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revision 1.28 by dimitri, Fri Feb 13 08:35:48 2004 UTC revision 1.81 by dimitri, Tue Dec 12 04:20:42 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  =================
4  cube-sphere integration.  UPDATES
5    
6    December 11, 2006: preparing for cube47, same as cube43
7    but with Arctic monthly river runoff climatology
8    
9    December 5, 2006: 216-CPU code for cube46
10    Changed diagnostics to accomodate JMCs latest and some
11    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
12    to speed up code.
13    
14    November 7, 2006: 216-CPU code for cube43
15    Bug fixes in growth.F routine and new set of diagnostics
16    
17    October 15, 2006: 216-CPU code for cube40
18    
19    September 28, 2006: 216-CPU code for cube38
20    
21    September 4, 2006
22    Modified 32*32*6*15 experiments to use grid_cs32.* files from
23     verification/tutorial_held_suarez_cs/input instead of
24     tile* files from verification/global_ocean.cs32x15/input
25    
26    August 8, 2006: 216-CPU code and input used for cube37
27    using "June 10, 2006" MITgcm code.
28    
29    for online T/S profile diagnostics all that is needed is
30      profiles_init_fixed
31      profiles_inloop
32    see pkg/ecco/ecco_cost_init_fixed.F
33        pkg/ecco/cost_averagesfields.F
34    
35    ##########################################################################
36    ##########################################################################
37    # Get forcing files, etc.
38    # Example below is for cube46 on /nobackup2a/menemenl
39    
40    cd /nobackup2a/menemenl
41    mkdir cube46
42    cd cube46
43    ln -sf ../run_template .
44    ln -sf ../ncep_rgau .
45    
46    
47  ##########################################################################  ##########################################################################
48  ##########################################################################  ##########################################################################
49  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
50    
51  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack    bash or sh shell:
52  cvs login ( CVS password: cvsanon )      $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
53  cvs co -r hrcube4 MITgcm_contrib/high_res_cube/README_ice      $ cvs login
54  cvs co -r hrcube4 MITgcm_contrib/high_res_cube/code-mods        ( enter the CVS password: "cvsanon" )
55  cvs co -r hrcube4 MITgcm_contrib/high_res_cube/matlab-grid-converter  
56  cvs co -r hrcube4 MITgcm_contrib/high_res_cube/input    tcsh or csh shell:
57  cvs co -r hrcube4 MITgcm_contrib/high_res_cube/results      $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
58  cvs co -r hrcube4 MITgcm_code      $ cvs login
59  cvs co -r hrcube4 MITgcm/verification/global_ocean.cs32x15        ( enter the CVS password: "cvsanon" )
60    
61    cvs co MITgcm_contrib/high_res_cube/README_ice
62    cvs co MITgcm_contrib/high_res_cube/code-mods
63    cvs co MITgcm_contrib/high_res_cube/input
64    cvs co MITgcm_contrib/high_res_cube/results
65    cvs co MITgcm_code
66    cvs co MITgcm/verification/global_ocean.cs32x15
67    cvs co MITgcm/verification/tutorial_held_suarez_cs/input
68    
69    
70  ##########################################################################  ##########################################################################
71  ##########################################################################  ##########################################################################
72  # 32*32*6*15, 1-cpu cube sphere  # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
73    
74  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
75  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
76  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
77    \cp SIZE.h_216 SIZE.h
78    \cp packages.conf_hr packages.conf
79    
80  cd ../build  cd ../build
81    \rm *
82    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
83    make depend
84    make -j
85    
86    cd ..
87    mkdir run
88    cd run
89    \rm *
90    \cp ../input/* .
91    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
92    ln -sf ../../../../run_template/* .
93    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
94    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
95    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
96    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38 pickup_seaice.0000000216
97    \cp ../build/mitgcmuv .
98    qsub job_altix
99    
100    
101    ##########################################################################
102    ##########################################################################
103    # 32*32*6*15, 1-cpu cube sphere
104    
105    cd MITgcm/verification/global_ocean.cs32x15/code
106    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
107    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
108    cd ../build
109    \rm *
110  ../../../tools/genmake2 -mods=../code  ../../../tools/genmake2 -mods=../code
111  make depend  make depend
112  make  make
   
113  cd ..  cd ..
