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revision 1.48 by dimitri, Wed Dec 29 23:05:12 2004 UTC revision 1.62 by dimitri, Sat Feb 25 16:59:00 2006 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: July 9, 2004.  Date last updated: February 25, 2005
3  Code and input used for integrating cube9.  216-CPU code and input used for integrating cube29.
4    
5    
6  ##########################################################################  ##########################################################################
# Line 13  cvs co MITgcm_contrib/high_res_cube/inpu Line 13  cvs co MITgcm_contrib/high_res_cube/inpu
13  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
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  
17    # remove check in config_check.F
18    > C-TRM     IF ( highOrderVorticity .AND. useCubedSphereExchange ) THEN
19    > C-TRM       WRITE(msgBuf,'(2A)')
20    > C-TRM    &   'CONFIG_CHECK: highOrderVorticity Scheme does not work',
21    > C-TRM    &   ' on CubedSphere grid'
22    > C-TRM       CALL PRINT_ERROR( msgBuf , myThid)
23    > C-TRM       STOP 'ABNORMAL END: S/R CONFIG_CHECK'
24    > C-TRM     ENDIF
25    
26    
27  ##########################################################################  ##########################################################################
# Line 42  comparison output is in: Line 50  comparison output is in:
50  to use matlab to look at the output  to use matlab to look at the output
51  matlab  matlab
52    
53  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...
54             'QNETtave','FVtave','FUtave','EmPmRtave'}
55      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]);
56      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
57  end  end
58    
59  heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);
60  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
61  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]);
62  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]);
63  clf  clf
64  subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
65  subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
66  subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
67  subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
68    
69    
70  ##########################################################################  ##########################################################################
# Line 78  cd run Line 87  cd run
87  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
88  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
89    
 comparison output is in:  
 ../../../../MITgcm_contrib/high_res_cube/results/output.txt  
   
 to use matlab to look at the output  
 matlab  
   
 for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  
     tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);  
     cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause  
 end  
   
 heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  
 mask=0*heff; mask(find(heff>.001))=1;  
 uice=mask.*permute(readbin(['UICE.0000000020.data'],[32,6,32]),[1 3 2]);  
 vice=mask.*permute(readbin(['VICE.0000000020.data'],[32,6,32]),[1 3 2]);  
 clf  
 subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  
 subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  
 subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  
 subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  
   
90    
91  ##########################################################################  ##########################################################################
92  ##########################################################################  ##########################################################################
93  # 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 ifort
94    
95  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
96  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
# Line 111  cd MITgcm/verification/global_ocean.cs32 Line 99  cd MITgcm/verification/global_ocean.cs32
99    
100  cd ../build  cd ../build
101  \rm *  \rm *
102  ../../../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
103  make depend  make depend
104  make -j  make -j
105    
# Line 152  qsub job_altix92_54t Line 140  qsub job_altix92_54t
140    
141  ##########################################################################  ##########################################################################
142  ##########################################################################  ##########################################################################
143  # 510*510*6*50, 216-cpu cube sphere on altix with ifort  # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
144  # requires input files in sudirectories run_template and ncep_rgau  # requires input files in sudirectories run_template and ncep_rgau
145  # these can be obained from lou:/u/menemenl/cube  # these can be obained from lou:/u/menemenl/cube
146    
# Line 166  cd ../build Line 154  cd ../build
154  \rm *  \rm *
155  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
156  make depend  make depend
157  make -j 4  make -j
158    
159    cd ..
160    mkdir run
161    cd run
162    \rm *
163    \cp ../input/* .
164    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
165    ln -sf ../../../../run_template/* .
166    \rm pickup*
167    ln -sf ../../../../run_template/pickup.0000000216.cube27 pickup.0000000216
168    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube27 pickup_seaice.0000000216
169    \cp ../build/mitgcmuv .
170    qsub job_altix
171    
172    
173    ##########################################################################
174    ##########################################################################
175    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
176    # uses s1500t_17x51 configuration
177    
178    cd MITgcm/verification/global_ocean.cs32x15/code
179    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
180    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
181    \cp SIZE.h_150 SIZE.h
182    \cp packages.conf_hr packages.conf
183    
184    cd ../build
185    \rm *
186    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
187    make depend
188    make -j
189    
190    cd ..
191    mkdir run
192    cd run
193    \rm *
194    \cp ../input/* .
195    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
196    ln -sf ../../../../run_template/* .
197    \rm pickup*
198    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
199    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
200    \cp ../build/mitgcmuv mitgcmuv150
201    qsub job_altix150
202    
203    
204    
205    
206    ##########################################################################
207    ##########################################################################
208    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
209    # uses s1500t_17x51 configuration
210    # example for running on c17-c20 using arrayd
211    
212    cd MITgcm/verification/global_ocean.cs32x15/code
213    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
214    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
215    \cp SIZE.h_375 SIZE.h
216    \cp packages.conf_hr packages.conf
217    
218    cd ../build
219    \rm *
220    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
221    make depend
222    make -j
223    
224    cd ..
225    mkdir run
226    cd run
227    \rm *
228    \cp ../input/* .
229    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
230    ln -sf ../../../../run_template/* .
231    \rm pickup*
232    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
233    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
234    \cp ../build/mitgcmuv .
235    job_c20_375cpu < /dev/null >&! output.run &
236    
237    
238    
239    
240    
241    
242    
243    
244    
245    
246    
247    
248    ##########################################################################
249    ##########################################################################
250    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
251    # uses s1500t_17x51 configuration
252    # example for running on c17-c20 using arrayd
253    
254    cd MITgcm/verification/global_ocean.cs32x15/code
255    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
256    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
257    \cp SIZE.h_375 SIZE.h
258    \cp packages.conf_hr packages.conf
259    
260    cd ../build
261    \rm *
262    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
263    make depend
264    make -j
265    
266    cd ..
267    mkdir run
268    cd run
269    \rm *
270    \cp ../input/* .
271    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
272    ln -sf ../../../../run_template/* .
273    \rm pickup*
274    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
275    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
276    \cp ../build/mitgcmuv .
277    job_c20_375cpu < /dev/null >&! output.run &
278    
279    
280    ##########################################################################
281    ##########################################################################
282    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
283    # uses s1500t_17x51 configuration
284    # example for running on c17-c20 using arrayd
285    
286    cd MITgcm/verification/global_ocean.cs32x15/code
287    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
288    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
289    \cp SIZE.h_500 SIZE.h
290    \cp packages.conf_hr packages.conf
291    
292    cd ../build
293    \rm *
294    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
295    make depend
296    make -j
297    
298    cd ..
299    mkdir run
300    cd run
301    \rm *
302    \cp ../input/* .
303    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
304    ln -sf ../../../../run_template/* .
305    \rm pickup*
306    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
307    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
308    \cp ../build/mitgcmuv .
309    job_c19_500cpu < /dev/null >&! output.run &
310    
311    
312    
313    
314    
315    ##########################################################################
316    ##########################################################################
317    # 510*510*6*50, 216-cpu cube sphere on cosmos
318    
319    cd MITgcm/verification/global_ocean.cs32x15/code
320    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
321    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
322    \cp SIZE.h_216 SIZE.h
323    \cp packages.conf_hr packages.conf
324    
325    module unload latest_intel80
326    module unload mpich-gm-intel80
327    module load latest_intel81
328    module load mpich-gm-intel81
329    
330    cd ../build
331    \rm *
332    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
333    make depend
334    make -j
335    
336  cd ..  cd ..
337  mkdir run  mkdir run
# Line 175  cd run Line 340  cd run
340  \cp ../input/* .  \cp ../input/* .
341  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
342  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
343  ln -sf pickup.0000290088.data.cube10 pickup.0000000216.data  \rm pickup*
344  ln -sf pickup_seaice.0000290088.data.cube10 pickup_seaice.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
345    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
346  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv .
347  qsub job_altix92  bsub < job_cosmos
348    
349    
350    
351    
352    
# Line 276  cd run Line 444  cd run
444  \cp ../input/* .  \cp ../input/* .
445  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
446  qsub job_orion  qsub job_orion
   
