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quick_tips.md

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Quick tips for interacting with the Alpine cluster

Full documentation here.

Login

Login at this link.

  • Open a terminal on the head node by selecting Clusters/Alpine
  • Start a VS Code interactive job Interactive Apps/vS Code-Server (Presets)

ssh Login

Directions to set up ssh are here

Command to log in using the created key

ssh -i ~/.ssh/id_rsa {user_name}@login-ci.rc.colorado.edu

Helpful commands

Submit a script

sbatch job_script.sh

Cancel a job

scancel job_id

Start an interactive job

sinteractive --partition=amilan --time=00:10:00 --ntasks=1

To view all jobs

squeue

To view just your jobs

squeue --user {user_name}

Transfer files

Set up Globus. Note, need to set up and use the CU Boulder Research Computing ACCESS.

Link to transfer

Rsync

rsync -avz --progress path/to/local/files {user_name}@login-ci.rc.colorado.edu:/home/{user_name}/path/to/alpine/location

Setting up Conda

To start conda

module load anaconda
conda init

By default conda will install in the home directory, but there is not enough room. Instead it needs to install into projects.

vim ~/.condarc

And add

pkgs_dirs:
  - /projects/$USER/.conda_pkgs
envs_dirs:
  - /projects/$USER/software/anaconda/envs

Now when you create a new environment, it will point to the correct location

Information for chainging the base directory of installing packages with conda is here

Checking usage

module load slurmtools

See usage stats

suuser {user_name}

See usage stats for the last year

suuser {user_name} 365

This is important to check because

The cumulative computing allocations of a single research group across all projects may not exceed 5 M SU/year or 2.5 M SU over 6 months

Check on jobs that have run (including wait times)

jobstats {user_name}

Check priority (greater than 1 is higher than average, less than 1 is lower than average)

levelfs {user_name}

View resources requested by a job

scontrol show job {job_id}