Accessing CyberShake Seismograms

This page details the process of identifying and accessing CyberShake seismograms.

Identifying Seismograms of Interest

The first step is to figure out which seismograms are of interest. You'll need to access the database to determine this; instructions are available at Accessing CyberShake Database Data. To do this, you'll need to know a) the site and run ID of the CyberShake run, and b) the source id, rupture id, and rupture variation id of the seismogram. You may have done this already. If not, you can determine the run ID by using MySQL to query the CyberShake database on focal.usc.edu. To determine a run ID, you will need to know values for a few parameters, such as the ERF, the velocity model, and the rupture variation generator version. Here's a sample query:

select R.Run_ID from CyberShake_Runs R, CyberShake_Sites S
where S.CS_Short_Name="LADT"    //Replace this with the site you want
and R.Site_ID=S.CS_Site_ID
and R.ERF_ID=35                 //35 corresponds to UCERF 2.  You'll always want to use this.
and R.SGT_Variation_ID=5        //This is the code used to generate the SGTs.  5 = Rob Graves' code.  6 = AWP-ODC.  7 = a newer, revised version of the Graves code.
and R.Rup_Var_Scenario_ID=4     //This is the code used to generated the rupture variations.  3 = Graves & Pitarka 2007.  4 = Graves & Pitarka 2010.  You'll probably want to  use 4.
and R.Velocity_Model_ID=1       //This is the velocity model.  1 = CVM-S4.  2 = CVM-H v11.2.  4 = CVM-H v11.9.
and (R.Max_Frequency=0.5 or R.Max_Frequency is null)    //This selects only deterministic (0.5 Hz) runs.  If you wanted only runs that include the stochastic high-frequency components, you would change this to "R.Max_Frequency=10.0"
and R.Status="Verified";        //This means the run completed successfully

From this you should be able to get a run ID. You could use this run ID to access all the seismograms (usually about 500,000) for the run, or you could continue to use the database to select seismograms for only certain events.

From an SRF file, you already have the source ID and run ID. The difference between rupture variations is the hypocenter locations and the slip distributions. The hypocenter locations are in the database, so you can look at them with a query like:

select Rup_Var_ID, Hypocenter_Lat, Hypocenter_Lon, Hypocenter_Depth from Rupture_Variations
where ERF_ID=35
and Source_ID=0
and Rupture_ID=0;

To understand the different slips, the easiest thing to do is to plot them.

Retrieving Seismograms

We are in the process of migrating seismograms from past CyberShake studies to Globus collections, to simplify access for users. Currently, only CyberShake Study 15.12 is available through Globus, but if you are interested in accessing seismograms from a different CyberShake study, please email software@scec.org to make a request.

Globus Account

To access the seismograms, you'll need to acquire a Globus account. If you don't already have one, you can create one using your email address by following the instructions here.

Connecting to the collection

To access the seismogram data, or intensity measure data beyond what is stored in the database, you'll need to transfer data from the Study 15.12 Globus collection to your destination system, either by using the Globus web-based interface or the Globus command-line interface.

Once you've connected to the collection, you can transfer the data anywhere with a Globus endpoint - details here. Many clusters, universities, and HPC centers have Globus endpoints set up already. If you can't find an endpoint where you need one, or you'd prefer to transfer the data to your local laptop or desktop, you can create your own endpoint using Globus Connect Personal.

Globus web-based interface

The simplest way to access CyberShake data is through the Globus web-based interface. You can access this collection by following this link.

Globus command-line interface

If you have a complex request (for example, you only want data for certain events) which is difficult to handle in the web GUI, or you would like to automate your transfers, Globus provides the Globus Command Line Interface(CLI). You can issue the same commands as in the web client, and additionally you can create a batch file which contains a list of all the files you'd like to download. With some versions of the CLI I have noticed a limit in terms of the number of files the CLI can handle at a time, so I would recommend no more than 100,000 files per batch file. If you use this approach, you'll need either the name of the collection, which is 'SCEC CyberShake Study 15.12', or the UUID for the collection, which is 2c328eb5-1c89-470d-ac1d-9fa693d28d86. Note that transfers made through the CLI will still be associated with your account, and you can monitor their progress through the web GUI.

Data organization

The data is organized by site name and run ID. So, for example, there's a directory for site ACTN and then run ID 4296. Inside this directory are all the seismograms, PSA, RotD, and duration files for site ACTN, run ID 4296. The filenames are <Seismogram | PeakVals | RotD | Duration>_<site>_<source ID>_<rupture ID>.<grm | bsa | rotd | dur> . The data for each run of Study 15.12 is approximately 90 GB.

Seismogram Format

The seismogram file Seismogram_<site>_<sourceID>_<ruptureID>.grm contains the seismograms for all the rupture variations for the given source ID.

