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revision 1.28 by dimitri, Fri Feb 13 08:35:48 2004 UTC revision 1.66 by dimitri, Fri Sep 29 08:37:00 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: February 13, 2004.  
3  This is the code used for cube4, the third 1992-2002 510x510x6  September 28, 2006: 216-CPU code for cube38
4  cube-sphere integration.  
5    September 4, 2006
6    Modified 32*32*6*15 experiments to use grid_cs32.* files from
7     verification/tutorial_held_suarez_cs/input instead of
8     tile* files from verification/global_ocean.cs32x15/input
9    
10    August 8, 2006
11    216-CPU code and input used for integrating cube37
12    using "June 10, 2006" MITgcm code.
13    
14    
15  ##########################################################################  ##########################################################################
16  ##########################################################################  ##########################################################################
17  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
18    
19  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  cvs co MITgcm_contrib/high_res_cube/README_ice
20  cvs login ( CVS password: cvsanon )  cvs co MITgcm_contrib/high_res_cube/code-mods
21  cvs co -r hrcube4 MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/input
22  cvs co -r hrcube4 MITgcm_contrib/high_res_cube/code-mods  cvs co MITgcm_contrib/high_res_cube/results
23  cvs co -r hrcube4 MITgcm_contrib/high_res_cube/matlab-grid-converter  cvs co MITgcm_code
24  cvs co -r hrcube4 MITgcm_contrib/high_res_cube/input  cvs co MITgcm/verification/global_ocean.cs32x15
25  cvs co -r hrcube4 MITgcm_contrib/high_res_cube/results  cvs co MITgcm/verification/tutorial_held_suarez_cs/input
 cvs co -r hrcube4 MITgcm_code  
 cvs co -r hrcube4 MITgcm/verification/global_ocean.cs32x15  
26    
27    
28  ##########################################################################  ##########################################################################
# Line 25  cvs co -r hrcube4 MITgcm/verification/gl Line 31  cvs co -r hrcube4 MITgcm/verification/gl
31    
32  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
33  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
34  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
   
35  cd ../build  cd ../build
36    \rm *
37  ../../../tools/genmake2 -mods=../code  ../../../tools/genmake2 -mods=../code
38  make depend  make depend
39  make  make
   
40  cd ..  cd ..
41  mkdir run  mkdir run
42  cd run  cd run
43    \rm *
44    \cp ../../tutorial_held_suarez_cs/input/grid* .
45  \cp ../input/* .  \cp ../input/* .
 \cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  
46  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
47  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
48    
# Line 46  comparison output is in: Line 52  comparison output is in:
52  to use matlab to look at the output  to use matlab to look at the output
53  matlab  matlab
54    
55  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...
56             'QNETtave','FVtave','FUtave','EmPmRtave'}
57      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]);
58      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
59  end  end
60    
61  heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);
62  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
63  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]);
64  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]);
65  clf  clf
66  subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
67  subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
68  subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
69  subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
70    
71    
72    ##########################################################################
73    ##########################################################################
74    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
75    
76    cd MITgcm/verification/global_ocean.cs32x15/code
77    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
78    \cp ../code_alt/code.176t_8x4/* .
79    cd ../build
80    \rm *
81    ../../../tools/genmake2 -mods=../code
82    make depend
83    make
84    cd ..
85    mkdir run
86    cd run
87    \rm *
88    \cp ../../tutorial_held_suarez_cs/input/grid* .
89    \cp ../input/* .
90    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
91    ../build/mitgcmuv >& output.txt
92    
93    
94  ##########################################################################  ##########################################################################
95  ##########################################################################  ##########################################################################
96  # 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
97    
98  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
99  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
100  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
101  \cp SIZE.h_mpi SIZE.h  \cp SIZE.h_mpi SIZE.h
102    
103  cd ../build  cd ../build
104  \rm *  \rm *
105  ../../../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
106  make depend  make depend
107  make  make -j
108    
109  cd ..  cd ..
