Contents of /MITgcm_contrib/gael/comm/course-idma2015/computing/iap-idma-readme


---- common to all matlab sessions ----

0) login as guest

1) open web browser, and download setup_gcmfaces_and_mitprof.csh
   from http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/gael/

note :
   for step 1, please be sure to use the download button
   of the browser rather than e.g. wget that can conflict 
   with the behavior of the CVS web interface

2) open terminal window, and proceed to download codes:
   csh
   mkdir iap-idma
   mv Downloads/setup_gcmfaces_and_mitprof.csh iap-idma/
   cd iap-idma
   source ./setup_gcmfaces_and_mitprof.csh

notes : 
   disk space requirement ~ 800M (plus class specific items)
   matlab requirement > 2011 (for native netcdf implementation)

---- for class #1 ----

1,2) see 'common to all classes' above

3) download idma_float_plot.m from http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/gael/comm/course-idma2015/computing/

4) in terminal window 
   mv ~/Downloads/idma_float_plot.m ~/iap-idma/.

5) download Argo etc
   cd ~/iap-idma
   mkdir release1
   wget --recursive ftp://mit.ecco-group.org/gforget/MITprof
   mv mit.ecco-group.org/gforget/MITprof release1/.

6) start matlab and run idma_float_plot.m
   matlab
   [p]=idma_float_plot('2900828');

notes :
   disk space requirement ~ 6.4G (plus 0.8G from steps 1,2)
   start matlab at command line : matlab -nodesktop

---- for class #2 ----

1,2) see 'common to all classes' above

3) start matlab and run gcmfaces_demo
   cd ~/iap-idma
   matlab
   addpath gcmfaces
   gcmfaces_demo
   exit
   
4) download ECCO climatology
   cd ~/iap-idma
   mkdir release1

   wget --recursive ftp://mit.ecco-group.org/gforget/nctiles_climatology/THETA
   wget --recursive ftp://mit.ecco-group.org/gforget/nctiles_climatology/SALT
   wget --recursive ftp://mit.ecco-group.org/gforget/nctiles_climatology/UVELMASS
   wget --recursive ftp://mit.ecco-group.org/gforget/nctiles_climatology/VVELMASS
   wget --recursive ftp://mit.ecco-group.org/gforget/nctiles_climatology/'ADVx_*'
   wget --recursive ftp://mit.ecco-group.org/gforget/nctiles_climatology/'ADVy_*'
   wget --recursive ftp://mit.ecco-group.org/gforget/nctiles_climatology/'DFxE_*'
   wget --recursive ftp://mit.ecco-group.org/gforget/nctiles_climatology/'DFyE_*'
   mv mit.ecco-group.org/gforget/nctiles_climatology release1/.

5) start matlab and run example_transports (or re-run gcmfaces_demo).
   cd ~/iap-idma
   matlab
   addpath gcmfaces
   gcmfaces_global
   diags=example_transports('v4');
   example_transports_disp(diags);

---- for class #4 ----

1) open web browser, and download setup_these_exps.csh
   from http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/gael/verification/

note :
   for step 1, please be sure to use the download button
   of the browser rather than e.g. wget that can conflict
   with the behavior of the CVS web interface

2) open terminal window, install MITgcm:

   mkdir iap-idma
   cd iap-idma
   csh
   setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
   cvs login
        ( enter the CVS password: "cvsanon" )
   cvs co -P MITgcm_verif_basic

3) install the ECCO v4 setups

   cd ~/iap-idma/MITgcm/verification
   mv ~/Downloads/setup_these_exps.csh .
   source ./setup_these_exps.csh
   mv global_oce_tmp_download/global_oce_* .
   rm -rf global_oce_tmp_download

4) run the ECCO v4 mini benchmark

   ./testreport -t global_oce_cs32

note :
   building the MITgcm (whether using genmake2 or via testreport) requires that your machine
   has : make or (preferably) GNU make, FORTRAN compiler, C compiler, [ba]sh and [t]csh shells

5) quick output plot

   cd ~/iap-idma
   matlab -nodesktop
   addpath gcmfaces
   gcmfaces_global

   cd ~/iap-idma/MITgcm/verification/global_oce_cs32/run
   grid_load('./',6,'compact');
   THETA=rdmds2gcmfaces('T.0000000008');
   figureL; qwckplot(THETA(:,:,1)); colorbar;

note :
   the matlab software needed for item #5 is assumed to have been 
   installed according to 'common to all matlab sessions'

