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

   Code Block
   language bash
   $ 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:  ftphttps://ucquakecore1pquakecoresoft.canterbury.ac.nz/seisfinder/private/gmsim/gmsim_pack_latest.tar.gz

   Code Block
   language bash
   $ wget ftphttps://ucquakecore1pquakecoresoft.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]

    

   Code Block
   language bash
   $ ./install.sh gmsim_pack_latest.tar.gz 20100904 Darfield 7.1

4. This starts the installation process.
   

    

   Code Block

   ========================================================================= 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)

   Code Block
   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.
   
   

   Code Block

   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. !!!

   Code Block
   theme Midnight language bash
   $ source /home/jonney/20100904_Darfield_m7p1_201705221509/path.sh

...

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

   Code Block

   $ 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% 459 623.7KB5KB/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

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

   Code Block
   language bash
   $ cd /nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350

6. Run the simulation on Low Frequency (LF)

1. 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

   Code Block
   language bash
   $ 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

   Code Block
   language bash
   $ 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.

   Code Block
   language bash
   $ ./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.*

   Code Block
   language bash
   $ ./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.

   Code Block
   language bash
   $ 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

   Code Block
   language bash
   $ 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

   Code Block
   language bash
   ./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

   Code Block
   language bash
   $ 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)

   Code Block
   language bash
   $ 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

   Code Block
   language bash
   $ ./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.*

   Code Block
   language bash
   ./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.

   Code Block
   language bash
   $ 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)

   Code Block
   language bash
   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

   Code Block
   language bash
   $ ./submit_bb.sh devel ['

   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

2. Run submit_emod3d.sh
   $ ./submit_emod3d.h
3. 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.*
4. use llsubmit to submit your job if you selected to not to auto submit.
5. Use llq to check if your job has finished. (job status: R= running, C= Complete, I = idle)
   $ llq -u user
6. 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

1. Run install_bb.sh, to setup the parameters
   $ ./install_bb.sh
2. Choose from the options according to simulation requirement
3. 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

1. /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)

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

   Run submit_bb.sh
   $ ./submit_bb.sh

   
   
   
   
   
   

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