in <module>
    from .arpack import *
  File "C:\Users\deban\anaconda3\lib\site-packages\scipy\sparse\linalg\eigen\arpack\arpack.py", line 42, in <module>
    from . import _arpack
ImportError: DLL load failed while importing _arpack: The specified procedure could not be found.

[ma-sadeghi]

I was able to install openpnm on my machine. Just to make sure you can do the same, do the followings:

1. Create a fresh virtual environment (called test) so if you have any broken dependencies, it's not going to affect your installation

conda create -n test python=3.8

2. Activate the test environment

conda activate test

3. Install openpnm

conda install openpnm

4. Test your installation

python -c "import openpnm"

If you were able to run the last step with no errors, chances are that there might be something wrong with your scipy installation in your default conda environment. One fix could be to update all packages (before, make sure to activate your base environment, since we're currently inside test.):

conda update --all

Let me know if it fixes you problem.

[ma-sadeghi]

Can you paste what you get when you run import openpnm; print(openpnm.__version__)?

[vtextremelab]

Sorry for delay. Just created an new environment in anaconda and reinstalled in there. Still is not working on example usage case. for above I get output below.
2.8.2

[loaa4]

Hi,
I've have the same problem of missing:'pore.area',
so i wonder whether there is a solution for this problem

[Mat10G]

Hi, I have also the same problem

[Mat10G]

Hello everyone, I post this message because I finally managed to install and run the OpenPNM examples. Then I will explain my configuration. I am on the Ubuntu 20.04 virtual machine and I have installed the latest version of Anaconda (Python 3.9). Then I created a workspace configured also in Python 3.9. I installed OpenPNM in the hard way specified on the online documentation ($ git clone https://github.com/PMEAL/OpenPNM) but by placing myself in the release branch and not the dev branch (git checkout insertpath/release). Then, when I open my anaconda browser under Linux I make sure to place myself in the right environment mentioned above and then I can launch my examples from JupyterNoteBook.

[debanik1]

I was able to install openpnm on my machine. Just to make sure you can do the same, do the followings: ...

Thanks for the inputs. I reinstalled numpy and scipy and it's working now.

[stathi02]

get this error when i try to import:

import openpnm

 <frozen importlib._bootstrap>:228: RuntimeWarning: scipy._lib.messagestream.MessageStream size changed, may indicate binary incompatibility. Expected 56 from C header, got 64 from PyObject

[jgostick]

can you put the full traceback? This is not a openpnm error message so we need to see where in the stack this gets triggered.

[Mat10G]

Hello, thank you for your quick response, I have this traceback. I downloaded OpenPNM with this function on my virtual machine : $ conda install -c conda-forge openpnm CRITICAL : front and back labels have been switched to obey the right-hand rule SOURCE : openpnm.network.Cubic.__init__ TIME STAMP : 2022-06-01 10:13:35,829 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.flow_shape_factors was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:35,980 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.hydraulic_conductance was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:35,980 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.poisson_shape_factors was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:35,981 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.diffusive_conductance was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:35,981 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.ad_dif_conductance was not run since the following property is missing: 'throat.hydraulic_conductance' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:35,982 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.thermal_conductance was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:35,984 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.electrical_conductance was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:35,984 ------------------------------------------------------------ ------------------------------------------------------------ WARNING : Inlets have non-zero volume, percolation curve won't start at 0. SOURCE : openpnm.algorithms.OrdinaryPercolation.get_intrusion_data TIME STAMP : 2022-06-01 10:13:36,552 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.flow_shape_factors was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:36,718 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.hydraulic_conductance was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:36,719 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.poisson_shape_factors was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:36,719 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.diffusive_conductance was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:36,720 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.ad_dif_conductance was not run since the following property is missing: 'throat.hydraulic_conductance' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:36,720 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.thermal_conductance was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:36,723 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.electrical_conductance was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:36,723 ------------------------------------------------------------ Traceback (most recent call last): File "/home/mathias/anaconda3/User_Guide.py", line 29, in <module> sf.run() File "/home/mathias/anaconda3/lib/python3.9/site-packages/openpnm/algorithms/ReactiveTransport.py", line 154, in run self._validate_data_health() File "/home/mathias/anaconda3/lib/python3.9/site-packages/openpnm/algorithms/GenericTransport.py", line 810, in _validate_data_health if np.isfinite(self.A.data).all() and np.isfinite(self.b).all(): File "/home/mathias/anaconda3/lib/python3.9/site-packages/openpnm/algorithms/GenericTransport.py", line 489, in _get_A self._build_A() File "/home/mathias/anaconda3/lib/python3.9/site-packages/openpnm/algorithms/GenericTransport.py", line 468, in _build_A g = phase[gvals] File "/home/mathias/anaconda3/lib/python3.9/site-packages/openpnm/phases/GenericPhase.py", line 99, in __getitem__ vals = super().__getitem__(key) File "/home/mathias/anaconda3/lib/python3.9/site-packages/openpnm/core/Base.py", line 283, in __getitem__ raise KeyError(key) KeyError: 'throat.hydraulic_conductance' Le mer. 1 juin 2022 à 00:50, jgostick ***@***.***> a écrit :

