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We can see new links to our external directories:

updatedfiles.png

And now we can get to them:

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Getting information about packages?

What’s Installed - How to find out:

In our notebook, we can see which modules are available by opening a new cell with the + button.

In our cell box, set as “code” use the python import command, followed by a space, then hit tab to get a list of options.

Hitting tab after import runs autocomplete options for the import command. This list of options has populated all modules available to us in our jupyter notebook:

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What’s Installed - Can we get a

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list in Python?

Yes. By running help('modules')
Note: the numpy library isn’t available

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What’s installed and how to use it: Python - help()

  • Generally, help ('modules <module_name>') will give us information on how to use the specific python library we’re importing as long as that library is installed.

  • Similar in functionality to the --help and man commands for shell.

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What’s Installed - Can we get a list in R?

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In R:

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What’s Installed - Query a specific package in R?

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What’s Installed and how to use it: In R - help()

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We’ve confirmed the package we need is unavailable:

Our output results in an error:

  • The error means this particular module is not available in the kernel we have loaded, despite being a commonly used software package for researchers and computations.

  • While many packages were listed when we autocompleted an import command, most of them were installed as part of the jupyter installation and underlying OS environment.

  • Most software we’d need to perform even more simple and common activities for our research would still need to be installed or made available somehow. What are our options?

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Option 1: Load a different kernel

Depending on the HPC’s native environment, you may have other kernels available.

Or not --->

MedBow currently has a minimal number of global kernels (purposefully).

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