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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
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.gzCode Block language bash $ wget ftphttps://ucquakecore1pquakecoresoft.canterbury.ac.nz/seisfinder/private/gmsim/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]
Code Block language bash $ ./install.sh gmsim_pack_latest.tar.gz 20100904 Darfield 7.1
- 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!!!! =========================================================================
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
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
...
After admin tells you that all files are uploaded to Fitzroy, Run setup_remote.sh
$setup_remote.sh usernameCode 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
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)
- Go to the Simulation Folder, located at /nesi/
user/run_nameInstallation completed ==================================================================================================== Instructions ==================================================================================================== For Simulation (Fitzroy) 1. cd /nesi/projects/nesi00213/RunFolder/
Code Block language bash $ cd /nesi/projects/nesi00213/RunFolder/ykh22/20100904_Darfield_m7p1_201705181350
Run submit_emod3d.sh
$ ./submit_emod3d.hCode Block language bash 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.*Code Block language bash use llsubmit to submit your job if you selected to not to auto submit.
Code Block language bash Use llq to check if your job has finished. (job status: R= running, C= Complete, I = idle)
$ llq -u userCode Block language bash 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.shCode Block language bash
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.shCode Block language bash Choose from the options according to simulation requirement
Code Block language bash Run submit_hf.sh
$ ./submit_hf.sh
note: if you prefer to change some detail configurations, press 2(no) for auto submit.*Code Block language bash
*: 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
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
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)
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
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.
Use llq to check if your job has finished. (job status: R= running, C= Complete, I = idle)
$ llq -u userCode 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
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.shCode 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
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.
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
Run install_bb.sh, to setup the parameters
Choose from the options according to simulation requirementCode 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
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
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.
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
Run submit_bb.sh
$ ./submit_bb.shCode Block language bash $ ./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
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.shCode Block language bash
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