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revision 1.22 by dimitri, Fri Feb 6 21:12:01 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: January 24, 2004.  Date last updated: February 25, 2005
3  This is the code used for cube2, the second 1992-2002 510x510x6  216-CPU code and input used for integrating cube29.
 cube-sphere integration.  
4    
5    
6  ##########################################################################  ##########################################################################
7  ##########################################################################  ##########################################################################
8  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
9    
10  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  cvs co MITgcm_contrib/high_res_cube/README_ice
11  cvs login ( CVS password: cvsanon )  cvs co MITgcm_contrib/high_res_cube/code-mods
12  cvs co -r hrcube_2 MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/input
13  cvs co -r hrcube_2 MITgcm_contrib/high_res_cube/code-mods  cvs co MITgcm_contrib/high_res_cube/results
14  cvs co -r hrcube_2 MITgcm_contrib/high_res_cube/matlab-grid-converter  cvs co MITgcm_code
15  cvs co -r hrcube_2 MITgcm_contrib/high_res_cube/input  cvs co MITgcm/verification/global_ocean.cs32x15
16  cvs co -r hrcube_2 MITgcm_contrib/high_res_cube/results  
17  cvs co -r hrcube_2 MITgcm_code  # remove check in config_check.F
18  cvs co -r hrcube_2 MITgcm/verification/global_ocean.cs32x15  > 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 25  cvs co -r hrcube_2 MITgcm/verification/g Line 30  cvs co -r hrcube_2 MITgcm/verification/g
30    
31  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
32  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
33  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
34    cd ../build
35  cd ..  \rm *
 mkdir build  
 cd build  
36  ../../../tools/genmake2 -mods=../code  ../../../tools/genmake2 -mods=../code
37  make depend  make depend
38  make  make
   
39  cd ..  cd ..
40  mkdir run  mkdir run
41  cd run  cd run
42    \rm *
43  \cp ../input/* .  \cp ../input/* .
 \cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  
44  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
45  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
46    
# Line 48  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    ##########################################################################
71    ##########################################################################
72    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
73    
74    cd MITgcm/verification/global_ocean.cs32x15/code
75    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
76    \cp ../code_alt/code.176t_8x4/* .
77    cd ../build
78    \rm *
79    ../../../tools/genmake2 -mods=../code
80    make depend
81    make
82    cd ..
83    mkdir run
84    cd run
85    \rm *
86    \cp ../input/* .
87    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
88    ../build/mitgcmuv >& output.txt
89    
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/* .
97  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
98  \cp SIZE.h_mpi SIZE.h  \cp SIZE.h_mpi SIZE.h
99    
100  cd ..  cd ../build
 mkdir build  
 cd build  
101  \rm *  \rm *
102  ../../../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
103  make depend  make depend
104  make  make -j
105    
106  cd ..  cd ..
107  mkdir run  mkdir run
108  cd run  cd run
109  \rm *  \rm *
110  \cp ../input/* .  \cp ../input/* .
 \cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  
111  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
112  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
113    
114    
115  ##########################################################################  ##########################################################################
116  ##########################################################################  ##########################################################################
117  # 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
118    # starting with pickup file from end of 1992
119  # requires input files in sudirectories run_template and ncep_rgau  # requires input files in sudirectories run_template and ncep_rgau
 # presently residing under orion:/tmp1/dmenem/cube  
120    
121  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
122  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
123  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
 \cp SIZE.h_54 SIZE.h  
124  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
 \cp mom_vi_hdissip.F_hr mom_vi_hdissip.F  
125    
126  cd ..  cd ../build
 mkdir build  
 cd build  
127  \rm *  \rm *
128  ../../../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
129  make depend  make depend
130  make  make -j
131    
132  cd ..  cd ..
133  mkdir run  mkdir run
# Line 118  cd run Line 135  cd run
135  \rm *  \rm *
136  \cp ../input/* .  \cp ../input/* .
137  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
138  qsub job_orion  qsub job_altix92_54t
139    
140    
141  ##########################################################################  ##########################################################################
142  ##########################################################################  ##########################################################################
143  # 510*510*6*50, 216-cpu cube sphere on altix with efc  # 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 132  cd MITgcm/verification/global_ocean.cs32 Line 149  cd MITgcm/verification/global_ocean.cs32
149  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
150  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_216 SIZE.h
151  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
152  \cp mom_vi_hdissip.F_hr mom_vi_hdissip.F  
153    cd ../build
154    \rm *
155    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
156    make depend
157    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 ..  cd ..
