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revision 1.10 by dimitri, Sun Dec 14 02:59:06 2003 UTC revision 1.51 by dimitri, Thu Feb 10 20:47:06 2005 UTC
# Line 1  Line 1 
1  Instructions for setting up a cube-sphere integration with sea-ice.  Instructions for setting up a cube-sphere integration with sea-ice.
2  Date last tested: December 11, 2003.  Date last tested: July 9, 2004.
3    Code and input used for integrating cube9.
4    
5    
6  ##########################################################################  ##########################################################################
7  ##########################################################################  ##########################################################################
8  # 32*32*6*15, 1-cpu cube sphere  # getting the code from anonymous CVS server
9    
10    cvs co MITgcm_contrib/high_res_cube/README_ice
11    cvs co MITgcm_contrib/high_res_cube/code-mods
12    cvs co MITgcm_contrib/high_res_cube/input
13    cvs co MITgcm_contrib/high_res_cube/results
14    cvs co MITgcm_code
15    cvs co MITgcm/verification/global_ocean.cs32x15
16    cvs co MITgcm/verification/testreport
17    
18  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  
19  cvs login ( CVS password: cvsanon )  ##########################################################################
20  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/README_ice  ##########################################################################
21  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/code-mods  # 32*32*6*15, 1-cpu cube sphere
 cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/matlab-grid-converter  
 cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/input  
 cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/results  
 cvs co -r checkpoint52d_pre MITgcm_code  
 cvs co -r checkpoint52d_pre MITgcm/verification/global_ocean.cs32x15  
22    
23  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
24  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
25  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
26  \rm mdsio_readfield.F  cd ../build
27    \rm *
 cd ..  
 mkdir build  
 cd build  
28  ../../../tools/genmake2 -mods=../code  ../../../tools/genmake2 -mods=../code
29  make depend  make depend
30  make  make
31    cd ..
32    mkdir run
33    cd run
34    \rm *
35    \cp ../input/* .
36    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
37    ../build/mitgcmuv >& output.txt
38    
39    comparison output is in:
40    ../../../../MITgcm_contrib/high_res_cube/results/output.txt
41    
42    to use matlab to look at the output
43    matlab
44    
45    for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}
46        tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);
47        cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
48    end
49    
50    heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);
51    mask=0*heff; mask(find(heff>.001))=1;
52    uice=mask.*permute(readbin(['UICE.0000000020.data'],[32,6,32]),[1 3 2]);
53    vice=mask.*permute(readbin(['VICE.0000000020.data'],[32,6,32]),[1 3 2]);
54    clf
55    subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')
56    subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')
57    subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')
58    subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')
59    
60    
61    ##########################################################################
62    ##########################################################################
63    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
64    
65    cd MITgcm/verification/global_ocean.cs32x15/code
66    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
67    \cp ../code_alt/code.176t_8x4/* .
68    cd ../build
69    \rm *
70    ../../../tools/genmake2 -mods=../code
71    make depend
72    make
73  cd ..  cd ..
74  mkdir run  mkdir run
75  cd run  cd run
76    \rm *
77  \cp ../input/* .  \cp ../input/* .
 \cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  
78  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
79  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
80    
# Line 41  comparison output is in: Line 83  comparison output is in:
83    
84  to use matlab to look at the output  to use matlab to look at the output
85  matlab  matlab
86    
87  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}
88      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);
89      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
90  end  end
91    
92    heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);
93    mask=0*heff; mask(find(heff>.001))=1;
94    uice=mask.*permute(readbin(['UICE.0000000020.data'],[32,6,32]),[1 3 2]);
95    vice=mask.*permute(readbin(['VICE.0000000020.data'],[32,6,32]),[1 3 2]);
96    clf
97    subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')
98    subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')
99    subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')
100    subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')
101    
102    
103  ##########################################################################  ##########################################################################
104  ##########################################################################  ##########################################################################
105  # 32*32*6*15, 2-cpu cube sphere on the altices with efc  # 32*32*6*15, 2-cpu cube sphere on the altices with efc
106    
 setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  
 cvs login ( CVS password: cvsanon )  
 cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/README_ice  
 cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/code-mods  
 cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/matlab-grid-converter  
 cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/input  
 cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/results  
 cvs co -r checkpoint52d_pre MITgcm_code  
 cvs co -r checkpoint52d_pre MITgcm/verification/global_ocean.cs32x15  
   
107  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
108  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
109  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
110  \cp SIZE.h_mpi SIZE.h  \cp SIZE.h_mpi SIZE.h
 \cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h  
 \rm mdsio_readfield.F  
111    
112  cd ..  cd ../build
113  mkdir build  \rm *
114  cd build  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
 ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi  
115  make depend  make depend
116  make  make -j
117    
118  cd ..  cd ..