The seismograms are velocity seismograms, with units of cm/s. The number of timesteps and dt depends on what frequency the run was performed at, as well as whether the run included stochastic high-frequency results, and can be determined by reading the header information.

The format is (binary):

<Rupture Variation 1 56-byte header>
<Rupture Variation 1, X component - NT 4-byte floats>
<Rupture Variation 1, Y component - NT 4-byte floats>
<Rupture Variation 2 56-byte header>
<Rupture Variation 2, X component - NT 4-byte floats>
<Rupture Variation 2, Y component - NT 4-byte floats>
...
<Rupture Variation n 56-byte header>
<Rupture Variation n, X component - NT 4-byte floats>
<Rupture Variation n, Y component - NT 4-byte floats>

However, the rupture variations are not necessarily in order in the file. So if you are only interested in a subset of the rupture variations, you will have to read the header data to find the rupture variations you are interested in. A description of the header structure is given in CyberShake_output_data_headers#Seismogram_header. C and Python examples to read the header information are provided there.

Sample Python and C code for reading out the seismogram contents for a seismogram with just 1 rupture variation is below. This code prints the 1000th timesteps for X and Y components, but obviously you could do whatever is needed with the arrays.

Python code

!/usr/bin/env python3

import sys
import struct

class Seismogram:

    def __init__(self, filename):
        self.filename = filename
        self.nt = 0
        self.dt = 0.0

    def parseHeader(self, header_str):
        #Find null terminator
        split_point = header_str[0:8].find(b'\x00')
        self.version = header_str[0:split_point].decode()
        if self.version!="12.10":
           print("Error: version does not match expected string '12.10', aborting.")
           sys.exit(2)
        #Find null terminator
        split_point = header_str[8:16].find(b'\x00')
        self.site = header_str[8:8+split_point].decode()
        self.source_id = struct.unpack('i', header_str[24:28])[0]
        self.rupture_id = struct.unpack('i', header_str[28:32])[0]
        self.rup_var_id = struct.unpack('i', header_str[32:36])[0]
        self.dt = struct.unpack('f', header_str[36:40])[0]
        self.nt = struct.unpack('i', header_str[40:44])[0]
        self.comps = struct.unpack('i', header_str[44:48])[0]
        self.x_flag = self.y_flag = self.z_flag = False
        if (self.comps & 1)==1:
            self.x_flag = True
        if (self.comps & 2)==2:
            self.y_flag = True
        if (self.comps & 4)==4:
            self.z_flag = True
        self.det_max_freq = struct.unpack('f', header_str[48:52])[0]
        self.stoch_max_freq = struct.unpack('f', header_str[52:56])[0]

    def readData(self):
        fp_in = open(self.filename, "rb")
        header_str = fp_in.read(56)
        self.parseHeader(header_str)
        data_str = fp_in.read(4*self.nt)
        self.x_data = struct.unpack("%df" % self.nt, data_str)
        data_str = fp_in.read(4*self.nt)
        self.y_data = struct.unpack("%df" % self.nt, data_str)
        fp_in.close()

if len(sys.argv)<2:
    print("Usage: %s <seismogram file>" % sys.argv[0])
    sys.exit(1)

seis_file = sys.argv[1]
s = Seismogram(seis_file)
s.readData()
print("seis_data[X][1000] = %f" % s.x_data[1000])
print("seis_data[Y][1000] = %f" % s.y_data[1000])

C code

#include <stdio.h>
#include <stdlib.h>
#define X 0
#define Y 1

struct seisheader {
 char version[8];
 char site_name[8];
 char padding[8];
 int source_id;
 int rupture_id;
 int rup_var_id;
 float dt;
 int nt;
 int comps;
 float det_max_freq;
 float stoch_max_freq;
};

int main(int argc, char** argv) {
        if (argc<2) {
                printf("Usage: %s <input seismogram>\n", argv[0]);
        }
        char* input_file = argv[1];
        FILE* fp_in = fopen(input_file, "rb");
        struct seisheader shead;
        fread(&shead, sizeof(struct seisheader), 1, fp_in);
        //Array with X and Y seismograms
        //seis_data[0] has X, seis_data[1] has Y
        float* seis_data[2];
        int i;
        for (i=0; i<2; i++) {
                seis_data[i] = malloc(sizeof(float)*shead.nt);
                fread(seis_data[i], sizeof(float), shead.nt, fp_in);
        }
        fclose(fp_in);
        printf("seis_data[X][1000] = %f\n", seis_data[X][1000]);
        printf("seis_data[Y][1000] = %f\n", seis_data[Y][1000]);
        for (i=0; i<2; i++) {
                free(seis_data[i]);
        }
}