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• Python packages: All Python packages that will be needed in programs using a package will need to be installed into the same environment, as the instance of Python from this environment will be used to run the programs. To install additional packages, activate the environment, install the packages (with conda if possible, otherwise with pip), then deactivate the environment.

• Installing PyPi packages with pip: If an attempt to install a package gives an error about trying to write to a location to which there isn't permission, this is usually a result of a PATH issue.

  • It is important to use the instance of pip that was installed in the conda environment, and not one from another location that may be available in the path.

  • The current path can be seen by running 'echo $PATH'.

  • Issues with incorrect directories being included, or occurring in the wrong order, in a path can usually be resolved by logging out and back in, loading Miniconda, then activating the necessary environment.

• Conda environment dependencies:

  Within the Conda documentation on Managing environments, specifically the section on Building identical conda environments, it states:

  • You can use explicit specification files to build an identical conda environment on the same operating system platform, either on the same machine or on a different machine.

  • An explicit spec file is not usually cross platform, and therefore has a comment at the top such as # platform: osx-64 showing the platform where it was created. This platform is the one where this spec file is known to work. On other platforms, the packages specified might not be available or dependencies might be missing for some of the key packages already in the spec.

  • Conda does not check architecture or dependencies when installing from a spec file. To ensure that the packages work correctly, make sure that the file was created from a working environment, and use it on the same architecture, operating system, and platform, such as linux-64 or osx-64.

  The Miniconda documentation states:

  • System requirements License:

    • Operating system: Windows 8 or newer, 64-bit macOS 10.13+, or Linux, including Ubuntu, RedHat, CentOS 7+, and others.

Common Error Messages

Error: /lib64/libk5crypto.so.3: undefined symbol: EVP_KDF_ctrl, version OPENSSL_1_1_1b

This error is typically associated when trying to use git after performing a module load miniconda3/<version>. For example:

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1. Use a newer version of git than provided by the base system. Perform a module spider git to see available versions and load.

2. If you’re using an active conda environment, then you can explicitly install conda into it via conda install -c anaconda git.

Error: json.decoder.JSONDecodeError: Expecting value: line

This may occur while trying to install packages, or creating a new environment.
Solution: Try conda clean -i in your account then re-perform the conda install step.
The clean command removes unused packages and caches, with the -i option removing the index cache that might have become corrupted..

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