Annotation of /MITgcm_contrib/LCML/cpl_aim+ocn/README

*****VERY IMPORTANT*****
The setbuildenv and setrunenv files need to be in the users' home
directory. They need to be modified for other compilers/libraries.
Eventually LEGEND will prepare them as well.

Load up Legend

Go to File->Open, put in 
/net/lagoon/scratch2/ce107/MITgcm_contrib/LCML/cpl_aim+ocn
or whereever you have untared/cvs co-ed the root directory
and choose cpl_aim+ocn.xml

To build the code:

A) Go to the top level menu and 
1) decide on the directory names.
2) run the script

B) Go deep into the Atmosphere build menu and 
1) set the choices for package, options etc in every case.
2) save the file in every case

C) Configure the Atmosphere genmake2 menu and run genmake2. This takes
a while.

D) Go up to the Atmosphere build menu, decide on the variables and 
run the script

E) Go deep into the Ocean build menu and 
1) set the choices for package, options etc in every case.
2) save the file in every case

F) Configure the Ocean genmake2 menu and run genmake2

G) Go up to the Ocean build menu, decide on the variables and 
run the script. This takes a while.

B) Go deep into the Coupler build menu and 
1) set the choices for Parameters in every case.
2) save the file in every case

C) Configure the Coupler genmake2 menu and run genmake2

D) Go up to the Coupler build menu, decide on the variables and 
run the script. This doesn't take too long.

To run the code:

A) Go deep into each menu and edit the data and execution parameter
files. Save them in the respective directories (savedirs) that you
sent in the top menu. 

*****VERY IMPORTANT*****
To retrieve values that work for this setup you can either import each
file's exported values (the names are self explanatory) or import a
top to bottom export for the runtime called
exportFromCpl_aim+ocn_runtime.xml

B) Go to the runtime menu for each component and run the script to
prepare the run directories 

C) To to the top runtime menu, edit the options if necessary and run
the script. 

LEGEND current faux-pass:
a) LEGEND is temperamental as of late. It seems to be far less so with
IBM java than with Sun Java so on batsi.mit.edu for example use module
add jdk/ibm/1.5.0 
java -jar Legend.jar
etc.
Available modules on batsi are seen as always by 
module avail
b) If you do not want to see PBS output that makes no sense do not
forget to remove the default PBS monitor from the options under
Tools. On the other hand this way you get a nice popup when an action
finishes unlike the standard case when you have to look for any
output.  
c) You can always edit a script before execution in the window it
appears in; Sun Java sometimes gets horribly worked up over it and
LEGEND needs to be killed.  
d) After an import the visual on the use box for a structure becomes
unticked even though it is actually true. The file output is correct
but the table display is misleading.
1	ce107	1.2	***VERY IMPORTANT***
2			The setbuildenv and setrunenv files need to be in the users' home
3			directory. They need to be modified for other compilers/libraries.
4			Eventually LEGEND will prepare them as well.
5
6			Load up Legend
7
8			Go to File->Open, put in
9			/net/lagoon/scratch2/ce107/MITgcm_contrib/LCML/cpl_aim+ocn
10			or whereever you have untared/cvs co-ed the root directory
11			and choose cpl_aim+ocn.xml
12
13	ce107	1.1	To build the code:
14
15			A) Go to the top level menu and
16			1) decide on the directory names.
17			2) run the script
18
19			B) Go deep into the Atmosphere build menu and
20			1) set the choices for package, options etc in every case.
21			2) save the file in every case
22
23	ce107	1.2	C) Configure the Atmosphere genmake2 menu and run genmake2. This takes
24			a while.
25	ce107	1.1
26			D) Go up to the Atmosphere build menu, decide on the variables and
27			run the script
28
29			E) Go deep into the Ocean build menu and
30			1) set the choices for package, options etc in every case.
31			2) save the file in every case
32
33			F) Configure the Ocean genmake2 menu and run genmake2
34
35			G) Go up to the Ocean build menu, decide on the variables and
36	ce107	1.2	run the script. This takes a while.
37	ce107	1.1
38			B) Go deep into the Coupler build menu and
39			1) set the choices for Parameters in every case.
40			2) save the file in every case
41
42			C) Configure the Coupler genmake2 menu and run genmake2
43
44	ce107	1.2	D) Go up to the Coupler build menu, decide on the variables and
45			run the script. This doesn't take too long.
46	ce107	1.1
47			To run the code:
48
49	ce107	1.2	A) Go deep into each menu and edit the data and execution parameter
50			files. Save them in the respective directories (savedirs) that you
51			sent in the top menu.
52
53			***VERY IMPORTANT***
54			To retrieve values that work for this setup you can either import each
55			file's exported values (the names are self explanatory) or import a
56			top to bottom export for the runtime called
57			exportFromCpl_aim+ocn_runtime.xml
58	ce107	1.1
59	ce107	1.2	B) Go to the runtime menu for each component and run the script to
60			prepare the run directories
61
62			C) To to the top runtime menu, edit the options if necessary and run
63			the script.
64	ce107	1.1
65			LEGEND current faux-pass:
66	ce107	1.2	a) LEGEND is temperamental as of late. It seems to be far less so with
67			IBM java than with Sun Java so on batsi.mit.edu for example use module
68			add jdk/ibm/1.5.0
69			java -jar Legend.jar
70			etc.
71			Available modules on batsi are seen as always by
72			module avail
73			b) If you do not want to see PBS output that makes no sense do not
74			forget to remove the default PBS monitor from the options under
75			Tools. On the other hand this way you get a nice popup when an action
76			finishes unlike the standard case when you have to look for any
77			output.
78			c) You can always edit a script before execution in the window it
79			appears in; Sun Java sometimes gets horribly worked up over it and
80			LEGEND needs to be killed.
81			d) After an import the visual on the use box for a structure becomes
82			unticked even though it is actually true. The file output is correct
83			but the table display is misleading.