Contents 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	last changed June 8, 2004
2
3	OBSERVATION SYSTEM SIMULATION EXPERIMENT
4
5	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
9	INSTALLATION
10
11	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	EnKF: empty
36
37	build: handy place to compile MITgcm
38
39	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	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
49	filter: source and data files to run the data assimilation and Kalman
50	filter.
51
52	run: empty
53
54	utils: assorted Matlab m-files
55
56
57	COMPILING AND TESTING THE MODEL
58
59	The following series of commands creates the MITgcm executable.
60
61	From the MITgcm root:
62
63	cd verification/osse/build
64	../../../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	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
77	The data assimilation code is made by typing ``make'' in the filter
78	directory, which creates an executable named ``osse''.
79
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.