Transtomo - Revision history

Tolumorayo: /* Build parameter files */

2017-08-30T21:40:17Z

Build parameter files

Tolumorayo: /* Build parameter files */

2017-08-30T21:33:22Z

Build parameter files

← Older revision		Revision as of 17:33, 30 August 2017
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	=Build parameter files=		=Build parameter files=
	'''Run [{{#filelink: single_job.sh}} ~~run_pytnonSbatch~~.sh] script, the single shell python caller, and the python code'''		'''Run [{{#filelink: single_job.sh}} run_pythonSbatch.sh] script, the single shell python caller, and the python code'''

	{{#fileanchor: ~~run_pytnonSbatch~~.sh}}		{{#fileanchor: run_pythonSbatch.sh}}
	<source lang=~~csh~~>		<source lang=bash>
	#!/bin/tcsh		#!/bin/tcsh
	#		#

Tolumorayo: /* Build parameter files */

2017-08-30T21:32:08Z

Build parameter files

← Older revision		Revision as of 17:32, 30 August 2017
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	{{#fileanchor: run_pytnonSbatch.sh}}		{{#fileanchor: run_pytnonSbatch.sh}}
	<source lang=~~tcsh~~>		<source lang=csh>
	#!/bin/tcsh		#!/bin/tcsh
	#		#
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	end		end
	</source>		</source>


	= Setting up parameter and data files=		= Setting up parameter and data files=

Tolumorayo at 21:31, 30 August 2017

2017-08-30T21:31:32Z

@@ Line 92: / Line 92: @@
 has been used. These two environment variables are absolutely crucial for
 compiling the mpi version of the code i.e. tomo mpi.
 = Setting up parameter and data files=

Tolumorayo: /* Setting up parameter and data files */

2017-08-28T23:18:17Z

Setting up parameter and data files

← Older revision		Revision as of 19:18, 28 August 2017
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	The First is the <code> <Input/Output-Data/Exhaust-directory> </code> that stores the input data, parameter files needed to start the <code>tomompi</code? code and results output generated after successful completion of the analysis. The datasets are organized by phase-velocity e.g. <code><Input/Output-Data/Exhaust-directory>/<folder> </code> where <code><folder></code> represents the 22 phase velocity datasets: L05-L40 and R05-R40. Here is a listing of the data directory:		The First is the <code> <Input/Output-Data/Exhaust-directory> </code> that stores the input data, parameter files needed to start the <code>tomompi</code? code and results output generated after successful completion of the analysis. The datasets are organized by phase-velocity e.g. <code><Input/Output-Data/Exhaust-directory>/<folder> </code> where <code><folder></code> represents the 22 phase velocity datasets: L05-L40 and R05-R40. Here is a listing of the data directory:

	* <code><Input/Output-Data/Exhaust-directory>/<folder></code?		* <code><Input/Output-Data/Exhaust-directory>/<folder></code>
	Holds the important observation data, source-receiver configuration and path location files e.g. observations.dat, paths.dat, sources.dat, etc.		Holds the important observation data, source-receiver configuration and path location files e.g. observations.dat, paths.dat, sources.dat, etc.

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	ags.		ags.

	* <run-shell-execute-directory>/tomoParamMPI.nml:		* <code> <run-shell-execute-directory>/tomoParamMPI.nml: </code>
	Parameter ~~�le~~ used by tomo single.sh for setting up all the required ~~in-~~		Parameter file used by tomo single.sh for setting up all the required input parameters used by tomo mpi. It sets up parameters like file paths, number of steps, distribution range, perturbation parameters, seed values for probability distribution, state of starting models etc. Note that we provide another parameter file: <code><run-shell-execute-directory>/rstrtTomoParamMPI.nml </code>for setting up parameters if the chain is to be restart from a specified initial model state (typically a high-resolution near-mean state).
	~~put~~ parameters used by tomo mpi. It sets up parameters like ~~�le~~ paths,
	number of steps, distribution range, perturbation parameters, seed values
	for probability distribution, state of starting models etc. Note that we
	provide another parameter ~~�le~~:
	<run-shell-execute-directory>/rstrtTomoParamMPI.nml for setting
	up parameters if the chain is to be restart from a ~~speci�ed~~ initial model
	state (typically a high resolution near-mean state).

