Madagascar - Recent changes [en]

SCons

Sfomel — Wed, 08 Sep 2010 17:47:05 GMT

SConstruct commands:

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	</pre>		</pre>

-	Obviously, one could also run similar commands with a shell script. What makes SCons convenient is the way it behaves when we make changes in the input files or in the script. Let us change, for example, the mute velocity parameter in the second <tt>Flow</tt> command. You can do it with an editor or on the command line as	+	Obviously, one could also run similar commands with a shell script. What makes SCons convenient is the way it behaves when we make changes in the input files or in the script. Let us change, for example, the mute velocity parameter in the second <tt>Flow</tt> command. You can do that with an editor or on the command line as
	<pre>		<pre>
	sed -i s/v0=0.31/v0=0.32/ SConstruct		sed -i s/v0=0.31/v0=0.32/ SConstruct
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	/RSF/bin/vppen yscale=2 vpstyle=n gridnum=2,1 wind.vpl mute.vpl > Fig/denmark.vpl		/RSF/bin/vppen yscale=2 vpstyle=n gridnum=2,1 wind.vpl mute.vpl > Fig/denmark.vpl
	</pre>		</pre>
-	We can see that <tt>scons</tt> executes only the ~~part~~ of the data processing flow that ~~was~~ affected by the change. By keeping track of dependencies, SCons makes it easier to modify existing workflows without the need to rerun everything after each change.	+	We can see that <tt>scons</tt> executes only the parts of the data processing flow that were affected by the change. By keeping track of dependencies, SCons makes it easier to modify existing workflows without the need to rerun everything after each change.

	=== SConstruct commands ===		=== SConstruct commands ===
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	* '''Flow(<target[s]>,<source[s]>,<command>,[options])''' defines a rule for creating targets from sources by running the specified command through Unix shell. For example...		* '''Flow(<target[s]>,<source[s]>,<command>,[options])''' defines a rule for creating targets from sources by running the specified command through Unix shell. For example...

-	* '''~~Plot~~'''	+	{\|class="wikitable" align="center" cellspacing="0" border="1"
		+	\|-
		+	! colspan="3" style="background:#ffdead;"\|Flow options
		+	\|-
		+	\| '''Name''' \|\| '''Default''' \|\| '''Meaning'''
		+	\|-
		+	\| stdout \|\| 1 \|\| if output to standard out (0 for output to <tt>/dev/null</tt>, -1 for no output)
		+	\|-
		+	\| stdin \|\| 1 \|\| if take input from standard in (0 for no input)
		+	\|-
		+	\| rsfflow \|\| 1 \|\| if using <tt>Madagascar</tt> commands
		+	\|-
		+	\| suffix \|\| '.rsf' \|\| default suffix for output files
		+	\|-
		+	\| prefix \|\| 'sf' \|\| default prefix for programs
		+	\|-
		+	\| src_suffix \|\| '.rsf' \|\| default suffix for input files
		+	\|-
		+	\| split \|\| [] \|\| split the flow for data parallel processing
		+	\|-
		+	\| reduce \|\| 'cat' \|\| how to reduce the output from data parallel processing
		+	\|-
		+	\| local \|\| 0 \|\| if execute on the local node when using data parallel processing on a cluster
		+	\|}

-	* '''Result'''

-	* '''~~End~~'''	+	* '''Plot(<target>,<source[s]>,<command>,[options])''' or '''Plot(<target>,<command>,[options])''' is similar to '''Flow''' but generates a graphics file (Vplot file) instead of an RSF file. If the source file is not specified, it is assumed that the name of the output file (without the <tt>.vpl</tt> suffix) is the same as the name of the input file (without the <tt>.rsf</tt> suffix).
		+
		+	{\|class="wikitable" align="center" cellspacing="0" border="1"
		+	\|-
		+	! colspan="3" style="background:#ffdead;"\|Plot options
		+	\|-
		+	\| '''Name''' \|\| '''Default''' \|\| '''Meaning'''
		+	\|-
		+	\| suffix \|\| '.vpl' \|\| default suffix for the output file
		+	\|-
		+	\| vppen \|\| None \|\| additional options to pass to <tt>vppen</tt>
		+	\|-
		+	\| view \|\| None \|\| if set, show the output on the screen instead of saving it in a file
		+	\|}
		+
		+	* '''Result(<target>,<source[s]>,<command>,[options])''' or '''Result(<target>,<command>,[options])''' is similar to '''Plot''', only the output graphics file is put not in the current directory but in a separate directory (<tt>./Fig</tt> by default). The output is intended for inclusion in papers and reports.
		+
		+	{\|class="wikitable" align="center" cellspacing="0" border="1"
		+	\|-
		+	! colspan="3" style="background:#ffdead;"\|Result options
		+	\|-
		+	\| '''Name''' \|\| '''Default''' \|\| '''Meaning'''
		+	\|-
		+	\| suffix \|\| '.vpl' \|\| default suffix for the output file
		+	\|}

-	~~=== Default~~ targets ~~===~~	+	* '''End()''' takes no arguments and signals the end of data processing rules. It provides the following targets, which operate on all previously specified '''Result''' figures.
		+	** '''scons view''' displays the resuts on the screen.
		+	** '''scons print''' sends the results to the printer (specified with '''PSPRINTER''' environmental variable).
		+	** '''scons lock''' copies the results to a location inside the '''DATAPATH''' tree.
		+	** '''scons test''' compares the previously "locked" results with the current results and aborts with an error in case of mismatch.

