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.