Difference between revisions of "Broadband User Guide v15.3.0"
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Once the unit tests all pass, proceed to the acceptance tests. If there are any failure or errors while running the unit tests, consult the Troubleshooting section at the end of this user guide for know issues and their solutions. | Once the unit tests all pass, proceed to the acceptance tests. If there are any failure or errors while running the unit tests, consult the Troubleshooting section at the end of this user guide for know issues and their solutions. | ||
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| + | On a Linux computer, the following commands will run the UnitTests.py as a background model. | ||
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| + | nohup ./AcceptTests.py > tests.log 2>&1 & | ||
== Running Acceptance Tests == | == Running Acceptance Tests == | ||
Revision as of 20:31, 21 April 2015
Version 15.3.0
If you find errors in this document or sections to be unclear, please contact software@scec.org. If possible, please send a description of how to reproduce the problem. This will help SCEC developers more quickly identify and resolve the problem you have identified.
Contents
Installing the Broadband Platform
Installing the Broadband Platform involves obtaining a copy of the code and building the required executables. You can either download the platform from the Broadband web site or check the code out of SCEC's Subversion repository. Most users should download the platform.
System Dependencies
The current version of the Broadband Platform is designed to run on standard 64-bit Linux machines and on Mac OS X. On Linux, testing has been performed on SCEC's development servers running Fedora Core 14 (kernel version 2.6.35.6-45.fc14.x86_64). On Mac OS X, testing was done on versions 10.9 (Mavericks) and 10.10 (Yosemite). In this guide we outline how to install the platform into your own account on a Linux or Mac computer using the simplest approach.
Software Dependencies
The Broadband Platform has certain software dependencies.
Required:
- Python v2.6+ with
- Matplotlib 1.0.1
- Numpy 1.4.1
- Scipy 0.7.2
- Pyproj 1.8.9
- GNU compilers (gcc, gfortran) v4.5.1
Mac OS X users should refer to our BBP on OS X Guide for installing the above dependencies to their system.
User Account Setup
For simplicity of installation, we recommend users use a bash shell for the Broadband Platform account. It is possible to get the platform running using other shell's, but we will focus on a bash shell installation. The user environment is a common source of problems since certain environment variables must be defined for the platform to work correctly.
To check your account, make sure you can run basic commands like ls and cd before proceeding.
Downloading the Platform
Download the main Broadband distribution file from the Broadband website. Users should also download the Greens' Functions files for the regions where simulations will be performed. Currently the platform supports the following regions:
- LABasin (this package is required to run the Unit and Acceptance tests)
- Mojave
- NoCal
- Western Japan
- Central Japan
- Eastern North America
- Eastern Canada
Additionally, users can optionally download validation packages for the following recorded events:
- Northridge (requires the LABasin GF package, this package is required to run the Acceptance tests)
- Loma Prieta (requires the NoCal GF package)
The installation instructions given later include a script that will confirm that the BBP files have been copied intact and unchanged onto your computer.
If multiple users are planning to use the platform on the same system, you only need one copy of the data files per machine. Each user will still need his or her own copy of the code files.
Alternatively, if you would like access to the latest version of the platform and get frequent but less thoroughly tested improvements, you can check out the platform from SCEC's Subversion repository. Only advanced users should take this approach, outlined in detail in the Advanced Users section.
Broadband Platform Directory Structure Setup
After confirming that all downloaded files are good, it is time to set up the directory structure used by the Broadband Platform. Start by creating a top-level directory for the Broadband Platform installation. In our example, we will use 'bbp' as this top-level directory. Assuming this directory will be installed in for the user "sarah":
$ cd /home/sarah $ mkdir bbp $ cd bbp
Now, untar the main Broadband distribution file (assuming all downloaded files are located in /home/sarah/downloads):
$ tar -xzvf /home/sarah/downloads/bbp-dist-15.3.0.tar.gz
This will create the "15.3.0" directory with the main distribution content. Now, create 2 more directories: one for the downloaded Greens' Functions and another for the optional Validation packages:
$ mkdir bbp_gf $ mkdir bbp_val
Go into the bbp_gf directory and untar each of the downloaded GF packages:
$ cd bbp_gf
For the LABasin package, the command would be:
$ tar -xzvf /home/sarah/downloads/labasin-velocity-model-15.3.0.tar.gz
Please untar any other GF packages that you desire to install.
Now, we need to do the same thing for the validation packages. Switch to the bbp_val directory and install any validation packages that were downloaded. For example, to install the Northridge validation package, users will need to:
$ cd /home/sarah/bbp/bbp_val $ tar -xzvf /home/sarah/downloads/northridge-validation-15.3.0.tar.gz
We are almost ready now. Users will need to create another directory, which will contain all the simulations that will be generated by the Broadband Platform. In this example, we will use "bbp_data", and will place it along with the other directories that we created above, using the commands:
$ cd /home/sarah/bbp $ mkdir bbp_data
The last step before we can proceed is to set up environment variables indicating where each of the above directories are located so that the Broadband Platform can find their locations. Using the example above, users will need to set up the following 6 environment variables. Just add the following lines to your .bash_profile file:
export BBP_DIR=/home/sarah/bbp/15.3.0/bbp export BBP_GF_DIR=/home/sarah/bbp/bbp_gf export BBP_VAL_DIR=/home/sarah/bbp/bbp_val export BBP_DATA_DIR=/home/sarah/bbp/bbp_data export PYTHONPATH=$BBP_DIR/comps:$PYTHONPATH export PATH=$BBP_DIR/comps:$BBP_DIR/utils/batch:$PATH
Note that users may need to log out and log in again in order for this change to take effect.
Building the Platform
Once users have downloaded and untar'ed the code and supporting packages, the final step is to compile the Broadband Platform. In order to successfully compile the project, you'll need to make sure the required compilers directories are in your PATH variable. Broadband requires the GNU Compilers, gcc, and gfortran to compile the scientific code. Using the example provided in the section above, users will need to go to the 'src' directory and compile the code. Before trying to compile the code, users can use the following command to make sure the needed compilers are present in their path:
$ which gcc
If you get a message like "no gcc in path" you will need to add the GNU compilers to your path. Once that is done, you can compile the code using the following commands:
$ cd /home/sarah/bbp/15.3.0/bbp/src $ make clean $ make
This will take a few minutes, and once it is done, you are ready to start using the Broadband Platform!
