CyberShake Code Base - Revision history

Scottcal: /* DirectSynth */

2025-11-26T19:57:56Z

DirectSynth

Scottcal: /* DirectSynth */

2025-11-26T19:46:28Z

DirectSynth

Scottcal: /* File types */

2025-11-26T19:44:04Z

File types

Scottcal at 16:34, 25 September 2024

2024-09-25T16:34:03Z

Show changes

Scottcal: /* RupGen-api */

2024-08-21T17:45:31Z

RupGen-api

Scottcal: /* Dependencies */

2024-08-21T17:41:22Z

Dependencies

Scottcal: /* Dependencies */

2024-08-21T17:13:50Z

Dependencies

Scottcal: /* Getpar */

2024-08-21T17:12:09Z

Getpar

Scottcal: /* Dependencies */

2024-08-21T17:06:50Z

Dependencies

Scottcal: /* Code Installation */

2024-08-21T17:03:22Z

Code Installation

@@ Line 552: / Line 552: @@
 === DirectSynth ===
-DirectSynth is the code we currently use to perform the post-processing.  For historical reasons, all of the codes used for CyberShake post-processing are documented here: [https://scec.usc.edu/it/Post-processing_options CyberShake post-processing options] (login required).
+DirectSynth is the code we currently use to perform the post-processing.  For historical reasons, all of the codes used for CyberShake post-processing are documented here: [https://scec.usc.edu/it/Post-processing_options CyberShake post-processing options] (login required).  The current version uses the [[Rupture_Variation_Generator_v5.5.2|Graves and Pitarka (2022) rupture generator]], RupGen-v5.5.2.
 <b>Purpose:</b> To perform reciprocity calculations and produce seismograms, intensity measures, and duration measures.
@@ Line 567: / Line 567: @@
 <b>Author:</b> Scott Callaghan, original seismogram synthesis code by Rob Graves, X and Y component PSA code by David Okaya, RotD code by Christine Goulet
-<b>Dependencies:</b> [[CyberShake Code Base#Getpar | Getpar]], [[CyberShake Code Base#libcfu | libcfu]], [[CyberShake Code Base#RupGen-api-v3.3.1 | RupGen-api-v3.3.1, [[CyberShake Code Base#FFTW | FFTW]], [[CyberShake Code Base#libmemcached | libmemcached]] (optional) and [[CyberShake Code Base#memcached | memcached]] (optional)
+<b>Dependencies:</b> [[CyberShake Code Base#Getpar | Getpar]], [[CyberShake Code Base#libcfu | libcfu]], [[CyberShake Code Base#RupGen-api-v5.5.2 | RupGen-api-v5.5.2, [[CyberShake Code Base#FFTW | FFTW]], [[CyberShake Code Base#libmemcached | libmemcached]] (optional) and [[CyberShake Code Base#memcached | memcached]] (optional)
 <b>Executable chain:</b>
-   direct_synth_v3.3.1.py (current version, uses the Graves & Pitarka (2014) rupture generator)
+   direct_synth.py
      utils/pegasus_wrappers/invoke_memcached.sh
        memcached
@@ Line 580: / Line 580: @@
 ##BASE_DIR should point to the top-level CyberShake install directory
 ##LIBCFU should point to the libcfu install directory
-##V3_3_1_RG_LIB should point to the RupGen-api-3.3.1/lib directory
+##CUR_RG_LIB should point to the RupGen-api-<version>/lib directory
 ##LDLIBS should have the correct paths to the libcfu and libmemcached lib directories
-##V3_3_1_RG_INC should point to the RupGen-api-3.3.1/include directory
+##CUR_RG_INC should point to the RupGen-api-<version>/include directory
 ##IFLAGS should have the correct paths to the libcfu and libmemcached include directories
-#Run 'make direct_synth_v3.3.1' in DirectSynth/src.
+#Run 'make direct_synth' in DirectSynth/src.
-You will also need to edit the hard-coded paths to memcached in direct_synth_v3.3.1.py, in lines 15 and 24.
+direct_synth.py has an if statement which, based on the wrapper to MPI on the target system (such as 'mpiexec', 'ibrun', or 'jsrun'), will set up the execution string.  You may need to add a new section of the if statement if a new MPI wrapper is used.  This is also the place to change the number of cores used per node.  You may also need to add hard-coded paths to memcached here.
 <b>Usage:</b>
 <pre>
-direct_synth_v3.3.1.py
+direct_synth.py
   stat=<site short name>
   slat=<site lat>
@@ Line 597: / Line 597: @@
   sgt_handlers=<number of SGT handler processes; must be enough for the SGTs to be read into memory>
   debug=<print logs for each process; 1 is yes, 0 no>
-  max_buf_mb=<buffer size in MB for each worker to use for storing SGT information>
+  max_buf_mb=<buffer size in MB for each worker to use for storing SGT information; 512 recommended>
   rupture_spacing=<'uniform' or 'random' hypocenter spacing>
   ntout=<nt for seismograms>
   dtout=<dt for seismograms>
   rup_list_file=<input file containing ruptures to process>
   sgt_xfile=<input SGT X file>
   sgt_yfile=<input SGT Y file>
   x_header=<input SGT X header>
   y_header=<input SGT Y header>
   det_max_freq=<maximum frequency of deterministic part>
   stoch_max_freq=<maximum frequency of stochastic part>
@@ Line 611: / Line 614: @@
   run_rotd=<'1' to run RotD calculations, '0' to not>
   run_durations=<'1' to run duration calculation, '0' to not>
-  simulation_out_pointsX=<'2', the number of components>
+  run_period_durations=<'1' to run period duration calculations, '0' to not>
   simulation_out_pointsY=1
   simulation_out_timesamples=<same as ntout>

