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Error installing ovito on Linux cluster

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Hello everybody,

i am having the following error when trying to install Ovito 3.3.5 with Python 3.8:

pip3 install ovito
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', OSError(0, 'Error'))': /simple/ovito/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', OSError(0, 'Error'))': /simple/ovito/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', OSError(0, 'Error'))': /simple/ovito/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', OSError(0, 'Error'))': /simple/ovito/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', OSError(0, 'Error'))': /simple/ovito/
ERROR: Could not find a version that satisfies the requirement ovito (from versions: none)
ERROR: No matching distribution found for ovito

 

and this error with conda install:

conda install -c https://conda.ovito.org/ -c conda-forge ovito=3.3.0
Collecting package metadata (current_repodata.json): failed

CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.ovito.org/linux-64/current_repodata.json&gt;
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
'https://conda.ovito.org/linux-64'

 

I hope somebody can help me.

Regards

Hi,

In both cases the error messages seem to indicate some sort of internet connection problem. In principle this can happen due to a temporary server outage or some connection or network configuration problem on your end. The OVITO pip package and the OVITO Anaconda packages are hosted on completely different servers though:

https://pypi.org/project/ovito/

https://conda.ovito.org/linux-64/

Are you able to open these URLs in your web browser? I just installed the OVITO Anaconda package on my computer and can confirm that the package server is currently working:

C:\Users\astuk>conda install -c https://conda.ovito.org -c conda-forge ovito=3.3.5
Collecting package metadata (current_repodata.json): done
Solving environment: done

Installing an older OVITO release, like you did (version 3.3.0), also works.

Hello Alexander

i can open these URLs but i am still getting the same error with conda install. Is it possible to solve this issue ?

Regards

Betim

I just realized that you work on a Linux cluster machine. Did you try to open these URLs from the Linux terminal? I'm not sure, but I still have the feeling that something, maybe a firewall, is blocking the access of the pip/conda package managers to these URLs.

If the pip and conda package management tools still fail, you can try to manually download the OVITO pip or or Anaconda packages and perform a manual installation from the Linux terminal. The pip package file ("wheel") can be downloaded from here:

https://pypi.org/project/ovito/#files

The Anaconda package is available here:

https://conda.ovito.org/linux-64/

In both cases you will have to pick the correct package for your OS and Python interpreter versions. Additionally, you will have to make sure all required dependencies are installed as well. In case of the Anaconda package, you find the list of other packages the OVITO package depends on in this metadata file: https://conda.ovito.org/linux-64/repodata.json

More instructions on how to manually install a pip wheel file can be found here: https://packaging.python.org/tutorials/installing-packages/

-Alexander

Hello Alexander,

i am getting the same result with the whl file:

python -m pip install ovito-3.3.5-cp38-cp38-manylinux1_x86_64.whl
Processing ./ovito-3.3.5-cp38-cp38-manylinux1_x86_64.whl
Requirement already satisfied: numpy in ./anaconda3/lib/python3.8/site-packages (from ovito==3.3.5) (1.19.2)
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', OSError(0, 'Error'))': /simple/pyside2/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', OSError(0, 'Error'))': /simple/pyside2/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', OSError(0, 'Error'))': /simple/pyside2/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', OSError(0, 'Error'))': /simple/pyside2/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', OSError(0, 'Error'))': /simple/pyside2/
ERROR: Could not find a version that satisfies the requirement PySide2>=5.15 (from ovito==3.3.5) (from versions: none)
ERROR: No matching distribution found for PySide2>=5.15 (from ovito==3.3.5)

The pip package manager on your system seems to be unable to download any packages at all. The error message above indicates that the PySide2 package is missing on your system, which is required by the ovito package. This basically means you will have to download the wheel files for every Python package required by OVITO (including their secondary dependencies) and install them by hand. For example, the wheel file containing the PySide2 package is available here: https://pypi.org/project/PySide2/

Be aware that it can be a cumbersome process to download and install all Python packages by hand. Perhaps it makes more sense to solve the original pip connection problem. Can you talk to the technical support staff for your Linux cluster and ask them for help in this matter?

One more advice: Do not mix pip and Anaconda packages. I can see from the error message above that you tried to install the OVITO pip wheel in an Anaconda Python interpreter. This is generally not a good idea, because our pip package is only made for standard CPython interpreters. If you work in an Anaconda environment, install only the OVITO package for Anaconda to avoid compatibility problems.

Quote from Alexander Stukowski on January 12, 2021, 1:18 pm

The pip package manager on your system seems to be unable to download any packages at all. The error message above indicates that the PySide2 package is missing on your system, which is required by the ovito package. This basically means you will have to download the wheel files for every Python package required by OVITO (including their secondary dependencies) and install them by hand. For example, the wheel file containing the PySide2 package is available here: https://pypi.org/project/PySide2/

Be aware that it can be a cumbersome process to download and install all Python packages by hand. Perhaps it makes more sense to solve the original pip connection problem. Can you talk to the technical support staff for your Linux cluster and ask them for help in this matter?

