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revision 1.40 by dimitri, Thu Jul 1 03:52:24 2004 UTC revision 1.58 by dimitri, Sun May 1 14:02:20 2005 UTC
# Line 1  Line 1 
1  Instructions for setting up a cube-sphere integration with sea-ice.  daInstructions for setting up a cube-sphere integration with sea-ice.
2  Date last tested: March 28, 2004.  Date last updated: February 17, 2005
3  Code and input used for integrating cube5.  Code and input used for integrating cube22.
4    
5    
6  ##########################################################################  ##########################################################################
# Line 11  cvs co MITgcm_contrib/high_res_cube/READ Line 11  cvs co MITgcm_contrib/high_res_cube/READ
11  cvs co MITgcm_contrib/high_res_cube/code-mods  cvs co MITgcm_contrib/high_res_cube/code-mods
12  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
13  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
 cvs co MITgcm_contrib/edge_problem  
14  cvs co MITgcm_code  cvs co MITgcm_code
15  cvs co MITgcm/verification/global_ocean.cs32x15  cvs co MITgcm/verification/global_ocean.cs32x15
16  cvs co MITgcm/verification/testreport  cvs co MITgcm/verification/testreport
# Line 43  comparison output is in: Line 42  comparison output is in:
42  to use matlab to look at the output  to use matlab to look at the output
43  matlab  matlab
44    
45  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...
46             'QNETtave','FVtave','FUtave','EmPmRtave'}
47      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]);
48      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
49  end  end
50    
51  heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);
52  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
53  uice=mask.*permute(readbin(['UICE.0000000020.data'],[32,6,32]),[1 3 2]);  uice=mask.*permute(readbin(['UICEtave.0000000020.data'],[32,6,32]),[1 3 2]);
54  vice=mask.*permute(readbin(['VICE.0000000020.data'],[32,6,32]),[1 3 2]);  vice=mask.*permute(readbin(['VICEtave.0000000020.data'],[32,6,32]),[1 3 2]);
55  clf  clf
56  subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
57  subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
58  subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
59  subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
60    
61    
62  ##########################################################################  ##########################################################################
# Line 79  cd run Line 79  cd run
79  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
80  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
81    
 comparison output is in:  
 ../../../../MITgcm_contrib/high_res_cube/results/output.txt  
82    
83  to use matlab to look at the output  ##########################################################################
84  matlab  ##########################################################################
85    # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
86    
87  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  cd MITgcm/verification/global_ocean.cs32x15/code
88      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
89      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
90  end  \cp SIZE.h_mpi SIZE.h
91    
92  heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  cd ../build
93  mask=0*heff; mask(find(heff>.001))=1;  \rm *
94  uice=mask.*permute(readbin(['UICE.0000000020.data'],[32,6,32]),[1 3 2]);  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
95  vice=mask.*permute(readbin(['VICE.0000000020.data'],[32,6,32]),[1 3 2]);  make depend
96  clf  make -j
97  subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  
98  subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  cd ..
99  subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  mkdir run
100  subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  cd run
101    \rm *
102    \cp ../input/* .
103    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
104    mpirun -np 2 ../build/mitgcmuv
105    
106    
107  ##########################################################################  ##########################################################################
108  ##########################################################################  ##########################################################################
109  # 32*32*6*15, 2-cpu cube sphere on the altices with efc  # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
110    # starting with pickup file from end of 1992
111    # requires input files in sudirectories run_template and ncep_rgau
112    
113  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
114  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
115  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
116  \cp SIZE.h_mpi SIZE.h  \cp packages.conf_hr packages.conf
117    
118  cd ../build  cd ../build
119  \rm *  \rm *
120  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
121  make depend  make depend
122  make  make -j
123    
124  cd ..  cd ..
125  mkdir run  mkdir run
# Line 122  cd run Line 127  cd run
127  \rm *  \rm *
128  \cp ../input/* .  \cp ../input/* .
