Annotation of /MITgcm_contrib/ocean_inversion_project/README

Ocean Inversion Project
=======================

Instructions for using pkg/ptracers to compute tracer
Green's functions for Gruber's ocean inversion project
(see quercus.igpp.ucla.edu/OceanInversion/ for details).

Preprocessed OceanInversion input files are available
under directories region_mask, takahashi, and
atm_co2 in this package.  All netcdf input files
have been converted to binary format in order to avoid
having to link netcdf library with MITgcm code.  See
respective README files in each directory for details.


===============================================
First check that pkg/ptracers works OK by using
salinity initial and boundary conditions
===============================================

1 ===> get MITgcm code from cvs repository

 CVSROOT=:pserver:cvsanon@mitgcm.org:/u/gcmpack
 cvs login ( CVS password: cvsanon )
 cvs co -r checkpoint51n_branch MITgcm_code
 cvs co -r checkpoint51n_branch MITgcm/verification/testreport
 cvs co -r checkpoint51n_branch MITgcm/verification/global_with_exf

2 ===> put MITgcm_contrib/ocean_inversion_project in MITgcm directory

 cd MITgcm
 cvs co -d ocean_inversion_project MITgcm_contrib/ocean_inversion_project

3 ===> compile and link

 mkdir bin exe
 cd bin
 cp ../verification/global_with_exf/code/* .
 cp ../ocean_inversion_project/code/* .
 rm ptracers_*.F PTRACERS_OPTIONS.h
 ../tools/genmake2
   (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
 make depend
 make

4 ===> execute

 cd ../exe
 cp ../verification/global_with_exf/input/eedata .
 cp ../verification/global_with_exf/input/data.* .
 cp ../verification/global_with_exf/input/POLY3.COEFFS .
 ln -sf ../verification/global_with_exf/input/*.bin .
 cp ../ocean_inversion_project/input/* .
 cp data.test data
 cp data.ptracers.test data.ptracers
 mitgcmuv > output.txt
  
5 ===> check that PTRACER output and salinity output are identical.

 diff PTRACER01.0000000020.001.001.data S.0000000020.001.001.data
 diff PTRACER30.0000000020.001.001.data S.0000000020.001.001.data
 diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data
 diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data


==========================================================
MPI instructions for carrying out a 3000-year quasi-stationary
integration using the global_ocean.90x40x15 configuration.
==========================================================

 cd MITgcm/exe
 rm *
 cd ../bin
 rm *
 cp ../verification/global_with_exf/code/* .
 cp ../ocean_inversion_project/code/* .
 rm PTRACERS_OPTIONS.h
 cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h
 cp SIZE.h_mpi SIZE.h
 ../tools/genmake2
   (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
 make depend
 make
 cd ../exe
 cp ../verification/global_with_exf/input/eedata .
 cp ../verification/global_with_exf/input/data.* .
 cp ../verification/global_with_exf/input/POLY3.COEFFS .
 ln -sf ../verification/global_with_exf/input/*.bin .
 cp ../ocean_inversion_project/input/* .
 ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
 ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
 cp data.stationary.1 data
 mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
   (on orion: qsub job.orion)

==========================================================
MPI instructions for carrying out time-dependent, 1765-2005,
anthropogenic carbon perturbation tracer experiments using
the global_ocean.90x40x15 configuration.
==========================================================

 cd MITgcm/exe
 rm *
 cd ../bin
 rm *
 cp ../verification/global_with_exf/code/* .
 cp ../ocean_inversion_project/code/* .
 cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h
 cp SIZE.h_mpi SIZE.h
 ../tools/genmake2
   (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
 make depend
 make
 cd ../exe
 cp ../verification/global_with_exf/input/eedata .
 cp ../verification/global_with_exf/input/data.* .
 cp ../verification/global_with_exf/input/POLY3.COEFFS .
 ln -sf ../verification/global_with_exf/input/*.bin .
 cp ../ocean_inversion_project/input/* .
 cp data.1765-2005 data
 ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
 ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
 ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
 mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
   (on orion: qsub job.orion.td)