	* <run-shell-execute-directory>/dwnldRslts.sh:		* <code><run-shell-execute-directory>/dwnldRslts.sh: </code>
	Script used to download results data from the remote deepthought2 ~~clus-~~		Script used to download results data from the remote deepthought2 cluster machine to the <outputData-prjDir> on the local machine for post-processing and visualization.
	~~ter~~ machine to the <outputData-prjDir> on the local machine for post-
	processing and visualization.

Tolumorayo: /* Setting up parameter and data files */

2017-08-28T23:13:32Z

Setting up parameter and data files

← Older revision		Revision as of 19:13, 28 August 2017
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	Now that the libraries and executable (binaries) environment is set up, the next stage is to set up the input parameters and the data environment necessary to stage the code on the cluster. There are two directories here:		Now that the libraries and executable (binaries) environment is set up, the next stage is to set up the input parameters and the data environment necessary to stage the code on the cluster. There are two directories here:

	The First is the <code> <Input/Output-Data/Exhaust-directory> </code> that stores the input data, parameter ~~�les~~ needed to start the ~~tomo mpi~~ code and results output generated after successful completion of the analysis. The datasets are organized by phase-velocity e.g. <Input/Output-Data/Exhaust-directory>/<folder> where <folder> represents the 22 phase velocity datasets: L05-L40 and R05-R40. Here is a listing of the data directory:		The First is the <code> <Input/Output-Data/Exhaust-directory> </code> that stores the input data, parameter files needed to start the <code>tomompi</code? code and results output generated after successful completion of the analysis. The datasets are organized by phase-velocity e.g. <code><Input/Output-Data/Exhaust-directory>/<folder> </code> where <code><folder></code> represents the 22 phase velocity datasets: L05-L40 and R05-R40. Here is a listing of the data directory:

	* <Input/Output-Data/Exhaust-directory>/<folder>		* <code><Input/Output-Data/Exhaust-directory>/<folder></code?
	Holds the important observation data, source-receiver ~~con�guration~~ and		Holds the important observation data, source-receiver configuration and path location files e.g. observations.dat, paths.dat, sources.dat, etc.
	path location ~~�les~~ e.g. observations.dat, paths.dat, sources.dat, etc.

	* <Input/Output-Data/Exhaust-directory>/<folder>/results		* <code><Input/Output-Data/Exhaust-directory>/<folder>/results </code>
	Stores the saved output after completed run e.g. output mean, ~~voroni~~-		Stores the saved output after completed run e.g. output mean, Voronoi-partition location and velocity history, misfit history, model save state, etc.)
	partition location and velocity history, ~~mis�t~~ history, model save state,
	etc.)

	* <Input/Output-Data/Exhaust-directory>/<folder>/restart		* <code> <Input/Output-Data/Exhaust-directory>/<folder>/restart </code>
	Stores the model states (i.e. high resolution tesselated model states or		Stores the model states (i.e. high resolution tesselated model states or intermediate model states) to be used in the case of a restart-able chain.
	intermediate model states) to be used in the case of a restart-able chain.

	The second is the <run-shell-execute-directory> where the shell SBATCH		The second is the <run-shell-execute-directory> where the shell <code>SBATCH</code> scripts for staging the code on the cluster Here are the files in this directory:
	scripts for staging the code on the cluster Here are the ~~�les~~ in this directory:		* <code><run-shell-execute-directory>/tomo sbatch.sh </code>:
	* <run-shell-execute-directory>/tomo sbatch.sh:
	Script runs tomo mpi for all 22 phase velocity maps. You can tweak this		Script runs tomo mpi for all 22 phase velocity maps. You can tweak this script to run single maps, specify an initial number of partitions, or to determine if you want to restart chains from set stages or particular input models. This is actually a wrapper script to tomo single.sh that does all the heavy lifting.
	script to run single maps, specify initial number of partitions, or to ~~de-~~		* <code><run-shell-execute-directory>/tomo single.sh </code>:
	~~termine~~ if you want to restart chains from set stages or particular ~~imput~~
	models. This is actually a wrapper script to tomo single.sh that does
	all the heavy lifting.
	* <run-shell-execute-directory>/tomo single.sh:
	Script used by tomo sbatch.sh above for running the tomo mpi on single		Script used by tomo sbatch.sh above for running the tomo mpi on single
	phase velocity maps, it also sets up all the required environment variables,		phase velocity maps, it also sets up all the required environment variables,

