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
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 .
- 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/site/site_search.py -m v18p6 /nesi/nobackup/nesi00213/RunFolder/Cybershake/v18p6/non_uniform_whole_nz_with_real_stations-hh400_v18p6_land.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", "$1}' > XXX.csv
4. Submit this job.
sbatch execute_hazard_search.sl
5. When the job has completed, check the last -10 lines of .out log file.
baes@mahuika02: ~/tmp$ 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_v18p6_SA_5p0/hazard_calcs.sh bash /home/baes/cybershake/v18p6/Hazard/hazard_search_v18p6_SA_5p0/deagg_calcs_im_value.sh bash /home/baes/cybershake/v18p6/Hazard/hazard_search_v18p6_SA_5p0/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_v18p6_SA_5p0 $ bash /nesi/project/nesi00213/deploy/seisfinder2/site/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.
baes@mahuika02: ~/cybershake/v18p6/Hazard/hazard_search_v18p6_SA_5p0$ 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