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revision 1.20 by dimitri, Sun Jan 25 06:33:20 2004 UTC revision 1.63 by dimitri, Sat Jun 10 15:47:23 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: June 10, 2006
3  This is the code used for cube2 the second 1992-2002 510x510x6  216-CPU code and input used for integrating cube37.
 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
 cvs co -r hrcube_2 MITgcm_contrib/high_res_cube/results  
 cvs co -r hrcube_2 MITgcm_code  
 cvs co -r hrcube_2 MITgcm/verification/global_ocean.cs32x15  
16    
17    
18  ##########################################################################  ##########################################################################
# Line 25  cvs co -r hrcube_2 MITgcm/verification/g Line 21  cvs co -r hrcube_2 MITgcm/verification/g
21    
22  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
23  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
24  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
25    cd ../build
26  cd ..  \rm *
 mkdir build  
 cd build  
27  ../../../tools/genmake2 -mods=../code  ../../../tools/genmake2 -mods=../code
28  make depend  make depend
29  make  make
   
30  cd ..  cd ..
31  mkdir run  mkdir run
32  cd run  cd run
33    \rm *
34  \cp ../input/* .  \cp ../input/* .
 \cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  
35  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
36  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
37    
# Line 48  comparison output is in: Line 41  comparison output is in:
41  to use matlab to look at the output  to use matlab to look at the output
42  matlab  matlab
43    
44  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...
45             'QNETtave','FVtave','FUtave','EmPmRtave'}
46      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]);
47      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
48  end  end
49    
50  heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);
51  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
52  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]);
53  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]);
54  clf  clf
55  subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
56  subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
57  subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
58  subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
59    
60    
61    ##########################################################################
62    ##########################################################################
63    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
64    
65    cd MITgcm/verification/global_ocean.cs32x15/code
66    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
67    \cp ../code_alt/code.176t_8x4/* .
68    cd ../build
69    \rm *
70    ../../../tools/genmake2 -mods=../code
71    make depend
72    make
73    cd ..
74    mkdir run
75    cd run
76    \rm *
77    \cp ../input/* .
78    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
79    ../build/mitgcmuv >& output.txt
80    
81    
82  ##########################################################################  ##########################################################################
83  ##########################################################################  ##########################################################################
84  # 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
85    
86  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
87  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
88  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
89  \cp SIZE.h_mpi SIZE.h  \cp SIZE.h_mpi SIZE.h
 \cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h  
90    
91  cd ..  cd ../build
 mkdir build  
 cd build  
92  \rm *  \rm *
93  ../../../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
94  make depend  make depend
95  make  make -j
96    
97  cd ..  cd ..
98  mkdir run  mkdir run
99  cd run  cd run
100  \rm *  \rm *
101  \cp ../input/* .  \cp ../input/* .
 \cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  
102  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
103  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
104    
105    
106  ##########################################################################  ##########################################################################
107  ##########################################################################  ##########################################################################
108  # 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
109    # starting with pickup file from end of 1992
110  # 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  
111    
112  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
113  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
114  \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  
 \cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h  
115  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
 \cp mom_vi_hdissip.F_hr mom_vi_hdissip.F  
116    
117  cd ..  cd ../build
 mkdir build  
 cd build  
118  \rm *  \rm *
119  ../../../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
120  make depend  make depend
121  make  make -j
122    
123  cd ..  cd ..
124  mkdir run  mkdir run
# Line 120  cd run Line 126  cd run
126  \rm *  \rm *
127  \cp ../input/* .  \cp ../input/* .
128  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
129  qsub job_orion  qsub job_altix92_54t
130    
131    
132  ##########################################################################  ##########################################################################
133  ##########################################################################  ##########################################################################
134  # 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
135  # requires input files in sudirectories run_template and ncep_rgau  # requires input files in sudirectories run_template and ncep_rgau
136  # these can be obained from lou:/u/menemenl/cube  # these can be obained from lou:/u/menemenl/cube
137    
# Line 133  cd MITgcm/verification/global_ocean.cs32 Line 139  cd MITgcm/verification/global_ocean.cs32
139  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
140  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
141  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_216 SIZE.h
 \cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h  
142  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
143  \cp mom_vi_hdissip.F_hr mom_vi_hdissip.F  
144    cd ../build
145    \rm *
146    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
147    make depend
148    make -j
149    
150    cd ..
