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 -hwill show the help for the script.python hazard_search.py -lreturns 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
- Go to /nesi/project/nesi00213/deploy/seisfinder2/CLI , and edit config
[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
2.
cp /nesi/project/nesi00213/deploy/seisfinder2/CLI/hazard/mahuika/execute_hazard_search.sl /nesi/project/nesi00213/deploy/seisfinder2/CLI
3. Edit execute_hazard_search.sl
#!/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 hazard_search.py -m v18p6 /nesi/project/nesi00213/deploy/cybershake/v18p6/non_uniform_whole_nz_with_real_stations-hh400_v18p6_land_lat_long.csv SA_5p0 date
To generate a list of locations .csv from a .ll file, you can use the following command
cat XXX.ll |awk '{ print $2", "$1}' > XXX.csv
4. sbatch execute_hazard_search.sl
sbatch execute_hazard_search.sl
5. When the job has completed, open .out log file. This creates a temp directory under TMPLOCATION_TO_CREATE_HAZARD_FILES specified, and places empirical files (symbolic links) and bash scripts that contain Python commands.
6. In this example. the temp location is /home/baes/cybershake/v18p6/Hazard/hazard_search_5F73LY_baes
7. In the temp dir, find hazard_calcs.sh. For entire cybershake, this can be very very long. We will be using SLURM's parallel for loop to run this in parallel, but it needs to be split to avoid SLURM complaining about too many lines.
8. Copy an .sl template to the temp dir and navigate to the directory.
cp /nesi/project/nesi00213/deploy/seisfinder2/CLI/hazard/mahuika/parallel_hazard_sl.template ~/cybershake/v18p6/Hazard/hazard_search_5F73LY_baes cd ~/cybershake/v18p6/Hazard/hazard_search_5F73LY_baes
9. Edit the template file, in particular, HAZARD_CALC_SH. (This step can be automated)
#!/bin/bash
# script version: slurm
# Please modify this file as needed, this is just a sample
#SBATCH --job-name=parallel_hazard_%NUM%
#SBATCH --account=nesi00213
#SBATCH --partition=large
#SBATCH --nodes=1
###SBATCH --ntasks=36
#SBATCH --ntasks-per-node=32
#SBATCH --cpus-per-task=1
#SBATCH --time=03:59:00
#SBATCH --output parallel_hazard-%NUM%.%j.out
#SBATCH --error parallel_hazard-%NUM%.%j.err
###SBATCH --mail-type=all
###SBATCH --mail-user=test@test.com
###SBATCH --mem-per-cpu=16G
###SBATCH -C avx
#OpenMP+Hyperthreading works well for VM
#SBATCH --hint=nomultithread
## END HEADER
source machine_env.sh
HAZARD_CALC_SH=/home/baes/cybershake/v18p6/Hazard/hazard_search_5F73LY_baes/hazard_calcs_uniq_%NUM%.sh
count=0
while IFS='' read -r line || [[ -n "$line" ]]; do
if [[ ${line:0:1} == '#' ]]
then
echo "comment:$line"
else
commands[count]=${line}
count=$(( $count + 1 ))
fi
done < $HAZARD_CALC_SH
for cmnd in "${commands[@]}"
do
srun -n1 --exclusive $cmnd &
done
wait
10. Run split_sh.sh to split the sh file into many smaller ones.
bash /nesi/project/nesi00213/deploy/seisfinder2/CLI/hazard/mahuika/split_sh.sh hazard_calcs.sh
This does a number of things. It filters out all the duplicates in the sh file, and split them into 1000 lines each to produce hazard_calcs_uniq_0.sh, hazard_calcs_uniq_1000.sh....hazard_calcs_uniq_xxxxx.sh and matching .sl files.
11. Copy .sl files to /nesi/project/nesi00213/deploy/seisfinder2/CLI/hazard/ (Can be automated)
cp *.sl /nesi/project/nesi00213/deploy/seisfinder2/CLI/hazard cd /nesi/project/nesi00213/deploy/seisfinder2/CLI/hazard
baes@mahuika02: /nesi/project/nesi00213/deploy/seisfinder2/CLI/hazard$ for sl in `ls parallel_hazard*.sl`; do sbatch $sl; done 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
13. Hazard map. When everything is completed, you can plot hazard map. For details, see https://github.com/ucgmsim/seisfinder2/tree/master/CLI/hazard
To do
- hazard_search.py should contain python commands with the full path to hazard_calc.py with all PYTHONPATH sorted. This will remove the need for copying .sl back to the code directory, enabling us to separate the code and working environment.
HAZARD_CALC_SH in parallel_hazard_sl.template can be automatically set by split_sh.sh
hazard_search.py can also copy .sl.tempalte and machine_env etc to the temp dir.