@@ Line 625: / Line 625: @@
 <b>Typical run configuration:</b> Parallel, typically on 3840 processors; for 750 GB SGTs with ~7000 ruptures, takes about 12 hours.
-<b>Input files:</b> [[CyberShake_Code_Base#RWG SGT|RWG SGT]], [[CyberShake_Code_Base#SGT header file|SGT headers]], [[CyberShake_Code_Base#rupture list file|rupture list file]], rupture geometry files
+<b>Input files:</b> [[CyberShake_Code_Base#RWG SGT|RWG SGT]], [[CyberShake_Code_Base#SGT header file|SGT headers]], [[CyberShake_Code_Base#rupture list file|rupture list file]], [[CyberShake_Code_Base#rupture variation info file|rupture variation info file]], [[CyberShake_Rupture_Files|rupture geometry files]]
 <b>Output files:</b> [[Accessing_CyberShake_Seismograms#Reading_Seismogram_Files | Seismograms]], [[Accessing_CyberShake_Peak_Acceleration_Data#Reading_Peak_Acceleration_Files | PSA files]], [[Accessing_CyberShake_Peak_Acceleration_Data#Reading_Peak_Acceleration_Files | RotD files]], [[Accessing_CyberShake_Duration_Data | Duration files]]

← Older revision		Revision as of 19:44, 26 November 2025
Line 1,760:		Line 1,760:

	Used by: Sub Stoch DAX generator, to add these values as command-line arguments to HF Synth and LF Site Response jobs.		Used by: Sub Stoch DAX generator, to add these values as command-line arguments to HF Synth and LF Site Response jobs.
		+
		+	=== rupture list file ===
		+
		+	Purpose: Contains a list of all the ruptures for which low-frequency seismograms should be synthesized. This file is used to construct the tasks in DirectSynth. The number of rows, columns, and magnitude are included because DirectSynth uses this information to determine how much memory the tasks will use. This file is constructed at abstract workflow creation time.
		+
		+	Filename convention: rupture_file_list_<site>_<run_id>
		+
		+	Format: Text format, with the number of ruptures and then 1 line per rupture:
		+
		+	<pre>
		+	<number of ruptures N>
		+	<rupture geometry filename 1> <number of hypocenters> <number of slips per hypocenter> <number of rows in the rupture geometry> <number of columns in the rupture geometry> <magnitude>
		+	<rupture geometry filename 2> <number of hypocenters> <number of slips per hypocenter> <number of rows in the rupture geometry> <number of columns in the rupture geometry> <magnitude>
		+	...
		+	<rupture geometry filename N> <number of hypocenters> <number of slips per hypocenter> <number of rows in the rupture geometry> <number of columns in the rupture geometry> <magnitude>
		+	</pre>
		+
		+	Used by: DirectSynth
		+
		+	=== rupture variation info file ===
		+
		+	Purpose: This file provides the rvfrac (rupture velocity speed as a fraction of shear wave velocity) and random seed for each rupture variation. It is constructed at abstract workflow creation time, using values from the database. It is highly recommended that these values are stored somewhere for reproducibility, and the same values should be used for all sites so that the rupture variations are the same for all sites.
		+
		+	Filename convention: rvfrac_seed_values_<site>_<run_id>
		+
		+	Format: Text format, with the number of rupture variations and then 1 line per rupture variation:
		+
		+	<pre>
		+	<number of rupture variations N>
		+	<source ID 1> <rupture ID 1> <rupture variation ID 1> <rvfrac> <random seed>
		+	<source ID 2> <rupture ID 2> <rupture variation ID 2> <rvfrac> <random seed>
		+	...
		+	<source ID N> <rupture ID N> <rupture variation ID N> <rvfrac> <random seed>
		+	</pre>
		+
		+	Used by: DirectSynth, when linked with RupGen-v5.5.2 or later
		+

	=== BBP 1D Velocity file ===		=== BBP 1D Velocity file ===

@@ Line 1,948: / Line 1,948: @@
 Special installation instructions:
 #If you want memcached support, edit the makefile in RuptureCodes/RupGen-api-5.5.2/src to uncomment lines 19-21 and edit line 19 to point to the libmemcached install directory.  You'll need to do the same to RuptureCodes/RupGen-api-5.5.2/src/GenRandV5.0/makefile, lines 35-37.
 #You may need to edit CFLAGS in RuptureCodes/RupGen-api-5.5.2/src/GenRandV5.5.2/makefile (lines 21-23) to point to the FFTW path; whether or not this is needed depends on the particular system.