One more advice: Do not mix pip and Anaconda packages. I can see from the error message above that you tried to install the OVITO pip wheel in an Anaconda Python interpreter. This is generally not a good idea, because our pip package is only made for standard CPython interpreters. If you work in an Anaconda environment, install only the OVITO package for Anaconda to avoid compatibility problems.

with conda it looks like it worked:

conda install ovito-3.3.5-py38h04863e7_0.tar.bz2
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

 

but when i start python and import ovito it does not work:

import ovito
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/bahtiri/anaconda3/lib/python3.8/site-packages/ovito/__init__.py", line 19, in <module>
from .plugins.PyScript import (version, version_string, gui_mode, headless_mode, Scene, scene, dataset, enable_logging)
ImportError: libavformat.so.58: cannot open shared object file: No such file or directory

 

 

i started python on the terminal*

python

import ovito

 

The conda install command does not automatically fetch required dependencies when installing a local package file. It does not even check if the required dependencies are present, which can result in a broken environment. Dependency checking is only performed by this command if you install a package from a conda channel, which requires a working internet connection. Without that, you are responsible for making sure that all requirements are met.

The OVITO module isn't working yet, because you haven't installed all third-party packages required by the ovito package. As mentioned above, they are listed in the repodata.json file:

        "ffmpeg >=4.3.1,<4.4.0a0",
        "libgcc-ng >=9.3.0",
        "libnetcdf >=4.7.4,<4.7.5.0a0",
        "libsodium >=1.0.18,<1.0.19.0a0",
        "libstdcxx-ng >=9.3.0",
        "numpy",
        "ospray_ovito 2.2.0.*",
        "pyside2",
        "python >=3.8,<3.9.0a0",
        "python_abi 3.8.* *_cp38",
        "qt >=5.12.9,<5.13.0a0",
        "tbb >=2020.2",
        "zlib >=1.2.11,<1.3.0a0"

Some of them are available from the main Anaconda Cloud channel, others must be installed from the conda-forge channel. The ospray_ovito package is provided by our own conda channel and can be manually downloaded here. The package file should be installed using the conda install command.

Quote from Alexander Stukowski on January 13, 2021, 10:49 am

The conda install command does not automatically fetch required dependencies when installing a local package file. It does not even check if the required dependencies are present, which can result in a broken environment. Dependency checking is only performed by this command if you install a package from a conda channel, which requires a working internet connection. Without that, you are responsible for making sure that all requirements are met.

The OVITO module isn't working yet, because you haven't installed all third-party packages required by the ovito package. As mentioned above, they are listed in the repodata.json file:

        "ffmpeg >=4.3.1,<4.4.0a0",
        "libgcc-ng >=9.3.0",
        "libnetcdf >=4.7.4,<4.7.5.0a0",
        "libsodium >=1.0.18,<1.0.19.0a0",
        "libstdcxx-ng >=9.3.0",
        "numpy",
        "ospray_ovito 2.2.0.*",
        "pyside2",
        "python >=3.8,<3.9.0a0",
        "python_abi 3.8.* *_cp38",
        "qt >=5.12.9,<5.13.0a0",
        "tbb >=2020.2",
        "zlib >=1.2.11,<1.3.0a0"

Some of them are available from the main Anaconda Cloud channel, others must be installed from the conda-forge channel. The ospray_ovito package is provided by our own conda channel and can be manually downloaded here. The package file should be installed using the conda install command.

I was able to install ovito by exporting the proxies:

pip install -U ovito
Collecting ovito
Using cached ovito-3.3.5-cp38-cp38-manylinux1_x86_64.whl (78.8 MB)
Requirement already satisfied: numpy in ./anaconda3/lib/python3.8/site-packages (from ovito) (1.19.2)
Collecting PySide2>=5.15
Using cached PySide2-5.15.2-5.15.2-cp35.cp36.cp37.cp38.cp39-abi3-manylinux1_x86_64.whl (164.3 MB)
Collecting shiboken2==5.15.2
Using cached shiboken2-5.15.2-5.15.2-cp35.cp36.cp37.cp38.cp39-abi3-manylinux1_x86_64.whl (956 kB)
Installing collected packages: shiboken2, PySide2, ovito
Successfully installed PySide2-5.15.2 ovito-3.3.5 shiboken2-5.15.2

When i start python and import ovito i am getting the following from the terminal:

python
Python 3.8.5 (default, Sep 4 2020, 07:30:14)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import ovito
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/bahtiri/anaconda3/lib/python3.8/site-packages/ovito/__init__.py", line 19, in <module>
from .plugins.PyScript import (version, version_string, gui_mode, headless_mode, Scene, scene, dataset, enable_logging)
File "/home/bahtiri/anaconda3/lib/python3.8/site-packages/ovito/plugins/__init__.py", line 12, in <module>
import PySide2.QtCore
File "/home/bahtiri/anaconda3/lib/python3.8/site-packages/shiboken2/files.dir/shibokensupport/__feature__.py", line 142, in _import
return original_import(name, *args, **kwargs)
ImportError: /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2: symbol krb5_ser_context_init, version krb5_3_MIT not defined in file libkrb5.so.3 with link time reference

 

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