Installation#

uataq reads the UATAQ data archive, and the archive lives on CHPC. So you install and use uataq on CHPC. This page takes you from a fresh login to a first read of real data in about five minutes.

Run the commands on a login node, the computer you land on when you ssh in. Login nodes are for light work: installing, editing, small reads. Bigger jobs go to a compute node through Slurm, CHPC’s job scheduler (see Use uataq in a Slurm job). If CHPC is new to you, start with CHPC’s documentation.

What you need#

  • A CHPC account in the lin group. The archive is stored in the Lin group’s space, and only members of the group can read it. The command groups lists your groups. If lin is not in the list, ask your advisor to have you added.

  • Python 3.11 or newer. The Python you get when you log in (python3) is version 3.6.8, which is too old, and pip install fails on it with an unhelpful error (see If something goes wrong). Step 2 loads a newer Python from CHPC.

That is all. You do not set any environment variable: uataq already knows where the archive is. (To read a copy of it, set LINGROUP_MEASUREMENTS_DIR to the copy’s measurements folder; see Reading a copy of the archive.)

Install#

  1. Check that you can read the archive.

    ls /uufs/chpc.utah.edu/common/home/lin-group25/measurements/data

    You should see a folder for each site the lin group records (asb, csp, dbk, and so on through wbb), and a few other folders that are not uataq sites. If you get an error instead, you do not have access yet. See What you need.

  2. Load a newer Python. CHPC installs its software as modules, and module load turns one on for your current session.

    module load python
python3 --version

    The second command should print Python 3.11 or newer (Python 3.11.3 in October 2026).

  3. Make a virtual environment. A virtual environment is a folder with its own copy of Python and its own packages. What you install for uataq stays there and does not disturb anything else.

    python3 -m venv ~/venvs/uataq
source ~/venvs/uataq/bin/activate

    (uataq) now appears at the start of your prompt. The folder takes about 0.4 GB. Keep it in your home directory, not in scratch: CHPC deletes scratch files that go unused for 60 days.

  4. Install uataq. pip is Python’s installer. uataq is not on PyPI (the usual package index), so you point pip at its GitHub repository. The @v2026.11.0 at the end names a release, the newest when this page was written (Update uataq, or pin a version shows how to find a newer one).

    pip install git+https://github.com/jmineau/uataq.git@v2026.11.0

    pip prints a long list while it works (about two minutes). The last line that matters starts with Successfully installed. A notice about a new pip release after it is harmless.

  5. Check that it reads real data. This reads one day of CO2 from the WBB site (William Browning Building, on the University of Utah campus):

    python -c "import uataq; print(uataq.get_obs('WBB', 'CO2', time_range='2025-06-02'))"

    It takes a couple of seconds and prints a table:

                         CO2d_ppm_cal  CO2d_ppm_raw instrument
Time_UTC
2025-06-02 00:00:01    431.852558      434.8026   lgr_ugga
2025-06-02 00:00:11    431.612346      434.5594   lgr_ugga
2025-06-02 00:00:21    431.812938      434.7615   lgr_ugga
2025-06-02 00:00:30    431.939531      434.8889   lgr_ugga
2025-06-02 00:00:40    432.130721      435.0815   lgr_ugga
...                           ...           ...        ...
2025-06-02 23:59:20    429.260744      431.1932   lgr_ugga
2025-06-02 23:59:29    429.139982      431.0713   lgr_ugga
2025-06-02 23:59:39    429.083069      431.0138   lgr_ugga
2025-06-02 23:59:49    429.033293      430.9635   lgr_ugga
2025-06-02 23:59:59    429.157492      431.0887   lgr_ugga

[8390 rows x 3 columns]

    If you see a table like this, the install works and you can read the archive. (The row count can change if the data are reprocessed.) import uataq alone is not a good test: it can succeed even when the archive is out of reach, so this step reads some data.

Next, read Your first data.

Other Pythons#

module load python gives CHPC’s default Python. Any version from 3.11 up works. module spider python lists the others. The steps above were tried with the modules python/3.11.3 (the default), python/3.12.12, python/3.13.5 and python/3.14.5. For 3.14.5, CHPC wants module load gcc/13.4.0 python/3.14.5.