151    mkdir run
152    cd run
153    \rm *
154    \cp ../input/* .
155    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
156    ln -sf ../../../../run_template/* .
157    \rm pickup* data.pkg data.seaice data.exf_clim data.exf data
158    \rm *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
159    ln -sf ../../../../run_template/pickup.0000000216.cube27 pickup.0000000216
160    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube27 pickup_seaice.0000000216
161    \cp ../build/mitgcmuv .
162    qsub job_altix
163    
164    
165    ##########################################################################
166    ##########################################################################
167    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
168    # uses s1500t_17x51 configuration
169    
170    cd MITgcm/verification/global_ocean.cs32x15/code
171    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
172    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
173    \cp SIZE.h_150 SIZE.h
174    \cp packages.conf_hr packages.conf
175    
176    cd ../build
177    \rm *
178    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
179    make depend
180    make -j
181    
182  cd ..  cd ..
183  mkdir build  mkdir run
184  cd build  cd run
185    \rm *
186    \cp ../input/* .
187    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
188    ln -sf ../../../../run_template/* .
189    \rm pickup*
190    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
191    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
192    \cp ../build/mitgcmuv mitgcmuv150
193    qsub job_altix150
194    
195    
196    
197    
198    ##########################################################################
199    ##########################################################################
200    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
201    # uses s1500t_17x51 configuration
202    # example for running on c17-c20 using arrayd
203    
204    cd MITgcm/verification/global_ocean.cs32x15/code
205    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
206    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
207    \cp SIZE.h_375 SIZE.h
208    \cp packages.conf_hr packages.conf
209    
210    cd ../build
211    \rm *
212    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
213    make depend
214    make -j
215    
216    cd ..
217    mkdir run
218    cd run
219    \rm *
220    \cp ../input/* .
221    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
222    ln -sf ../../../../run_template/* .
223    \rm pickup*
224    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
225    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
226    \cp ../build/mitgcmuv .
227    job_c20_375cpu < /dev/null >&! output.run &
228    
229    
230    
231    
232    
233    
234    
235    
236    
237    
238    
239    
240    ##########################################################################
241    ##########################################################################
242    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
243    # uses s1500t_17x51 configuration
244    # example for running on c17-c20 using arrayd
245    
246    cd MITgcm/verification/global_ocean.cs32x15/code
247    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
248    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
249    \cp SIZE.h_375 SIZE.h
250    \cp packages.conf_hr packages.conf
251    
252    cd ../build
253    \rm *
254    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
255    make depend
256    make -j
257    
258    cd ..
259    mkdir run
260    cd run
261    \rm *
262    \cp ../input/* .
263    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
264    ln -sf ../../../../run_template/* .
265    \rm pickup*
266    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
267    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
268    \cp ../build/mitgcmuv .
269    job_c20_375cpu < /dev/null >&! output.run &
270    
271    
272    ##########################################################################
273    ##########################################################################
274    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
275    # uses s1500t_17x51 configuration
276    # example for running on c17-c20 using arrayd
277    
278    cd MITgcm/verification/global_ocean.cs32x15/code
279    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
280    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
281    \cp SIZE.h_500 SIZE.h
282    \cp packages.conf_hr packages.conf
283    
284    cd ../build
285    \rm *
286    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
287    make depend
288    make -j
289    
290    cd ..
291    mkdir run
292    cd run
293    \rm *
294    \cp ../input/* .
295    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
296    ln -sf ../../../../run_template/* .
297    \rm pickup*
298    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
299    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
300    \cp ../build/mitgcmuv .
301    job_c19_500cpu < /dev/null >&! output.run &
302    
303    
304    
305    
306    
307    ##########################################################################
308    ##########################################################################
309    # 510*510*6*50, 216-cpu cube sphere on cosmos
310    
311    cd MITgcm/verification/global_ocean.cs32x15/code
312    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
313    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
314    \cp SIZE.h_216 SIZE.h
315    \cp packages.conf_hr packages.conf
316    
317    module unload latest_intel80
318    module unload mpich-gm-intel80
319    module load latest_intel81
320    module load mpich-gm-intel81
321    
322    cd ../build
323    \rm *
324    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
325    make depend
326    make -j
327    
328    cd ..
