Annotation 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	gforget	1.2
2	gforget	1.3	---- common to all matlab sessions ----
3	gforget	1.2
4	gforget	1.1	0) login as guest
5
6	gforget	1.2	1) open web browser, and download setup_gcmfaces_and_mitprof.csh
7			from http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/gael/
8	gforget	1.1
9	gforget	1.4	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	gforget	1.2	2) open terminal window, and proceed to download codes:
15			csh
16	gforget	1.1	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	gforget	1.2	disk space requirement ~ 800M (plus class specific items)
23	gforget	1.1	matlab requirement > 2011 (for native netcdf implementation)
24
25	gforget	1.2	---- 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	gforget	1.3	5) download Argo etc
35			cd ~/iap-idma
36	gforget	1.2	mkdir release1
37			wget --recursive ftp://mit.ecco-group.org/gforget/MITprof
38			mv mit.ecco-group.org/gforget/MITprof release1/.
39
40	gforget	1.3	6) start matlab and run idma_float_plot.m
41	gforget	1.2	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	gforget	1.3	1,2) see 'common to all classes' above
51
52	gforget	1.1	3) start matlab and run gcmfaces_demo
53	gforget	1.3	cd ~/iap-idma
54	gforget	1.2	matlab
55	gforget	1.1	addpath gcmfaces
56			gcmfaces_demo
57	gforget	1.3	exit
58	gforget	1.1
59	gforget	1.2	4) download ECCO climatology
60	gforget	1.3	cd ~/iap-idma
61	gforget	1.1	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	gforget	1.3	cd ~/iap-idma
75			matlab
76	gforget	1.1	addpath gcmfaces
77			gcmfaces_global
78			diags=example_transports('v4');
79			example_transports_disp(diags);
80
81	gforget	1.6	---- for class #4 ----
82	gforget	1.5
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	gforget	1.6	2) open terminal window, install MITgcm:
92	gforget	1.5
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	gforget	1.9	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	gforget	1.5	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	gforget	1.1
133	gforget	1.6	---- for class #5 ----
134
135	gforget	1.7	1,2) same as class #4 except with
136			cvs co -P MITgcm
137	gforget	1.9	instead of
138			cvs co -P MITgcm_verif_basic
139	gforget	1.6
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	gforget	1.9	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	gforget	1.6	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	gforget	1.8	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	gforget	1.6	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	gforget	1.7	* 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	gforget	1.6
171			note :
172	gforget	1.7	* in the cases of adjustment.cs-32x32x1, tutorial_held_suarez_cs,
173	gforget	1.6	and tutorial_plume_on_slope the matlab programs expect that
174			the experiment duration was increased (see iap-idma-exercises)