110  mkdir run  mkdir run
111  cd run  cd run
112  \rm *  \rm *
113    \cp ../../tutorial_held_suarez_cs/input/grid* .
114  \cp ../input/* .  \cp ../input/* .
 \cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  
115  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
116  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
117    
118    
119  ##########################################################################  ##########################################################################
120  ##########################################################################  ##########################################################################
121  # 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
122    # starting with pickup file from end of 1992
123    # requires input files in sudirectories run_template and ncep_rgau
124    
125    cd MITgcm/verification/global_ocean.cs32x15/code
126    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
127    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
128    \cp packages.conf_hr packages.conf
129    
130    cd ../build
131    \rm *
132    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
133    make depend
134    make -j
135    
136    cd ..
137    mkdir run
138    cd run
139    \rm *
140    \cp ../input/* .
141    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
142    qsub job_altix92_54t
143    
144    
145    ##########################################################################
146    ##########################################################################
147    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
148    # requires input files in sudirectories run_template and ncep_rgau
149    # these can be obained from lou:/u/menemenl/cube
150    
151    cd MITgcm/verification/global_ocean.cs32x15/code
152    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
153    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
154    \cp SIZE.h_216 SIZE.h
155    \cp packages.conf_hr packages.conf
156    
157    cd ../build
158    \rm *
159    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
160    make depend
161    make -j
162    
163    cd ..
164    mkdir run
165    cd run
166    \rm *
167    \cp ../input/* .
168    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
169    ln -sf ../../../../run_template/* .
170    \rm pickup* data.pkg data.seaice data.exf_clim data.exf data bathy_Hmin50.bin
171    \rm *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
172    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
173    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38 pickup_seaice.0000000216
174    \cp ../build/mitgcmuv .
175    qsub job_altix
176    
177    
178    ##########################################################################
179    ##########################################################################
180    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
181    # uses s1500t_17x51 configuration
182    
183    cd MITgcm/verification/global_ocean.cs32x15/code
184    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
185    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
186    \cp SIZE.h_150 SIZE.h
187    \cp packages.conf_hr packages.conf
188    
189    cd ../build
190    \rm *
191    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
192    make depend
193    make -j
194    
195    cd ..
196    mkdir run
197    cd run
198    \rm *
199    \cp ../input/* .
200    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
201    ln -sf ../../../../run_template/* .
202    \rm pickup*
203    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
204    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
205    \cp ../build/mitgcmuv mitgcmuv150
206    qsub job_altix150
207    
208    
209    
210    
211    ##########################################################################
212    ##########################################################################
213    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
214    # uses s1500t_17x51 configuration
215    # example for running on c17-c20 using arrayd
216    
217    cd MITgcm/verification/global_ocean.cs32x15/code
218    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
219    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
220    \cp SIZE.h_375 SIZE.h
221    \cp packages.conf_hr packages.conf
222    
223    cd ../build
224    \rm *
225    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
226    make depend
227    make -j
228    
229    cd ..
230    mkdir run
231    cd run
232    \rm *
233    \cp ../input/* .
234    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
235    ln -sf ../../../../run_template/* .
236    \rm pickup*
237    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
238    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
239    \cp ../build/mitgcmuv .
240    job_c20_375cpu < /dev/null >&! output.run &
241    
242    
243    
244    
245    
246    
247    
248    
249    
250    
251    
252    
253    ##########################################################################
254    ##########################################################################
255    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
256    # uses s1500t_17x51 configuration
257    # example for running on c17-c20 using arrayd
258    
259    cd MITgcm/verification/global_ocean.cs32x15/code
260    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
261    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
262    \cp SIZE.h_375 SIZE.h
263    \cp packages.conf_hr packages.conf
264    
265    cd ../build
266    \rm *
267    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
268    make depend
269    make -j
270    
271    cd ..
272    mkdir run
273    cd run
274    \rm *
275    \cp ../input/* .
276    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
277    ln -sf ../../../../run_template/* .
278    \rm pickup*
279    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
280    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
281    \cp ../build/mitgcmuv .