114  mkdir run  mkdir run
115  cd run  cd run
116    \rm *
117    \cp ../../tutorial_held_suarez_cs/input/grid* .
118  \cp ../input/* .  \cp ../input/* .
 \cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  
119  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
120  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
121    
# Line 46  comparison output is in: Line 125  comparison output is in:
125  to use matlab to look at the output  to use matlab to look at the output
126  matlab  matlab
127    
128  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
129      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);           'surForcT','oceTAUX','oceTAUY','surForcS'}
130        tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
131      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
132  end  end
133    
134  heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
135  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
136  uice=mask.*permute(readbin(['UICE.0000000020.data'],[32,6,32]),[1 3 2]);  uice=mask.*permute(readbin(['SIuice.0000000072.data'],[32,6,32]),[1 3 2]);
137  vice=mask.*permute(readbin(['VICE.0000000020.data'],[32,6,32]),[1 3 2]);  vice=mask.*permute(readbin(['SIvice.0000000072.data'],[32,6,32]),[1 3 2]);
138  clf  clf
139  subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
140  subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
141  subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
142  subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
143    
144    
145    ##########################################################################
146    ##########################################################################
147    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
148    
149    cd MITgcm/verification/global_ocean.cs32x15/code
150    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
151    \cp ../code_alt/code.176t_8x4/* .
152    cd ../build
153    \rm *
154    ../../../tools/genmake2 -mods=../code
155    make depend
156    make
157    cd ..
158    mkdir run
159    cd run
160    \rm *
161    \cp ../../tutorial_held_suarez_cs/input/grid* .
162    \cp ../input/* .
163    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
164    ../build/mitgcmuv >& output.txt
165    
166    
167  ##########################################################################  ##########################################################################
168  ##########################################################################  ##########################################################################
169  # 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
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/s12t_16x32/* .  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
174  \cp SIZE.h_mpi SIZE.h  \cp SIZE.h_mpi SIZE.h
175    
176  cd ../build  cd ../build
177  \rm *  \rm *
178  ../../../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
179  make depend  make depend
180  make  make -j
181    
182  cd ..  cd ..
183  mkdir run  mkdir run
184  cd run  cd run
185  \rm *  \rm *
186    \cp ../../tutorial_held_suarez_cs/input/grid* .
187  \cp ../input/* .  \cp ../input/* .
 \cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  
188  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
189  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
190    
191    
192  ##########################################################################  ##########################################################################
193  ##########################################################################  ##########################################################################
194  # 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
195    # starting with pickup file from end of 1992
196    # requires input files in sudirectories run_template and ncep_rgau
197    
198    cd MITgcm/verification/global_ocean.cs32x15/code
199    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
200    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
201    \cp packages.conf_hr packages.conf
202    
203    cd ../build
204    \rm *
205    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
206    make depend
207    make -j
208    
209    cd ..
210    mkdir run
211    cd run
212    \rm *
213    \cp ../input/* .
214    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
215    qsub job_altix92_54t
216    
217    
218    ##########################################################################
219    ##########################################################################
220    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
221    # uses s1500t_17x51 configuration
222    
223    cd MITgcm/verification/global_ocean.cs32x15/code
224    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
225    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
226    \cp SIZE.h_150 SIZE.h
227    \cp packages.conf_hr packages.conf
228    
229    cd ../build
230    \rm *
231    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
232    make depend
233    make -j
234    
235    cd ..
236    mkdir run
237    cd run
238    \rm *
239    \cp ../input/* .
240    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
241    ln -sf ../../../../run_template/* .
242    \rm pickup*
243    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
244    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
245    \cp ../build/mitgcmuv mitgcmuv150
246    qsub job_altix150
247    
248    
249    ##########################################################################
250    ##########################################################################
251    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
252    # uses s1500t_17x51 configuration
253    # example for running on c17-c20 using arrayd
254    
255    cd MITgcm/verification/global_ocean.cs32x15/code
256    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
257    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
258    \cp SIZE.h_375 SIZE.h
259    \cp packages.conf_hr packages.conf
260    
261    cd ../build
262    \rm *
263    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
264    make depend
265    make -j
266    
267    cd ..
268    mkdir run
269    cd run
270    \rm *
271    \cp ../input/* .
272    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
273    ln -sf ../../../../run_template/* .
274    \rm pickup*
275    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
276    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
277    \cp ../build/mitgcmuv .
