Posted in 2019

How to prevent interuptions of ssh connections to Mistral?

If your ssh connections to mistral are interrupted after short periods without keyboard activities and you get an error message containing ‘broken pipe’ string, try to set the ServerAliveInterval parameter appropriately. This parameter can be set as a command-line option to ssh:

In the example above, ssh will send a message with a response request to the server if no packets have been received from the server in the past 60 seconds.

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Which MPI library and compiler should I use?

For model simulations in production mode, the recommended combination is to

Choose an Intel compiler version that has been validated to work with your model. Lacking a verified version, just use the most recent version (module intel/18.0.4 at the time of this writing) and validate that yourself.

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How do I share files with members of another project?

You can use ACLs to achieve this. As a member of project group ax0001, you would have to create a directory in your project’s work for example

It could be any other place on Lustre file systems where you have write access. Then you grant project bx0002 permissions to this directory

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Why do I receive .Xauthority file error messages?

When you open a new terminal session on mistral with X forwarding turned on (ssh -X ...), the .Xauthority file in your home directory gets updated by the xauth program. This file is used to keep X authentication keys in order to prevent unauthorized connections to your local display.

Sometimes, the .Xauthority file cannot be updated due to issues with the lustre01 file system, where your home directory is located, on mistral and you might experience an error message like:

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I want to add my own packages to Python or R but they won’t compile

Python and R, among other scripting languages, allow users to create customized environments including their own set of packages.

For Python you use virtualenv or conda, R can also add locally installed packages.

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