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

1. Get the current working version of gm_sim_pkg by using git clone:

   $ git clone git@github.com:ucgmsim/gm_sim_pkg.git

2. Navigate into gm_sim_pkg directory and download the latest package from the FTP server: https://quakecoresoft.canterbury.ac.nz/seisfinder/private/gmsim/gmsim_pack_latest.tar.gz

   $ wget https://quakecoresoft.canterbury.ac.nz/seisfinder/private/gmsim/gmsim_pack_latest.tar.gz

3. 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]

    

   $ ./install.sh gmsim_pack_latest.tar.gz 20100904 Darfield 7.1

4. This starts the installation process.
   

    

   ========================================================================= Event Name: 20100904_Darfield_m7p1 Run Name: 20100904_Darfield_m7p1_201705221509 Package to be installed: /home/jonney/gm_sim_pkg/gmsim_pack_20170522_1443.tar.gz Run directory: /home/jonney/20100904_Darfield_m7p1_201705221509 ========================================================================= 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 /home/jonney/code from /home/jonney/20100904_Darfield_m7p1_201705221509/code >>> Updating vs30-mapping data location: /home/jonney/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/jonney/tmp/vm_data/Data >>> Writing gmsim.cfg ========================================================================= Done!!!! =========================================================================

5. This has created the directory structure for managing the ground motion simulation for 2010 September 4 Darfield earthquake (Mw7.1)

   20100904_Darfield_m7p1_201705221509/ ├── GM │ ├── Obs │ │ ├── Data │ │ └── Figures │ ├── Sim │ │ ├── Data │ │ └── Figures │ └── Validation │ ├── Data │ └── Figures ├── Impact │ ├── Landslide │ └── PAGER ├── Src │ ├── Data │ ├── Figures │ └── Model ├── Stat └── VM ├── Data ├── Figures ├── Model └── Velocity-Model └── Data -> /home/jonney/tmp/vm_data/Data

6. Follow the instruction shown on screen to create required Models and files.
   
   

   Instructions: Everyone: !!!!!!!!!!!!!! source /home/jonney/20100904_Darfield_m7p1_201705221509/path.sh !!!!!!!!!!!!!! VM: 1. cd /home/jonney/20100904_Darfield_m7p1_201705221509/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 /home/jonney/20100904_Darfield_m7p1_201705221509/Src 2. config_src.py 3. make_src.sh Obs: 1. cd /home/jonney/20100904_Darfield_m7p1_201705221509/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. !!!

   $ source /home/jonney/20100904_Darfield_m7p1_201705221509/path.sh

2. How to create a Velocity Model

1. Go to the VM directory that instruction has provided

   $ cd /home/jonney/20100904_Darfield_m7p1_201705221509/VM

2. Execute config_vm.py to generate params_vel.py, a config file used for velocity modelling. The command is in the following format.
   
   $ config_vm.py magnitude centroid_Depth Latitude Longitude

   /home/jonney/20100904_Darfield_m7p1_201705221509/VM : config_vm.py -h usage: config_vm.py [-h] [--model_version MODEL_VERSION] [--min_vs MIN_VS] [--topo_type TOPO_TYPE] [--hh HH] [--extent_zmin EXTENT_ZMIN] [--extent_x EXTENT_X] [--extent_y EXTENT_Y] [--extent_zmax EXTENT_ZMAX] [--sim_duration SIM_DURATION] [--flo FLO] [--rot ROT] [--code CODE] [--output_dir OUTPUT_DIR] [--slice_params_dir SLICE_PARAMS_DIR] mag centroidDepth lon lat positional arguments: mag centroidDepth lon lat optional arguments: -h, --help show this help message and exit --model_version MODEL_VERSION --min_vs MIN_VS --topo_type TOPO_TYPE --hh HH --extent_zmin EXTENT_ZMIN --extent_x EXTENT_X --extent_y EXTENT_Y --extent_zmax EXTENT_ZMAX --sim_duration SIM_DURATION --flo FLO --rot ROT --code CODE --output_dir OUTPUT_DIR --slice_params_dir SLICE_PARAMS_DIR

   Three parameters mag, centroidDepth, lon, lat are mandatory. You can set other options with --option, such as --hh 0.2 or manually set by editing params_vel.py


   /home/jonney/20100904_Darfield_m7p1_201705221509/VM : config_vm.py 7.1 46.00 172.3 -43.6 --hh 0.2 --rot -10 --extent_x 140 --extent_y 120 --extent_zmax 46.0 --sim_duration 100 mag = 7.1 centroidDepth = 46.0 lon= 172.3 lat = -43.6 ############ Generated params_vel.py # If you edited this file manually, run 'test_vm_params.py' for integrity check !!! # Section I. Basic parameters (Manual Edit allowed) mag = '7.1' centroidDepth = '46.00' MODEL_LAT = '-43.6' MODEL_LON = '172.3' MODEL_ROT = '-10.0' hh = '0.200' min_vs = '0.5' model_version = '1.65' topo_type = 'BULLDOZED' output_directory = 'Rapid_Model' extracted_slice_parameters_directory = 'SliceParametersNZ/SliceParametersExtracted.txt' code = 'rt' # Section II. Derived parameters that can be manually editted extent_x = '140.0' extent_y = '120.0' extent_zmax = '46.0' extent_zmin = '0.0' sim_duration = '100.0' flo = '0.5' # Section III. Automated values. DO NOT EDIT (Manual changes will be ignored) nx = ' 700' ny = ' 600' nz = '230' sufx = '_rt01-h0.200' ############ Estimated Wallclock time nx=700 ny=600 nz=230 sim_duration=100 num_procs=512 Maximum: 0:55:02 Average: 0:17:16.597834 Minimum: 0:11:58.613082