278    job_c20_375cpu < /dev/null >&! output.run &
279    
280    
281    ##########################################################################
282    ##########################################################################
283    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
284    # uses s1500t_17x51 configuration
285    # example for running on c17-c20 using arrayd
286    
287    cd MITgcm/verification/global_ocean.cs32x15/code
288    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
289    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
290    \cp SIZE.h_375 SIZE.h
291    \cp packages.conf_hr packages.conf
292    
293    cd ../build
294    \rm *
295    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
296    make depend
297    make -j
298    
299    cd ..
300    mkdir run
301    cd run
302    \rm *
303    \cp ../input/* .
304    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
305    ln -sf ../../../../run_template/* .
306    \rm pickup*
307    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
308    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
309    \cp ../build/mitgcmuv .
310    job_c20_375cpu < /dev/null >&! output.run &
311    
312    
313    ##########################################################################
314    ##########################################################################
315    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
316    # uses s1500t_17x51 configuration
317    # example for running on c17-c20 using arrayd
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/s1500t_17x51/* .
322    \cp SIZE.h_500 SIZE.h
323    \cp packages.conf_hr packages.conf
324    
325    cd ../build
326    \rm *
327    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
328    make depend
329    make -j
330    
331    cd ..
332    mkdir run
333    cd run
334    \rm *
335    \cp ../input/* .
336    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
337    ln -sf ../../../../run_template/* .
338    \rm pickup*
339    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
340    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
341    \cp ../build/mitgcmuv .
342    job_c19_500cpu < /dev/null >&! output.run &
343    
344    
345    ##########################################################################
346    ##########################################################################
347    # 510*510*6*50, 216-cpu cube sphere on cosmos
348    
349    cd MITgcm/verification/global_ocean.cs32x15/code
350    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
351    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
352    \cp SIZE.h_216 SIZE.h
353    \cp packages.conf_hr packages.conf
354    
355    module unload latest_intel80
356    module unload mpich-gm-intel80
357    module load latest_intel81
358    module load mpich-gm-intel81
359    
360    cd ../build
361    \rm *
362    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
363    make depend
364    make -j
365    
366    cd ..
367    mkdir run
368    cd run
369    \rm *
370    \cp ../input/* .
371    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
372    ln -sf ../../../../run_template/* .
373    \rm pickup*
374    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
375    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
376    \cp ../build/mitgcmuv .
377    bsub < job_cosmos
378    
379    
380    ##########################################################################
381    ##########################################################################
382    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
383  # requires input files in sudirectories run_template and ncep_rgau  # requires input files in sudirectories run_template and ncep_rgau
384  # presently residing under orion:/tmp1/dmenem/cube  # presently residing under orion:/tmp1/dmenem/cube
385    
# Line 101  cd MITgcm/verification/global_ocean.cs32 Line 391  cd MITgcm/verification/global_ocean.cs32
391    
392  cd ../build  cd ../build
393  \rm *  \rm *
394  ../../../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
395  make depend  make depend
396  make  make -j
397    
398  cd ..  cd ..
399  mkdir run  mkdir run
# Line 128  cd MITgcm/verification/global_ocean.cs32 Line 418  cd MITgcm/verification/global_ocean.cs32
418    
419  cd ../build  cd ../build
420  \rm *  \rm *
421  ../../../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
422  make depend  make depend
423  make  make -j
424    
425  cd ..  cd ..
426  mkdir run  mkdir run
# Line 143  qsub job_orion41 Line 433  qsub job_orion41
433    
434  ##########################################################################  ##########################################################################
435  ##########################################################################  ##########################################################################
436  # 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
437  # requires input files in sudirectories run_template and ncep_rgau  # requires input files in sudirectories run_template and ncep_rgau
438  # these can be obained from lou:/u/menemenl/cube  # presently residing under orion:/tmp1/dmenem/cube
439    
440  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
441  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
442  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
443  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_50 SIZE.h
444  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
445    
446  cd ../build  cd ../build
447  \rm *  \rm *
448  ../../../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
449  make depend  make depend
450  make  make -j
451    
452  cd ..  cd ..
453  mkdir run  mkdir run
# Line 165  cd run Line 455  cd run
455  \rm *  \rm *
456  \cp ../input/* .  \cp ../input/* .
457  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
458  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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