==========================================================
Instructions for carrying out time-dependent, 1765-2005,
anthropogenic carbon perturbation tracer experiments using
global_ocean.90x40x15 configuration and netcdf output.
This assumes that the appropriate libnetcdf.a exists
and that it be specified in the genmake2 option file.
==========================================================

 cd MITgcm/exe
 rm *
 cd ../bin
 rm *
 cp ../verification/global_with_exf/code/* .
 cp ../ocean_inversion_project/code/* .
 cp PTRACERS_OPTIONS.h.netcdf PTRACERS_OPTIONS.h
 cp ../ocean_inversion_project/write_netCDF/*  .
 \rm mk_output.F

### need customized option file; example below is for nireas
 ../tools/genmake2 -of linux_ia32_g77_netcdf

 make depend
 make
 cd ../exe
 cp ../verification/global_with_exf/input/eedata .
 cp ../verification/global_with_exf/input/data.* .
 cp ../verification/global_with_exf/input/POLY3.COEFFS .
 ln -sf ../verification/global_with_exf/input/*.bin .
 cp ../ocean_inversion_project/input/* .
 cp data.1765-2005.1 data
 ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
 ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
 ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
 mitgcmuv > output .txt &


======================================================

==========================================================
Instructions for generating netcdf output files on orion
==========================================================

cd ocean_inversion_project/write_netCDF
setenv F_UFMTENDIAN big

(check that defaults in  mk_output.F are appropriate)

efc -W0 -WB mk_output.F write_nc_phys.F nc_util.F \
     handle_errors.F write_nc_basisfnctns.F \
     write_nc_diag_0D.F write_nc_diag_2D.F \
     -I/u2/dmenem/software/netcdf-3.5.0/include \
     -L/u2/dmenem/software/netcdf-3.5.0/lib -lnetcdf
a.out


======================================================

% some matlab code for looking at fort.10 debug files
load fort.10
tak=zeros(90,40,12);
for n=1:length(fort)
 m=fort(n,1); i=fort(n,2); j=fort(n,3);
 if i>0&i<91&j>0&j<41, tak(i,j,m)=fort(n,4); end
end
lon=2:4:360; lat=-78:4:78;
clf, contourf(lon,lat,mean(tak(:,:,1),3)',-10:10)
caxis([-6 6]), colorbar, plotland

% some matlab code for looking at PTRACER output files
salt=readbin('S.0000000020.001.001.data',[90 40 15],1);
tracer=zeros(90,40,15,30);
for i=1:30
 fn=['PTRACER' myint2str(i) '.0000000020.001.001.data'];
 tracer(:,:,:,i)=readbin(fn,[90 40 15],1);
 clf, mypcolor(tracer(:,:,1,i)'); pause(1)
end
tmp=sum(tracer,4); clf, mypcolor(tmp(:,:,1)')
mypcolor(


% some matlab code for checking that one year's worth of
% tracer uptake is approximately 1e18 mols.
lon=2:4:360; lat=-78:4:78;
thk=[50 70 100 140 190 240 290 340 390 440 490 540 590 640 690];
mask=readbin('hFacC.001.001.data',[90 40 15],1);
tracer=zeros(90,40,15,30); sumtracer=zeros(30,1);
for i=1:30, mydisp(i)
 fn=['PTRACER' myint2str(i) '.0000001800.001.001.data'];
 tracer(:,:,:,i)=readbin(fn,[90 40 15],1);
 for j=1:length(lat)
  for k=1:length(thk)
   sumtracer(i) = sumtracer(i) + sum(tracer(:,j,k,i).*mask(:,j,k)) * ...
                  thk(k) * (4*1.113195e+05)^2 * cos(pi*lat(j)/180);
  end
 end
end
plot(1:30,0*sumtracer,1:30,sumtracer)