   


3. You can manually edit params_vel.py. But you are strongly advised to run test_vm_params.py to validate your params_vel.py if manually edited. Note that values in Section II will be automatically computed based on the values in Section I, but user can manually edit them. However, any manual changes made to Section III will be ignored. 
   In the example, we execute test_vm_params.py after manually editing the value for "code" from "rt" to "nz". This creates new params_vel.py after making a backup of the original, and shows the difference between two. Notice " | " where a difference is observed (line 30).

   /home/jonney/20100904_Darfield_m7p1_201705221509/VM :test_vm_params.py ##################### Backing up params_vel.py to params_vel.py.bak ##################### params_vel.py updated diff -y params_vel.py.bak params_vel.py # If you edited this file manually, run 'test_vm_params.py' f # If you edited this file manually, run 'test_vm_params.py' f # Section I. Basic parameters (Manual Edit allowed) # Section I. Basic parameters (Manual Edit allowed) mag = '7.1' mag = '7.1' centroidDepth = '46.00' centroidDepth = '46.00' MODEL_LAT = '-43.6' MODEL_LAT = '-43.6' MODEL_LON = '172.3' MODEL_LON = '172.3' MODEL_ROT = '-10.0' MODEL_ROT = '-10.0' hh = '0.200' hh = '0.200' min_vs = '0.5' min_vs = '0.5' model_version = '1.65' model_version = '1.65' topo_type = 'BULLDOZED' topo_type = 'BULLDOZED' output_directory = 'Rapid_Model' output_directory = 'Rapid_Model' extracted_slice_parameters_directory = 'SliceParametersNZ/Sli extracted_slice_parameters_directory = 'SliceParametersNZ/Sli code = 'nz' code = 'nz' # Section II. Derived parameters that can be manually editted # Section II. Derived parameters that can be manually editted extent_x = '140.0' extent_x = '140.0' extent_y = '120.0' extent_y = '120.0' extent_zmax = '46.0' extent_zmax = '46.0' extent_zmin = '0.0' extent_zmin = '0.0' sim_duration = '100.0' sim_duration = '100.0' flo = '0.5' flo = '0.5' # Section III. Automated values. DO NOT EDIT (Manual changes # Section III. Automated values. DO NOT EDIT (Manual changes nx = ' 700' nx = ' 700' ny = ' 600' ny = ' 600' nz = '230' nz = '230' sufx = '_rt01-h0.200' | sufx = '_nz01-h0.200' ############ Estimated Wallclock time nx=700 ny=600 nz=230 sim_duration=100 num_procs=512 Maximum: 0:55:02 Average: 0:17:16.597834 Minimum: 0:11:58.613082

4. Run make_vm.sh to create the Velocity Model

   /home/jonney/20100904_Darfield_m7p1_201705221509/VM :make_vm.sh Executing genDomain.py Reading domain extents. Reading of domain extents. Complete. Writing generate velocity model shell scrip. Writing generate velocity model shell scrip. Complete. Generating velocity model. ========================================== Running GENERATE_VELOCITY_MOD. ========================================== ... ========================================== Completed running GENERATE_VELOCITY_MOD. ========================================== ... ========================================== Running EXTRACT_VELOCITY_SLICES. ========================================== ... ========================================== Completed running EXTRACT_VELOCITY_SLICES. ========================================== ... /nesi/projects/nesi00213/tools/gen_model_cords geoproj=1 gridfile=./Rapid_Model/Rapid_Model/Velocity_Model/gridfile_nz01-h0.200 gridout=./Rapid_Model/Rapid_Model/Velocity_Model/gridout_nz01-h0.200 center_origin=1 do_coords=1 nzout=1 name=./Rapid_Model/Rapid_Model/Velocity_Model/model_coords_nz01-h0.200 gzip=0 latfirst=0 modellon=172.3 modellat=-43.6 modelrot=-10.0 1> ./Rapid_Model/Rapid_Model/Velocity_Model/model_params_nz01-h0.200 2>/dev/null Generating model params and cords. Complete. Moving velocity model plots. Moving velocity model plots. Complete. Removing generated scripts. Rapid model generation complete. Model/20100904_Darfield_m7p1/v1.65_200m !!!!! Ask Admin to upload: Give him the path: /home/jonney/20100904_Darfield_m7p1_201705221509/VM !!!!!

5. Under the working directory VM, a subdirectory is created Model/20100904_Darfield_m7p1/v1.65_200m which contains the velocity model.

   /home/jonney/20100904_Darfield_m7p1_201705221509/VM/Model/20100904_Darfield_m7p1/v1.65_200m :ls gridfile_nz01-h0.200 Info model_coords_nz01-h0.200 params_vel.py vp3dfile.p gridout_nz01-h0.200 model_bounds_nz01-h0.200 model_params_nz01-h0.200 rho3dfile.d vs3dfile.s

6. Give the admin (Sung) the path to the VM working directory and request to upload the model. The admin will need to execute sendme.sh in the VM directory.

