ProbShakemap

ProbShakemap is a Python toolbox that propagates source uncertainty from an ensemble of earthquake scenarios to ground motion predictions at a grid of target points. It accounts for model uncertainty by accommodating multiple GMMs and their inherent variability. The package includes SeisEnsMan, a tool for generating the ensemble of event-compatible source scenarios. The output consists of a set of products aiding the user to explore and visualize the predictive distribution of ground motion at each target point. Designed for Urgent Computing applications.

Dependencies

• Shakemap
• OpenQuake
• Docker

Command line usage

usage: ProbShakemap.py [-h] [--imt {PGA,PGV,SA0.3),SA(1.0),SA(3.0}] [--tool {StationRecords,Save_Output,QueryHDF5}]
                       [--prob_tool {GetStatistics,GetDistributions,EnsemblePlot} [{GetStatistics,GetDistributions,EnsemblePlot} ...]]
                       [--numGMPEsRealizations NUMGMPESREALIZATIONS] [--num_processes NUM_PROCESSES]
                       [--imt_min IMT_MIN] [--imt_max IMT_MAX] [--station_file STATION_FILE] [--scenario SCENARIO]
                       [--pois_file POIS_FILE] [--deg_round DEG_ROUND] [--pois_subset] [--n_pois N_POIS]
                       [--max_distance MAX_DISTANCE] [--pois_selection_method {random,azimuth_uniform}]
                       [--reuse_pois_subset] [--vector_npy] [--fileScenariosWeights FILESCENARIOSWEIGHTS]

ProbShakemap Toolbox

optional arguments:
  -h, --help            show this help message and exit

input params:
  --imt {PGA,PGV,SA(0.3),SA(1.0),SA(3.0)}
                        Intensity measure type (IMT)
  --tool {StationRecords,Save_Output,QueryHDF5}
                        Tool(s) to use
  --prob_tool {GetStatistics,GetDistributions,EnsemblePlot} [{GetStatistics,GetDistributions,EnsemblePlot} ...]
                        ProbShakemap Tool(s) to use
  --numGMPEsRealizations NUMGMPESREALIZATIONS
                        Total number of GMPEs random samples
  --num_processes NUM_PROCESSES
                        Number of CPU cores for code parallelization
  --imt_min IMT_MIN     Minimum value for the selected IMT (for plot only)
  --imt_max IMT_MAX     Maximum value for the selected IMT (for plot only)
  --station_file STATION_FILE
                        Shakemap .json station file
  --scenario SCENARIO   Scenario number
  --pois_file POIS_FILE
                        Filename with latitude and longitude of POIs
  --deg_round DEG_ROUND
                        Rounding precision for latitude and longitude
  --pois_subset         Extract a subset of POIs
  --n_pois N_POIS       Number of POIs in the subset
  --max_distance MAX_DISTANCE
                        Max distance from epicenter of POIs in the subset
  --pois_selection_method {random,azimuth_uniform}
                        Selection method for the POIs of the subset
  --reuse_pois_subset   Reuse the subset of POIs already extracted in POIs.txt
  --vector_npy          Store ground motion distributions at all POIs (vector.npy)
  --fileScenariosWeights FILESCENARIOSWEIGHTS
                        File with scenarios weights

REQUIRED TO RUN

1. INGV shakemap Docker Image --> INGV shakemap Docker Image is the INGV configuration of the USGS Shakemap Docker Image incorporating specific GMMs and Vs30 map for the Italian region. Except for that, the two products are equivalent. See below for instructions on how to install the INGV shakemap Docker Image.
2. POIs file --> two space-separated columns .txt file with LAT and LON of the POIs. The file must be put in the folder INPUT_FILES.
3. input_file.txt --> file containing the inputs required by OpenQuake and Shakemap. The file must be put in the folder INPUT_FILES (do not rename it). Be sure to set ID_Event equal to the event_id folder name (see Setting ProbShakemap section below).

• TectonicRegionType: as defined in OpenQuake tectonic regionalisation.
• Magnitude_Scaling_Relationship: as required from openquake.hazardlib.scalerel.
• Rupture_aratio: rupture aspect ratio as required from openquake.hazardlib.geo.surface.PlanarSurface.from_hypocenter
• ID_Event: Shakemap ID of the event.
• Vs30file: GMT .grd Vs30 file; if not provided, set it to None. Default Vs30 value (760 m/s) will be used instead.
• CorrelationModel: as required from openquake.hazardlib.correlation.
• CrosscorrModel: as required from openquake.hazardlib.cross_orrelation.
• vs30_clustering: True value means that Vs30 values are expected to show clustering (as required from openquake.hazardlib.correlation).
• truncation_level: number of standard deviations for truncation of the cross-correlation model distribution (as required from openquake.hazardlib.cross_correlation). Note that the truncation feature is lost if you use correlation (see OpenQuake documentation). This parameter is only accounted for when 'NoCrossCorrelation' is selected by the user.
• seed: Random seed to ensure reproducibility in sampling from the GMMs.

4. fileScenariosWeights.txt --> File with scenarios weights (optional). The file must be put in the folder INPUT_FILES (do not rename it).

