This guide is for someone who would like to run a simulation with current library and packaging.
Step-by-step guide
1. How to create a working folder
Get the current working version of
gm_sim_pkg
by using git clone:Bash_code$ git clone git@github.com:ucgmsim/gm_sim_pkg.git
Navigate into
gm_sim_pkg
directory and download the lastest package from the FTP server: ftp://ucquakecore1p.canterbury.ac.nz/seisfinder/gmsim_pack_latest.tar.gzBash_code$ wget ftp://ucquakecore1p.canterbury.ac.nz/seisfinder/gmsim_pack_latest.tar.gz
Use
install.sh
to install the package just downloaded in the following format:./install.sh gmsim_pack_latest.tar.gz [event_date] [event_location] [event_magnitude]
Bash_code$ ./install.sh gmsim_pack_latest.tar.gz 20100904 Darfield 7.1
- This starts the installation process.
========================================================================= Event Name: 20100904_Darfield_m7p1 Run Name: 20100904_Darfield_m7p1_201705191345 Package to be installed: /home/seb56/gm_sim_pkg/gmsim_pack_20170517_1425.tar.gz Run directory: /nesi/projects/nesi00213/RealTime/20100904_Darfield_m7p1_201705191345 ========================================================================= Do you wish to proceed? (Y/N) y ========================================================================= Creating directory structure ========================================================================= /home/seb56/tmp already exists. /nesi/projects/nesi00213/RealTime/code already exists. ========================================================================= Extracting the package ========================================================================= ./ ./code/ ./code/wrapper/ ./code/wrapper/setup_remote.sh ./code/wrapper/make_vm.sh ./code/wrapper/make_stat.sh... ./GM/Sim/ ./GM/Sim/Data/ ./GM/Sim/Figures/ ./Stat/ ========================================================================= Updating the data ========================================================================= From https://github.com/ucgmsim/vm_data * branch master -> FETCH_HEAD Already up-to-date. ========================================================================= Final touch ========================================================================= >>> Moving to /nesi/projects/nesi00213/RealTime/code from /nesi/projects/nesi00213/RealTime/20100904_Darfield_m7p1_201705191345/code >>> Updating vs30-mapping data location: /nesi/projects/nesi00213/RealTime/code/Vs30-mapping collecting md5sum for file check Existing KRIGE_NZGD00_allNZ.Rdata is already good: No need to update >>> Making a symbolic link to /home/seb56/tmp/vm_data/Data >>> Writing gmsim.cfg ========================================================================= Done!!!!=========================================================================
Follow the instruction shown on screen to create required Models and files.
Instructions: Everyone: !!!!!!!!!!!!!! source /nesi/projects/nesi00213/RealTime/20100904_Darfield_m7p1_201705191345/path.sh !!!!!!!!!!!!!! VM: 1. cd /nesi/projects/nesi00213/RealTime/20100904_Darfield_m7p1_201705191345/VM 2. config_vm.py mag centroidDepth lon lat 3. test_vm_params.py (if params_vel.py edited) 4. make_vm.sh Source: 1. cd /nesi/projects/nesi00213/RealTime/20100904_Darfield_m7p1_201705191345/Src 2. config_src.py 3. make_src.sh Obs: 1. cd /nesi/projects/nesi00213/RealTime/20100904_Darfield_m7p1_201705191345/GM/Obs 2. config_obs.py geoNet_ftp_url 3. make_obs.sh
!!! Before you move on, make sure you do the first line give in the instruction. !!!Bash_code$ source /nesi/projects/nesi00213/RealTime/20100904_Darfield_m7p1_201705191345/path.sh
2. How to create a Velocity Model
Go to the VM directory that instruction has provided
Bash_code$ cd /nesi/projects/nesi00213/RealTime/20100904_Darfield_m7p1_201705191345/VM
e.g. $ cd /home/jonney/20100904_Darfield_m7p1_201705181350/VM- Create the config file that is needed for generating a Velocity Model
$ config_vm.py magnitude centroid_Depth Latitude Longitude
e.g. $ config_vm.py 7.1 46.00 172.3 -43.6 - Edit the parameter file to your requirements with prefered editor
e.g. $ vim params_vel.py - If you have edited the params_vel.py, please run test_vm_params.py
$ test_vm_params.py - Run make_vm.sh to create the Velocity Model
$ make_vm.sh - Follow the instruction given on the screen to provide a path to a admin.