Tolumorayo: /* Running tomo mpi with parameter/data �files */

2017-08-28T23:10:12Z

Running tomo mpi with parameter/data �files

@@ Line 93: / Line 93: @@
 compiling the mpi version of the code i.e. tomo mpi.
-= Running tomo mpi with parameter/data �files =
+= Setting up parameter and data files=
-Tolulope Olugboji (oluboji@umd.edu)
+Now that the libraries and executable (binaries) environment is set up, the next stage is to set up the input parameters and the data environment necessary to stage the code on the cluster. There are two directories here:

Tolumorayo at 23:05, 28 August 2017

2017-08-28T23:05:07Z

← Older revision		Revision as of 19:05, 28 August 2017
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	Work is also ongoing to extend the code to invert for azimuthal anisotropy <code>transtomo</code>. This documentation will provide details on this update when it's available. Feel free to contact me for any other questions on how to use		Work is also ongoing to extend the code to invert for azimuthal anisotropy <code>transtomo</code>. This documentation will provide details on this update when it's available. Feel free to contact me for any other questions on how to use
	this code and set it up on the deepthought2 cluster here at the University of Maryland.		this code and set it up on the deepthought2 cluster here at the University of Maryland.

			= Directory Listing =
			Here is a listing of the important directories that need to be set up on the
			cluster to organize and set things up.

			<source>
			1 <Home􀀀directory>
			2 /homes/username(olugboji)
			3 <Code􀀀data􀀀directory>
			4 /lustre/username(olugboji)/transdimsurfacewavetomography/
			5 <Code􀀀binary􀀀directory>
			6 /home/deepthought2/username(olugboji)/bin/
			7 <Run􀀀shell􀀀execute􀀀directory>
			8 /homes/username(olugboji)/binShell
			9 <Input/Output􀀀Data/Exhaust􀀀directory>
			10 /lustre/username(olugboji)/tomoParamFiles/
			11 <rjMcMC􀀀library􀀀directory>
			12 /home/deepthought2/olugboji
			13
			14 % Data that need to be backed up from the local store to the ...
			cluster directory ..
			15
			16 <local􀀀prjDir>
			17 :/Documents/UMD Seismo/
			18 <local􀀀code􀀀store>
			19 <local􀀀prjDir>iEarthSoftware/transdimsurfacewavetomography
			20 <local􀀀data􀀀store>
			21 <local􀀀prjDir>transdimUSANT/All Ta Sta/
			22 <local􀀀restrt􀀀models>
			23 <local􀀀prjDir>transdimUSANT/All Ta Sta/VorModels/inModels
			24
			25 %.. Data from cluster exhaust to local directory
			26 0.11
			27 0.22
			</source>


			= Login into deepthought2 =
			<code> ssh -X username@login.deepthought2.umd.edu </code>


			= Updating and compiling source code =
			The followng are the sequence of steps necessary to compile the and install the
			required libraries and other source code �les:
			2
			• Update the <code-data-directory> with the latest version of the source
			code (available on <local-prjDir> or @ <gitHub directory> (see direc-
			tory listing in 2 above)
			• Compile and install the RJMCMC library (<code-data-directory>/RJMCMC 1.0.11/)
			also see README �le. On the cluster this involves the following steps:
			> cd path to <code-data-directory>/RJMCMC 1.0.11/
			> module load openmpi
			> ./configure --prefix=<rjMcMC-library-directory>
			> make
			> make install
			This is the only way to install the RJMCMC library on the cluster. Attempt-
			ing to do a sudo make install will fail since the user does not have root
			access on the cluster.
			• On successfull install of the RJMCMC library, the user can then go ahead to
			compile and install the tomo mpi and tomo code into the <code-binary-directory>.
			It is from this directory that the SBATCH shell scripts in <run-shell-execute-directory>
			load the binary executables. Here are the steps to do this:
			> cd path to <Code-data-directory>/tomo-0.9.16 2
			> setenv PKG CONFIG PATH /home/deepthought2/olugboji/lib/pkg-config
			> module load openmpi
			> ./configure -RJMCMC FLAGS=-I<rjMcMC-library-directory>
			-I<$MPI INC> - RJMCMC LIBS=-L<$MPI LIB> -lm -lmpi -lrjmcmc
			> make
			> cp tomo* <code-binary-directory>
			*Note: if the configure command fails, then just run the command with
			empty values for the parameter
			ags RJMCMC FLAGS and RJMCMC LIBS, and
			then go into the makefile and update the relevant
			ags with the speci�ed
			include and load
			ags. Also note that the two MPI environment variables:
			$MPI INC and $MPI LIB are only set after the module load mpi command
			has been used. These two environment variables are absolutely crucial for
			compiling the mpi version of the code i.e. tomo mpi.