---- for class #5 ----

1,2) same as class #4 except with
   cvs co -P MITgcm
     instead of
   cvs co -P MITgcm_verif_basic

3) run MITgcm benchmarks

   ./testreport -t 'adjustment.128x64x1 advect_cs advect_xy'
   ./testreport -t 'adjustment.cs-32x32x1 tutorial_held_suarez_cs tutorial_plume_on_slope'

note : 
   building the MITgcm (whether using genmake2 or via testreport) requires that your machine 
   has : make or (preferably) GNU make, FORTRAN compiler, C compiler, [ba]sh and [t]csh shells

4) quick output plot for adjustment.128x64x1

   cd ~/iap-idma
   matlab -nodesktop
   addpath gcmfaces
   gcmfaces_global

   cd ~/iap-idma/MITgcm/verification/adjustment.128x64x1/run
   mitgcm_plot_adju_128;

   note : to download mitgcm_plot_adju_128.m etc. go to
   http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/gael/comm/course-idma2015/computing/

5) repeat step #4 for different experiments:

   adjustment.128x64x1          mitgcm_plot_adju_128.m
   advect_cs                    mitgcm_plot_adv_cs.m
   advect_xy                    mitgcm_plot_adv_xy.m
*  adjustment.cs-32x32x1        mitgcm_plot_adju_cs32.m
*  tutorial_held_suarez_cs      mitgcm_plot_held_suarez.m
*  tutorial_plume_on_slope      mitgcm_plot_plume.m