INSTALLATION

Set ProbShakemap

Clone the INGV shakemap GitHub repository (tag v4.1.3) into your working directory:

git clone --branch v4.1.3 https://github.com/INGV/shakemap.git

The folder shakemap/data/shakemap_profiles/world/data includes, as an example, the event-id folder for Norcia earthquake (8863681/current). The event-id folder contains the file event.xml, with basic information about the event. You need to create an event-id/current folder for each new event and provide the corresponding event.xml file. The latter can be built easily: start from the event.xml file provided for the Norcia example and then edit latitude, longitude, magnitude and time, the only information needed by SeisEnsMan to download the event QUAKEML file (see below). Make sure the event-id is the same you provided in input_file.txt. The Vs30 file (global_italy_vs30_clobber.grd) is placed in the Docker folder /home/shake/shakemap_data/vs30 after building the image. The file includes a specific Vs30 model for italy (Michelini et al., 2020).

Start Docker (download it from here) and build the shakemap Docker Image:

cd shakemap
DOCKER_BUILDKIT=1 docker build --no-cache --build-arg ENV_UID=$(id -u) --build-arg ENV_GID=$(id -g) --tag shakemap4:4.1.3 .

Download ProbShakemap:

git clone https://github.com/INGV/ProbShakemap.git

The ProbShakemap folder contains the input file, the list of scenarios and the POIs file related to the Amatrice earthquake example. Move the folder content to the 'world' folder (needed to preserve all the files after shutting down Docker):

mv ./ProbShakemap/* ./data/shakemap_profiles/world/ && rm -rf ./ProbShakemap

Install SeisEnsMan

SeisEnsMan generates an ensemble of N earthquake source scenarios that are compatible with the event under consideration, given the past seismicity in the region and the known faults. It utilizes the information from the event.xml file to automatically download the event's QUAKEML file and generate the event_stat.json file. The latter contains all the necessary parameters for creating the ensemble of scenarios. Examples of event-specific JSON files can be found in the SeisEnsManV2/IO/EarlyEst folder.

To install all Python libraries required by SeisEnsMan, first create and activate the environment SeisEnsMan:

python -m venv SeisEnsMan

On macOS and Linux:

source [path_to]SeisEnsMan/bin/activate

On Windows:

[path_to]SeisEnsMan\Scripts\activate

Then use the file requirements.txt provided in the folder SeisEnsManV2 to install the required libraries:

python3 -m pip install -r requirements.txt

HOW TO RUN

Generate the scenarios ensemble

Create the event-id/current folder for the event and provide the corresponding event.xml file. This will be used by SeisEnsMan to download the event QUAKEML file needed for generating the ensemble of event-compatible scenarios. Activate the environment SeisEnsMan and move to SeisEnsManV2 directory in path/to/shakemap/data/shakemap_profiles/world/. Then run the following command (set the --nb_scen parameter to the desired number of scenarios in the ensemble):

./line_call.sh

After being generated, the ensemble of scenarios is saved in INPUT_FILES/ENSEMBLE folder, ready to be queried by ProbShakemap. Any other old file has been moved to the BACKUP folder. Before running ProbShakemap, make sure to deactivate the environment SeisEnsMan:

deactivate

Run ProbShakemap

Start Docker and move back to shakemap directory, then run:

docker run -it --rm -v $(pwd)/data/shakemap_profiles:/home/shake/shakemap_profiles -v $(pwd)/data/local:/home/shake/.local --entrypoint=bash shakemap4:4.1.3
sm_profile -l
cd /home/shake/shakemap_profiles/world

ProbShakemap comes with three utility tools: StationRecords, Save_Output and QueryHDF5.

TOOL: StationRecords

Plot data from Shakemap file stationlist.json (the file must be placed in the event-id/current folder).

python ProbShakemap.py --imt PGA --tool StationRecords --imt_min 0.01 --imt_max 10 --station_file stationlist.json

OUTPUT

Data_stationfile_{imt}.pdf: Plot data from Shakemap .json station file for the selected IMT (PGA in the example).

TOOL: Save_Output

Run the probabilistic analysis and save the output to a .HDF5 file with the following hierarchical structure.

scenario --> POI --> GMPEs realizations

python ProbShakemap.py --imt PGA --tool Save_Output --num_processes 8 --pois_file POIs.txt --numGMPEsRealizations 10

OUTPUT

SIZE_{num_scenarios}_ENSEMBLE_{IMT}.hdf5

TOOL: QueryHDF5

Navigate and query the .HDF5 file.

python ProbShakemap.py --tool QueryHDF5 --imt PGA --scenario 10 --pois_file POIs.txt

OUTPUT

GMF_info.txt: Print the ground motion fields for the selected scenario at the POIs listed in POIs.txt.