119  mkdir run  mkdir run
120  cd run  cd run
121    \rm *
122  \cp ../input/* .  \cp ../input/* .
 \cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  
123  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
124  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
125    
126    
127  ##########################################################################  ##########################################################################
128  ##########################################################################  ##########################################################################
129  # 510*510*6*50, 54-cpu cube sphere on the altices with efc  # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
130    # starting with pickup file from end of 1992
131    # requires input files in sudirectories run_template and ncep_rgau
132    
133    cd MITgcm/verification/global_ocean.cs32x15/code
134    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
135    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
136    \cp packages.conf_hr packages.conf
137    
138    cd ../build
139    \rm *
140    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
141    make depend
142    make -j
143    
144  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  cd ..
145  cvs login ( CVS password: cvsanon )  mkdir run
146  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/README_ice  cd run
147  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/code-mods  \rm *
148  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/matlab-grid-converter  \cp ../input/* .
149  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/input  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
150  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/results  qsub job_altix92_54t
151  cvs co -r checkpoint52d_pre MITgcm_code  
152  cvs co -r checkpoint52d_pre MITgcm/verification/global_ocean.cs32x15  
153    ##########################################################################
154    ##########################################################################
155    # 510*510*6*50, 216-cpu cube sphere on altix with ifort
156    # requires input files in sudirectories run_template and ncep_rgau
157    # these can be obained from lou:/u/menemenl/cube
158    
159  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
160  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
161  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
162  \cp SIZE.h_54 SIZE.h  \cp SIZE.h_216 SIZE.h
163  \cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h  \cp packages.conf_hr packages.conf
 \rm mdsio_readfield.F  
164    
165  cd ..  cd ../build
166  mkdir build  \rm *
167  cd build  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
 ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi  
168  make depend  make depend
169  make  make -j 4
170    
171  cd ..  cd ..
172  mkdir run  mkdir run
173  cd run  cd run
174    \rm *
175  \cp ../input/* .  \cp ../input/* .
176  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
177  \cp data_hr data  ln -sf ../../../../run_template/* .
178  \ln -sf ../../../../run_template/tile00* .  \rm pickup*
179  \ln -sf ../../../../run_template/LEV* .  ln -sf ../../../../run_template/pickup.0000316440.cube20 pickup.0000000216.data
180  \ln -sf ../../../../run_template/BATHY_18360x85_filled.bin .  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube20 pickup_seaice.0000000216.data
181  qsub job_orion  \cp ../build/mitgcmuv .
182    qsub job_altix92
183    
184    
185    
186    
187    
188    
189  ##########################################################################  ##########################################################################
190  ##########################################################################  ##########################################################################
191  # 510*510*6*50, 216-cpu cube sphere on the altices with efc  # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
192    # requires input files in sudirectories run_template and ncep_rgau
193  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  # these can be obained from lou:/u/menemenl/cube
 cvs login ( CVS password: cvsanon )  
 cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/README_ice  
 cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/code-mods  
 cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/matlab-grid-converter  
 cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/input  
 cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/results  
 cvs co -r checkpoint52d_pre MITgcm_code  
 cvs co -r checkpoint52d_pre MITgcm/verification/global_ocean.cs32x15  
194    
195  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
196  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
197  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
198  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_216 SIZE.h
199  \cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h  \cp packages.conf_diagnostics packages.conf
200  \rm mdsio_readfield.F  
201    cd ../build
202    \rm *
203    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
204    make depend
205    make -j 4
206    
207  cd ..  cd ..
208  mkdir build  mkdir run
209  cd build  cd run
210  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi  \rm *
211    \cp ../input/* .
212    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
213    ln -sf ../../../../run_template/* .
214    \rm pickup*
215    ln -sf ../../../../run_template/pickup.0000316440.cube20 pickup.0000000216.data
216    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube20 pickup_seaice.0000000216.data
217    \cp ../build/mitgcmuv .