Broadband Platform Source Distribution Directory Structure
The platform consists of several top-level directories:
- 15.3.0 - Contains the source code, executables, scripts, and tests
- bbp_gf - Contrains the Green's Functions for the several regions supported by the Broadband Platform
- bbp_val - Contains the Validation Events that can be used with the Broadband Platform
- bbp_data - Contains the inputs, outputs, logs, and other temporary files generated by Broadband simulations. Please note that indata, logs, outdata, run, tmpdata, and xml sub-directories will be created when the Broadband Platform is first run, so they do not need to be created by the user.
The 15.3.0 directory has the bbp and doc sub-directories, containing the software distribution and some documentation and examples respectively. The bbp sub-directory contains the following folders:
- comps - Broadband modules required to run work-flows.
- mod_data - Data files used by the various simulation modules.
- plot - Scripts and data required to generate plots.
- src - Broadband science modules source code and supporting files.
- tests- Set of unit and acceptance tests.
- utils - Includes the batch utilities used for cluster operation
And the $BBP_DATA_DIR directory includes the following sub-directories:
- indata - Input data for simulations
- logs- Log files for simulations
- outdata - Output data from simulations
- run - Directory where user input files can be placed
- tmpdata - Temporary files generated during Broadband simulations
- xml - XML files with simulation parameters
In general, you will be interacting with the run directory for input files, comps to run the platform, tests to test the platform, and outdata to examine data products.
Adding aliases
You may find it helpful to add aliases, so you can quickly and easily move to different broadband directories with a single command. We recommend creating aliases for the comps, run, and outdata directories.
If you are using the Bash shell, you can create aliases by adding the following lines to ~/.bash_profile:
alias comps='cd $BBP_DIR/comps' alias run='cd $BBP_DATA_DIR/run' alias outd='cd $BBP_DATA_DIR/outdata'
Log out and log back in. You'll notice that now you can type the alias command as a shortcut to change directories:
$ pwd /home/sarah $ comps $ pwd /home/sarah/bbp/15.3.0/bbp/comps
This can be a useful way to navigate around the broadband platform directories.
Running the Tests
The Broadband Platform contains three kinds of tests. The checksum tests verify that the data files were copied correctly and you have all the files that are expected. Unit tests run each module using a set of input files, and compare the results against known outputs. They verify that each module has been built and is working correctly. Acceptance tests verify that the modules are working correctly together. They test the Platform end-to-end using different combinations with known inputs and compare the results. Each method (for both user-defined and validation events) are tested as checks against integration errors. Both unit and acceptance tests require the LABasin Greens' Functions package to be installed. The acceptance tests also require users to install the Northridge validation package.
Running Checksum Tests
To run the checksum tests, change to the checksums directory and run md5sum_check.py.
$ cd utils/checksums $ ./md5sum_check.py
It takes about 5 minutes to compute the checksums. If a checksum disagrees, that means that the contents of the datafile were not what was expected. Try reinstalling the data files and try again. If you continue to get a checksum error, contact support.
Once the checksums agree, move on to the unit tests.
If the script above pass, you can move onto the unit tests. But if you want to check the integrity of any individual BBP distribution file, these md5sum tests can be run for any BBP distribution file. After downloading the needed files to your local Linux or Mac OS X computer, users can calculate their checksums and compare them to the checksums on the Broadband web site to verify that you have the correct files. For Linux, if you type:
$ which md5sum
You should get something like /usr/bin/md5sum. If you see the message 'no md5sum in...', contact your Linux system administrator and ask to have md5sum added to your path.
Once you have the md5sum command installed on your system, you can type:
$ md5sum downloaded_file.tar.gz
where "downloaded_file.tar.gz" is the file downloaded from the Broadband website. Users should do this once for each of the downloaded files to make sure they have successfully downloaded the files. The easiest way to do it, it to have all .tar.gz distribution files and all .md5 files in the same directory and type:
$ md5sum -c *.md5
You should see a confirmation that each of the downloaded files are OK.
For Mac OS X, you can use the "md5" command, which works similarly to "md5sum". You can type:
$ md5 *.tar.gz
And you should see a list of md5 sums on the screen. Then compare them against the ones in the .md5 files to make sure they match.
Running Unit Tests
In order to run the unit tests, users should go to the tests directory and type:
$ cd /home/sarah/bbp/15.3.0/bbp/tests $ ./UnitTests.py
The tests should begin and will take between 30-60 minutes to run, depending on your computer speed. At the end of each test, a "ok" should be printed if the test was successful. At the end, the program will print the number of tests that passed and the number of tests that failed. If a test has failed, first check that you have built the executables.You can rerun just the specific test that failed (test_<module>.py). If the test is still failing, also verify that you have the ref_data directory, since it contains the input and reference files. If you're looking for more information about the failure, you can consult the Unit Tests log file in $BBP_DATA_DIR/logs/unit_tests.log . If you can't determine the reason for the failure, contact support.
Once the unit tests all pass, proceed to the acceptance tests. If there are any failure or errors while running the unit tests, consult the Troubleshooting section at the end of this user guide for know issues and their solutions.
On a Linux computer, the following commands will run the UnitTests.py as a background model.
nohup ./AcceptTests.py > tests.log 2>&1 &
Running Acceptance Tests
Make sure the unit tests pass before moving on to the acceptance tests. To run the acceptance tests, users should:
$ cd /home/sarah/bbp/15.3.0/bbp/tests $ ./AcceptTests.py
There will be one test for each method in the platform, for both the validation mode (historical events) and the scenario modes (hypotethical earthquakes). These tests will take somewhere between 2 and 3 hours to run, depending on how fast the computer is.
When they're complete, the console will either print "OK" or how many tests failed. Acceptance test failures indicate that the modules are not integrated correctly. Like with the unit tests, verify that you have the ref_data directory. If a certain acceptance test fails, you can get more information by consulting the acceptance test logs in $BBP_DATA_DIR/logs/acceptance_test_logs/<test that failed>.log . If you can't determine the reason for the failure, contact support.
