Help needed: ImportError: No module named anytree

[Vitaliy]

Hello,

I have just updated MOOSE and I got this error message while running the tests. The installation and compilation went smooth and successful no errors or warnings, but tests do not work. But the actual problem works, only test run does not work.

Traceback (most recent call last):

  File "./run_tests", line 7, in <module>

    from TestHarness import TestHarness

  File "/home/project/moose/python/TestHarness/__init__.py", line 10, in <module>

    from TestHarness import TestHarness

  File "/home/project/moose/python/TestHarness/TestHarness.py", line 22, in <module>

    import util

  File "/home/project/moose/python/TestHarness/util.py", line 12, in <module>

    from mooseutils import colorText

  File "/home/project/moose/python/mooseutils/__init__.py", line 13, in <module>

    from hit_load import hit_load, HitNode, hit_parse

  File "/home/project/moose/python/mooseutils/hit_load.py", line 3, in <module>

    import anytree

ImportError: No module named anytime

Thanks,

Vitaliy

[Miller, Jason M]

The 'anytree' module is include in the latest moose-environment packages. Its possible you are using something non-standard? Specifically, anytree is available when one loads our miniconda or moose-tools module.

Jason

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[Vitaliy]

this is that I was thinking on the first place. I reinstalled moose environment package for Linux cluster single user, but the same error appeared again. echo $PETSC_DIR returns the correct path (/home/moose-compilers/petsc/petsc-3.8.3/gcc-opt). Again, my actual problem works, even tests work if I run it separately, only ./run_test command does not. Also, the output file is not store at the location of the input file, but in the root directory. How do I load MOOSE modules on linux cluster, because module load does not return anything.

Thanks,

Vitaliy 

On Thursday, February 22, 2018 at 8:34:38 AM UTC-6, jason.miller wrote:

The 'anytree' module is include in the latest moose-environment packages. Its possible you are using something non-standard? Specifically, anytree is available when one loads our miniconda or moose-tools module.

Jason

On Thu, Feb 22, 2018 at 7:23 AM, Vitaliy <vityu...@gmail.com> wrote:

Hello,

I have just updated MOOSE and I got this error message while running the tests. The installation and compilation went smooth and successful no errors or warnings, but tests do not work. But the actual problem works, only test run does not work.

Traceback (most recent call last):

  File "./run_tests", line 7, in <module>

    from TestHarness import TestHarness

  File "/home/project/moose/python/TestHarness/__init__.py", line 10, in <module>

    from TestHarness import TestHarness

  File "/home/project/moose/python/TestHarness/TestHarness.py", line 22, in <module>

    import util

  File "/home/project/moose/python/TestHarness/util.py", line 12, in <module>

    from mooseutils import colorText

  File "/home/project/moose/python/mooseutils/__init__.py", line 13, in <module>

    from hit_load import hit_load, HitNode, hit_parse

  File "/home/project/moose/python/mooseutils/hit_load.py", line 3, in <module>

    import anytree

ImportError: No module named anytime

Thanks,

Vitaliy

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[Miller, Jason M]

Oh I see... since this is a non-moose-environment install... looks like we need to update our cluster single/multi user installation instructions, to reflect the new requirements to python. Not sure you will need all of the following python modules, but here is a list the MOOSE group expects to have available (because they use the moose-environment package)

<install miniconda, or leverage your operating system's package management system, to install the following>

  python modules: coverage reportlab mako numpy scipy scikit-learn h5py hdf5 scikit-image requests vtk=7.1.0 pyyaml matplotlib pip lxml pyflakes pandas conda-build mock yaml pyqt swig

And also, the PIP specific stuff (pip install):

  markdown python-markdown-math pybtex bs4 jinja2 livereload daemonlite pylint==1.6.5 lxml pylatexenc anytree

The _exact_ thing we are doing to supply the above in the moose-environment package:

...install miniconda, and with miniconda installed:

  conda install -c idaholab python=2.7 coverage reportlab mako numpy scipy scikit-learn h5py hdf5 scikit-image requests vtk=7.1.0 pyyaml matplotlib pip lxml pyflakes pandas conda-build mock yaml pyqt swig --yes

...install pip, and with pip install:

  pip install --no-cache-dir markdown python-markdown-math pybtex bs4 jinja2 livereload daemonlite pylint==1.6.5 lxml pylatexenc anytree

Looks like you may only need to perform `pip install anytree`. But, there is no telling what other python modules you might need, so what I'd do, is make sure all those modules are installed.

Jason

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[Slaughter, Andrew E]

This is bug that we introduced recently, the test system should not be relying on "anytree". I will get this fixed soon(ish).

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[Vitaliy]

thanks guys! I have installed the missing packages and everything works now

Ran 560 tests in 29.3 seconds

560 passed, 41 skipped, 0 pending,

Vitaliy

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