   /home/jonney/20100904_Darfield_m7p1_201705221509/VM/sendme.sh SCP Upload tool Establishing SSH connection to: fitzroy.nesi.org.nz 22 ... Node size : 4 **************************************** /home/nesi00213...del/20100904_Darfield_m7p1/v1.65_200m/Info 49 Bytes Completed /home/nesi00213...904_Darfield_m7p1/v1.65_200m/params_vel.py 756 Bytes Completed /home/nesi00213...d_m7p1/v1.65_200m/model_params_nz01-h0.200 381 Bytes Completed /home/nesi00213...field_m7p1/v1.65_200m/gridfile_nz01-h0.200 155 Bytes Completed /home/nesi00213...d_m7p1/v1.65_200m/model_bounds_nz01-h0.200 96.3 KiB Completed /home/nesi00213...rfield_m7p1/v1.65_200m/gridout_nz01-h0.200 52.4 KiB Completed /home/nesi00213...d_m7p1/v1.65_200m/model_coords_nz01-h0.200 15.2 MiB Completed /home/nesi00213...100904_Darfield_m7p1/v1.65_200m/vs3dfile.s 368.5 MiB Completed /home/nesi00213...00904_Darfield_m7p1/v1.65_200m/rho3dfile.d 368.5 MiB Completed /home/nesi00213...100904_Darfield_m7p1/v1.65_200m/vp3dfile.p 368.5 MiB Completed Node 1: /home/nesi00213...100904_Darfield_m7p1/v1.65_200m/vs3dfile.s 368.5 MiB/368.5 MiB 100.0% Node 2: /home/nesi00213...00904_Darfield_m7p1/v1.65_200m/rho3dfile.d 368.5 MiB/368.5 MiB 100.0% Node 3: /home/nesi00213...100904_Darfield_m7p1/v1.65_200m/vp3dfile.p 368.5 MiB/368.5 MiB 100.0%

7. Files have been successfully uploaded to Fitzroy.

   baes@nesi2 /nesi/projects/nesi00213/VelocityModels/NZ/20100904_Darfield_m7p1/v1.65_200m :ls Info gridout_nz01-h0.200 model_coords_nz01-h0.200 params_vel.py vp3dfile.p gridfile_nz01-h0.200 model_bounds_nz01-h0.200 model_params_nz01-h0.200 rho3dfile.d vs3dfile.s

   
   
   

3. How to create Rupture Model (Source)

1. Go to the Src directory that instruction has provided

   $ cd /home/jonney/20100904_Darfield_m7p1_201705221509/Src

2. Create the config file that is needed for generating a Rupture Model
   
   

   $config_src.py -h usage: config_src.py [-h] {1,2,3,4} ... positional arguments: {1,2,3,4} Choose the type of srf you want to generate, usage of each type use: gen_src_params.py type -h 1 Generate type 1 srf (Point source srf). 2 Generate type 2 srf (Point source to Finite Fault srf). 3 Generate type 3 srf (Finite Fault descriptor to Finite Fault srf). 4 Generate type 4 srf (Multiple Segment Finite Fault srf). optional arguments: -h, --help show this help message and exit

   The extra options may differ from type to type. Use: "config_src.py type -h" will show you all the options can be provided for that type of source. 

   example of showing options for type 2:

   $ config_src.py 2 -h usage: config_src.py 2 [-h] [--LAT [LAT]] [--LON [LON]] [--MAG [MAG]] [--STK [STK]] [--RAK [RAK]] [--DIP [DIP]] [--DT [DT]] [--DEPTH [DEPTH]] [--SEED [SEED]] [--RVFRAC [RVFRAC]] [--ROUGH [ROUGH]] [--SLIP_COV [SLIP_COV]] [--MWSR [MWSR]] [--STOCH [STOCH]] [--GENSLIP [GENSLIP]] [--PREFIX [PREFIX]] optional arguments: -h, --help show this help message and exit --LAT [LAT] latitude (float) --LON [LON] longitude (float) --MAG [MAG] magnitude (float) --STK [STK] strike (int) --RAK [RAK] rake (int) --DIP [DIP] dip (int) --DT [DT] rupture timestep --DEPTH [DEPTH] --SEED [SEED] --RVFRAC [RVFRAC] --ROUGH [ROUGH] --SLIP_COV [SLIP_COV] --MWSR [MWSR] Mw Scaling Relation (string), one of:HanksBakun2002,BerrymanEtAl2002,VillamorEtAl2001 --STOCH [STOCH] String to set stoch gener ation. Default vaule will be used if not specified --GENSLIP [GENSLIP] Version of genslip --PREFIX [PREFIX] The prefix you want for SRF files. defualt= source. Ending with _ will auto append extra info to file name. Defualt value will be used if not specified.