Since the acceptance tests can take a long time to run, you may wish to resume where you left off. This feature is supported automatically. If you do not wish to resume, delete the resume file in $BBP_DATA_DIR/logs/resume.txt. If there are any failure or errors while running the acceptance tests, consult the Troubleshooting section at the end of this user guide for known issues and their solutions.
To run the acceptance tests in a terminal background process, on a Linux computer, the following command will run the tests as a background process, and redirect stderr and stdout to a "tests.log" file.
$ nohup ./AcceptTests.py > tests.log 2>&1 &
Here is an example output from the tests.log file created by running this command line above.
-bash-4.1$ more tests.log
nohup: ignoring input test_user-CSM (__main__.BBP2G_Acceptance_Tests) ... Number of tests to run: 12 ok test_user-EXSIM (__main__.BBP2G_Acceptance_Tests) ... ok test_user-GP (__main__.BBP2G_Acceptance_Tests) ... ok test_user-SDSU (__main__.BBP2G_Acceptance_Tests) ... ok test_user-UCSB (__main__.BBP2G_Acceptance_Tests) ... ok test_valid-northridge-CSM (__main__.BBP2G_Acceptance_Tests) ... ok test_valid-northridge-EXSIM (__main__.BBP2G_Acceptance_Tests) ... ok test_valid-northridge-GP (__main__.BBP2G_Acceptance_Tests) ... ok test_valid-northridge-GP_seis (__main__.BBP2G_Acceptance_Tests) ... ok test_valid-northridge-SDSU (__main__.BBP2G_Acceptance_Tests) ... ok test_valid-northridge-SDSU_seis (__main__.BBP2G_Acceptance_Tests) ... ok test_valid-northridge-UCSB (__main__.BBP2G_Acceptance_Tests) ... ok ---------------------------------------------------------------------- Ran 12 tests in 28116.825s OK
Performing Simulations
The platform supports two kinds of simulations, validation events and user-defined events. Validation simulations are performed using a historical event, and are directly compared to observed seismograms using goodness-of-fit. User-defined events are run using a rupture description provided by the user which may not necessarily be a historical earthquake.
When you run a simulation, the platform assigns an ID to it. This ID can be used to track the simulation and locate the output data products.
To supply input files to the platform, put them in the run directory. This directory is located in the $BBP_DATA_DIR directory and it is created by the platform when it is first ran. Extensions are important - the platform recognizes station lists (.stl), SRF files (.srf), and simple source descriptions (.src). For example, when selecting a station file, the Broadband Platform will list all the .stl files in the run directory and will prompt the user to select one.
Methods
To perform a simulation, a user selects a method, including optional modules. Currently, the Broadband Platform supports the following methods:
- Graves & Pitarka (GP)
- SDSU
- UCSB
- Composite Source Model (CSM - Under development)
- EXSIM
Modules
The Broadband Platform consists of a series of modules. There are two main types of modules, science modules and utility modules. Science modules are those for which the platform has multiple implementations, provided by different coding research groups. Utility modules only have 1 implementation and are used by all simulations. A schematic of the available modules and their flow relationships is shown below in the following sections.
Science Modules
All simulations must include a module that creates synthetic seismograms. In some methods, there are separate low-frequency and high-frequency modules, while in other methods, these two steps are done by a single module. Rupture generation and site response are optional science modules. Users may select the following different implementations of each of these modules:
- Rupture generation: GP, UCSB
- Low-frequency: GP, UCSB, CSM, EXSIM
- High-frequency: GP, UCSB, SDSU, CSM, EXSIM
- Site response: GP, UCSB, SDSU
Utility Modules
Two spectral response utility modules are automatically run after the seismogram synthesis is completed and the optional site response module. Additionally, users may select an optional goodness-of-fit (GoF) utility module to run at the conclusion of the simulation. The Broadband Platform currently supports both the GP and SDSU GoF modules and the users can select to run one, or both (or none) of these modules.
Validation Simulations
To run a validation simulation, go to the data/run directory and run run_bbp.py. The platform will ask you a series of questions. Answer 'y' to "Do you want to perform a validation run?"
$ cd $BBP_DATA_DIR/run $ run_bbp.py Welcome to the SCEC Broadband Platform version 15.3.0. ================================================================================ Please select the Broadband Platform mode of operation: * Validation - Simulates a historical event * Scenario - Runs a user-defined hypothetical event Do you want to perform a validation simulation (y/n)? y ================================================================================ Please select a validation event from the list below: (1) Northridge (2) Loma Prieta ? ...
No input files are required by the user. However, you may wish to customize the validation simulation by selecting an alternate source description (src file) or a reduced station list to speed up the computations. You can put your own source description andor station list into the run directory (the format is described in section 6.3) or you can tell the platform where each file is located by using an absolute path. Note that any stations which do not have observed seismograms will not be included in the automatically generated goodness-of-fit comparison.
In addition to the low-frequency modules which compute seismograms using 1D Green's Tensors, certain methods allow validation events to be also run using precomputed seismograms to supply the low-frequency.
User-defined Simulations
To run a user-defined simulation, two input files are required, a source description (src file) and a station list (stl file). For certain methods, the source description can either be in SRF format or a simple source description (the format is described in section 5.1). Other methods will always require a simple source description (src file). To run a user-defined simulation, run run_bbp.py.
$ cd $BBP_DATA_DIR/run $ run_bbp.py Welcome to the SCEC Broadband Platform version 15.3.0. ================================================================================ Please select the Broadband Platform mode of operation: * Validation - Simulates a historical event * Scenario - Runs a user-defined hypothetical event Do you want to perform a validation simulation (y/n)? n ================================================================================ The Broadband Platform provides the following velocity models, which also include several method-specific and region-specific parameters. Please select a velocity model (either number or name is ok): (1) NOCAL (2) Mojave (3) LABasin (4) CentralJapan (5) Canada1k (6) WesternJapan (7) CEUS1k ? ...
