Annotation of /MITgcm_contrib/osse/README

last changed June 8, 2004

OBSERVATION SYSTEM SIMULATION EXPERIMENT

OSSE is an MITgcm configuration to simulate data assimilation with a
deterministic ensemble Kalman filter and a model of a rotating tank of
water with an ice bucket at the center.

INSTALLATION 

At the time of this writing, the OSSE requires MITgcm checkpoint48 to
compile and run.  MITgcm can be obtained from
<http://mitgcm.org/source_code.html>.  If downloading from the CVS
server, use the command

cvs co -r 'checkpoint48' MITgcm

in order to specify the correct version.  Read the instructions on the
the webpage before trying to use the CVS server.

The OSSE directory tree can be obtained from the MITgcm CVS repository
with the command

cvs co MITgcm_contrib/osse

The code and its revision history can be browsed at 

<http://dev.mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/osse/>

A good place to put the osse directory tree is in MITgcm/verification,
where examples and test examples of MITgcm configurations are kept.

CONTENTS

EnKF: empty

build: handy place to compile MITgcm

code: modifications to MITgcm to run in cyclindrical coordinates.  At
the time of this writing, it requires checkpoint48 to compile and run.

codemod: modification to MITgcm to run with checkpoint 54.  Not quite
ready for prime time.

da: location for ensemble members and initialization and input files 

input: initialization and input files for running MITgcm

filter: source and data files to run the data assimilation and Kalman
filter.

run: empty

utils: assorted Matlab m-files 


COMPILING AND TESTING THE MODEL

The following series of commands creates the MITgcm executable.  

From the MITgcm root:

cd verification/osse/build  
../../../tools/genmake -mods=../code  # creates makefile
make depend       # contructs Fortran code from model codebase
make              # makes executable mitgcmuv

Try a test run, while redirecting the standard output to a file.  The
input directory contains files that should be present in the working
directory when you run mitgcmuv.  Assuming that you compiled the 
MITgcm executable in the build/ directory, you would run 
``../build/mitgcmuv >& output.txt''  It is recommended that you copy the
contents of the directory input/ to a different directory for running 
-- mitgcmuv does not change them, but they can be lost in the multitudes 
of output files.

The data assimilation code is made by typing ``make'' in the filter
directory, which creates an executable named ``osse''.  

Before running osse, the initial ensemble needs to be set up by
running the mkens script in verification/osse/da.  mkens creates the
directories, symbolically links files necessary to run the model, and
copies in the initial ensemble files.  osse should be run from the
directory verification/osse/da/inits since it expects the ensemble
members to be one directory above.  It also expects to have in its
working directory the file iobsloc-003.txt, which contains the
locations of the observations.  This file is located in
verification/osse/da/inits.
1	afe	1.3	last changed June 8, 2004
2	afe	1.1
3	afe	1.3	OBSERVATION SYSTEM SIMULATION EXPERIMENT
4	afe	1.2
5	afe	1.3	OSSE is an MITgcm configuration to simulate data assimilation with a
6			deterministic ensemble Kalman filter and a model of a rotating tank of
7			water with an ice bucket at the center.
8	afe	1.1
9	afe	1.3	INSTALLATION
10	afe	1.1
11	afe	1.3	At the time of this writing, the OSSE requires MITgcm checkpoint48 to
12			compile and run. MITgcm can be obtained from
13			<http://mitgcm.org/source_code.html>. If downloading from the CVS
14			server, use the command
15
16			cvs co -r 'checkpoint48' MITgcm
17
18			in order to specify the correct version. Read the instructions on the
19			the webpage before trying to use the CVS server.
20
21			The OSSE directory tree can be obtained from the MITgcm CVS repository
22			with the command
23
24			cvs co MITgcm_contrib/osse
25
26			The code and its revision history can be browsed at
27
28			<http://dev.mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/osse/>
29
30			A good place to put the osse directory tree is in MITgcm/verification,
31			where examples and test examples of MITgcm configurations are kept.
32
33			CONTENTS
34
35	afe	1.6	EnKF: empty
36
37			build: handy place to compile MITgcm
38
39	afe	1.3	code: modifications to MITgcm to run in cyclindrical coordinates. At
40			the time of this writing, it requires checkpoint48 to compile and run.
41
42	afe	1.6	codemod: modification to MITgcm to run with checkpoint 54. Not quite
43			ready for prime time.
44
45			da: location for ensemble members and initialization and input files
46
47			input: initialization and input files for running MITgcm
48	afe	1.4
49	afe	1.3	filter: source and data files to run the data assimilation and Kalman
50			filter.
51	afe	1.4
52	afe	1.6	run: empty
53
54	afe	1.4	utils: assorted Matlab m-files
55
56
57	afe	1.6	COMPILING AND TESTING THE MODEL
58	afe	1.4
59			The following series of commands creates the MITgcm executable.
60
61			From the MITgcm root:
62
63	afe	1.5	cd verification/osse/build
64	afe	1.4	../../../tools/genmake -mods=../code # creates makefile
65			make depend # contructs Fortran code from model codebase
66			make # makes executable mitgcmuv
67
68			Try a test run, while redirecting the standard output to a file. The
69			input directory contains files that should be present in the working
70	afe	1.6	directory when you run mitgcmuv. Assuming that you compiled the
71			MITgcm executable in the build/ directory, you would run
72			``../build/mitgcmuv >& output.txt'' It is recommended that you copy the
73			contents of the directory input/ to a different directory for running
74			-- mitgcmuv does not change them, but they can be lost in the multitudes
75			of output files.
76	afe	1.4
77			The data assimilation code is made by typing ``make'' in the filter
78	afe	1.6	directory, which creates an executable named ``osse''.
79	afe	1.5
80			Before running osse, the initial ensemble needs to be set up by
81			running the mkens script in verification/osse/da. mkens creates the
82			directories, symbolically links files necessary to run the model, and
83			copies in the initial ensemble files. osse should be run from the
84			directory verification/osse/da/inits since it expects the ensemble
85			members to be one directory above. It also expects to have in its
86			working directory the file iobsloc-003.txt, which contains the
87			locations of the observations. This file is located in
88			verification/osse/da/inits.