   
 ##########################################################################  
 ##########################################################################  
 # matlab script for generating pChkptFreq  
   
 nTimeSteps=26352;  
 for niter0=216:26352:(26352*12)  
  pChkptFreq=(niter0+nTimeSteps)*1200;  
  day=pChkptFreq/24/60/60;  
  disp(['niter0=' int2str(niter0) ',day=' int2str(day) ', ' ...  
  datestr(datenum(1992,1,1)+day) ', pChkptFreq=' int2str(pChkptFreq)])  
 end  
   
 niter0 = 216   , day = 369 , 04-Jan-1993, pChkptFreq = 31881600  
 niter0 = 26568 , day = 735 , 05-Jan-1994, pChkptFreq = 63504000  
 niter0 = 52920 , day = 1101, 06-Jan-1995, pChkptFreq = 95126400  
 niter0 = 79272 , day = 1467, 07-Jan-1996, pChkptFreq = 126748800  
 niter0 = 105624, day = 1833, 07-Jan-1997, pChkptFreq = 158371200  
 niter0 = 131976, day = 2199, 08-Jan-1998, pChkptFreq = 189993600  
 niter0 = 158328, day = 2565, 09-Jan-1999, pChkptFreq = 221616000  
 niter0 = 184680, day = 2931, 10-Jan-2000, pChkptFreq = 253238400  
 niter0 = 211032, day = 3297, 10-Jan-2001, pChkptFreq = 284860800  
 niter0 = 237384, day = 3663, 11-Jan-2002, pChkptFreq = 316483200  
 niter0 = 263736, day = 4029, 12-Jan-2003, pChkptFreq = 348105600  
 niter0 = 290088, day = 4395, 13-Jan-2004, pChkptFreq = 379728000  
   
   
   
   
   
   
 #!/bin/csh  
 \cp data.pkg_hr data.pkg  
 \cp data.seaice_hr data.seaice  
 \cp data.exf_clim_hr data.exf_clim  
   
 \cp data_hr92 data  
 ./modpickup  
 \cp data.exf_hr92 data.exf  
 /opt/sgi/mpt/1.11-85/bin/mpirun.real -v -a a2k c20 216 runon 221-436 mitgcmuv  
 mkdir out.1992  
 \mv STDOUT.0000 *.data pickup*.meta out.1992  
 \cp data* out.1992  
 \rm STD* *.meta  
   
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