129  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
130  mpirun -np 2 ../build/mitgcmuv  qsub job_altix92_54t
131    
132    
133  ##########################################################################  ##########################################################################
134  ##########################################################################  ##########################################################################
135  # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc  # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
136  # requires input files in sudirectories run_template and ncep_rgau  # requires input files in sudirectories run_template and ncep_rgau
137  # presently residing under orion:/tmp1/dmenem/cube  # these can be obained from lou:/u/menemenl/cube
138    
139  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
140  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
141  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
142  \cp SIZE.h_54 SIZE.h  \cp SIZE.h_216 SIZE.h
143  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
144    
145  cd ../build  cd ../build
146  \rm *  \rm *
147  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
148  make depend  make depend
149  make  make -j
150    
151  cd ..  cd ..
152  mkdir run  mkdir run
# Line 149  cd run Line 154  cd run
154  \rm *  \rm *
155  \cp ../input/* .  \cp ../input/* .
156  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
157  qsub job_orion  ln -sf ../../../../run_template/* .
158    \rm pickup*
159    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216.data
160    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216.data
161    \cp ../build/mitgcmuv .
162    qsub job_altix
163    
164    ##########################################################################
165    ##########################################################################
166    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
167    # uses s1500t_17x51 configuration
168    
169    cd MITgcm/verification/global_ocean.cs32x15/code
170    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
171    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
172    \cp SIZE.h_150 SIZE.h
173    \cp packages.conf_hr packages.conf
174    
175    cd ../build
176    \rm *
177    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
178    make depend
179    make -j
180    
181    cd ..
182    mkdir run
183    cd run
184    \rm *
185    \cp ../input/* .
186    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
187    ln -sf ../../../../run_template/* .
188    \rm pickup*
189    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216.data
190    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216.data
191    \cp ../build/mitgcmuv mitgcmuv150
192    qsub job_altix150
193    
194    
195    
196    
197    
198    
199    
200    
201    
202    
203    
204    
205    
206    
207    
208  ##########################################################################  ##########################################################################
209  ##########################################################################  ##########################################################################
210  # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc  # 510*510*6*50, 1500-tile, 375-cpu, excludes land
211  # starting with pickup file from end of 1992  # uses s1500t_17x51 configuration
212  # requires input files in sudirectories run_template and ncep_rgau  # example for running on c17-c20 using arrayd
213    
214  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
215  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
216  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
217    \cp SIZE.h_375 SIZE.h
218  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
219    
220  cd ../build  cd ../build
221  \rm *  \rm *
222  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
223  make depend  make depend
224  make  make -j
225    
226  cd ..  cd ..
227  mkdir run  mkdir run
# Line 175  cd run Line 229  cd run
229  \rm *  \rm *
230  \cp ../input/* .  \cp ../input/* .
231  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
232  qsub job_altix93_newIO  ln -sf ../../../../run_template/* .
233    \rm pickup*
234    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216.data
235    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216.data
236    \cp ../build/mitgcmuv .
237    job_c20_375cpu < /dev/null >&! output.run &
238    
239    
240  ##########################################################################  ##########################################################################
241  ##########################################################################  ##########################################################################
242  # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc  # 510*510*6*50, 1500-tile, 500-cpu, excludes land
243  # requires input files in sudirectories run_template and ncep_rgau  # uses s1500t_17x51 configuration
244  # presently residing under orion:/tmp1/dmenem/cube  # example for running on c17-c20 using arrayd
245    
246  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
247  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
248  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
249  \cp SIZE.h_41 SIZE.h  \cp SIZE.h_500 SIZE.h
250  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
251    
252  cd ../build  cd ../build
253  \rm *  \rm *
254  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
255  make depend  make depend
256  make  make -j
257    
258  cd ..  cd ..
259  mkdir run  mkdir run
# Line 202  cd run Line 261  cd run
261  \rm *  \rm *
262  \cp ../input/* .  \cp ../input/* .
263  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
264  qsub job_orion41  ln -sf ../../../../run_template/* .
265    \rm pickup*
266    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216.data
267    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216.data
268    \cp ../build/mitgcmuv .