…

can you put the full traceback? This is not a openpnm error message so we need to see where in the stack this gets triggered. — Reply to this email directly, view it on GitHub <#2183 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AYWXRI3UGDPDQ7A63KVNI63VM2JS5ANCNFSM5LPNCCPQ> . You are receiving this because you commented.Message ID: ***@***.***>

[jgostick]

This means that one or more of your geometry values is not computed correctly, like you have nans in the throat lenght of something. THen all the 'downstream' calculations will complain and warn you. When you run stokes flow it does not work because the data is not available. Try printing your geometry and seeing which properties have invalid values (i.e. print(geo))

[Mat10G]

I think there is something wrong with the function : sf.run(). It is impossible to execute so I can't calculate the permeability in the UserGuide example. Le mer. 1 juin 2022 à 10:21, Mathias Gazay ***@***.***> a écrit :

…

Hello, thank you for your quick response, I have this traceback. I downloaded OpenPNM with this function on my virtual machine : $ conda install -c conda-forge openpnm CRITICAL : front and back labels have been switched to obey the right-hand rule SOURCE : openpnm.network.Cubic.__init__ TIME STAMP : 2022-06-01 10:13:35,829 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.flow_shape_factors was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:35,980 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.hydraulic_conductance was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:35,980 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.poisson_shape_factors was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:35,981 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.diffusive_conductance was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:35,981 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.ad_dif_conductance was not run since the following property is missing: 'throat.hydraulic_conductance' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:35,982 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.thermal_conductance was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:35,984 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.electrical_conductance was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:35,984 ------------------------------------------------------------ ------------------------------------------------------------ WARNING : Inlets have non-zero volume, percolation curve won't start at 0. SOURCE : openpnm.algorithms.OrdinaryPercolation.get_intrusion_data TIME STAMP : 2022-06-01 10:13:36,552 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.flow_shape_factors was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:36,718 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.hydraulic_conductance was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:36,719 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.poisson_shape_factors was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:36,719 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.diffusive_conductance was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:36,720 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.ad_dif_conductance was not run since the following property is missing: 'throat.hydraulic_conductance' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:36,720 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.thermal_conductance was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:36,723 ------------------------------------------------------------ ------------------------------------------------------------ ERROR : throat.electrical_conductance was not run since the following property is missing: 'pore.area' SOURCE : openpnm.core.ModelsMixin._regen TIME STAMP : 2022-06-01 10:13:36,723 ------------------------------------------------------------ Traceback (most recent call last): File "/home/mathias/anaconda3/User_Guide.py", line 29, in <module> sf.run() File "/home/mathias/anaconda3/lib/python3.9/site-packages/openpnm/algorithms/ReactiveTransport.py", line 154, in run self._validate_data_health() File "/home/mathias/anaconda3/lib/python3.9/site-packages/openpnm/algorithms/GenericTransport.py", line 810, in _validate_data_health if np.isfinite(self.A.data).all() and np.isfinite(self.b).all(): File "/home/mathias/anaconda3/lib/python3.9/site-packages/openpnm/algorithms/GenericTransport.py", line 489, in _get_A self._build_A() File "/home/mathias/anaconda3/lib/python3.9/site-packages/openpnm/algorithms/GenericTransport.py", line 468, in _build_A g = phase[gvals] File "/home/mathias/anaconda3/lib/python3.9/site-packages/openpnm/phases/GenericPhase.py", line 99, in __getitem__ vals = super().__getitem__(key) File "/home/mathias/anaconda3/lib/python3.9/site-packages/openpnm/core/Base.py", line 283, in __getitem__ raise KeyError(key) KeyError: 'throat.hydraulic_conductance' Le mer. 1 juin 2022 à 00:50, jgostick ***@***.***> a écrit : > can you put the full traceback? This is not a openpnm error message so we > need to see where in the stack this gets triggered. > > — > Reply to this email directly, view it on GitHub > <#2183 (reply in thread)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AYWXRI3UGDPDQ7A63KVNI63VM2JS5ANCNFSM5LPNCCPQ> > . > You are receiving this because you commented.Message ID: > ***@***.***> >