% check that tracer flux is 1e18 mols / year
nb_seconds_per_year=31556880;
lon=2:4:360; lat=-78:4:78;
mask=readbin('hFacC.data',[90 40 15],1);
tracer=zeros(90,40,30); sumtracer=zeros(30,1);
for i=1:30, mydisp(i)
 fn=['PtrFlux' myint2str(i) '.0000000180.data'];
 tracer(:,:,i)=readbin(fn,[90 40],1);
 for j=1:length(lat)
    sumtracer(i) = sumtracer(i) + sum(tracer(:,j,i).*mask(:,j,1)) * ...
        nb_seconds_per_year* (4*1.113195e+05)^2 * cos(pi*lat(j)/180);
  end
end
plot(1:30,0*sumtracer,1:30,sumtracer-mmean(sumtracer))
1	dimitri	1.1	Ocean Inversion Project
2			=======================
3
4			Instructions for using pkg/ptracers to compute tracer
5			Green's functions for Gruber's ocean inversion project
6	dimitri	1.3	(see quercus.igpp.ucla.edu/OceanInversion/ for details).
7
8			Preprocessed OceanInversion input files are available
9			under directories region_mask, takahashi, and
10			atm_co2 in this package. All netcdf input files
11			have been converted to binary format in order to avoid
12			having to link netcdf library with MITgcm code. See
13			respective README files in each directory for details.
14	dimitri	1.1
15
16	dimitri	1.2	===============================================
17			First check that pkg/ptracers works OK by using
18			salinity initial and boundary conditions
19			===============================================
20
21			1 ===> get MITgcm code from cvs repository
22
23	dimitri	1.21	CVSROOT=:pserver:cvsanon@mitgcm.org:/u/gcmpack
24	dimitri	1.2	cvs login ( CVS password: cvsanon )
25	dimitri	1.21	cvs co -r checkpoint51n_branch MITgcm_code
26			cvs co -r checkpoint51n_branch MITgcm/verification/testreport
27			cvs co -r checkpoint51n_branch MITgcm/verification/global_with_exf
28	dimitri	1.2
29			2 ===> put MITgcm_contrib/ocean_inversion_project in MITgcm directory
30
31			cd MITgcm
32			cvs co -d ocean_inversion_project MITgcm_contrib/ocean_inversion_project
33
34	dimitri	1.3	3 ===> compile and link
35	dimitri	1.2
36	dimitri	1.21	mkdir bin exe
37	dimitri	1.2	cd bin
38			cp ../verification/global_with_exf/code/* .
39			cp ../ocean_inversion_project/code/* .
40	dimitri	1.12	rm ptracers_*.F PTRACERS_OPTIONS.h
41	dimitri	1.11	../tools/genmake2
42			(on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
43	dimitri	1.2	make depend
44			make
45
46			4 ===> execute
47
48			cd ../exe
49	dimitri	1.3	cp ../verification/global_with_exf/input/eedata .
50			cp ../verification/global_with_exf/input/data.* .
51			cp ../verification/global_with_exf/input/POLY3.COEFFS .
52			ln -sf ../verification/global_with_exf/input/*.bin .
53	dimitri	1.2	cp ../ocean_inversion_project/input/* .
54	dimitri	1.3	cp data.test data
55			cp data.ptracers.test data.ptracers
56	dimitri	1.4	mitgcmuv > output.txt
57	dimitri	1.2
58	dimitri	1.5	5 ===> check that PTRACER output and salinity output are identical.
59	dimitri	1.2
60			diff PTRACER01.0000000020.001.001.data S.0000000020.001.001.data
61			diff PTRACER30.0000000020.001.001.data S.0000000020.001.001.data
62	dimitri	1.14	diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data
63			diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data
64	dimitri	1.3
65	dimitri	1.1
66	dimitri	1.8	==========================================================
67			MPI instructions for carrying out a 3000-year quasi-stationary
68			integration using the global_ocean.90x40x15 configuration.
69			==========================================================
70