3. How to create Rupture Model (Source)
- Go to the Src directory that instruction has provided
e.g. $ cd /home/jonney/20100904_Darfield_m7p1_201705181350/Src - Create the config file that is needed for generating a Rupture Model
$ config_src.py type
e.g. $ config_src.py 2 - Go to the folder provided by instrutions
e.g. $ cd /home/jonney/20100904_Darfield_m7p1_201705181350/Src/Model/20100904_Darfield_m7p1/t2_103245_20170518_175214 - Edit the setSrfParams.py
note: every variables with #!!!PLEASE SPECIFY!!!# must be provided - Create the Model using make_src.sh
e.g. $ make_src.sh - Follow the instruction given on the screen to provide a path to a admin.
4. How to create observation files
note: you can skip this part if you are running for a future event (not yet happened)
- Go to the Obs directory that instruction has provided
e.g. $ cd /home/jonney/20100904_Darfield_m7p1_201705181350/GM/Obs - Create the config file that is needed
$ config_obs.py geoNet_ftp_url
e.g. $ config_obs.py ftp://ftp.geonet.org.nz/strong/processed/Proc/2010/09_Sep/2010-09-04_045556/Vol1/data/ - Run make_obs.sh to generate all the files
e.g. $ make_obs.sh - Follow the instruction given on the screen to provide a path to a admin.
5. How to setup the simulation
- After admin tells you that all files are uploaded to Fitzroy, Run setup_remote.sh
$ setup_remote.sh username
e.g $ setup_remote.sh jonney
6. Run the simulation on Low Frequency (LF)
- Go to the Simulation Folder, located at /nesi/projects/nesi00213/RunFolder/user/run_name
e.g. $ cd /nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350 - Run submit_emod3d.sh
$ ./submit_emod3d.h - It will ask you to enter a wall_clock_limit and if it should auto submit the job.
note: if you prefer to change some detail configurations, press 2(no) for auto submit.* - use llsubmit to submit your job if you selected to not to auto submit.
- Use llq to check if your job has finished. (job status: R= running, C= Complete, I = idle)
$ llq -u user - After Emod3d finished, run submit_post_emod3d.sh
note: if you prefer to change some detail configurations, press 2(no) for auto submit.*
$ ./submit_post_emod3d.sh
7. Run the simulation on High Frequency (HF)
note: this part can run before LF is finished
- Run install_bb.sh, to setup the parameters
$ ./install_bb.sh - Choose from the options according to simulation requirement
- Run submit_hf.sh
$ ./submit_hf.sh
note: if you prefer to change some detail configurations, press 2(no) for auto submit.*
*: use llsubmit to submit your job if you selected not to auto submit. $ llsubmit job.ll
8. Run the Simulation on Broadband (BB)
Note: This part MUST wait untill both LF and HF are finished
- Run submit_bb.sh
$ ./submit_bb.sh
Related articles
=========================================================================
Event Name: 20100904_Darfield_m7p1
Run Name: 20100904_Darfield_m7p1_201705191345
Package to be installed: /home/seb56/gm_sim_pkg/gmsim_pack_20170517_1425.tar.gz
Run directory: /nesi/projects/nesi00213/RealTime/20100904_Darfield_m7p1_201705191345
=========================================================================
Do you wish to proceed? (Y/N) y
=========================================================================
Creating directory structure
=========================================================================
/home/seb56/tmp already exists.
/nesi/projects/nesi00213/RealTime/code already exists.
=========================================================================
Extracting the package
=========================================================================
./
./code/
./code/wrapper/
./code/wrapper/setup_remote.sh
./code/wrapper/make_vm.sh
./code/wrapper/make_stat.sh
...
./GM/Sim/
./GM/Sim/Data/
./GM/Sim/Figures/
./Stat/
=========================================================================
Updating the data
=========================================================================
From https://github.com/ucgmsim/vm_data
* branch master -> FETCH_HEAD
Already up-to-date.
=========================================================================
Final touch
=========================================================================
>>> Moving to /nesi/projects/nesi00213/RealTime/code from /nesi/projects/nesi00213/RealTime/20100904_Darfield_m7p1_201705191345/code
>>> Updating vs30-mapping data
location: /nesi/projects/nesi00213/RealTime/code/Vs30-mapping
collecting md5sum for file check
Existing KRIGE_NZGD00_allNZ.Rdata is already good: No need to update
>>> Making a symbolic link to /home/seb56/tmp/vm_data/Data
>>> Writing gmsim.cfg
=========================================================================
Done!!!!
=========================================================================