   And example of creating type 2 Source file:

   $ config_src.py 2 --LAT -43.6 --LON 172.3 TYPE = 2 LAT = -43.6 LON = 172.3 PREFIX = Srf/source SEED = 103245 STOCH = Stoch GENSLIP = 3.3 #################### the params below are not specified, please manually edit setSrfParams.py to specify the value. #################### MAG = STK = RAK = DIP = DT = RVFRAC = ROUGH = SLIP_COV = DEPTH = MWSR = ==================================================================================================== Cannot find folder /home/jonney/20100904_Darfield_m7p1_201705221509/Src/Model/20100904_Darfield_m7p1. Attemp to create... Created Folder: /home/jonney/20100904_Darfield_m7p1_201705221509/Src/Model/20100904_Darfield_m7p1 no existing folder with type 2, Using sub-folder name: t2_103245 #################### Please go to: cd /home/jonney/20100904_Darfield_m7p1_201705221509/Src/Model/20100904_Darfield_m7p1/t2_103245 to manually edit all the parameters that is empty in setSrfParams.py and run make_src.sh ####################

   
   If config_src.sh has been run more than once, it will ask you if you want to update/replace a current param or create a new one.

   You can choose to create a new sub-folder with time stamp or replace the old files.

   example of creating new folder:

   $ config_src.py 2 --LAT -43.6 --LON 172.3 --MAG 7.1 --STK 150.0 --RAK 6.0 TYPE = 2 LAT = -43.6 LON = 172.3 MAG = 7.1 STK = 150.0 RAK = 6.0 PREFIX = Srf/source SEED = 103245 STOCH = Stoch GENSLIP = 3.3 #################### the params below are not specified, please manually edit setSrfParams.py to specify the value. #################### DIP = DT = RVFRAC = ROUGH = SLIP_COV = DEPTH = MWSR = ==================================================================================================== ==================================================================================================== select the src folder you want to place the setSrfParams.py into ==================================================================================================== 1. Create new setSrfParams.py 2. t2_103245 Enter the number you wish to select (1-2):1 ==================================================================================================== Do you want to create a sub-folder: t2_103245_20170524_171346? ==================================================================================================== 1. Yes 2. No Enter the number you wish to select (1-2):1 #################### Please go to: cd /home/jonney/20100904_Darfield_m7p1_201705221509/Src/Model/220100904_Darfield_m7p1/t2_103245_20170524_171346 to manually edit all the parameters that is empty in setSrfParams.py and run make_src.sh ####################

   If you choose to replace existing params, it will show a comparison between two params(old on the left, new on the right).
   Example of replacing a old param file:

   $ config_src.py 2 --LAT -43.6 --LON 172.3 --MAG 7.1 --STK 1.0 --RAK 1.0 --DT 0.025 TYPE = 2 LAT = -43.6 LON = 172.3 MAG = 7.1 STK = 1.0 RAK = 1.0 DT = 0.025 PREFIX = Srf/source SEED = 103245 STOCH = Stoch GENSLIP = 3.3 #################### the params below are not specified, please manually edit setSrfParams.py to specify the value. #################### DIP = RVFRAC = ROUGH = SLIP_COV = DEPTH = MWSR = ==================================================================================================== ==================================================================================================== select the src folder you want to place the setSrfParams.py into ==================================================================================================== 1. Create new setSrfParams.py 2. t2_103245 3. t2_103245_20170524_171346 Enter the number you wish to select (1-3):2 diff -y /home/jonney/20100904_Darfield_m7p1_201705221509/Src/Model/20100904_Darfield_m7p1/t2_103245/setSrfParams.py /home/jonney/20100904_Darfield_m7p1_201705221509/Src/Model/20100904_Darfield_m7p/params.tmp ## Sets Variables for SRF/Stoch Generation ## Sets Variables for SRF/Stoch Generation #################### #################### #!!!Important!! #!!!Important!! #################### #################### #Please change the values accordingly if '#!!!PLEASE SPECIFY! #Please change the values accordingly if '#!!!PLEASE SPECIFY! # TYPE: # TYPE: # 1: point source to point source srf # 1: point source to point source srf # 2: point source to finite fault srf # 2: point source to finite fault srf # 3: finite fault to finite fault srf # 3: finite fault to finite fault srf # 4: multi-segment finite fault srf # 4: multi-segment finite fault srf TYPE = 2 TYPE = 2 # specify basename for gsf, srf and stoch file created # specify basename for gsf, srf and stoch file created # PREFIX for gsf/srf/stoch files # PREFIX for gsf/srf/stoch files # if prefix ends with '_', automatic naming follows # if prefix ends with '_', automatic naming follows PREFIX = 'Srf/source' PREFIX = 'Srf/source' # directory for Stoch file(s) # directory for Stoch file(s) # set to None to not produce the stoch file # set to None to not produce the stoch file STOCH = 'Stoch' STOCH = 'Stoch' # rupture timestep (float), e.g. DT = 0.025 # rupture timestep (float), e.g. DT = 0.025 DT = #!!!PLEASE SPECIFY!!!# | DT = 0.025 # latitude (float), e.g. LAT = -43.5095 # latitude (float), e.g. LAT = -43.5095 LAT = -43.6 LAT = -43.6 # longitude (float), e.g. LON = 172.1811 # longitude (float), e.g. LON = 172.1811 LON = 172.3 LON = 172.3 ... ... SEED = 103245 SEED = 103245 # Mw Scaling Relation (string), one of: # Mw Scaling Relation (string), one of: # HanksBakun2002, BerrymanEtAl2002, VillamorEtAl2001 # HanksBakun2002, BerrymanEtAl2002, VillamorEtAl2001 MWSR = ''#!!!PLEASE SPECIFY!!!# MWSR = ''#!!!PLEASE SPECIFY!!!# ==================================================================================================== do you want to replace this param file? ==================================================================================================== 1. Yes 2. No Enter the number you wish to select (1-2):1 #################### Please go to: cd /home/jonney/20100904_Darfield_m7p1_201705221509/Src/Model/20100904_Darfield_m7p1/t2_103245 to manually edit all the parameters that is empty in setSrfParams.py and run make_src.sh ####################

