Usage#

This page contains information on using PySEP in non-standard environments

Running PySEP on UAF Chinook#

Chinook is University of Alaska Fairbanks’ (UAF) high performance computer. We can run PySEP on Chinook using Docker containers through Singularity/Apptainer.

PySEP has been containerized directly, and any changes pushed to the repo will trigger the container to rebuild, keeping everything up-to-date. The following code snippet downloads the correct SCOPED container. and runs the PySEP help message on Chinook.

module load singularity
singularity pull ghcr.io/seisscoped/pysep:centos7
singularity exec -c pysep_centos7.sif pysep -h

To run a data download we will need to mount the local filesystem into the container using the --bind command. Using the Anchorage example event:

singularity exec -c --bind $(pwd):/home1 pysep_centos7.sif \
    bash -c "cd /home1/; pysep -p mtuq_workshop_2022 -e 2009-04-07T201255_ANCHORAGE.yaml"

In the above example, the -c/--contain flag preserves the internal container filesystem, the -B/--bind flag binds the current working directory on Chinook (i.e., pwd)to a directory called /home1 within the container, and then the bash -c command changes to this /home1 directory and runs PySEP. Files are subsequently saved to the local filesystem in our current working directory.

RecSec, the record section plotting tool, can be run from the command line using a similar format. With the Anchorange example files we just generated:

cd 2009-04-07T201255_SOUTHERN_ALASKA/
singularity exec -c --bind $(pwd):/home1 ../pysep_centos7.sif \
    bash -c "cd /home1; recsec --pysep_path SAC/ --min_period 10 --save record_section_tmin10.png"

Accessing LLNL Waveform Database#

PySEP interfaces with the databases of:

  • W. Walter et al. (2006) An assembled western United States dataset for regional seismic analysis ISSO 9660 CD, LLNL release UCRL-MI-222502

    Download link: https://ds.iris.edu/mda/18-001

To use the LLNL database, you will require an additional dependency that is not listed in the package setup files. To install this dependency run the following in your pysep Conda environment.

conda install -c conda-forge pandas basemap pytest
git clone https://github.com/krischer/llnl_db_client.git
cd llnl_db_client
pip install .

Documentation for the llnl_db_client dependency can be be found here.

When running PySEP, to use the LLNL waveform database, set the input parameter client as:

client: 'LLNL'

PySEP will automatically use the llnl_db_client dependency to acquire event, station and waveform data from the local files donwloaded from IRIS.