191  mkdir build  mkdir run
192  cd build  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 ..
337    mkdir run
338    cd run
339    \rm *
340    \cp ../input/* .
341    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
342    ln -sf ../../../../run_template/* .
343    \rm pickup*
344    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 .
347    bsub < job_cosmos
348    
349    
350    
351    
352    
353    
354    
355    
356    
357    
358    
359    
360    
361    
362    
363    
364    
365    
366    
367    
368    ##########################################################################
369    ##########################################################################
370    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
371    # requires input files in sudirectories run_template and ncep_rgau
372    # presently residing under orion:/tmp1/dmenem/cube
373    
374    cd MITgcm/verification/global_ocean.cs32x15/code
375    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
376    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
377    \cp SIZE.h_54 SIZE.h
378    \cp packages.conf_hr packages.conf
379    
380    cd ../build
381  \rm *  \rm *
382  ../../../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
383  make depend  make depend
384  make  make -j
385    
386  cd ..  cd ..
387  mkdir run  mkdir run
# Line 148  cd run Line 389  cd run
389  \rm *  \rm *
390  \cp ../input/* .  \cp ../input/* .
391  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
392  qsub job_altix  qsub job_orion
393    
394    
395  ##########################################################################  ##########################################################################
396  ##########################################################################  ##########################################################################
397  # matlab script for generating pChkptFreq  # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
398    # requires input files in sudirectories run_template and ncep_rgau
399    # presently residing under orion:/tmp1/dmenem/cube
400    
401  nTimeSteps=26352;  cd MITgcm/verification/global_ocean.cs32x15/code
402  for niter0=216:26352:(26352*11)  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
403   pChkptFreq=(niter0+nTimeSteps)*1200;  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
404   day=pChkptFreq/24/60/60;  \cp SIZE.h_41 SIZE.h
405   disp(['niter0=' int2str(niter0) ',day=' int2str(day) ', ' ...  \cp packages.conf_hr packages.conf
  datestr(datenum(1992,1,1)+day) ', pChkptFreq=' int2str(pChkptFreq)])  
 end  
406    
407  niter0 = 216   , day = 369 , 04-Jan-1993, pChkptFreq = 31881600  cd ../build
408  niter0 = 26568 , day = 735 , 05-Jan-1994, pChkptFreq = 63504000  \rm *
409  niter0 = 52920 , day = 1101, 06-Jan-1995, pChkptFreq = 95126400  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
410  niter0 = 79272 , day = 1467, 07-Jan-1996, pChkptFreq = 126748800  make depend
411  niter0 = 105624, day = 1833, 07-Jan-1997, pChkptFreq = 158371200  make -j
412  niter0 = 131976, day = 2199, 08-Jan-1998, pChkptFreq = 189993600  
413  niter0 = 158328, day = 2565, 09-Jan-1999, pChkptFreq = 221616000  cd ..
414  niter0 = 184680, day = 2931, 10-Jan-2000, pChkptFreq = 253238400  mkdir run
415  niter0 = 211032, day = 3297, 10-Jan-2001, pChkptFreq = 284860800  cd run
416  niter0 = 237384, day = 3663, 11-Jan-2002, pChkptFreq = 316483200  \rm *
417  niter0 = 263736, day = 4029, 12-Jan-2003, pChkptFreq = 348105600  \cp ../input/* .
418    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
419    qsub job_orion41
420    
421    
422    ##########################################################################
423    ##########################################################################
424    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
425    # requires input files in sudirectories run_template and ncep_rgau
426    # presently residing under orion:/tmp1/dmenem/cube
427    
428    cd MITgcm/verification/global_ocean.cs32x15/code
429    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
430    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
431    \cp SIZE.h_50 SIZE.h
432    \cp packages.conf_hr packages.conf
433    
434    cd ../build
435    \rm *
436    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
437    make depend
438    make -j
439    
440    cd ..
441    mkdir run
442    cd run
443    \rm *
444    \cp ../input/* .
445    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
446    qsub job_orion
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