269    job_c19_500cpu < /dev/null >&! output.run &
270    
271    
272    
273    
274    
275    
276    
277    
278    
279    
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283    
284    
285    
286    
287    
288    
289    
290    
291    
292    
293    
294  ##########################################################################  ##########################################################################
295  ##########################################################################  ##########################################################################
296  # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc  # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
297  # requires input files in sudirectories run_template and ncep_rgau  # requires input files in sudirectories run_template and ncep_rgau
298  # presently residing under orion:/tmp1/dmenem/cube  # presently residing under orion:/tmp1/dmenem/cube
299    
300  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
301  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
302  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
303  \cp SIZE.h_50 SIZE.h  \cp SIZE.h_54 SIZE.h
304  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
305    
306  cd ../build  cd ../build
307  \rm *  \rm *
308  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
309  make depend  make depend
310  make  make -j
311    
312  cd ..  cd ..
313  mkdir run  mkdir run
# Line 234  qsub job_orion Line 320  qsub job_orion
320    
321  ##########################################################################  ##########################################################################
322  ##########################################################################  ##########################################################################
323  # 510*510*6*50, 216-cpu cube sphere on altix with efc  # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
324  # requires input files in sudirectories run_template and ncep_rgau  # requires input files in sudirectories run_template and ncep_rgau
325  # these can be obained from lou:/u/menemenl/cube  # presently residing under orion:/tmp1/dmenem/cube
326    
327  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
328  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
329  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
330  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_41 SIZE.h
331  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
332    
333  cd ../build  cd ../build
334  \rm *  \rm *
335  ../../../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_altix
336  make depend  make depend
337  make  make -j
338    
339  cd ..  cd ..
340  mkdir run  mkdir run
# Line 256  cd run Line 342  cd run
342  \rm *  \rm *
343  \cp ../input/* .  \cp ../input/* .
344  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
345  qsub job_altix  qsub job_orion41
346    
347    
348  ##########################################################################  ##########################################################################
349  ##########################################################################  ##########################################################################
350  # matlab script for generating pChkptFreq  # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
351    # requires input files in sudirectories run_template and ncep_rgau
352    # presently residing under orion:/tmp1/dmenem/cube
353    
354  nTimeSteps=26352;  cd MITgcm/verification/global_ocean.cs32x15/code
355  for niter0=216:26352:(26352*12)  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
356   pChkptFreq=(niter0+nTimeSteps)*1200;  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
357   day=pChkptFreq/24/60/60;  \cp SIZE.h_50 SIZE.h
358   disp(['niter0=' int2str(niter0) ',day=' int2str(day) ', ' ...  \cp packages.conf_hr packages.conf
  datestr(datenum(1992,1,1)+day) ', pChkptFreq=' int2str(pChkptFreq)])  
 end  
359    
360  niter0 = 216   , day = 369 , 04-Jan-1993, pChkptFreq = 31881600  cd ../build
361  niter0 = 26568 , day = 735 , 05-Jan-1994, pChkptFreq = 63504000  \rm *
362  niter0 = 52920 , day = 1101, 06-Jan-1995, pChkptFreq = 95126400  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
363  niter0 = 79272 , day = 1467, 07-Jan-1996, pChkptFreq = 126748800  make depend
364  niter0 = 105624, day = 1833, 07-Jan-1997, pChkptFreq = 158371200  make -j
365  niter0 = 131976, day = 2199, 08-Jan-1998, pChkptFreq = 189993600  
366  niter0 = 158328, day = 2565, 09-Jan-1999, pChkptFreq = 221616000  cd ..
367  niter0 = 184680, day = 2931, 10-Jan-2000, pChkptFreq = 253238400  mkdir run
368  niter0 = 211032, day = 3297, 10-Jan-2001, pChkptFreq = 284860800  cd run
369  niter0 = 237384, day = 3663, 11-Jan-2002, pChkptFreq = 316483200  \rm *
370  niter0 = 263736, day = 4029, 12-Jan-2003, pChkptFreq = 348105600  \cp ../input/* .
371  niter0 = 290088, day = 4395, 13-Jan-2004, pChkptFreq = 379728000  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
372    qsub job_orion
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