[Mat10G]

Okay thank you for your answer, I did it and I obtain only valid values I think. Maybe I am running a too young version for this kind of example. [image: image.png] Le mer. 1 juin 2022 à 14:53, jgostick ***@***.***> a écrit :

…

This means that one or more of your geometry values is not computed correctly, like you have nans in the throat lenght of something. THen all the 'downstream' calculations will complain and warn you. When you run stokes flow it does not work because the data is not available. Try printing your geometry and seeing which properties have invalid values (i.e. print(geo)) — Reply to this email directly, view it on GitHub <#2183 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AYWXRI6NQO5M3NFE2JTEDETVM5MMBANCNFSM5LPNCCPQ> . You are receiving this because you commented.Message ID: ***@***.***>

[stathi02]

Same here. I am trying to run this simple example from the tutorial:

_import openpnm as op

Define geometrical parameters

Lc = 1e-4
Nx, Ny, Nz = (10, 10, 10)

Generate network, geometry, phase, and physics

pn = op.network.Cubic(shape=[Nx, Ny, Nz], spacing=Lc)
geo = op.geometry.SpheresAndCylinders(network=pn, pores=pn.Ps, throats=pn.Ts)
print(geo)
Hg = op.phases.Mercury(network=pn)
phys = op.physics.Standard(network=pn, phase=Hg, geometry=geo)

Create algorithm and run simulation

mip = op.algorithms.Porosimetry(network=pn, phase=Hg)
mip.set_inlets(pores=pn.pores(['left', 'right', 'top', 'bottom']))
mip.run()_

and i get

runfile('C:/Users/stath/.spyder-py3/temp.py', wdir='C:/Users/stath/.spyder-py3')

CRITICAL : front and back labels have been switched to obey the right-hand rule
SOURCE : openpnm.network.Cubic.init
TIME STAMP : 2022-06-01 21:23:39,349

---

ERROR : throat.flow_shape_factors was not run since the following property is
missing: 'pore.area'
SOURCE : openpnm.core.ModelsMixin._regen
TIME STAMP : 2022-06-01 21:23:39,374

---

ERROR : throat.hydraulic_conductance was not run since the following property is
missing: 'pore.area'
SOURCE : openpnm.core.ModelsMixin._regen
TIME STAMP : 2022-06-01 21:23:39,376

---

ERROR : throat.poisson_shape_factors was not run since the following property is
missing: 'pore.area'
SOURCE : openpnm.core.ModelsMixin._regen
TIME STAMP : 2022-06-01 21:23:39,377

---

ERROR : throat.diffusive_conductance was not run since the following property is
missing: 'pore.area'
SOURCE : openpnm.core.ModelsMixin._regen
TIME STAMP : 2022-06-01 21:23:39,379

---

ERROR : throat.ad_dif_conductance was not run since the following property is
missing: 'throat.hydraulic_conductance'
SOURCE : openpnm.core.ModelsMixin._regen
TIME STAMP : 2022-06-01 21:23:39,380

---

ERROR : throat.thermal_conductance was not run since the following property is
missing: 'pore.area'
SOURCE : openpnm.core.ModelsMixin._regen
TIME STAMP : 2022-06-01 21:23:39,385

---

ERROR : throat.electrical_conductance was not run since the following property is
missing: 'pore.area'
SOURCE : openpnm.core.ModelsMixin._regen
TIME STAMP : 2022-06-01 21:23:39,386

――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
openpnm.geometry.SpheresAndCylinders : geo_01
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――

Properties Valid Values

――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
1 pore.diameter 1000 / 1000
2 pore.max_size 1000 / 1000
3 pore.seed 1000 / 1000
4 pore.volume 1000 / 1000
5 throat.cross_sectional_area 2700 / 2700
6 throat.diameter 2700 / 2700
7 throat.diffusive_size_factors.pore1 2700 / 2700
8 throat.diffusive_size_factors.pore2 2700 / 2700
9 throat.diffusive_size_factors.th... 2700 / 2700
10 throat.hydraulic_size_factors.pore1 2700 / 2700
11 throat.hydraulic_size_factors.pore2 2700 / 2700
12 throat.hydraulic_size_factors.th... 2700 / 2700
13 throat.length 2700 / 2700
14 throat.max_size 2700 / 2700
15 throat.volume 2700 / 2700
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――

Labels Assigned Locations

――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
1 pore.all 1000
2 throat.all 2700
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――

I understand that pore.area is missing