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Cluster environment description update #49

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CameronTEllis opened this issue May 23, 2019 · 0 comments
Open

Cluster environment description update #49

CameronTEllis opened this issue May 23, 2019 · 0 comments

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@CameronTEllis
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A naive student tried to get started on the cluster environment and had trouble so here are some recommendation of how to change the get started text.

The tabs for 'Cluster' and 'Cluster (admin)' should be renamed to something like 'Cluster (personal only)' and 'Cluster (shared)' and then each has a description at the top like:

"

Cluster (personal only)

Use these instructions if you wish to create a personal environment on a cluster. You will set a conda environment that you have access to and can use for running these tutorials. You are expected to have knowledge of SLURM parameters, your cluster, to launch the Jupyter notebooks and run batch jobs. Your cluster administrator can help you with setting the SLURM parameters. If other people have already set up these tutorials or intend to, it might be better to use the instructions for 'Cluster (shared)'.
"

"

Cluster (shared)

Use these instructions to set up an environment that can be used multiple users on a cluster. Included are instructions for an admin to create a shared environment and the users need to change some of the tutorial scripts to accommodate This will likely involve creating modules that can be loaded by other users and downloading data to a shared location. You are expected to have knowledge of SLURM parameters, your cluster, to launch the Jupyter notebooks and run batch jobs. Your cluster administrator can help you with setting the SLURM parameters. If you only wish to set up the tutorials for yourself, it might be better to use the instructions for 'Cluster (personal use)'
"

In the current 'Cluster' tab it lists the same instructions twice:

"Check your environment
Check file setup_environment.sh for CONDA_ENV=mybrainiak
Check configuration='cluster'"

It would be good to have a line added to the current 'Cluster' and 'Cluster (admin)' tabs say something like:

"When running the 'run_jupyter_remote_server.sh' script, two problems often arise.

  1. if you submit this as a job you may get an issue where the script cannot be run interactively. If so, change the first line of this file to read: #!/bin/bash
  2. depending on your cluster configuration, your server name may be inappropriately referenced. This will mean that the suggested host name this script outputs will be wrong (typically because it just finds the name of the node you are on). In such cases, you can manually edit the server name in the setup_environment.sh script."

Why do we tell them to use run_jupyter_remote_server when launching on a cluster? Why not use the run_jupyter_remote_cluster.sh for this use? The only difference is using MPI

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