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revision 1.44 by dimitri, Sun Oct 17 12:27:50 2004 UTC revision 1.90 by dimitri, Wed Feb 7 01:30:48 2007 UTC
# Line 1  Line 1 
1    
2  Instructions for setting up a cube-sphere integration with sea-ice.  Instructions for setting up a cube-sphere integration with sea-ice.
3  Date last tested: July 9, 2004.  
4  Code and input used for integrating cube9.  Forcing fields and other input files needed for the CS510
5    configuration can be obtained from
6    http://ecco2.org/products/model_setups/cs510.html
7    
8    =================
9    UPDATES
10    
11    February 6, 2006: cube56, same as cube 50 with SEAICEuseFlooding
12    
13    February 1, 2006: back to cube50 default (bottomDragQuadratic = 0.002)
14                      removed UVEL and VVEL from diagnostics
15    
16    January 5, 2006: cube51, like cube50 but with bottomDragQuadratic = 0.0012
17    
18    January 5, 2006: cube50, like cube48 but with snow advection
19    
20    December 30, 2006: updates for cube49, the first
21    "blend" integration.
22    
23    December 11, 2006: preparing for cube47, same as cube43
24    but with Arctic monthly river runoff climatology.
25    
26    December 5, 2006: 216-CPU code for cube46
27    Changed diagnostics to accomodate JMCs latest and some
28    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
29    to speed up code.
30    
31    November 7, 2006: 216-CPU code for cube43
32    Bug fixes in growth.F routine and new set of diagnostics
33    
34    October 15, 2006: 216-CPU code for cube40
35    
36    September 28, 2006: 216-CPU code for cube38
37    
38    September 4, 2006
39    Modified 32*32*6*15 experiments to use grid_cs32.* files from
40     verification/tutorial_held_suarez_cs/input instead of
41     tile* files from verification/global_ocean.cs32x15/input
42    
43    August 8, 2006: 216-CPU code and input used for cube37
44    using "June 10, 2006" MITgcm code.
45    
46    for online T/S profile diagnostics all that is needed is
47      profiles_init_fixed
48      profiles_inloop
49    see pkg/ecco/ecco_cost_init_fixed.F
50        pkg/ecco/cost_averagesfields.F
51    
52    ##########################################################################
53    ##########################################################################
54    # Get forcing files, etc.
55    # Example below is for cube46 on /nobackup2a/menemenl
56    
57    cd /nobackup2a/menemenl
58    mkdir cube47
59    cd cube47
60    ln -sf ../run_template .
61    ln -sf ../ncep_rgau .
62    
63    
64  ##########################################################################  ##########################################################################
65  ##########################################################################  ##########################################################################
66  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
67    
68      bash or sh shell:
69        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
70        $ cvs login
71          ( enter the CVS password: "cvsanon" )
72    
73      tcsh or csh shell:
74        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
75        $ cvs login
76          ( enter the CVS password: "cvsanon" )
77    
78  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
79  cvs co MITgcm_contrib/high_res_cube/code-mods  cvs co MITgcm_contrib/high_res_cube/code-mods
80  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
81  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
82  cvs co MITgcm_code  cvs co MITgcm_code
83  cvs co MITgcm/verification/global_ocean.cs32x15  cvs co MITgcm/verification/global_ocean.cs32x15
84  cvs co MITgcm/verification/testreport  cvs co MITgcm/verification/tutorial_held_suarez_cs/input
85    
86    
87    ##########################################################################
88    ##########################################################################
89    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
90    
91    cd MITgcm/verification/global_ocean.cs32x15/code
92    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
93    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
94    \cp SIZE.h_216 SIZE.h
95    \cp packages.conf_hr packages.conf
96    
97    cd ../build
98    \rm *
99    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
100    make depend
101    make -j
102    
103    cd ..
104    mkdir run
105    cd run
106    \rm *
107    \cp ../input/* .
108    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
109    ln -sf ../../../../run_template/* .
110    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
111    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
112    ln -sf ../../../../run_template/pickup.0000000216.cube49 pickup.0000000216
113    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube48 pickup_seaice.0000000216
114    \cp ../build/mitgcmuv .
115    qsub job_altix
116    
117    
118  ##########################################################################  ##########################################################################
# Line 23  cvs co MITgcm/verification/testreport Line 122  cvs co MITgcm/verification/testreport
122  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
123  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
124  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
125    \rm CPP_EEOPTIONS.h
126  cd ../build  cd ../build
127  \rm *  \rm *
128  ../../../tools/genmake2 -mods=../code  ../../../tools/genmake2 -mods=../code
# Line 32  cd .. Line 132  cd ..
132  mkdir run  mkdir run
133  cd run  cd run
134  \rm *  \rm *
135    \cp ../../tutorial_held_suarez_cs/input/grid* .
136  \cp ../input/* .  \cp ../input/* .
137  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
138  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 42  comparison output is in: Line 143  comparison output is in:
143  to use matlab to look at the output  to use matlab to look at the output
144  matlab  matlab
145    
146  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
147      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);           'surForcT','oceTAUX','oceTAUY','surForcS'}
148        tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
149      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
150  end  end
151    
152  heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
153  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
154  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]);
155  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]);
156  clf  clf
157  subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
158  subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
159  subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
160  subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
161    
162    
163  ##########################################################################  ##########################################################################
# Line 74  cd .. Line 176  cd ..
176  mkdir run  mkdir run
177  cd run  cd run
178  \rm *  \rm *
179    \cp ../../tutorial_held_suarez_cs/input/grid* .
180  \cp ../input/* .  \cp ../input/* .
181  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
182  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
183    
 comparison output is in:  
 ../../../../MITgcm_contrib/high_res_cube/results/output.txt  
   
 to use matlab to look at the output  
 matlab  
   
 for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  
     tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);  
     cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause  
 end  
   
 heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  
 mask=0*heff; mask(find(heff>.001))=1;  
 uice=mask.*permute(readbin(['UICE.0000000020.data'],[32,6,32]),[1 3 2]);  
 vice=mask.*permute(readbin(['VICE.0000000020.data'],[32,6,32]),[1 3 2]);  
 clf  
 subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  
 subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  
 subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  
 subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  
   