Preview of an example output file:

GMF realizations at Site_LAT:43.2846_LON:12.7778 for Scenario_10: [0.17520797, 0.21844997, 0.093965515, 0.27266037, 0.079073295, 0.09725358, 0.08347481, 0.06693749, 0.005907976, 0.060873847]
GMF realizations at Site_LAT:43.1846_LON:12.8778 for Scenario_10: [0.100996606, 0.35003924, 0.24363522, 0.19941418, 0.15757227, 0.1009447, 0.19146584, 0.06460667, 0.03146108, 0.097111605]
GMF realizations at Site_LAT:43.0846_LON:13.4778 for Scenario_10: [0.18333985, 0.11954803, 0.2914887, 0.050770156, 0.07628956, 0.17871241, 0.10297835, 0.15162756, 0.020328628, 0.04087482]

---

PROB_TOOLS

ProbShakemap comes with three 'prob tools': GetStatistics, GetDistributions and EnsemblePlot. The outputs are intended to assist the user in exploring the ground-motion predictive distributions at a set of POIs.

TOOL: GetStatistics

Calculate, save and plot the statistics of the ground motion predictive distributions at all POIs.

python ProbShakemap.py --imt PGA --prob_tool GetStatistics --num_processes 8 --pois_file POIs.txt --numGMPEsRealizations 10 --imt_min 0.001 --imt_max 1

OUTPUT

• npy files with the statistics (saved in the npyFiles folder)
• map view of the statistics in vector_stat.npy (saved in the STATISTICS folder)

Output saved in the npyFiles folder:

• vector_stat.npy: dictionary of statistics computed for the ground motion distributions at all POIs: 'Mean', 'Median','Percentile 10','Percentile 20','Percentile 80','Percentile 90','Percentile 5','Percentile 95','Percentile 2.5','Percentile 97.5';
• (OPTIONAL, with command --vector_npy) vector.npy: a 2D array that stores the ground-motion distributions at all POIs. The array has dimensions (num_pois, num_GMPEsRealizations * num_scenarios), where num_GMPEsRealizations represents the number of realizations per scenario, and num_scenarios is the total number of scenarios in the ensemble.

TOOL: GetDistributions

Plot the cumulative distribution of the predicted ground-motion values and main statistics at a specific POI together with the ground-motion value recorded at the closest station (or at a POI coincident with the station, if available).

Note: the Shakemap file stationlist.json must be placed in the event-id/current folder.

python ProbShakemap.py --imt PGA --prob_tool GetDistributions --num_processes 8 --pois_file POIs.txt --numGMPEsRealizations 10 --imt_min 0.001 --imt_max 10 --station_file stationlist.json

OUTPUT

• POIs_Map.pdf: Spatial map of the POIs
• Distr_POI-{POI_idx}.pdf: Plot of Datum-Ensemble comparison at a given POI

TOOL: EnsemblePlot

Plot and summarize the key statistical features of the distribution of predicted ground-motion values at the POIs.

python ProbShakemap.py --imt PGA --prob_tool EnsemblePlot --num_processes 8 --pois_file POIs.txt --numGMPEsRealizations 10

OUTPUT

• POIs_Map.pdf: Spatial map of the POIs
• Ensemble_Spread_Plot_{imt}.pdf: Boxplot

POIs SUBSET OPTION

When using the tools QueryHDF5, GetStatistics, GetDistributions and EnsemblePlot, you can require to extract a subset of POIs within a maximum distance from the event epicenter following one of the following spatial distributions: random and azimuthally uniform. This changes the command line to:

python ProbShakemap.py [...] --pois_subset --n_pois 12 --max_distance 50 --pois_selection_method azimuth_uniform

If azimuthally uniform is selected, POIs are chosen within a ring in the range max_distance +- max_distance/10.

MULTIPLE TOOLS AT THE SAME TIME

ProbShakemap can handle multiple tools at the same time. Be aware that, in this case, the same settings will apply (ie,--imt_min, --imt_max, --pois_subset etc.).

python ProbShakemap.py --imt PGA --prob_tool GetDistributions EnsemblePlot --num_processes 8 --pois_file POIs.txt --numGMPEsRealizations 10 --imt_min 0.001 --imt_max 10 --station_file stationlist.json --pois_subset --n_pois 12 --max_distance 50 --pois_selection_method azimuth_uniform

HPC

ProbShakemap can be executed on a HPC cluster. Note that this implies converting the Docker image into Singularity’s native format, namely the Singularity Image Format (SIF). The .sif image of the shakemap Docker image can be provided upon request. See an example of bash file to run the code on a HPC cluster at run_code.bash. IMPORTANT: the number set at --ntasks-per-node must coincide with num_processes.

Contact

If you need support write to [email protected].

Contributions & Acknowledgements

Jacopo Selva coded the GetStatistics tool; Louise Cordrie authored the SeisEnsMan tool and tested ProbShakemap on the INGV-Bologna ADA cluster. I thank Valentino Lauciani for testing and developing the INGV Shakemap Docker and Licia Faenza for testing ProbShakemap. I also thank Michele Proietto (@https://github.com/miproietto) for assisting us in building the Docker image on the HPC cluster using Singularity.

Citation

If you use ProbShakemap in your research, please cite using the following citation:

@software{Stallone_ProbShakemap,
author = {Stallone, Angela and Cordrie, Louise  and Selva, Jacopo},
title = {{ProbShakemap}},
url = {https://github.com/INGV/ProbShakemap}
}