	=== Command-line options ===		=== Command-line options ===

Sandbox

Nick — Sat, 04 Sep 2010 05:28:51 GMT

Brochure:

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	The intent is to provide a middle ground between "fragment of useful information stranded in a forum post/in author's head" and "finished page ready for being posted to the world with pride". This sort of information benefits much more from collaborative editing than finished pages that are incrementally improved after creation.		The intent is to provide a middle ground between "fragment of useful information stranded in a forum post/in author's head" and "finished page ready for being posted to the world with pride". This sort of information benefits much more from collaborative editing than finished pages that are incrementally improved after creation.

-	=~~Pages under construction~~=	+	=Brochure=
-	* [[Manual]]	+	For being handed over at conferences, displayed at booths of institutions using it and contributing to it if they will, etc.
-	* [[Library Reference]]	+
-	* [[Parallel Computing]]	+	Purpose: Giving the users reasons why they should use Madagascar
-	* [[Madagascar ~~for non-seismologists]]~~	+
-	* [[Task-centric program list]]	+	The brochure is handled by the reader in two ways: most often, closed (so pages 1 and 6 are the most important), or opened and read in a manner similar to that of a book, in which case the order of pages is the one below:
-	* [[IP self-~~audit]]~~	+
-	* [[SU to ~~m8r dictionary]]~~	+	{\| border="1"
-	* [[~~SEPlib to m8r dictionary~~]]	+	\| 5
-	* [[~~Graphics development with vplot~~]]	+	\| 6
		+	\| 1
		+	\|-
		+	\| 2
		+	\| 3
		+	\| 4
		+	\|}
		+
		+	An example we can learn from – the SU brochure. It looks a bit dry though -- A brochure needs more graphics than that. Graphics may need to be in uniform tones, so as to not increase the cost of printing (glossy paper, photographic quality costs).
		+
		+	[[Image:SU brochure 1.jpg]]
		+
		+	[[Image:SU brochure 2.jpg]]

	=Info from the blog/mailing lists/forums=		=Info from the blog/mailing lists/forums=

Image:SU brochure 2.jpg

Nick — Sat, 04 Sep 2010 05:00:59 GMT

uploaded "[[Image:SU brochure 2.jpg]]"

New page

Guide to madagascar API

Nick — Thu, 02 Sep 2010 20:03:47 GMT

Python interface:

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	import numpy		import numpy
-	import rsf	+	import rsf.api as rsf

	par = rsf.Par()		par = rsf.Par()
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	<python>		<python>
	import numpy		import numpy
-	import rsf	+	import rsf.api as rsf
	</python>		</python>

-	The script starts with importing the <tt>numpy</tt> and	+	The script starts with importing the <tt>numpy</tt> module and the
-	<tt>rsf</tt> ~~modules~~.	+	<tt>rsf</tt> API.
	<python>		<python>
	par = rsf.Par()		par = rsf.Par()
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	<python>		<python>
-	import numpy, rsf	+	import numpy, rsf.api

-	input = rsf.Input('test.rsf')	+	input = rsf.api.Input('test.rsf')
	n1 = input.int("n1")		n1 = input.int("n1")
	n2 = input.int("n2")		n2 = input.int("n2")
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	<python>		<python>
	#!/usr/bin/env python		#!/usr/bin/env python
-	import rsf, numpy, sys, pylab	+	import rsf.api, numpy, sys, pylab

-	input = rsf.Input('test.rsf')	+	input = rsf.api.Input('test.rsf')
	n1 = input.int("n1")		n1 = input.int("n1")
	n2 = input.int("n2")		n2 = input.int("n2")

SCons

Sfomel — Wed, 01 Sep 2010 18:27:05 GMT

SConstruct commands:

←Older revision		Revision as of 18:27, 1 September 2010
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	env.Program('hello',['hello.c', 'main.c'])		env.Program('hello',['hello.c', 'main.c'])
	</python>		</python>
		+
		+	and produce something like
		+
		+	<pre>
		+	bash$ scons -Q
		+	gcc -o hello.o -c -Wall -g hello.c
		+	gcc -o main.o -c -Wall -g main.c
		+	gcc -o hello hello.o main.o
		+	</pre>
		+
		+	to compile the <tt>hello</tt> program from the source files <tt>hello.c</tt> and <tt>main.c</tt>.
		+
		+	<tt>Madagascar</tt> uses SCons to compile its programs from the source. The more frequent usage, however, comes from adopting SCons to manage data processing flows.

	== Data processing flows with <tt>rsf.proj</tt> ==		== Data processing flows with <tt>rsf.proj</tt> ==
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	\|}		\|}

-	=== Seismic Unix data processing flows with <tt>rsf.suproj</tt> ===	+	== Seismic Unix data processing flows with <tt>rsf.suproj</tt> ==

	== Document creation with <tt>rsf.tex</tt> ==		== Document creation with <tt>rsf.tex</tt> ==
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	== Book and report creation with <tt>rsf.book</tt> ==		== Book and report creation with <tt>rsf.book</tt> ==
		+
		+	=== SConstruct commands ===
		+
		+	* '''Book'''
		+
		+	* '''Papers'''
		+
		+	* '''End'''
		+
		+	=== Default targets ===