71			cd MITgcm/exe
72			rm *
73			cd ../bin
74			rm *
75			cp ../verification/global_with_exf/code/* .
76			cp ../ocean_inversion_project/code/* .
77	dimitri	1.12	rm PTRACERS_OPTIONS.h
78	dimitri	1.8	cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h
79			cp SIZE.h_mpi SIZE.h
80	dimitri	1.11	../tools/genmake2
81			(on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
82	dimitri	1.8	make depend
83			make
84			cd ../exe
85			cp ../verification/global_with_exf/input/eedata .
86			cp ../verification/global_with_exf/input/data.* .
87			cp ../verification/global_with_exf/input/POLY3.COEFFS .
88			ln -sf ../verification/global_with_exf/input/*.bin .
89			cp ../ocean_inversion_project/input/* .
90			ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
91			ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
92	dimitri	1.17	cp data.stationary.1 data
93			mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
94	dimitri	1.19	(on orion: qsub job.orion)
95	dimitri	1.12
96			==========================================================
97	dimitri	1.19	MPI instructions for carrying out time-dependent, 1765-2005,
98	dimitri	1.12	anthropogenic carbon perturbation tracer experiments using
99			the global_ocean.90x40x15 configuration.
100			==========================================================
101
102			cd MITgcm/exe
103			rm *
104			cd ../bin
105			rm *
106			cp ../verification/global_with_exf/code/* .
107			cp ../ocean_inversion_project/code/* .
108	dimitri	1.19	cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h
109			cp SIZE.h_mpi SIZE.h
110	dimitri	1.12	../tools/genmake2
111			(on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
112	dimitri	1.13	make depend
113			make
114			cd ../exe
115			cp ../verification/global_with_exf/input/eedata .
116			cp ../verification/global_with_exf/input/data.* .
117			cp ../verification/global_with_exf/input/POLY3.COEFFS .
118			ln -sf ../verification/global_with_exf/input/*.bin .
119			cp ../ocean_inversion_project/input/* .
120			cp data.1765-2005 data
121			ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
122			ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
123			ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
124	dimitri	1.19	mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
125			(on orion: qsub job.orion.td)
126	dimitri	1.13
127
128			==========================================================
129			Instructions for carrying out time-dependent, 1765-2005,
130			anthropogenic carbon perturbation tracer experiments using
131			global_ocean.90x40x15 configuration and netcdf output.
132			This assumes that the appropriate libnetcdf.a exists
133			and that it be specified in the genmake2 option file.
134			==========================================================
135
136			cd MITgcm/exe
137			rm *
138			cd ../bin
139			rm *
140			cp ../verification/global_with_exf/code/* .
141			cp ../ocean_inversion_project/code/* .
142			cp PTRACERS_OPTIONS.h.netcdf PTRACERS_OPTIONS.h
143			cp ../ocean_inversion_project/write_netCDF/* .
144	dimitri	1.20	\rm mk_output.F
145	dimitri	1.13
146			### need customized option file; example below is for nireas
147			../tools/genmake2 -of linux_ia32_g77_netcdf
148
149	dimitri	1.12	make depend
150			make
151			cd ../exe
152			cp ../verification/global_with_exf/input/eedata .
153			cp ../verification/global_with_exf/input/data.* .
154			cp ../verification/global_with_exf/input/POLY3.COEFFS .