If you already use conda, make an environment with Python 3.11 or newer and run the same pip install inside it. This works too, and the environment takes 0.6 GB in ~/.conda/envs:

module load miniforge3
conda create -y -n uataq python=3.12
conda activate uataq
pip install git+https://github.com/jmineau/uataq.git@v2026.11.0

Each time you log in#

Activate the environment before you use uataq:

source ~/venvs/uataq/bin/activate

You do not need module load python again: the environment remembers which Python it uses. If it ever stops working after CHPC changes its modules, delete the folder (rm -rf ~/venvs/uataq) and redo steps 2 to 4.

Use uataq in Jupyter#

CHPC runs Jupyter in your browser through Open OnDemand. To use your uataq environment there, install Jupyter into it once:

source ~/venvs/uataq/bin/activate
pip install jupyterlab

It takes a minute or two and about 0.25 GB more. Then open the Jupyter app in Open OnDemand, choose Custom (Environment setup below) as the Python version, and enter these two lines in the environment setup box:

module load python
source ~/venvs/uataq/bin/activate

Your notebooks then run the environment’s Python, with uataq. (The two lines are CHPC’s instructions for a custom environment; the environment itself was tested up to a Jupyter kernel that imports uataq.)

Update uataq, or pin a version#

The install above names a release by its tag, @v2026.11.0. Each release has a tag of the form vYYYY.M.PATCH. The releases page lists them, newest first. To update later, run the install again with --upgrade and the newest tag:

pip install --upgrade git+https://github.com/jmineau/uataq.git@v2026.11.0

For results you will publish, keep the tag you installed and write the version down. pip show uataq prints the version you have:

pip show uataq

To try changes made since the last release, leave off the @ and the tag. That installs the code on the main branch, which these docs may not yet describe (the version switcher in the header has a dev copy that does).

Use uataq in a Slurm job#

A login node is for light work, such as a year of one site’s CO2 and CH4 at the final level (how long that takes: A year or more). For several years or many sites, the raw level, or reads in several processes, write a job script. The job only has to activate the environment:

#!/bin/bash
#SBATCH --account=lin-np
#SBATCH --partition=lin-np
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem=8G
#SBATCH --time=00:30:00

source ~/venvs/uataq/bin/activate
python my_script.py

Save it as my_job.sh and submit it with sbatch my_job.sh. lin-np is the Lin group’s own set of compute nodes. If sbatch refuses the account, mychpc batch lists the accounts and partitions you can use. See CHPC’s Slurm guide for the rest.

Reading a copy of the archive#

uataq reads the Lin group’s measurements from the group’s dedicated measurements space. To read a copy instead (a snapshot kept for a paper, or a test tree), set LINGROUP_MEASUREMENTS_DIR to the copy’s measurements folder, the one that holds data and pipeline. Unset or empty, it means the archive itself.

export LINGROUP_MEASUREMENTS_DIR=/path/to/measurements

uataq looks the variable up each time it needs a path, so setting it in Python after import uataq works too (os.environ["LINGROUP_MEASUREMENTS_DIR"] = ...), with one exception: the pipeline’s configuration files (data_config.json and site_config.csv) are read once, when uataq is imported, so set the variable before the import if the copy’s configuration differs. A value that is not a directory raises FileNotFoundError naming the variable. The Horel group’s folders have no such variable.

If something goes wrong#

pip install ends with FileNotFoundError: ... setup.py

You are on CHPC’s system Python 3.6, which cannot install uataq. Run module load python, delete the environment if you made it before that (rm -rf ~/venvs/uataq), and redo steps 2 to 4.

FileNotFoundError saying LINGROUP_MEASUREMENTS_DIR is not a directory

The variable is set to a path that does not exist. Fix the path, or run unset LINGROUP_MEASUREMENTS_DIR to read the archive itself.

The ls in step 1, or the read in step 5, fails

You are probably not in the lin group yet. Run groups and see What you need.

The steps on this page were last checked in October 2026 on a Notchpeak login node.