You may then choose the method you would like to run:
The Broadband Platform includes several scientific methods that can be used to calculate synthetic seismograms. Choose a Method to use in this Broadband scenario simulation: (1) GP (Graves & Pitarka) (2) UCSB (3) SDSU (4) EXSIM (5) Composite Source Model (CSM - Under Development) ?
Logging
During the run, log files will be produced in logs/<simulation ID>/<simulation ID>.<module name>.log. If the platform fails, this is a good place to look to determine the error. Additionally, any fatal errors will be recorded in fatal_error.log.
Metadata capturing all the executable calls is located in tmpdata/<simulation ID>/metadata.txt for careful tracing of exactly what was called. Both the log files and metadata can be useful if troubleshooting an issue.
Data Products
The platform produces a variety of data products. All data products are located in outdata/<simulation ID>. The ouput folder has a index-<simulation ID>.html file with a listing of all the data products in the output folder. You can open the index file on your browser window and then click through all data products. Image files can be displayed by clicking on the link to the file in the index.html page. The .bbp and .list files will be displayed as text files in the browser. On Mac OS X, you can see these data products by opening the outdata folder in Finder and double clicking on the specific file. On most Linux systems, you can show images using display:
$ display <PNG file>
Make sure you have X11 forwarding enabled.
Station Map
To help visualize the stations in relationship to the fault, the platform produces a PNG file displaying station locations with red circles and the fault plane with a black line. You can find this file in outdata/<simulation ID>/station_map.png.
The Broadband Platform also produces a station_map.kml file that can be opened in Google Earth and will show the fault location and stations with their labels. This file is useful to identify the individual stations on the map.
Seismograms
When running the Broadband Platform, you have the option to generate plots of velocity and acceleration seismograms for each station. Plots of these files can be found in outdata/<simulation ID>/<simulation ID>.<station>_<velocity or acceleration>_seis.png.
The raw seismogram data is available in outdata/<simulation ID>/<simulation ID>.<station>.vel.bbp (velocity) and outdata/<simulation ID>.<station>.acc.bbp (acceleration). Its format is described in section 6.4.
Response Spectra
The Respect and RotD50 codes, run at the end of each simulation, calculates the response spectra for each station. The raw Respect and RotD50 data is located at
outdata/<simulation ID>/<simulation ID>.<station>.rsp outdata/<simulation ID>/<simulation ID>.<station>.rd50
in the format described in section 6.5 and section 6.6.
Goodness-of-fit
If you run a goodness-of-fit module, several additional data products are produced. Two goodness-of-fit modules are available in Broadband.
- GP Goodness-of-fit:
The goodness-of-fit comparison is performed by comparing the response spectra of a set of calculated seismograms to seismograms from another simulation or observed seismograms. For each station involved in the comparison, a plot comparing the response spectra calculated by the Respect module can be found in outdata/<simulation ID>/<comparison label>_<simulation ID>_<station>_rsp.png. Similarly, a plot comparing the response spectra calculated by the RotD50 module can be found in outdata/<simulation ID>/<comparison label>_<simulation ID>/<station>rotd50.png. A plot showing the seismograms on top and bottom can be found at outdata/<comparison label>_<simulation ID>_<station>_overlay.png. The seismogram comparison plot also includes a comparison of the arias duration. Finally, two goodness-of-fit plots are generated, one using the data from Respect, and a second one with data from RotD50. These plots can be found at gof-<comparison label>-<simulation ID>_r0-<cutoff distance>.png and gof-<comparison label>-<simulation ID>_r0-<cutoff distance>-rotd50.png.
Note that at least 3 stations must be run for goodness-of-fit to be valid. If fewer than 3 stations are run, no goodness of fit calculation will be performed.
- SDSU Goodness-of-fit:
The SDSU goodness-of-fit module can compute several GoF measures. A detailed list of these GoF measure is listed here: SDSU MO-Gof. The goodness-of-fit comparison is performed by comparing the synthetic seismogram to the observed seismogram for each of the sites. For each GoF measure computed, a summary file labeled GOF_<measure>.list is generated with the GoF values for each of the sites. A weighted sum of GoF measures called site-fit is available in gof_summaray.txt file. If the simulation was run with three or more sites in the station list, GoF map plots will be available in the output directory as <simulation ID>_<Gof measure>_map.png. If PGA or PGV GoF values are computed a set of overlay plots showing the observed and synthetic seismograms on top and bottom will be available as outdata/gof_plots/<simulation ID>_<station>_match_<format>_overlay.png files.
Rupture files
When a user-defined event is simulated, the user has the option to run a rupture generator. This generator produces an SRF file, found in outdata/<simulation ID>/*.srf. This file can be put in the run directory and used in future runs. Additionally, the platform produces a plot of the cumulative slip on the fault surface, outdata/<simulation ID>/<SRF prefix>.png.
Platform Modes
The platform can be run in multiple modes. The default is interactive mode, in which the user is prompted to answer a series of questions. Once all the information has been gathered, the simulation run begins.
For a large number of runs, or if the user is repeating a specific run, this can be tedious. The platform provides two other ways to describe a run, with an option file or an XML description.
An option file provides responses to all the questions that the platform poses. The format is described in section 6.7, but it's basically a text file, 1 entry per line, with support for comments. It can be fed to the platform using the -o option.
The platform will also accept XML files containing a full description of a run. The schema for these files is given in section 6.8. These files are also produced by the platform after every simulation, and placed in xml/<simulation ID>.xml. So if you want to rerun a simulation, you can point the platform to the XML file from that simulation using the -x option. Note that a new simulation ID will be assigned to the run, so there is no risk of overwriting previous simulation results.
Available Options
To get a list of the current available options, run run_bbp.py with the -h flag.
$ ./run_bbp.py --help Usage: run_bbp.py [options] Options: -h, --help show this help message and exit -x XML_FILE, --xml-file=XML_FILE Run using XML description of workflow -s SIM_ID, --sim-id=SIM_ID Force a sim id -o OPTFILE, --option-file=OPTFILE File containing responses to interactive platform prompts -v, --version Broadband platform version -g, --generate-only Generates the XML description but does not run the platform -l LOG_FILE, --log=LOG_FILE Directs output to a file, use to run BBP in background -m, --no-xml Do not generate xml -r RESUME_MODULE, --resume=RESUME_MODULE Resume workflow from a certain module -e END_MODULE, --end=END_MODULE End workflow after a certain module --expert Turns on expert mode
Examples
Below are some examples that you can try using the sample files in the examples directory. You will need to have the Northridge Validation Package installed to use this example, which also requires that the LABasin Green's Functions package be installed in the Broadband Platform. Make sure all the tests pass before you try this.