218    qsub job_altix92
219    
220    
221    
222    
223    
224    
225    
226    
227    
228    
229    
230    
231    
232    
233    
234    
235    
236    
237    ##########################################################################
238    ##########################################################################
239    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
240    # requires input files in sudirectories run_template and ncep_rgau
241    # presently residing under orion:/tmp1/dmenem/cube
242    
243    cd MITgcm/verification/global_ocean.cs32x15/code
244    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
245    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
246    \cp SIZE.h_54 SIZE.h
247    \cp packages.conf_hr packages.conf
248    
249    cd ../build
250    \rm *
251    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
252  make depend  make depend
253  make  make -j
254    
255  cd ..  cd ..
256  mkdir run  mkdir run
257  cd run  cd run
258    \rm *
259  \cp ../input/* .  \cp ../input/* .
260  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
 \cp data_hr data  
 \cp data.pkg_hr data.pkg  
 \ln -sf ../../../../run_template/tile00* .  
 \ln -sf ../../../../run_template/LEV* .  
 \ln -sf ../../../../run_template/BATHY_18360x85_filled.bin .  
261  qsub job_orion  qsub job_orion
262    
263    
264    ##########################################################################
265    ##########################################################################
266    # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
267    # requires input files in sudirectories run_template and ncep_rgau
268    # presently residing under orion:/tmp1/dmenem/cube
269    
270    cd MITgcm/verification/global_ocean.cs32x15/code
271    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
272    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
273    \cp SIZE.h_41 SIZE.h
274    \cp packages.conf_hr packages.conf
275    
276    cd ../build
277    \rm *
278    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
279    make depend
280    make -j
281    
282    cd ..
283    mkdir run
284    cd run
285    \rm *
286    \cp ../input/* .
287    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
288    qsub job_orion41
289    
290    
291    ##########################################################################
292    ##########################################################################
293    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
294    # requires input files in sudirectories run_template and ncep_rgau
295    # presently residing under orion:/tmp1/dmenem/cube
296    
297    cd MITgcm/verification/global_ocean.cs32x15/code
298    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
299    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
300    \cp SIZE.h_50 SIZE.h
301    \cp packages.conf_hr packages.conf
302    
303    cd ../build
304    \rm *
305    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
306    make depend
307    make -j
308    
309    cd ..
310    mkdir run
311    cd run
312    \rm *
313    \cp ../input/* .
314    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
315    qsub job_orion
316    
317    
318    ##########################################################################
319    ##########################################################################
320    # matlab script for generating pChkptFreq
321    
322    nTimeSteps=26352;
323    for niter0=216:26352:(26352*12)
324     pChkptFreq=(niter0+nTimeSteps)*1200;
325     day=pChkptFreq/24/60/60;
326     disp(['niter0=' int2str(niter0) ',day=' int2str(day) ', ' ...
327     datestr(datenum(1992,1,1)+day) ', pChkptFreq=' int2str(pChkptFreq)])
328    end
329    
330    niter0 = 216   , day = 369 , 04-Jan-1993, pChkptFreq = 31881600
331    niter0 = 26568 , day = 735 , 05-Jan-1994, pChkptFreq = 63504000
332    niter0 = 52920 , day = 1101, 06-Jan-1995, pChkptFreq = 95126400
333    niter0 = 79272 , day = 1467, 07-Jan-1996, pChkptFreq = 126748800
334    niter0 = 105624, day = 1833, 07-Jan-1997, pChkptFreq = 158371200
335    niter0 = 131976, day = 2199, 08-Jan-1998, pChkptFreq = 189993600
336    niter0 = 158328, day = 2565, 09-Jan-1999, pChkptFreq = 221616000
337    niter0 = 184680, day = 2931, 10-Jan-2000, pChkptFreq = 253238400
338    niter0 = 211032, day = 3297, 10-Jan-2001, pChkptFreq = 284860800
339    niter0 = 237384, day = 3663, 11-Jan-2002, pChkptFreq = 316483200
340    niter0 = 263736, day = 4029, 12-Jan-2003, pChkptFreq = 348105600
341    niter0 = 290088, day = 4395, 13-Jan-2004, pChkptFreq = 379728000
342    
343    
344    
345    
346    
347    
348    #!/bin/csh
349    \cp data.pkg_hr data.pkg
350    \cp data.seaice_hr data.seaice
351    \cp data.exf_clim_hr data.exf_clim
352    
353    \cp data_hr92 data
354    ./modpickup
355    \cp data.exf_hr92 data.exf
356    /opt/sgi/mpt/1.11-85/bin/mpirun.real -v -a a2k c20 216 runon 221-436 mitgcmuv
357    mkdir out.1992
358    \mv STDOUT.0000 *.data pickup*.meta out.1992
359    \cp data* out.1992
360    \rm STD* *.meta
361    
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