3. Go to the folder provided by instrutions

   $ cd /home/jonney/20100904_Darfield_m7p1_201705221509/Src/Model/20100904_Darfield_m7p1/t2_103245

4. Edit the setSrfParams.py
   note: every variables with #!!!PLEASE SPECIFY!!!# must be provided

   $ vim setSrfParams.py 1 ## Sets Variables for SRF/Stoch Generation 2 #################### 3 #!!!Important!! 4 #################### 5 #Please change the values accordingly if '#!!!PLEASE SPECIFY!!!#' 6 7 # TYPE: 8 # 1: point source to point source srf 9 # 2: point source to finite fault srf 10 # 3: finite fault to finite fault srf 11 # 4: multi-segment finite fault srf 12 TYPE = 2 13 # specify basename for gsf, srf and stoch file created 14 # PREFIX for gsf/srf/stoch files 15 # if prefix ends with '_', automatic naming follows 16 PREFIX = 'Srf/source' 17 # directory for Stoch file(s) 18 # set to None to not produce the stoch file 19 STOCH = 'Stoch' 20 # rupture timestep (float), e.g. DT = 0.025 21 DT = 0.025 22 # latitude (float), e.g. LAT = -43.5095 23 LAT = -43.6 24 # longitude (float), e.g. LON = 172.1811 25 LON = 172.3 26 # depth (float), ex. DEPTH = 2.0 27 DEPTH = 2.0#!!!PLEASE SPECIFY!!!# 28 # magnitude (float), e.g. MAG = 5.5 ... ... 40 ## roughness of fault only for genslip 5.0+ 41 ## 0.1 is a good value to use - Rob Graves 42 ## 0.0050119 = (10^(-2.3)) - Shi & Day 2014. Used as default in 5.2.3a 43 #ROUGH = #!!!PLEASE SPECIFY!!!# 44 ## (float), e.g. RVFRAC = 0.8 45 #RVFRAC = #!!!PLEASE SPECIFY!!!# 46 ## (float), e.g. SLIP_COV = 0.85 47 #SLIP_COV = #!!!PLEASE SPECIFY!!!# 48 # seed for stoch, e.g. SEED = 103245 49 SEED = 103245 50 # Mw Scaling Relation (string), one of: 51 # HanksBakun2002, BerrymanEtAl2002, VillamorEtAl2001 52 MWSR = ''#!!!PLEASE SPECIFY!!!#

5. Create the Model using make_src.sh

   $ make_src.sh Ececuting createSRF.py Executing /nesi/projects/nesi00213/tools/genslip-v3.3read_erf=0write_srf=1read_gsf=1write_gsf=0infile=Srf/source.gsfmag=5.500000nx=58ny=58ns=1nh=1seed=103245velfile=/home/jonney/code/SrfGen//lp_generic1d-gp01_v1.vmodshypo=0.000000dhypo=2.877200dt=0.025000plane_header=1srf_version=2.0rvfrac=Noneshal_vrup=0.6deep_vrup=0.6fdrup_time=1alpha_rough=Noneslip_sigma=None seed=103245 mag= 5.50 median mag= 5.52 nslip= 1 nhypo= 1 random_seed =103245 nx= 58 ny= 58 dx= 0.0992 dy= 0.0992 0: 172.30055 -43.59977 58 58 5.7543 5.7543 150.0 54.0 0.0000 **** 16.5000 16.5000 ratio (negative slip)/(positive slip)= 0.002216 mom= 1.99526e+24 avgslip= 48 maxslip= 98 orig_sigma= 0.403256 ... new_sigma= 0.396138 rt_scalefac= 7.388430 ravg= 1.00000e+00 rmed= 9.86539e-01 rmin= 3.09826e-01 rmax= 1.93412e+00 seg= 0 nstk= 58 nx= 3 nxdiv= 3 nxsum= 58 ndip= 58 ny= 3 nydiv= 3 nysum= 58 Plotting SRF as square plot... ... /home/jonney/20100904_Darfield_m7p1_201705221509/gmsim.cfg making a symbolic link from source_map.png to /home/jonney/20100904_Darfield_m7p1_201705221509/Src/Figures/source_map.png making a symbolic link from source_square.png to /home/jonney/20100904_Darfield_m7p1_201705221509/Src/Figures/source_square.png attempt_upload.sh /home/jonney/20100904_Darfield_m7p1_201705221509/Src/Model/20100904_Darfield_m7p1/t2_103245 /nesi/projects/nesi00213/RupModel/20100904_Darfield_m7p1 baes seb56 !!!!! Ask Admin to upload: Give him the path: /home/jonney/20100904_Darfield_m7p1_201705221509/Src !!!!!