You should be in the run directory when you start these examples. If you set the aliases defined above, type:
$ run
Otherwise, type a path to the run directory. The Run directory provides a collection point, a staging area, when you are assembling the input files to be used in a simulation:
$ cd $BBP_DATA_DIR/run
Running a Northridge Full Validation Simulation
You don't need to move any files for this. Notice that we will be using the EXSIM method, which will generate results quickly.
$ run_bbp.py Welcome to the SCEC Broadband Platform version 15.3.0 ================================================================================ Please select the Broadband Platform mode of operation: * Validation - Simulates a historical event * Scenario - Runs a user-defined hypothetical event Do you want to perform a validation simulation (y/n)? y ================================================================================ Please select a validation event from the list below: (1) Loma Prieta (2) Northridge ? 2 ================================================================================ The Broadband Platform includes several scientific methods that can be used to calculate synthetic seismograms. Choose a Method to use in this Broadband validation simulation: (1) GP (Graves & Pitarka) (2) UCSB (3) SDSU (4) EXSIM (5) Composite Source Model (CSM - Under Development) ? 4 ================================================================================ SRC file: /home/sarah/bbp/bbp_val/Northridge/common/nr_v14_02_1.src ================================================================================ STL file: /home/sarah/bbp/bbp_val/Northridge/common/nr_stats-ver_9_2013.stl Running ExSim ...
This simulation should take about 30 minutes (as opposed to about 12+ hours if using some of the other methods). Once it's complete, the platform will tell you:
You can find results in $BBP_DATA_DIR/outdata/<simulation ID>
In that directory you will find:
- HTML Directory Listing (index-<simulation ID>.html)
- Velocity seismograms (<simulation ID>.<station>.vel.bbp)
- Acceleration seismograms (<simulation ID>.<station>.acc.bbp)
- Plots of velocity seismograms (<simulation ID>.<station>_velocity_seis.png)
- Plots of acceleration seismograms (<simulation ID>.<station>_acceleration_seis.png)
- Response spectra Respect files (<simulation ID>.<station>.rsp)
- Response spectra RotD50 files (<simulation ID>.<station>.rd50)
- Plots comparing simulated and observed seismograms (Northridge_<simulation ID>_<station>_overlay.png)
- Plots comparing simulated and observed Respect response spectra (Northridge_<simulation ID>_<station>_rsp.png)
- Plots comparing simulated and observed RotD50 response spectra (Northridge_<simulation ID>_<station>_rotd50.png)
- Overall Respect goodness-of-fit plots (gof-Northridge-<simulation ID>_r0-120.png)
- Overall RotD50 goodness-of-fit plots (gof-Northridge-<simulation ID>_r0-120-rd50.png)
Sample Northridge Validation simulation, custom stations
Validation runs can take a long time. The time needed to generate each low-frequency seismogram will generaly increase with the magnitude of the event, taking more than 1 hour per station for earthquakes with Mw > 7.2. Sometimes you might want to run with a reduced station list so the simulation will run faster.
Copy the station list from $BBP_DIR/doc/examples/northridge_3_stations into the run directory, which should be $BBP_DATA_DIR/run. Take a look at the format of the station file:
$ more northridge_3_stations.stl #Required: lon, lat, station name, Vs30 #Optional: low freq corner, high freq corner #lon lat station Vs30 LF corn HF corn -118.6417 34.5640 cast 450 0.120 111.11 -118.4180 34.0628 lacn 278 0.140 111.11 -118.8811 34.2886 moor 405 0.160 111.11
Now, run the platform, using a different station list. To do this, you will need to use the Broadband Platform "expert" mode. See below:
$ run_bbp.py --expert
Welcome to the SCEC Broadband Platform version 15.3.0.
================================================================================
Please select the Broadband Platform mode of operation:
* Validation - Simulates a historical event
* Scenario - Runs a user-defined hypothetical event
Do you want to perform a validation simulation (y/n)? y
================================================================================
Please select a validation event from the list below:
(1) Loma Prieta
(2) Northridge
? 2
================================================================================
The Broadband Platform includes several scientific methods that can be used to
calculate synthetic seismograms.
Choose a Method to use in this Broadband validation simulation:
(1) GP (Graves & Pitarka)
(2) GP Seis (using precomp seismograms)
(3) UCSB
(4) SDSU
(5) SDSU Seis (using precomp seismograms)
(6) EXSIM
(7) Composite Source Model (CSM - Under Development)
? 1
================================================================================
When starting a simulation from a source description (SRC) file, the Broadband Platform
workflow should include a rupture generator. Answer 'yes' here unless providing
a complex Standard Rupture Format (SRF) file.
Do you want to run the rupture generator (y/n)? y
================================================================================
Each validation package includes a default source description (SRC) file for a historical event.
Would you like to provide a different file instead of the default file provided?
Answer 'no' here if you would like to use the standard source file for this event.
Do you want to provide a custom source file (y/n)? n
================================================================================
SRC file: /home/sarah/bbp/bbp_val/Northridge/common/nr_v14_02_1.src
================================================================================
Station Selection
=================
Would you like to:
(1) generate seismograms for all stations in the validation package
OR
(2) provide a custom list with a subset of the stations
? 2
Do you want to
(1) select a BBP station list in /home/sarah/bbb/bbp_data/run
OR
(2) enter the path of a BBP station list file
? 1
You will see a list of station list files that you have in your run directory. For this example, we only have the northridge_3_stations.stl file that we copied from the examples directory. You could have more files in the run directory if you have already tried other unit and acceptance tests. For this example, just select the northridge_3_stations.stl file.
