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Account & Access

Complete this step before the workshop begins. Getting your Alpine account active can take up to 15 minutes, so do not leave it for the day of.

1. Request an Alpine Account

Follow the instructions at the CSU Research Computing portal:

Get Started with Alpine, CSU Research Computing

Your account should become active within 15 minutes.

Please reach out to the workshop organizers directly to have an account set up for you. Do not attempt to create an account through the CSU portal.

2. Log in via Open OnDemand

The easiest way to access Alpine is through the Open OnDemand web interface, no SSH client or VPN required.

  1. Navigate to ondemand-rmacc.rc.colorado.edu
  2. Log in with your institutional credentials
  3. In the top menu, go to Clusters → Alpine Shell Access

This opens a terminal in your browser connected to an Alpine login node. You should see something like this:

Alpine Shell, login node
Welcome to Alpine - University of Colorado Research Computing Important notes: - Do not run jobs on login nodes - Scratch storage is not backed up - For help: rc-help@colorado.edu

Alternative: SSH

If you prefer a local terminal, you can connect via SSH instead: 

ssh YOUR_USERNAME@login.rc.colorado.edu
See the CURC documentation for full SSH login instructions, including two-factor authentication setup.

3. Workshop Flight Test

The QIIME2 environment needs to be tested before the workshop.

1. Enter a compile node:

From the login shell, run:

acompile
Alpine Shell, entering compile node
acompile salloc: Granted job allocation 1234567 salloc: Waiting for resource configuration salloc: Nodes c3cpu-a2-u1-1 are ready for job [jsmith@c3cpu-a2-u1-1 ~]$

Your prompt changes from a login node (login-ciXX) to a compute node (c3cpu-...), confirming you are on the compile node.

2. Copy the test script:

cp /pl/active/courses/2026_summer/CSU_2026/qiime_script_2026.sh /projects/$USER
Alpine Shell, copy install script
cp /pl/active/courses/2026_summer/CSU_2026/qiime_script_2026.sh /projects/$USER # No output means success

3. Navigate to your projects directory and confirm the script is there:

cd /projects/$USER
ls
Alpine Shell, verify script
cd /projects/jsmith@colostate.edu ls qiime_script_2026.sh

Note

Replace jsmith@colostate.edu with your actual CSU NetID and email address.

4. Run the test script:

sbatch qiime_script_2026.sh
Alpine Shell, running install (~2 min)
chmod +x qiime_script_2026.sh ./qiime_script_2026.sh ✅ TMPDIR added to ~/.bashrc permanently. ========== DIRECTORY INFORMATION ========= HOME: /home/jsmith@colostate.edu (2GB capacity) PROJECT: /project/jsmith@colostate.edu (250GB capacity) SCRATCH: /scratch/alpine/jsmith@colostate.edu (10TB, purged after 90 days) TMPDIR: /scratch/alpine/jsmith@colostate.edu(used for temp installs) Available /tmp space: 60G ✅ /tmp has sufficient space. Workshop Directory: /pl/active/courses/2026_summer/CSU_2026 ✅ You have access to the workshop directory. ========== NODE TYPE CHECK ========= ✅ You are on a compute node. Proceeding with software checks. ========== QIIME2 SOFTWARE TEST ========= Loading qiime2/2026.1_amplicon... Running: qiime --help ✅ Qiime2 loaded successfully. Version: q2cli version 2026.1.0 Run `qiime info` for more version details. 🎉 Success! You’re ready for the workshop! ========== END OF FLIGHT TEST ========= If you experience issues, please send the output file to: rc2-request@colostate.edu

Verify Your Setup

After the script finishes, confirm QIIME2 loads correctly:

module purge
module load qiime2/2026.1_amplicon
qiime info
Alpine Shell, verify QIIME2
module purge module load qiime2/2026.1_amplicon qiime info System versions Python version: 3.9.x QIIME 2 release: 2026.1 QIIME 2 version: 2026.1.0 Installed plugins alignment 2026.1.0 composition 2026.1.0 dada2 2026.1.0 diversity 2026.1.0 feature-classifier 2026.1.0 feature-table 2026.1.0 fragment-insertion 2026.1.0 longitudinal 2026.1.0 metadata 2026.1.0 quality-control 2026.1.0 sample-classifier 2026.1.0 taxa 2026.1.0

If you see this output, you are ready for the workshop. If you see an error, email rc-help@Colorado.EDU with the full output.

Questions?

Contact the Research Computing help desk: rc-help@Colorado.EDU

Additional Alpine documentation: curc.readthedocs.io

Next: Environment Setup