6. Under the working directory Src, a subdirectory is created

   $ ls /home/jonney/20100904_Darfield_m7p1_201705221509/Src/Model/20100904_Darfield_m7p1/t2_103245 cnrs.txt Info params_plot.py params_plot.pyc setSrfParams.py setSrfParams.pyc Srf Stoch

7. Give the admin (Sung) the path to the Src working directory and request to upload the model. The admin will need to execute sendme.sh in the Src directory.

4. How to create observation files

note: you can skip this part if you are running for a future event (not yet happened)

1. Go to the Obs directory that instruction has provided

   cd /home/jonney/20100904_Darfield_m7p1_201705221509/GM/Obs

2. Create the config file that is needed
   $ config_obs.py geoNet_ftp_url

   $ config_obs.py Usage: /home/jonney/code/wrapper/config_obs.py URL eg. URL: ftp://ftp.geonet.org.nz/strong/processed/Proc/2011/02_Feb/2011-02-22_012009/Vol1/data

   $ config_obs.py ftp://ftp.geonet.org.nz/strong/processed/Proc/2010/09_Sep/2010-09-04_045556/Vol1/data Done!

   
   
   

3. Run make_obs.sh to generate all the files

   $ make_obs.sh Reading input from /home/jonney/20100904_Darfield_m7p1_201705221509/GM/Obs/event_info.txt /home/jonney/code/Vs30-mapping Downloading data ... Finished downloading data in 0.3 secs Creating stations list ... Done in 0.0 secs Creating Vs30 files ... Done Vs30 calcs in 21.0 secs Processing .V1A files ... Done processing in 21.2 secs Creating acc and vel plots for all Observed SMSs ... Done plotting acc, vel in 47.2 secs. Creating pSA plots for all Observed SMSs ... Done pSA plots in 55.8 secs. Writting IMs for GMT plotting ... Done in 5.1 secs. Relocate plots to Figures directory Attempting to upload station info to Fitzroy /home/jonney/20100904_Darfield_m7p1_201705221509/gmsim.cfg !!!!! Ask Admin to upload: Give him the path: /home/jonney/20100904_Darfield_m7p1_201705221509/GM/Obs !!!!!

4. The Vs30 and station files will be under working directory Stat/event_name

   $ ls /home/jonney/20100904_Darfield_m7p1_201705221509/Stat/20100904_Darfield_m7p1 20100904_Darfield_m7p1.kml 20100904_Darfield_m7p1.vs30 Info Vs30_stderr.txt 20100904_Darfield_m7p1.ll 20100904_Darfield_m7p1.vs30ref Vs30.out Vs30_stdout.txt

5. Give the admin (Sung) the path to the Obs working directory and request to upload the model. The admin will need to execute sendme.sh in the Obs directory.

5. How to setup the simulation

1. After admin tells you that all files are uploaded to Fitzroy, Run setup_remote.sh
   $setup_remote.sh username

   $ setup_remote.sh ykh22 /home/jonney/20100904_Darfield_m7p1_201705181350/gmsim.cfg vel_mod_dir: /nesi/projects/nesi00213/VelocityModels/NZ/20100904_Darfield_m7p1/v1.65_400m srf_path: /nesi/projects/nesi00213/RupModel/20100904_Darfield_m7p1/t2_103245/Srf/source.srf stat_path: /nesi/projects/nesi00213/StationInfo/20100904_Darfield_m7p1/20100904_Darfield_m7p1.ll remote_user: ykh22 remote cfg: /home/ykh22/gmsim.cfg scp /home/jonney/20100904_Darfield_m7p1_201705181350/gmsim.cfg ykh22@fitzroy.nesi.org.nz:/home/ykh22/gmsim.cfg gmsim.cfg 100% 459 23.5KB/s 0.5KB/s 00:00 Generation of model params has been skipped. Re-directing related params to files under /nesi/projects/nesi00213/VelocityModels/NZ/20100904_Darfield_m7p1/v1.65_400m /nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350 Permission /nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350 : 750 **************************************************************************************************** **************************************************************************************************** Producing statcords and FD_STATLIST. It may take a minute or two /nesi/projects/nesi00213/StationInfo/20100904_Darfield_m7p1/20100904_Darfield_m7p1.ll From: /nesi/projects/nesi00213/StationInfo/20100904_Darfield_m7p1/20100904_Darfield_m7p1.ll To: /nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350/fd_nz01-h0.400.statcords /nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350/fd_nz01-h0.400.ll Done Installation completed ==================================================================================================== Instructions ==================================================================================================== For Simulation (Fitzroy) 1. cd /nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350 2. Edit params.py and run_emod3d.ll.template 3. ./submit_emod3d.sh 4. ./submit_post_emod3d.sh or ./submit_post_emod3d_mpi.sh (parallel) 5. ./install_bb.sh 6. ./submit_hf.sh and ./submit_bb.sh For Plotting (hypocentre) 1. Plotting station based data (IMs, Vs30, Obs PGA, pSA): plot_stations.py {datafile}.ll 2. Plotting timeslice-based data (PGV,MMI,animation): plot_transfer.py auto /nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350 3. PGV,MMI: plot_ts_sum.py Timeslice sequence: plot_ts.py

2. The location on Fitzroy will be under /nesi/projects/nesi00213/RunFolder/username/event

   $ cd /nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350

6. Run the simulation on Low Frequency (LF)

1. Go to the Simulation Folder, located at /nesi/projects/nesi00213/RunFolder/user/run_name

   $ cd /nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350

2. Run submit_emod3d.sh

   It will ask you to enter a wall_clock_limit and if it should auto submit the job.