Here are the BBP station list files in the run directory. Please select one: (1) northridge_3_stations.stl ? 1 ================================================================================ STL file: /home/sarah/bbp/bbp_data/run/northridge_3_sta.stl ================================================================================ Site Response ============= Running a site response module is an optional step while running a Broadband Platform simulation. It requires a station list file containing the Vs30 values for each station location. Do you want to run the site response module (y/n)? n ================================================================================ Do you want to generate velocity seismograms' plots (y/n)? y ================================================================================ Do you want to generate acceleration seismograms' plots (y/n)? y ================================================================================ The Broadband Platform can generate comparison plots of the validation data against GMPEs to show how GMPEs match the recorded data for a certain event. Do you want to generate a GMPE comparison plot (y/n)? y ================================================================================ Please select a GMPE set to use in the comparison (number of name are ok): (1) CENA GROUP 1 (2) NGA-West1 (3) NGA-West2 ? 2 ================================================================================ Goodness-of-Fit Plot ==================== Running a goodness-of-fit (GoF) module is an optional step while running a Broadband Platform simulation. It creates a comparison plot showing how well the calculated seismograms fit recorded data. Do you want to run a goodness-of-fit module (y/n)? y ================================================================================ Users can optionally select a Goodness of Fit module to plot a comparison of how well the simulated seismograms match the recorded data in a historical event. Choose a Goodness of Fit (GOF) Module: (1) GP (2) SDSU (3) Both ? 1
Again, when the run completes, in about 15 minutes, you can find results in the output directory. You'll notice far fewer files, as only 3 stations were run instead of 133. The goodness-of-fit plots won't look very good - more stations are really needed to get an accurate plot. In the $BBP_DIR/doc/examples/northridge_3_stations/results directory you will find pre-calculated results for a few of the methods (GP and UCSB). You should obtain results equivalent to those.
Sample User-defined Southern California simulation with source description
Next let's try running a user-defined event. Copy the files $BBP_DIR/examples/scenario_1_station/nr_one_stat.stl and $BBP_DIR/examples/scenario_1_station/user_eq.src to the $BBP_DATA_DIR/run directory. user_eq.src is a simple source description. Its format is outlined in section 6.1.
$ run_bbp.py Welcome to the SCEC Broadband Platform version 15.3.0. ================================================================================ Please select the Broadband Platform mode of operation: * Validation - Simulates a historical event * Scenario - Runs a user-defined hypothetical event Do you want to perform a validation simulation (y/n)? n ================================================================================ The Broadband Platform provides the following velocity models, which also include several method-specific and region-specific parameters. Please select a velocity model (either number or name is ok): (1) Mojave (2) LABasin (3) CentralJapan (4) LOMAP (5) WesternJapan ? 2
Since we are running a Southern California event, we select the LABasin velocity model, as it is the one that most closely matches the location of our rupture and stations.
================================================================================
The Broadband Platform includes several scientific methods that can be used
to calculate synthetic seismograms.
Choose a Method to use in this Broadband scenario simulation:
(1) GP (Graves & Pitarka)
(2) UCSB
(3) SDSU
(4) EXSIM
(5) Composite Source Model (CSM - Under Development)
? 1
================================================================================
The source description (SRC) file contains a description of the hypothetical
(or scenario) earthquake, including information like location, geometry,
magnitude, and mechanism.
Do you want to
(1) select a source description in /Users/fsilva/Work/svn/temp/bbp_sims/run
OR
(2) enter the path of a source description file
? 1
Here are the source description files in the run directory.
Please select one:
(1) user_eq.src
? 1
Do you want to
(1) select a BBP station list in /home/sarah/bbp/bbp_data/run
OR
(2) enter the path of a BBP station list file
? 1
Here are the BBP station list files in the run directory.
Please select one:
(1) nr_one_stat.stl
(2) nr_three_stat.stl
? 1
Running Genslip
...
Since this run only includes one station, it will run in about 5 minutes. In the output directory you'll notice there are no goodness-of-fit or files, since this is not a validation simulation. However, there is also a map file (station_map.png and station_map.kml), showing the fault plane and the stations, and a plot of the rupture slip (user_eq.png). The SRF generated by the rupture generator is in user_eq.srf; this file could be used in future runs. The filenames of the rupture slip plot and SRF are taken from the rupture description filename.
File Formats
This section offers descriptions of various file formats in the broadband platform.
Simple source description
This is the format for the simple source description. It is not whitespace sensitive. The filename must end in .src for the platform to identify it as a source description.
MAGNITUDE = <moment magnitude> FAULT_LENGTH = <length of fault> DLEN = <DX, along length> FAULT_WIDTH = <down-dip fault width> DWID = <DY, along width> DEPTH_TO_TOP = <depth of fault below surface> STRIKE = <strike> RAKE = <rake> DIP = <dip> LAT_TOP_CENTER = <latitude of top center point in fault plane> LON_TOP_CENTER = <longitude of top center point in fault plane> HYPO_ALONG_STK = <along strike location of hypocenter (0.0 = middle)> HYPO_DOWN_DIP = <down dip location of hypocenter (0.0 = top)> SEED = <random seed used in calculations> CORNER_FREQ = <corner frequency to use>
SRF rupture description
Details of the Standard Rupture Format (SRF) are given in more detail in the accompanying document. The general fault surface is represented by a distribution of point sources, and it can support one or more planes. The platform produces SRFs as output from rupture generators, but a user can also supply an SRF file as input for user-defined simulations. SRF filenames must end with the suffix .srf for the platform to correctly identify them.
Station File List
The user may specify a list of stations, matching the following format:
#optional %comment # lines <lon> <lat> <stat name> <Vs30> <LF corner> <HF corner> <stat info> ...
The station list filename needs to end in .stl for the platform to recognize it as a station list.
BBP seismograms
All intermediate and output seismograms are produced in a 4-column text format, whether velocity or acceleration.
# optional % comment # lines <timestamp> <North/South> <East/West> <Up/Down> ...
Time is in seconds and motion is in cm/s (velocity) or cm/s/s (acceleration) unless otherwise specified in the header. Velocity filenames end in .vel.bbp; accelerations in .acc.bbp.
Respect Response Spectra
The Respect response spectra file is in a 4-column text format.