282    job_c20_375cpu < /dev/null >&! output.run &
283    
284    
285    ##########################################################################
286    ##########################################################################
287    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
288    # uses s1500t_17x51 configuration
289    # example for running on c17-c20 using arrayd
290    
291    cd MITgcm/verification/global_ocean.cs32x15/code
292    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
293    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
294    \cp SIZE.h_500 SIZE.h
295    \cp packages.conf_hr packages.conf
296    
297    cd ../build
298    \rm *
299    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
300    make depend
301    make -j
302    
303    cd ..
304    mkdir run
305    cd run
306    \rm *
307    \cp ../input/* .
308    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
309    ln -sf ../../../../run_template/* .
310    \rm pickup*
311    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
312    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
313    \cp ../build/mitgcmuv .
314    job_c19_500cpu < /dev/null >&! output.run &
315    
316    
317    
318    
319    
320    ##########################################################################
321    ##########################################################################
322    # 510*510*6*50, 216-cpu cube sphere on cosmos
323    
324    cd MITgcm/verification/global_ocean.cs32x15/code
325    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
326    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
327    \cp SIZE.h_216 SIZE.h
328    \cp packages.conf_hr packages.conf
329    
330    module unload latest_intel80
331    module unload mpich-gm-intel80
332    module load latest_intel81
333    module load mpich-gm-intel81
334    
335    cd ../build
336    \rm *
337    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
338    make depend
339    make -j
340    
341    cd ..
342    mkdir run
343    cd run
344    \rm *
345    \cp ../input/* .
346    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
347    ln -sf ../../../../run_template/* .
348    \rm pickup*
349    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
350    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
351    \cp ../build/mitgcmuv .
352    bsub < job_cosmos
353    
354    
355    
356    
357    
358    
359    
360    
361    
362    
363    
364    
365    
366    
367    
368    
369    
370    
371    
372    
373    ##########################################################################
374    ##########################################################################
375    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
376  # requires input files in sudirectories run_template and ncep_rgau  # requires input files in sudirectories run_template and ncep_rgau
377  # presently residing under orion:/tmp1/dmenem/cube  # presently residing under orion:/tmp1/dmenem/cube
378    
# Line 101  cd MITgcm/verification/global_ocean.cs32 Line 384  cd MITgcm/verification/global_ocean.cs32
384    
385  cd ../build  cd ../build
386  \rm *  \rm *
387  ../../../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
388  make depend  make depend
389  make  make -j
390    
391  cd ..  cd ..
392  mkdir run  mkdir run
# Line 128  cd MITgcm/verification/global_ocean.cs32 Line 411  cd MITgcm/verification/global_ocean.cs32
411    
412  cd ../build  cd ../build
413  \rm *  \rm *
414  ../../../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
415  make depend  make depend
416  make  make -j
417    
418  cd ..  cd ..
419  mkdir run  mkdir run
# Line 143  qsub job_orion41 Line 426  qsub job_orion41
426    
427  ##########################################################################  ##########################################################################
428  ##########################################################################  ##########################################################################
429  # 510*510*6*50, 216-cpu cube sphere on altix with efc  # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
430  # requires input files in sudirectories run_template and ncep_rgau  # requires input files in sudirectories run_template and ncep_rgau
431  # these can be obained from lou:/u/menemenl/cube  # presently residing under orion:/tmp1/dmenem/cube
432    
433  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
434  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
435  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
436  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_50 SIZE.h
437  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
438    
439  cd ../build  cd ../build
440  \rm *  \rm *
441  ../../../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
442  make depend  make depend
443  make  make -j
444    
445  cd ..  cd ..
446  mkdir run  mkdir run
# Line 165  cd run Line 448  cd run
448  \rm *  \rm *
449  \cp ../input/* .  \cp ../input/* .
450  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
451  qsub -l ignore_ded=1 job_altix  qsub job_orion
   
   
 ##########################################################################  
 ##########################################################################  
 # matlab script for generating pChkptFreq  
   
 nTimeSteps=26352;  
 for niter0=216:26352:(26352*11)  
  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  
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