   $ ./submit_emod3d.h devel ==================================================================================================== Fetching WallClock time estimation from DB ==================================================================================================== [3.4182194616977223e-07, 1.0417627567533496e-07, 6.560775746124221e-11] nx=350 ny=300 nz=115 sim_duration=100 num_procs=512 Maximum: 0:06:52.750000 Average: 0:02:05.792853 Minimum: 0:00:00.079221 ==================================================================================================== Enter the WallClock time limit you will like to use: 5:30:00 ==================================================================================================== Also submit the job for you? 1. Yes 2. No Enter the number you wish to select (1-2):1 Loadleveler script run_emod3d_source.ll written Submitting run_emod3d_source.ll

   note: if you prefer to change some detail configurations, press 2(no) for auto submit.*

   $ ./submit_emod3d.sh devel ==================================================================================================== Fetching WallClock time estimation from DB ==================================================================================================== [3.4182194616977223e-07, 1.0417627567533496e-07, 6.560775746124221e-11] nx=350 ny=300 nz=115 sim_duration=100 num_procs=512 Maximum: 0:06:52.750000 Average: 0:02:05.792853 Minimum: 0:00:00.079221 ==================================================================================================== Enter the WallClock time limit you will like to use: 5:30:00 ==================================================================================================== Also submit the job for you? 1. Yes 2. No Enter the number you wish to select (1-2):2 Loadleveler script run_emod3d_source.ll written User chose to submit the job manually

    

   use llsubmit to submit your job if you selected to not to auto submit.

   $ llsubmit run_emod3d_source.ll llsubmit: Processed command file through Submit Filter: "/gpfs_external/admin/LL_Oper_job_filter.py". llsubmit: The job "f2n7.1440438" has been submitted.

3. Use llq to check if your job has finished. (job status: R= running, C= Complete, I = idle)
   $ llq -u user

   $ llq -u ykh22 Id Owner Submitted ST PRI Class Running On ------------------------ ---------- ----------- -- --- ------------ ----------- f2n7.1440438.0 ykh22 5/25 04:10 I 50 General

4. 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

   ./submit_post_emod3d.sh devel Also submit the job for you? 1. Yes 2. No Enter the number you wish to select (1-2):2 Loadleveler script post_emod3d_source.ll written User chose to submit the job manually

5. submit the job after you manually edited the post_emod3d_source.ll

   $ llsubmit post_emod3d_source.ll llsubmit: Processed command file through Submit Filter: "/gpfs_external/admin/LL_Oper_job_filter.py". llsubmit: The job "f2n7.1440439" with 3 job steps has been submitted.

6. Use llq to check if your job has finished. (job status: R= running, C= Complete, I = idle)

   $ llq -u ykh22 Id Owner Submitted ST PRI Class Running On ------------------------ ---------- ----------- -- --- ------------ ----------- f2n7.1440439.0 ykh22 5/25 04:14 R 50 General f2n7.1440439.2 ykh22 5/25 04:14 C 50 General f2n7.1440439.1 ykh22 5/25 04:14 C 50 General

7. Run the simulation on High Frequency (HF)

note: this part can run before LF is finished

1. Run install_bb.sh, to setup the parameters
   Choose from the options according to simulation requirement

   $ ./install_bb.sh devel Info: Old version of params.py supporting singular kappa and sdrop **************************************************************************************************** EMOD3D HF/BB Preparationi Ver.devel **************************************************************************************************** ==================================================================================================== Select one of 1D Velocity models (from /nesi/projects/nesi00213/VelocityModel/Mod-1D) ==================================================================================================== 1. /nesi/projects/nesi00213/VelocityModel/Mod-1D/Cant1D_v1-midQ.1d 2. /nesi/projects/nesi00213/VelocityModel/Mod-1D/Cant1D_v1.1d 3. /nesi/projects/nesi00213/VelocityModel/Mod-1D/Cant1D_v2-midQ.1d 4. /nesi/projects/nesi00213/VelocityModel/Mod-1D/banks.1d 5. /nesi/projects/nesi00213/VelocityModel/Mod-1D/foothills.1d 6. /nesi/projects/nesi00213/VelocityModel/Mod-1D/foothills_v2.1d 7. /nesi/projects/nesi00213/VelocityModel/Mod-1D/plains.1d Enter the number you wish to select (1-7):3 /nesi/projects/nesi00213/VelocityModel/Mod-1D/Cant1D_v2-midQ.1d ==================================================================================================== - Vel. Model 1D: Cant1D_v2-midQ - hf_sim_bin: hb_high_v5.4.5_np2mm+ - hf_rvfac: 0.8 - hf_sdrop: 50 - hf_kappa: 0.045 - srf file: /nesi/projects/nesi00213/RupModel/20100904_Darfield_m7p1/t2_103245/Srf/source.srf /nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350/LF/source/params_uncertain.py /nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350/HF/Cant1D_v2-midQ_hfnp2mm+_rvf0p8_sd50_k0p045/source/params_bb_uncertain.py [Errno 17] File exists Permission /nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350/HF/Cant1D_v2-midQ_hfnp2mm+_rvf0p8_sd50_k0p045 : 750 Permission /nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350/BB/Cant1D_v2-midQ_hfnp2mm+_rvf0p8_sd50_k0p045 : 750