# optional % comment # lines <period (sec)> <North/South> <East/West> <Up/Down> ...
The platform samples Respect response spectra at 112 periods, 0.01-20 sec and outputs pseudo spectral acceleration in units of g.
RotD50 Response Spectra
The RotD50 response spectra file is in a 4-column text format.
# optional # comment # lines
<period (sec)> <PSA North/South> <PSA East/West> <RotD50> ...
The platform samples RotD50 response spectra at 63 periods, 0.01-10 sec and outputs pseudo spectral acceleration in units of g.
Option File
Option files contain responses to the prompts in the platform. You can use them with the -o option to run_bbp.py. The responses have to match the prompts exactly. For example, if you craft an option file assuming a certain order of station lists (stl) or source descriptions (src) files in the run directory and there is a different set of files there it will potentially cause the Broadband Platform to pick a wrong file or possibly abort. Whenever a list of method, files, velocity models, or validation events is presented, the user can use either name or number to select that option. Picking the name avoids problems with the ordering. Option files are recommended to perform a series of runs with different inputs or different modules. If you have a run you perform regularly, it's better practice to run the platform with the -g option and the option file to produce an XML description, which are more complete descriptions of the workflow.
#optional comments %using either symbol n #comments y % can go 1 # here LABasin # velocity model ...
Use with:
$ ./run_bbp.py -o <option file>
XML workflow description schema
Each time the platform is invoked, an XML file is produced describing the workflow, obeying the following schema:
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema">
<xs:element name= "BBP_Run_Specification" minOccurs= "1" maxOccurs= "1">
<xs:attribute name="version" type = "xs:string" use = "required" />
<xs:complexType>
<xs:sequence>
<xs:element name= "Validation_Run" minOccurs= "0" maxOccurs = "1">
<xs:attribute name= "event" type= "xs:string" use= "required" />
<xs:attribute name= "input_station_file" type = "xs:string" />
<xs:attribute name= "subset" type = "xs:boolean" use = "required" />
</xs:element>
<xs:element name= "BBP_Modules">
<xs:complexType>
<xs:sequence>
<xs:element name = "BBP_Module" maxOccurs = "unbounded" >
<xs:complexType>
<xs:sequence>
<xs:element name= "name" type="xs:string" />
<xs:element name= "staged_files" >
<xs:complexType>
<xs:sequence>
<xs:element name="file" type="xs:string" maxOccurs= "unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name= "arguments" >
<xs:complexType>
<xs:sequence>
<xs:element name="argument" type="xs:string" maxOccurs="unbounded">
<xs:attribute name= "type" type= "xs:string" user= "required" />
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
These files are difficult to construct by hand, but can be generated using the -g flag when running run_bbp.py.
Advanced Users
Alternatively, if you would like access to the latest version of the platform, to get frequent but less thoroughly tested improvements, you can check out the platform from SCEC's Subversion version control repository on source.usc.edu. Only advanced users should follow this approach. If you are unsure, you should download the code as outlined in Downloading the Platform and skip this section.
You may need to request access from the SCEC system administrator, John Yu (johnyu@usc.edu). Make sure you have subversion in your path before beginning.
Once you have access, you'll need to decide if you want a stable tagged version, or the latest version in the repository. For a stable version, open a terminal window on the system of your choice and type:
$ svn checkout https://source.usc.edu/svn/broadband/tags/<stable version> <stable version>
For the latest version, type:
$ svn checkout https://source.usc.edu/svn/broadband/trunk trunk
This will check out the project to your local machine. It contains the source code, tests, and some example files. You also need to obtain a copy of the Broadband Platform Green's Functions packages. They are too large to be stored in version control. You can get the .tar.gz files for the Green's Functions from the same download site you obtained this guide.
Periodically you should check for updates to the code. To do so, go to your trunk directory and type
$ svn update
This will pull down any code updates that have been made in the repository. After you update, make the code again (detailed in section 1.6) so that any code changes are captured in the executables.
User Support
If you run into bugs with the platform, you can open a trouble ticket at the Broadband Trac site.
Check to see if there has already been a ticket opened for the bug. If you are unable to get the platform to run, you can get direct user support by emailing software@scec.org.
Appendix A: Troubleshooting
If you experience trouble building the platform or successfully running test and simulations, try the following solutions.
Build Errors
The instruction for installing Broadband Platform are listed in Section 1: "Installing the Second-Generation Broadband Platform" of the User guide. If after following all steps listed in this section of the user guide the build fails, check if the failure is listed in this section and try the solution to fix the issue you are facing.
Unit/Acceptance Test Warnings and Errors
Unit and Acceptance tests are provided to verify the Broadband platform and it's supporting modules built by the user are functioning as designed. Under certain circumstances, some of these test might fail or print a warning message. While some of these failures might indicate serious problems that will have to be addressed before the platform can used, it is acceptable to ignore some of the warnings. This section lists some issues and their solutions.
test_bbtoolbox
The test_bbtoolbox unit test will fail on Mac OS X. This is due to the raytracing code in the SDSU method not working on Mac OS X. This is a known issue and we hope to have this issue resolved in a future version of the Broadband Platform.
test_gof
In certain environments, the test_gof unit test will display a series of warning messages regarding the availability of certain fonts used in the plots. The user would see a number of messages like:
/usr/lib64/python2.7/site-packages/matplotlib/font_manager.py:1242: UserWarning: findfont: Font family ['STIXSizeThreeSym'] not found. Falling back to Bitstream Vera Sans /usr/lib64/python2.7/site-packages/matplotlib/font_manager.py:1242: UserWarning: findfont: Font family ['STIXSizeFourSym'] not found. Falling back to Bitstream Vera Sans
These messages do not indicate a failure of the unit test. At the end of this test you will still see the "ok" status, indicating that the test was successful.
test_user-SDSU
test_valid-northridge-SDSU
test_valid-northridge-SDSU_seis
All acceptance tests for the SDSU method will fail on Mac OS X due to the raytracing code in the SDSU method. This is a known issue and we hope to have this resolved in an upcoming version of the Broadband Platform.
Runtime Warnings and Errors
Below is a list of known issues in the current Broadband 13.9.0 release that can sometimes cause a simulation to fail.
