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This document explains how to use the implementation of hazard_search.py. Note that it currently works for CyberShake17p9 (v17p9) version only.

  • ssh your_login@dev01-quakecore.canterbury.ac.nz (if you don't have a login contact Melody or Daniel)
  • cd /var/www/seisfinder2/CLI
  • You will find lots of scripts, enter values in hazard_search_config.ini. A sample config for v17p9 is shown below:
    • [v17p9]
      TMPLOCATION_TO_CREATE_HAZARD_FILES = /rcc/home/projects/quakecore/cybershake/v17p9/Hazard/
      EMPIRICAL_FILES_LOCATION = /rcc/home/projects/quakecore/cybershake/v17p9/Empiricals
      FAULT_LIST_CSV_FILE_LOCATION = /rcc/home/projects/quakecore/cybershake/v17p9/cyber_shake_file_v17p9.csv

       

  • The one that you need to run is hazard_search.py.
    • python hazard_search.py -h will show the help for the script.
    • python hazard_search.py -l returns all the simulation groups we currently have (disabled and we only have v17p9).
    • python hazard_search.py -s cybershake_version latitude longitude IM (or --single cybershake_version latitude longitude IM) will create a temporary directory for you and will copy (if they exist) the empirical file for the closest station that we have for the given latitude and longitude. It will print some instructions on how to calculate hazard and deaggregation.
    • python hazard_search.py -m cybershake_version csv_file IM (or --multi cybershake_version csv_file IM) takes as input a CSV file containing latitude,longitude lines for several locations of interest. As previously, it will copy all the relevant empirical files to a temporary folder. The instructions printed will  be shorter, but you will be provided some bash scripts to automate the execution.

 

Running hazard search for entire Cybershake on Mahuika

You may wish to install python packages geopy, psycopg2, numpy, pyarrow, etc. Use pip install --user to install missing packages.

pip install geopy, psycopg2, numpy, pyarrow --user



  1. Create a temporary directory. Let's say ~/tmp and copy 2 files to here

    baes@mahuika02: ~/tmp$ cp /nesi/project/nesi00213/deploy/seisfinder2/CLI/hazard_search_config.ini .
baes@mahuika02: ~/tmp$ cp /nesi/project/nesi00213/deploy/seisfinder2/CLI/hazard/mahuika/execute_hazard_search.sl .

     

     

  2. Go to ~/tmp and edit hazard_search_config.ini

[database]
SQLITE_DB_PATH = /home/baes/seisfinderdb.db

[v18p6]
TMPLOCATION_TO_CREATE_HAZARD_FILES = /home/baes/cybershake/v18p6/Hazard/
EMPIRICAL_FILES_LOCATION = /nesi/project/nesi00213/deploy/empiricals/v18p5
FAULT_LIST_CSV_FILE_LOCATION = /nesi/project/nesi00213/deploy/cybershake/v18p6/fault_list.csv
LL_FILE = /nesi/project/nesi00213/deploy/cybershake/v18p6/non_uniform_whole_nz_with_real_stations-hh400_v18p6_land.ll
IM_PATH= /nesi/project/nesi00213/deploy/cybershake/v18p6/IMs

 

3. Edit  execute_hazard_search.sl, especially the line starting with "srun" at the bottom.

#!/bin/bash
# script version: slurm
# Please modify this file as needed, this is just a sample
#SBATCH --job-name=hazard_search_multi
#SBATCH --account=nesi00213
#SBATCH --partition=prepost
#SBATCH --ntasks=1
####SBATCH --cpus-per-task=36
#SBATCH --time=00:59:00
#SBATCH --output hazard_search_multi-%j.out
#SBATCH --error hazard_search_multi-%j.err
###SBATCH --mail-type=all
###SBATCH --mail-user=test@test.com
###SBATCH --mem-per-cpu=16G
###SBATCH -C avx
#OpenMP+Hyperthreading works well for VM
###SBATCH --hint=nomultithread
## END HEADER
source machine_env.sh
date
srun python /nesi/project/nesi00213/deploy/seisfinder2/CLI/hazard_search.py -m v18p6 /nesi/project/nesi00213/deploy/cybershake/v18p6/non_uniform_whole_nz_with_real_stations-hh400_v18p6_land_lat_long.csv PGA
date

To generate a list of locations .csv from a .ll file, you can use the following command

cat XXX.ll |awk '{ print $2", "$1}' > XXX.csv

 

4.  Submit this job. 

 

sbatch execute_hazard_search.sl


5. When the job has completed, check the last -10 lines of .out log file.

 

baes@mahuika02: ~/tmp$ tail -10 hazard_search_multi-85422.out
Instructions in the multicase are not written in extense as it is not useful.                    Please use the scripts below
Please go to hazard/
Then run the scripts created as:
bash /home/baes/cybershake/v18p6/Hazard/hazard_search_5F73LY_baes/hazard_calcs.sh
bash /home/baes/cybershake/v18p6/Hazard/hazard_search_5F73LY_baes/deagg_calcs_im_value.sh
bash /home/baes/cybershake/v18p6/Hazard/hazard_search_5F73LY_baes/deagg_calcs_exceedance_rate.sh
Note: The IM_VALUE and EXCEEDANCE should be adjusted on the deagg_* scripts
Mon Sep  3 03:30:39 UTC 2018

This means it has created a temp directory /home/baes/cybershake/v18p6/Hazard/hazard_search_5F73LY_baes and  placed empirical files (symbolic links) and bash scripts that contain Python commands. 

6. Let's call this temp location  a working directory.

7. There is hazard_calcs.sh in the working directory.  For entire cybershake, this can be very very long. We will be using SLURM's parallel for loop to run this in parallel, but it needs to be split to avoid SLURM complaining about too many lines. This involves quite a bit of steps, but it can be largely automated by executing prepare_hpc_hazard_calc.sh. Go to the working directory, and execute it. You just need to supply the path to the working directory.

baes@mahuika02: ~/cybershake/v18p6/Hazard/hazard_search_5F73LY_baes $ bash /nesi/project/nesi00213/deploy/seisfinder2/CLI/hazard/mahuika/prepare_hpc_hazard_calc.sh .

The above does EVERYTHING for you. It copies the .sl template to the working directory, splits the hazard_calc.sh, and generates all the .sl files ready for submission.

8. Submit jobs: sbatch each .sl or use submit_all.sh, which submits all the jobs at one.

 

baes@mahuika02: ~/cybershake/v18p6/Hazard/hazard_search_5F73LY_baes$ bash ./submit_all.sh
Submitted batch job 69390
Submitted batch job 69391
Submitted batch job 69392
Submitted batch job 69393
Submitted batch job 69394
Submitted batch job 69395
Submitted batch job 69396
Submitted batch job 69397
Submitted batch job 69398
Submitted batch job 69399
Submitted batch job 69400
Submitted batch job 69401
Submitted batch job 69402
Submitted batch job 69403
Submitted batch job 69404
Submitted batch job 69405
Submitted batch job 69406
Submitted batch job 69407
Submitted batch job 69408

 

9. Hazard map: When everything is completed, you can submit the following .sl script that has been automatically generated for you. Just edit the exceedance value if required.  For details, see https://github.com/ucgmsim/seisfinder2/tree/master/CLI/hazard

baes@mahuika02: ~/cybershake/v18p6/Hazard/hazard_search_5F73LY_baes$ sbatch execute_hazard_map.sl

 

 


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