184    
185  ##########################################################################  ##########################################################################
186  ##########################################################################  ##########################################################################
187  # 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
188    
189  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
190  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
# Line 111  cd MITgcm/verification/global_ocean.cs32 Line 193  cd MITgcm/verification/global_ocean.cs32
193    
194  cd ../build  cd ../build
195  \rm *  \rm *
196  ../../../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
197  make depend  make depend
198  make -j  make -j
199    
# Line 119  cd .. Line 201  cd ..
201  mkdir run  mkdir run
202  cd run  cd run
203  \rm *  \rm *
204    \cp ../../tutorial_held_suarez_cs/input/grid* .
205  \cp ../input/* .  \cp ../input/* .
206  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
207  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
# Line 152  qsub job_altix92_54t Line 235  qsub job_altix92_54t
235    
236  ##########################################################################  ##########################################################################
237  ##########################################################################  ##########################################################################
238  # 510*510*6*50, 216-cpu cube sphere on altix with efc  # 510*510*6*50, 1500-tile, 150-cpu, excludes land
239  # requires input files in sudirectories run_template and ncep_rgau  # uses s1500t_17x51 configuration
 # these can be obained from lou:/u/menemenl/cube  
240    
241  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
242  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
243  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
244  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_150 SIZE.h
245  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
246    
247  cd ../build  cd ../build
248  \rm *  \rm *
249  ../../../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
250    make depend
251    make -j
252    
253    cd ..
254    mkdir run
255    cd run
256    \rm *
257    \cp ../input/* .
258    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
259    ln -sf ../../../../run_template/* .
260    \rm pickup*
261    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
262    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
263    \cp ../build/mitgcmuv mitgcmuv150
264    qsub job_altix150
265    
266    
267    ##########################################################################
268    ##########################################################################
269    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
270    # uses s1500t_17x51 configuration
271    # example for running on c17-c20 using arrayd
272    
273    cd MITgcm/verification/global_ocean.cs32x15/code
274    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
275    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
276    \cp SIZE.h_375 SIZE.h
277    \cp packages.conf_hr packages.conf
278    
279    cd ../build
280    \rm *
281    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
282  make depend  make depend
283  make -j 16  make -j
284    
285  cd ..  cd ..
286  mkdir run  mkdir run
# Line 175  cd run Line 289  cd run
289  \cp ../input/* .  \cp ../input/* .
290  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
291  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
292  ln -sf pickup.0000290088.data.cube10 pickup.0000000216.data  \rm pickup*
293  ln -sf pickup_seaice.0000290088.data.cube10 pickup_seaice.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
294    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
295  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv .
296  qsub job_altix92  job_c20_375cpu < /dev/null >&! output.run &
297    
298    
299    ##########################################################################
300    ##########################################################################
301    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
302    # uses s1500t_17x51 configuration
303    # example for running on c17-c20 using arrayd
304    
305    cd MITgcm/verification/global_ocean.cs32x15/code
306    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
307    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
308    \cp SIZE.h_375 SIZE.h
309    \cp packages.conf_hr packages.conf
310    
311    cd ../build
312    \rm *
313    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
314    make depend
315    make -j
316    
317    cd ..
318    mkdir run
319    cd run
320    \rm *
321    \cp ../input/* .
322    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
323    ln -sf ../../../../run_template/* .
324    \rm pickup*
325    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
326    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
327    \cp ../build/mitgcmuv .
328    job_c20_375cpu < /dev/null >&! output.run &
329    
330    
331    ##########################################################################
332    ##########################################################################
333    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
334    # uses s1500t_17x51 configuration
335    # example for running on c17-c20 using arrayd
336    
337    cd MITgcm/verification/global_ocean.cs32x15/code
338    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
339    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
340    \cp SIZE.h_500 SIZE.h
341    \cp packages.conf_hr packages.conf
342    
343    cd ../build
344    \rm *
345    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
346    make depend
347    make -j
348    
349    cd ..
350    mkdir run
351    cd run
352    \rm *
353    \cp ../input/* .
354    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
355    ln -sf ../../../../run_template/* .
356    \rm pickup*
357    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
358    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
359    \cp ../build/mitgcmuv .
360    job_c19_500cpu < /dev/null >&! output.run &
361    
362    
363    ##########################################################################
364    ##########################################################################
365    # 510*510*6*50, 216-cpu cube sphere on cosmos
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_216 SIZE.h
371    \cp packages.conf_hr packages.conf
372    
373    module unload latest_intel80
374    module unload mpich-gm-intel80
375    module load latest_intel81
376    module load mpich-gm-intel81
377    
378    cd ../build
379    \rm *
380    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
381    make depend
382    make -j
383    
384    cd ..
385    mkdir run
386    cd run
387    \rm *
388    \cp ../input/* .
389    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
390    ln -sf ../../../../run_template/* .
391    \rm pickup*
392    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
393    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
394    \cp ../build/mitgcmuv .
395    bsub < job_cosmos
396    
397    
398  ##########################################################################  ##########################################################################
# Line 276  cd run Line 474  cd run
474  \cp ../input/* .  \cp ../input/* .
475  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
476  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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