note :
   * in the cases of adjustment.cs-32x32x1, tutorial_held_suarez_cs,
   and tutorial_plume_on_slope the matlab programs expect that
   the experiment duration was increased (see iap-idma-exercises)
1
2	---- common to all matlab sessions ----
3
4	0) login as guest
5
6	1) open web browser, and download setup_gcmfaces_and_mitprof.csh
7	from http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/gael/
8
9	note :
10	for step 1, please be sure to use the download button
11	of the browser rather than e.g. wget that can conflict
12	with the behavior of the CVS web interface
13
14	2) open terminal window, and proceed to download codes:
15	csh
16	mkdir iap-idma
17	mv Downloads/setup_gcmfaces_and_mitprof.csh iap-idma/
18	cd iap-idma
19	source ./setup_gcmfaces_and_mitprof.csh
20
21	notes :
22	disk space requirement ~ 800M (plus class specific items)
23	matlab requirement > 2011 (for native netcdf implementation)
24
25	---- for class #1 ----
26
27	1,2) see 'common to all classes' above
28
29	3) download idma_float_plot.m from http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/gael/comm/course-idma2015/computing/
30
31	4) in terminal window
32	mv ~/Downloads/idma_float_plot.m ~/iap-idma/.
33
34	5) download Argo etc
35	cd ~/iap-idma
36	mkdir release1
37	wget --recursive ftp://mit.ecco-group.org/gforget/MITprof
38	mv mit.ecco-group.org/gforget/MITprof release1/.
39
40	6) start matlab and run idma_float_plot.m
41	matlab
42	[p]=idma_float_plot('2900828');
43
44	notes :
45	disk space requirement ~ 6.4G (plus 0.8G from steps 1,2)
46	start matlab at command line : matlab -nodesktop
47
48	---- for class #2 ----
49
50	1,2) see 'common to all classes' above
51
52	3) start matlab and run gcmfaces_demo
53	cd ~/iap-idma
54	matlab
55	addpath gcmfaces
56	gcmfaces_demo
57	exit
58
59	4) download ECCO climatology
60	cd ~/iap-idma
61	mkdir release1
62
63	wget --recursive ftp://mit.ecco-group.org/gforget/nctiles_climatology/THETA
64	wget --recursive ftp://mit.ecco-group.org/gforget/nctiles_climatology/SALT
65	wget --recursive ftp://mit.ecco-group.org/gforget/nctiles_climatology/UVELMASS
66	wget --recursive ftp://mit.ecco-group.org/gforget/nctiles_climatology/VVELMASS
67	wget --recursive ftp://mit.ecco-group.org/gforget/nctiles_climatology/'ADVx_*'
68	wget --recursive ftp://mit.ecco-group.org/gforget/nctiles_climatology/'ADVy_*'
69	wget --recursive ftp://mit.ecco-group.org/gforget/nctiles_climatology/'DFxE_*'
70	wget --recursive ftp://mit.ecco-group.org/gforget/nctiles_climatology/'DFyE_*'
71	mv mit.ecco-group.org/gforget/nctiles_climatology release1/.
72
73	5) start matlab and run example_transports (or re-run gcmfaces_demo).
74	cd ~/iap-idma
75	matlab
76	addpath gcmfaces
77	gcmfaces_global
78	diags=example_transports('v4');
79	example_transports_disp(diags);
80
81	---- for class #4 ----
82
83	1) open web browser, and download setup_these_exps.csh
84	from http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/gael/verification/
85
86	note :
87	for step 1, please be sure to use the download button
88	of the browser rather than e.g. wget that can conflict
89	with the behavior of the CVS web interface
90
91	2) open terminal window, install MITgcm:
92
93	mkdir iap-idma
94	cd iap-idma
95	csh
96	setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
97	cvs login
98	( enter the CVS password: "cvsanon" )
99	cvs co -P MITgcm_verif_basic
100
101	3) install the ECCO v4 setups
102
103	cd ~/iap-idma/MITgcm/verification
104	mv ~/Downloads/setup_these_exps.csh .
105	source ./setup_these_exps.csh
106	mv global_oce_tmp_download/global_oce_* .
107	rm -rf global_oce_tmp_download
108
109	4) run the ECCO v4 mini benchmark
110
111	./testreport -t global_oce_cs32
112
113	note :
114	building the MITgcm (whether using genmake2 or via testreport) requires that your machine
115	has : make or (preferably) GNU make, FORTRAN compiler, C compiler, [ba]sh and [t]csh shells
116
117	5) quick output plot
118
119	cd ~/iap-idma
120	matlab -nodesktop
121	addpath gcmfaces
122	gcmfaces_global
123
124	cd ~/iap-idma/MITgcm/verification/global_oce_cs32/run
125	grid_load('./',6,'compact');
126	THETA=rdmds2gcmfaces('T.0000000008');
127	figureL; qwckplot(THETA(:,:,1)); colorbar;
128
129	note :
130	the matlab software needed for item #5 is assumed to have been
131	installed according to 'common to all matlab sessions'
132
133	---- for class #5 ----
134
135	1,2) same as class #4 except with
136	cvs co -P MITgcm
137	instead of
138	cvs co -P MITgcm_verif_basic
139
140	3) run MITgcm benchmarks
141
142	./testreport -t 'adjustment.128x64x1 advect_cs advect_xy'
143	./testreport -t 'adjustment.cs-32x32x1 tutorial_held_suarez_cs tutorial_plume_on_slope'
144
145	note :
146	building the MITgcm (whether using genmake2 or via testreport) requires that your machine
147	has : make or (preferably) GNU make, FORTRAN compiler, C compiler, [ba]sh and [t]csh shells
148
149	4) quick output plot for adjustment.128x64x1
150
151	cd ~/iap-idma
152	matlab -nodesktop
153	addpath gcmfaces
154	gcmfaces_global
155
156	cd ~/iap-idma/MITgcm/verification/adjustment.128x64x1/run
157	mitgcm_plot_adju_128;
158
159	note : to download mitgcm_plot_adju_128.m etc. go to
160	http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/gael/comm/course-idma2015/computing/
161
162	5) repeat step #4 for different experiments:
163
164	adjustment.128x64x1 mitgcm_plot_adju_128.m
165	advect_cs mitgcm_plot_adv_cs.m
166	advect_xy mitgcm_plot_adv_xy.m
167	* adjustment.cs-32x32x1 mitgcm_plot_adju_cs32.m
168	* tutorial_held_suarez_cs mitgcm_plot_held_suarez.m
169	* tutorial_plume_on_slope mitgcm_plot_plume.m
170
171	note :
172	* in the cases of adjustment.cs-32x32x1, tutorial_held_suarez_cs,
173	and tutorial_plume_on_slope the matlab programs expect that
174	the experiment duration was increased (see iap-idma-exercises)