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revision 1.41 by dimitri, Fri Jul 9 23:54:52 2004 UTC revision 1.64 by dimitri, Tue Aug 8 13:45:43 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: August 8, 2006
3  Code and input used for integrating cube9.  216-CPU code and input used for integrating cube37
4    using "June 10, 2006" MITgcm code.
5    
6    
7  ##########################################################################  ##########################################################################
# Line 11  cvs co MITgcm_contrib/high_res_cube/READ Line 12  cvs co MITgcm_contrib/high_res_cube/READ
12  cvs co MITgcm_contrib/high_res_cube/code-mods  cvs co MITgcm_contrib/high_res_cube/code-mods
13  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
14  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
15  cvs co MITgcm_contrib/edge_problem  cvs co MITgcm_code
16  cvs co -r checkpoint54b_post MITgcm_code  cvs co MITgcm/verification/global_ocean.cs32x15
 cvs co -r checkpoint54b_post MITgcm/verification/global_ocean.cs32x15  
 cvs co -r checkpoint54b_post MITgcm/verification/testreport  
17    
18    
19  ##########################################################################  ##########################################################################
# 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 *
# 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_altix  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
148  make depend  make depend
149  make -j  make -j
150    
# 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* data.pkg data.seaice data.exf_clim data.exf data
159    \rm *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
160    ln -sf ../../../../run_template/pickup.0000000216.cube27 pickup.0000000216
161    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube27 pickup_seaice.0000000216
162    \cp ../build/mitgcmuv .
163    qsub job_altix
164    
165    
166  ##########################################################################  ##########################################################################
167  ##########################################################################  ##########################################################################
168  # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc  # 510*510*6*50, 1500-tile, 150-cpu, excludes land
169  # starting with pickup file from end of 1992  # uses s1500t_17x51 configuration
 # requires input files in sudirectories run_template and ncep_rgau  
170    
171  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
172  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
173  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
174    \cp SIZE.h_150 SIZE.h
175  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
176    
177  cd ../build  cd ../build
178  \rm *  \rm *
179  ../../../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
180  make depend  make depend
181  make -j  make -j
182    
# Line 175  cd run Line 186  cd run
186  \rm *  \rm *
187  \cp ../input/* .  \cp ../input/* .
188  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
189  qsub job_altix92_54t  ln -sf ../../../../run_template/* .
190    \rm pickup*
191    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
192    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
193    \cp ../build/mitgcmuv mitgcmuv150
194    qsub job_altix150
195    
196    
197    
198    
199  ##########################################################################  ##########################################################################
200  ##########################################################################  ##########################################################################
201  # 510*510*6*50, 216-cpu cube sphere on altix with efc  # 510*510*6*50, 1500-tile, 375-cpu, excludes land
202  # requires input files in sudirectories run_template and ncep_rgau  # uses s1500t_17x51 configuration
203  # these can be obained from lou:/u/menemenl/cube  # example for running on c17-c20 using arrayd
204    
205  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
206  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
207  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
208  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_375 SIZE.h
209  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
210    
211  cd ../build  cd ../build
212  \rm *  \rm *
213  ../../../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
214  make depend  make depend
215  make -j  make -j
216    
# Line 202  cd run Line 220  cd run
220  \rm *  \rm *
221  \cp ../input/* .  \cp ../input/* .
222  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
223  qsub job_altix92  ln -sf ../../../../run_template/* .
224    \rm pickup*
225    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
226    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
227    \cp ../build/mitgcmuv .
228    job_c20_375cpu < /dev/null >&! output.run &
229    
230    
231    
# Line 215  qsub job_altix92 Line 238  qsub job_altix92
238    
239    
240    
241    ##########################################################################
242    ##########################################################################
243    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
244    # uses s1500t_17x51 configuration
245    # example for running on c17-c20 using arrayd
246    
247    cd MITgcm/verification/global_ocean.cs32x15/code
248    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
249    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
250    \cp SIZE.h_375 SIZE.h
251    \cp packages.conf_hr packages.conf
252    
253    cd ../build
254    \rm *
255    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
256    make depend
257    make -j
258    
259    cd ..
260    mkdir run
261    cd run
262    \rm *
263    \cp ../input/* .
264    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
265    ln -sf ../../../../run_template/* .
266    \rm pickup*
267    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
268    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
269    \cp ../build/mitgcmuv .
270    job_c20_375cpu < /dev/null >&! output.run &
271    
272    
273    ##########################################################################
274    ##########################################################################
275    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
276    # uses s1500t_17x51 configuration
277    # example for running on c17-c20 using arrayd
278    
279    cd MITgcm/verification/global_ocean.cs32x15/code
280    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
281    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
282    \cp SIZE.h_500 SIZE.h
283    \cp packages.conf_hr packages.conf
284    
285    cd ../build
286    \rm *
287    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
288    make depend
289    make -j
290    
291    cd ..
292    mkdir run
293    cd run
294    \rm *
295    \cp ../input/* .
296    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
297    ln -sf ../../../../run_template/* .
298    \rm pickup*
299    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
300    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
301    \cp ../build/mitgcmuv .
302    job_c19_500cpu < /dev/null >&! output.run &
303    
304    
305    
306    
307    
308    ##########################################################################
309    ##########################################################################
310    # 510*510*6*50, 216-cpu cube sphere on cosmos
311    
312    cd MITgcm/verification/global_ocean.cs32x15/code
313    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
314    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
315    \cp SIZE.h_216 SIZE.h
316    \cp packages.conf_hr packages.conf
317    
318    module unload latest_intel80
319    module unload mpich-gm-intel80
320    module load latest_intel81
321    module load mpich-gm-intel81
322    
323    cd ../build
324    \rm *
325    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
326    make depend
327    make -j
328    
329    cd ..
330    mkdir run
331    cd run
332    \rm *
333    \cp ../input/* .
334    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
335    ln -sf ../../../../run_template/* .
336    \rm pickup*
337    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
338    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
339    \cp ../build/mitgcmuv .
340    bsub < job_cosmos
341    
342    
343    
# Line 230  qsub job_altix92 Line 352  qsub job_altix92
352    
353    
354    
355    
356    
357    
358    
359    
360    
361    ##########################################################################
362    ##########################################################################
363    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
364    # requires input files in sudirectories run_template and ncep_rgau
365    # presently residing under orion:/tmp1/dmenem/cube
366    
367    cd MITgcm/verification/global_ocean.cs32x15/code
368    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
369    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
370    \cp SIZE.h_54 SIZE.h
371    \cp packages.conf_hr packages.conf
372    
373    cd ../build
374    \rm *
375    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
376    make depend
377    make -j
378    
379    cd ..
380    mkdir run
381    cd run
382    \rm *
383    \cp ../input/* .
384    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
385    qsub job_orion
386    
387    
388  ##########################################################################  ##########################################################################
389  ##########################################################################  ##########################################################################
390  # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc  # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
# Line 282  cd run Line 437  cd run
437  \cp ../input/* .  \cp ../input/* .
438  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
439  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  
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