← Older revision		Revision as of 17:41, 21 August 2024
Line 1,951:		Line 1,951:
	#You may need to edit CFLAGS in RuptureCodes/RupGen-api-5.5.2/src/GenRandV5.5.2/makefile (lines 21-23) to point to the FFTW path; whether or not this is needed depends on the particular system.		#You may need to edit CFLAGS in RuptureCodes/RupGen-api-5.5.2/src/GenRandV5.5.2/makefile (lines 21-23) to point to the FFTW path; whether or not this is needed depends on the particular system.
	#Run 'make' in RupGen-api-5.5.2 to make the librupgen.a library.		#Run 'make' in RupGen-api-5.5.2 to make the librupgen.a library.
		+
		+	=== SCEC Broadband Platform ===
		+
		+	Purpose: To generate high-frequency stochastic seismograms for broadband CyberShake runs.
		+
		+	How to obtain: Follow installation instructions at https://github.com/SCECcode/bbp .

@@ Line 1,940: / Line 1,940: @@
 Special installation instructions: Sometimes installing can be a challenge, because it can't find the memcached install.  You may have to set the path to memcached either as an argument to configure, or you may even need to edit the configuration and makefiles directory.  Install into the utils directory.
-=== RupGen-api-v3.3.1 ===
+=== RupGen-api ===
-Purpose: To generate rupture variations from a rupture geometry for a given hypocenter and slip, using the Graves & Pitarka (2014) rupture generator (version 3.3.1).
+Purpose: To generate rupture variations from a rupture geometry for a given hypocenter and slip using the Graves & Pitarka rupture generator.  The current version is 5.5.2.
-How to obtain: Check out from http://source.usc.edu/svn/cybershake/import/trunk/RuptureCodes/RupGen-api-3.3.1 .
+How to obtain: Check out from https://github.com/SCECcode/cybershake-core/tree/main/RuptureCodes/RupGen-api-5.5.2 .
 Special installation instructions:
-#If you want memcached support, edit the makefile in RuptureCodes/RupGen-api-3.3.1/src to uncomment lines 19-21 and edit line 19 to point to the libmemcached install directory.  You'll need to do the same to RuptureCodes/RupGen-api-3.3.1/src/GenRandV3.3.1/makefile, lines 35-37.
+#If you want memcached support, edit the makefile in RuptureCodes/RupGen-api-5.5.2/src to uncomment lines 19-21 and edit line 19 to point to the libmemcached install directory.  You'll need to do the same to RuptureCodes/RupGen-api-5.5.2/src/GenRandV5.0/makefile, lines 35-37.
-#You may need to edit CFLAGS in RuptureCodes/RupGen-api-3.3.1/src/GenRandV3.3.1/makefile (lines 21-23) to point to the FFTW path; whether or not this is needed depends on the particular system.
+#You may need to edit CFLAGS in RuptureCodes/RupGen-api-5.5.2/src/GenRandV5.5.2/makefile (lines 21-23) to point to the FFTW path; whether or not this is needed depends on the particular system.
-#Run 'make' in RupGen-api-3.3.1 to make the librupgen.a library.
+#Run 'make' in RupGen-api-5.5.2 to make the librupgen.a library.

@@ Line 1,884: / Line 1,884: @@
 Purpose: A library written in C which enables parsing of key-value command-line parameters, and enforcement of required parameters.  Rob Graves uses it in his codes.
-How to obtain: Rob supplied a copy; it is in the CyberShake repository at http://source.usc.edu/svn/cybershake/import/trunk/Getpar/ .
+How to obtain: Rob supplied a copy; it is in the CyberShake repository at https://github.com/SCECcode/cybershake-core/tree/main/Getpar .
 Special installation instructions: Run 'make' in Getpar/getpar/src; this will make the library, libget.a, and install it in the lib directory, where CyberShake codes will expect it.

@@ Line 1,890: / Line 1,890: @@
 === MySQLdb ===
-Purpose: MySQL bindings for Python 2.
+This library has been deprecated in favor of pymysql.
-How to obtain: https://sourceforge.net/projects/mysql-python/ .  Documentation is at http://mysql-python.sourceforge.net/MySQLdb.html .
+=== pymysql ===
-Special installation instructions: Standard python install (python setup.py build; python setup.py install).  Many clusters have MySQLdb installed in one of their python installations, but it might take some experimenting to find it.  For example, the bwpy module on Blue Waters does NOT have it installed, but if you run 'unload module bwpy' and try again, you will find it.
+Purpose: MySQL bindings for Python.
 === UCVM ===

← Older revision		Revision as of 17:03, 21 August 2024
Line 16:		Line 16:

	Most of the codes below contain a main directory. Inside that is a bin directory, with binaries; a src directory with code requiring compilation; and wrappers, in the main directory.		Most of the codes below contain a main directory. Inside that is a bin directory, with binaries; a src directory with code requiring compilation; and wrappers, in the main directory.
		+
		+	If you are looking for compilation instructions, a general guide is available [[CyberShake compilation guide \| here]].

	=== Configuration file ===		=== Configuration file ===