SDSU Method: BBToolbox exits with code 174
The current version of SDSU's BBToolbox code can sometimes fail with an exit code of 174. This will cause the Broadband simulation to stop immediately and a message similar to the one below will be recorded in the bbtoolbox log file (which is located in the simulation's log directory at $BBP_DATA_DIR/logs/<simulation_id>:
*** Welcome to the Broad-Band Toolbox (v1.5) *** Initialising the code, please type input filename ... rl= 131 rl= 131 Starting slug3d: by J. Vidale, 1988, UCSC Starting punch: by J. Hole, 1993, UBC-Stanford -- travel-times written to :time3d_P.out -- selected velocity file :vel3d_P.bin WARNING: Computing only to max radius = 1001 Completed radius = 10 Completed radius = 20 Completed radius = 30 Completed radius = 40 Completed radius = 50 Completed radius = 60 Completed radius = 70 Completed radius = 80 Completed radius = 90 Completed radius = 100 Completed radius = 110 wavefront done Starting slug3d: by J. Vidale, 1988, UCSC Starting punch: by J. Hole, 1993, UBC-Stanford -- travel-times written to :time3d_S.out -- selected velocity file :vel3d_S.bin WARNING: Computing only to max radius = 1001 forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source BBtoolbox.exe 000000000043A28B Unknown Unknown Unknown BBtoolbox.exe 0000000000403A8B Unknown Unknown Unknown BBtoolbox.exe 000000000040372C Unknown Unknown Unknown libc.so.6 000000337641ECDD Unknown Unknown Unknown BBtoolbox.exe 0000000000403629 Unknown Unknown Unknown
This message reflects an issue in the raytracer code used by BBToolbox that will cause the code to fail with certain geometries. The SDSU team is currently working on a fix to this issue and we expect a future version of the Platform to include the fix. Meanwhile, the user can try to change the problem geometry in order to avoid the error. This can be done by overriding the geometry that is calculated based on the stations and rupture (using a larger x/y/z grid will not affect the simulation results but can sometimes solve this raytracer issue). To see what is the current problem geometry, users can look for the following line in the .bbpar file (located in the $BBP_DATA_DIR/indata/<simulation_id> directory:
/* GRID DEFINITION [X-Y-Z] FOR RAYTRACING: "FAR-SIDE" (IN KM) */ 130.0 140.0 125.0
To specify a different geometry to be used by BBToolbox's raytracer, users can include the following keys in the SRC file:
GRID_X = xxx GRID_Y = yyy GRID_Z = zzz
Where xxx, yyy, and zzz are the new dimensions for the raytracer to use (specified in km).
SDSU Method: BBToolbox exits with code 139
The current version of SDSU's BBToolbox code can sometimes fail with an exit code of 139. We are working with the modelers to resolve this issue, but it appears related to memory management issues in the code. We have found that it is sometimes useful to increase the stack size (if one is set). This should be done before the simulation starts, with the command below (for bash):
$ ulimit -s unlimited
UCSB Method: Site Response module
In the current version of the Broadband Platform, the UCSB site response module is producing unusually high amplitudes. This is likely due to a unit mismatch between the new versions of the source and wave propagation codes, and the old version of the site response module. Therefore, the UCSB method site response module should not be used in this release. We are currently working on a fix and will have a solution implemented by the next release of the Platform.
Related Entries
References
- Douglas S. Dreger and Thomas H. Jordan (2015) Introduction to the Focus Section on Validation of the SCEC Broadband Platform V14.3 Simulation Methods Seismological Research Letters, January/February 2015, v. 86, p. 15-16, doi:10.1785/0220140233
- Christine A. Goulet, Norman A. Abrahamson, Paul G. Somerville, and Katie E. Wooddell (2015) The SCEC Broadband Platform Validation Exercise: Methodology for Code Validation in the Context of Seismic‐Hazard Analyses Seismological Research Letters, January/February 2015, v. 86, p. 17-26, doi:10.1785/0220140104
- Philip J. Maechling, Fabio Silva, Scott Callaghan, and Thomas H. Jordan (2015) SCEC Broadband Platform: System Architecture and Software Implementation Seismological Research Letters, January/February 2015, v. 86, p. 27-38, First published on December 17, 2014, doi:10.1785/0220140125
- Douglas S. Dreger, Gregory C. Beroza, Steven M. Day, Christine A. Goulet, Thomas H. Jordan, Paul A. Spudich, and Jonathan P. Stewart (2015) Validation of the SCEC Broadband Platform V14.3 Simulation Methods Using Pseudospectral Acceleration Data Seismological Research Letters, January/February 2015, v. 86, p. 39-47, First published on December 17, 2014, doi:10.1785/0220140118
- Gail M. Atkinson and Karen Assatourians (2015) Implementation and Validation of EXSIM (A Stochastic Finite‐Fault Ground‐Motion Simulation Algorithm) on the SCEC Broadband Platform Seismological Research Letters, January/February 2015, v. 86, p. 48-60, First published on December 17, 2014, doi:10.1785/0220140097
- Jorge G. F. Crempien and Ralph J. Archuleta (2015) UCSB Method for Simulation of Broadband Ground Motion from Kinematic Earthquake Sources Seismological Research Letters, January/February 2015, v. 86, p. 61-67, First published on December 17, 2014, doi:10.1785/0220140103
- John G. Anderson The Composite Source Model for Broadband Simulations of Strong Ground Motions Seismological Research Letters, January/February 2015, v. 86, p. 68-74, First published on December 17, 2014, doi:10.1785/0220140098
- Robert Graves and Arben Pitarka (2015) Refinements to the Graves and Pitarka (2010) Broadband Ground‐Motion Simulation Method Seismological Research Letters, January/February 2015, v. 86, p. 75-80, First published on December 17, 2014, doi:10.1785/0220140101
- Kim Olsen and Rumi Takedatsu (2015) The SDSU Broadband Ground‐Motion Generation Module BBtoolbox Version 1.5 Seismological Research Letters, January/February 2015, v. 86, p. 81-88, First published on December 17, 2014, doi:10.1785/0220140102
