Plumed on Google Colab

[joan.c...@gmail.com]

Dear all,

This one is a bit odd but here it goes:

I am planning to run some gromacs/plumed calculations on a free Google Colab notebook. Since the free tier has a limited run time and the space is wiped clean every time the VM is killed, I was wondering if if would be possible to download the executables and just upload them instead of installing plumed from scratch every time. Would I only need to save the /usr/local/plumed directory, or are there any other files that plumed looks for?

Thank you!

Joan

[Giovanni Bussi]

Hi!

This is a nice idea, and it would be great if you want to share the result with other people :-) We might even release a precompiled tar compatible with colab instances.

What I would suggest is to:

- configure with --prefix /usr/local/plumed-$version

- make a tgz of that whole directory

- add to PATH /usr/local/plumed-$version/bin and to LIBRARY_PATH and LD_LIBRARY_PATH /usr/local/plumed-$version/lib

Does it make sense?

I guess there's no API to create this stuff with a single command on the command line (so that we could do it directly on GitHub Actions). Am I right? If so, maybe we might prepare a simple script that does the entire operation, and remember to do within a colab instance every now and then.

Giovanni

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[Joan Clark Nicolas]

Hi Giovanni,

It does work, not sure if the speed is as good as it should be, but it's good enough. I have it scripted in a notebook that I can share when I get access to my computer.

Cheers

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[Joan Clark Nicolas]

Dear all,

As mentioned a few weeks ago, here are 2 notebooks to install gmx-plumed in google colab and then run it using only the executables (could probs be combined into 1 but that made it easier for me). They are edits of the notebooks I use which are based on my own plumed fork so there may be some typos here and there, but they should be easy to fix.

Hope that is useful

Mr. Joan Clark-Nicolas