2. Run submit_hf.sh
   note: if you prefer to change some detail configurations, press 2(no) for auto submit.*

   ./install_bb.sh devel Info: Old version of params.py supporting singular kappa and sdrop **************************************************************************************************** EMOD3D HF/BB Preparationi Ver.devel **************************************************************************************************** ==================================================================================================== Select one of 1D Velocity models (from /nesi/projects/nesi00213/VelocityModel/Mod-1D) ==================================================================================================== 1. /nesi/projects/nesi00213/VelocityModel/Mod-1D/Cant1D_v1-midQ.1d 2. /nesi/projects/nesi00213/VelocityModel/Mod-1D/Cant1D_v1.1d 3. /nesi/projects/nesi00213/VelocityModel/Mod-1D/Cant1D_v2-midQ.1d 4. /nesi/projects/nesi00213/VelocityModel/Mod-1D/banks.1d 5. /nesi/projects/nesi00213/VelocityModel/Mod-1D/foothills.1d 6. /nesi/projects/nesi00213/VelocityModel/Mod-1D/foothills_v2.1d 7. /nesi/projects/nesi00213/VelocityModel/Mod-1D/plains.1d Enter the number you wish to select (1-7):3 /nesi/projects/nesi00213/VelocityModel/Mod-1D/Cant1D_v2-midQ.1d ==================================================================================================== - Vel. Model 1D: Cant1D_v2-midQ - hf_sim_bin: hb_high_v5.4.5_np2mm+ - hf_rvfac: 0.8 - hf_sdrop: 50 - hf_kappa: 0.045 - srf file: /nesi/projects/nesi00213/RupModel/20100904_Darfield_m7p1/t2_103245/Srf/source.srf /nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350/LF/source/params_uncertain.py /nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350/HF/Cant1D_v2-midQ_hfnp2mm+_rvf0p8_sd50_k0p045/source/params_bb_uncertain.py [Errno 17] File exists Permission /nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350/HF/Cant1D_v2-midQ_hfnp2mm+_rvf0p8_sd50_k0p045 : 750 Permission /nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350/BB/Cant1D_v2-midQ_hfnp2mm+_rvf0p8_sd50_k0p045 : 750 ykh22@nesi1 /nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350 :./submit_hf.sh devel SERIAL ['/nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350/HF/Cant1D_v2-midQ_hfnp2mm+_rvf0p8_sd50_k0p045/source'] Also submit the job for you? 1. Yes 2. No Enter the number you wish to select (1-2):1 Cant1D_v2-midQ_hfnp2mm+_rvf0p8_sd50_k0p045__source Loadleveler script run_hf_Cant1D_v2-midQ_hfnp2mm+_rvf0p8_sd50_k0p045__source.ll written Submitting run_hf_Cant1D_v2-midQ_hfnp2mm+_rvf0p8_sd50_k0p045__source.ll

3.  use llsubmit to submit your job if you selected not to auto submit.

   $ llsubmit run_hf_Cant1D_v2-midQ_hfnp2mm+_rvf0p8_sd50_k0p045__source.ll llsubmit: Processed command file through Submit Filter: "/gpfs_external/admin/LL_Oper_job_filter.py". llsubmit: The job "f4n7.1495670" has been submitted.

4. Use llq to check if your job has finished. (job status: R= running, C= Complete, I = idle)

   llq -u ykh22Id Owner Submitted ST PRI Class Running On ------------------------ ---------- ----------- -- --- ------------ ----------- f4n7.1495670.0 ykh22 5/25 03:04 R 50 General f7n13

8. Run the Simulation on Broadband (BB)

Note: This part MUST wait untill both LF and HF are finished

1. Run submit_bb.sh
   $ ./submit_bb.sh

   $ ./submit_bb.sh devel ['/nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350/BB/Cant1D_v2-midQ_hfnp2mm+_rvf0p8_sd50_k0p045/source'] Also submit the job for you? 1. Yes 2. No Enter the number you wish to select (1-2):1 Cant1D_v2-midQ_hfnp2mm+_rvf0p8_sd50_k0p045__source Loadleveler script run_bb_Cant1D_v2-midQ_hfnp2mm+_rvf0p8_sd50_k0p045__source.ll written Submitting run_bb_Cant1D_v2-midQ_hfnp2mm+_rvf0p8_sd50_k0p045__source.ll

2. Use llq to check if your job has finished. (job status: R= running, C= Complete, I = idle)

   llq -u ykh22Id Owner Submitted ST PRI Class Running On ------------------------ ---------- ----------- -- --- ------------ ----------- f2n7.1440499.0 ykh22 5/25 03:04 R 50 General f7n13

   
   
   
   
   
   

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