			= Running tomo mpi with parameter/data �files =
			Now that the libraries and executable (binaries) environment is set up, the next stage is setting up the input parameters and the data environment necessary to stage the code on the cluster. There are two directories here: First is the
			Input/Output-Data/Exhaust-directory and the second is the

			Tolulope Olugboji (oluboji@umd.edu)

Tolumorayo at 23:01, 28 August 2017

2017-08-28T23:01:11Z

← Older revision		Revision as of 19:01, 28 August 2017
Line 5:		Line 5:

	= Overview =		= Overview =
	This documentation outlines steps for compiling and running the extended version of transtomo on the deepthought2 cluster at the University of Maryland. This version of transtomo is a personal adaptation and improvement of the freely distributed copy on [http://www.iearth.org.au/ iEarth geophysics scientific software]. This version includes the following improvements:		This documentation outlines steps for compiling and running the extended version of <code>transtomo</code> on the deepthought2 cluster at the University of Maryland. This version of <code>transtomo</code> is a personal adaptation and improvement of the freely distributed copy on [http://www.iearth.org.au/ iEarth geophysics scientific software]. This version includes the following improvements:

	* Functionality to load, initialize, and restart chains from models stored in ASCII files		* Functionality to load, initialize, and restart chains from models stored in ASCII files
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	* Functionality to lock cells that do not participate in the update of travel time data		* Functionality to lock cells that do not participate in the update of travel time data

	Work is also ongoing to extend the code to invert for azimuthal anisotropy ~~transtomoAni~~. This documentation will provide details on this update when it's available. Feel free to contact me for any other questions on how to use		Work is also ongoing to extend the code to invert for azimuthal anisotropy <code>transtomo</code>. This documentation will provide details on this update when it's available. Feel free to contact me for any other questions on how to use
	this code and set it up on the deepthought2 cluster here at the University of Maryland.		this code and set it up on the deepthought2 cluster here at the University of Maryland.

Tolumorayo at 22:59, 28 August 2017

2017-08-28T22:59:40Z

← Older revision		Revision as of 18:59, 28 August 2017
Line 5:		Line 5:

	= Overview =		= Overview =
	This documentation outlines steps for compiling and running the extended version of transtomo on the deepthought2 cluster at the University of Maryland.		This documentation outlines steps for compiling and running the extended version of transtomo on the deepthought2 cluster at the University of Maryland. This version of transtomo is a personal adaptation and improvement of the freely distributed copy on [http://www.iearth.org.au/ iEarth geophysics scientific software]. This version includes the following improvements:

	~~This version of transtomo is a personal adaptation and improvement of the freely distributed copy on iEarth geophysics scientific software. This version~~		* Functionality to load, initialize, and restart chains from models stored in ASCII files
	~~includes the following improvements:~~		* Functionality to resample and save full chain history in ASCII files

	* Functionality to load, initialize, and restart chains from models stored in ~~ascii~~ files
	* Functionality to resample and save full chain history in ~~ascii~~ files
	* Functionality to lock cells that do not participate in the update of travel time data		* Functionality to lock cells that do not participate in the update of travel time data

	Work is also ongoing to extend the code to invert for azimuthal anisotropy transtomoAni. This documentation will provide details on this update when it's available. Feel free to contact me for any other questions on how to use		Work is also ongoing to extend the code to invert for azimuthal anisotropy transtomoAni. This documentation will provide details on this update when it's available. Feel free to contact me for any other questions on how to use
	this code and set it up on the deepthought2 cluster here at the University of Maryland.		this code and set it up on the deepthought2 cluster here at the University of Maryland.