155			ln -sf ../verification/global_with_exf/input/*.bin .
156			cp ../ocean_inversion_project/input/* .
157	dimitri	1.18	cp data.1765-2005.1 data
158	dimitri	1.12	ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
159			ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
160			ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
161			mitgcmuv > output .txt &
162	dimitri	1.19
163
164			======================================================
165
166			==========================================================
167			Instructions for generating netcdf output files on orion
168			==========================================================
169
170			cd ocean_inversion_project/write_netCDF
171			setenv F_UFMTENDIAN big
172
173			(check that defaults in mk_output.F are appropriate)
174
175			efc -W0 -WB mk_output.F write_nc_phys.F nc_util.F \
176			handle_errors.F write_nc_basisfnctns.F \
177			write_nc_diag_0D.F write_nc_diag_2D.F \
178			-I/u2/dmenem/software/netcdf-3.5.0/include \
179			-L/u2/dmenem/software/netcdf-3.5.0/lib -lnetcdf
180			a.out
181	dimitri	1.8
182
183	dimitri	1.3	======================================================
184	dimitri	1.1
185	dimitri	1.3	% some matlab code for looking at fort.10 debug files
186			load fort.10
187			tak=zeros(90,40,12);
188			for n=1:length(fort)
189			m=fort(n,1); i=fort(n,2); j=fort(n,3);
190			if i>0&i<91&j>0&j<41, tak(i,j,m)=fort(n,4); end
191			end
192			lon=2:4:360; lat=-78:4:78;
193			clf, contourf(lon,lat,mean(tak(:,:,1),3)',-10:10)
194			caxis([-6 6]), colorbar, plotland
195
196			% some matlab code for looking at PTRACER output files
197	dimitri	1.4	salt=readbin('S.0000000020.001.001.data',[90 40 15],1);
198	dimitri	1.3	tracer=zeros(90,40,15,30);
199			for i=1:30
200			fn=['PTRACER' myint2str(i) '.0000000020.001.001.data'];
201			tracer(:,:,:,i)=readbin(fn,[90 40 15],1);
202			clf, mypcolor(tracer(:,:,1,i)'); pause(1)
203			end
204			tmp=sum(tracer,4); clf, mypcolor(tmp(:,:,1)')
205	dimitri	1.4	mypcolor(
206
207	dimitri	1.3
208			% some matlab code for checking that one year's worth of
209			% tracer uptake is approximately 1e18 mols.
210			lon=2:4:360; lat=-78:4:78;
211			thk=[50 70 100 140 190 240 290 340 390 440 490 540 590 640 690];
212	dimitri	1.7	mask=readbin('hFacC.001.001.data',[90 40 15],1);
213	dimitri	1.3	tracer=zeros(90,40,15,30); sumtracer=zeros(30,1);
214			for i=1:30, mydisp(i)
215	dimitri	1.7	fn=['PTRACER' myint2str(i) '.0000001800.001.001.data'];
216	dimitri	1.3	tracer(:,:,:,i)=readbin(fn,[90 40 15],1);
217			for j=1:length(lat)
218			for k=1:length(thk)
219	dimitri	1.7	sumtracer(i) = sumtracer(i) + sum(tracer(:,j,k,i).mask(:,j,k)) ...
220	dimitri	1.3	thk(k) * (41.113195e+05)^2 cos(pi*lat(j)/180);
221			end
222	dimitri	1.1	end
223	dimitri	1.3	end
224	dimitri	1.4	plot(1:30,0*sumtracer,1:30,sumtracer)
225	dimitri	1.21
226
227			% check that tracer flux is 1e18 mols / year
228			nb_seconds_per_year=31556880;
229			lon=2:4:360; lat=-78:4:78;
230			mask=readbin('hFacC.data',[90 40 15],1);
231			tracer=zeros(90,40,30); sumtracer=zeros(30,1);
232			for i=1:30, mydisp(i)
233			fn=['PtrFlux' myint2str(i) '.0000000180.data'];
234			tracer(:,:,i)=readbin(fn,[90 40],1);
235			for j=1:length(lat)
236			sumtracer(i) = sumtracer(i) + sum(tracer(:,j,i).mask(:,j,1)) ...
237			nb_seconds_per_year* (41.113195e+05)^2 cos(pi*lat(j)/180);
238			end
239			end
240			plot(1:30,0*sumtracer,1:30,sumtracer-mmean(sumtracer))