329    mkdir run
330    cd run
331    \rm *
332    \cp ../input/* .
333    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
334    ln -sf ../../../../run_template/* .
335    \rm pickup*
336    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
337    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
338    \cp ../build/mitgcmuv .
339    bsub < job_cosmos
340    
341    
342    
343    
344    
345    
346    
347    
348    
349    
350    
351    
352    
353    
354    
355    
356    
357    
358    
359    
360    ##########################################################################
361    ##########################################################################
362    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
363    # requires input files in sudirectories run_template and ncep_rgau
364    # presently residing under orion:/tmp1/dmenem/cube
365    
366    cd MITgcm/verification/global_ocean.cs32x15/code
367    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
368    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
369    \cp SIZE.h_54 SIZE.h
370    \cp packages.conf_hr packages.conf
371    
372    cd ../build
373  \rm *  \rm *
374  ../../../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
375  make depend  make depend
376  make  make -j
377    
378  cd ..  cd ..
379  mkdir run  mkdir run
# Line 151  cd run Line 381  cd run
381  \rm *  \rm *
382  \cp ../input/* .  \cp ../input/* .
383  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
384  qsub job_altix  qsub job_orion
385    
386    
387  ##########################################################################  ##########################################################################
388  ##########################################################################  ##########################################################################
389  # matlab script for generating pChkptFreq  # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
390    # requires input files in sudirectories run_template and ncep_rgau
391    # presently residing under orion:/tmp1/dmenem/cube
392    
393  nTimeSteps=26352;  cd MITgcm/verification/global_ocean.cs32x15/code
394  for niter0=216:26352:(26352*11)  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
395   pChkptFreq=(niter0+nTimeSteps)*1200;  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
396   day=pChkptFreq/24/60/60;  \cp SIZE.h_41 SIZE.h
397   disp(['niter0=' int2str(niter0) ',day=' int2str(day) ', ' ...  \cp packages.conf_hr packages.conf
  datestr(datenum(1992,1,1)+day) ', pChkptFreq=' int2str(pChkptFreq)])  
 end  
398    
399  niter0 = 216   , day = 369 , 04-Jan-1993, pChkptFreq = 31881600  cd ../build
400  niter0 = 26568 , day = 735 , 05-Jan-1994, pChkptFreq = 63504000  \rm *
401  niter0 = 52920 , day = 1101, 06-Jan-1995, pChkptFreq = 95126400  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
402  niter0 = 79272 , day = 1467, 07-Jan-1996, pChkptFreq = 126748800  make depend
403  niter0 = 105624, day = 1833, 07-Jan-1997, pChkptFreq = 158371200  make -j
404  niter0 = 131976, day = 2199, 08-Jan-1998, pChkptFreq = 189993600  
405  niter0 = 158328, day = 2565, 09-Jan-1999, pChkptFreq = 221616000  cd ..
406  niter0 = 184680, day = 2931, 10-Jan-2000, pChkptFreq = 253238400  mkdir run
407  niter0 = 211032, day = 3297, 10-Jan-2001, pChkptFreq = 284860800  cd run
408  niter0 = 237384, day = 3663, 11-Jan-2002, pChkptFreq = 316483200  \rm *
409  niter0 = 263736, day = 4029, 12-Jan-2003, pChkptFreq = 348105600  \cp ../input/* .
410    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
411    qsub job_orion41
412    
413    
414    ##########################################################################
415    ##########################################################################
416    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
417    # requires input files in sudirectories run_template and ncep_rgau
418    # presently residing under orion:/tmp1/dmenem/cube
419    
420    cd MITgcm/verification/global_ocean.cs32x15/code
421    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
422    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
423    \cp SIZE.h_50 SIZE.h
424    \cp packages.conf_hr packages.conf
425    
426    cd ../build
427    \rm *
428    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
429    make depend
430    make -j
431    
432    cd ..
433    mkdir run
434    cd run
435    \rm *
436    \cp ../input/* .
437    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
438    qsub job_orion
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