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revision 1.50 by dimitri, Tue Jan 18 18:33:15 2005 UTC revision 1.85 by dimitri, Sat Dec 30 19:33:35 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: July 9, 2004.  
3  Code and input used for integrating cube9.  Forcing fields and other input files needed for the CS510
4    configuration can be obtained from
5    http://ecco2.org/products/model_setups/cs510.html
6    
7    =================
8    UPDATES
9    
10    December 30, 2006: updates for cube49, the first
11    "blend" integration.
12    
13    December 11, 2006: preparing for cube47, same as cube43
14    but with Arctic monthly river runoff climatology.
15    
16    December 5, 2006: 216-CPU code for cube46
17    Changed diagnostics to accomodate JMCs latest and some
18    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
19    to speed up code.
20    
21    November 7, 2006: 216-CPU code for cube43
22    Bug fixes in growth.F routine and new set of diagnostics
23    
24    October 15, 2006: 216-CPU code for cube40
25    
26    September 28, 2006: 216-CPU code for cube38
27    
28    September 4, 2006
29    Modified 32*32*6*15 experiments to use grid_cs32.* files from
30     verification/tutorial_held_suarez_cs/input instead of
31     tile* files from verification/global_ocean.cs32x15/input
32    
33    August 8, 2006: 216-CPU code and input used for cube37
34    using "June 10, 2006" MITgcm code.
35    
36    for online T/S profile diagnostics all that is needed is
37      profiles_init_fixed
38      profiles_inloop
39    see pkg/ecco/ecco_cost_init_fixed.F
40        pkg/ecco/cost_averagesfields.F
41    
42    ##########################################################################
43    ##########################################################################
44    # Get forcing files, etc.
45    # Example below is for cube46 on /nobackup2a/menemenl
46    
47    cd /nobackup2a/menemenl
48    mkdir cube47
49    cd cube47
50    ln -sf ../run_template .
51    ln -sf ../ncep_rgau .
52    
53    
54  ##########################################################################  ##########################################################################
55  ##########################################################################  ##########################################################################
56  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
57    
58      bash or sh shell:
59        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
60        $ cvs login
61          ( enter the CVS password: "cvsanon" )
62    
63      tcsh or csh shell:
64        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
65        $ cvs login
66          ( enter the CVS password: "cvsanon" )
67    
68  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
69  cvs co MITgcm_contrib/high_res_cube/code-mods  cvs co MITgcm_contrib/high_res_cube/code-mods
70  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
71  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
72  cvs co MITgcm_code  cvs co MITgcm_code
73  cvs co MITgcm/verification/global_ocean.cs32x15  cvs co MITgcm/verification/global_ocean.cs32x15
74  cvs co MITgcm/verification/testreport  cvs co MITgcm/verification/tutorial_held_suarez_cs/input
75    
76    
77    ##########################################################################
78    ##########################################################################
79    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
80    
81    cd MITgcm/verification/global_ocean.cs32x15/code
82    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
83    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
84    \cp SIZE.h_216 SIZE.h
85    \cp packages.conf_hr packages.conf
86    
87    cd ../build
88    \rm *
89    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
90    make depend
91    make -j
92    
93    cd ..
94    mkdir run
95    cd run
96    \rm *
97    \cp ../input/* .
98    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
99    ln -sf ../../../../run_template/* .
100    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
101    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
102    ln -sf ../../../../run_template/pickup.0000000216.cube49 pickup.0000000216
103    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube49 pickup_seaice.0000000216
104    \cp ../build/mitgcmuv .
105    qsub job_altix
106    
107    
108  ##########################################################################  ##########################################################################
# Line 32  cd .. Line 121  cd ..
121  mkdir run  mkdir run
122  cd run  cd run
123  \rm *  \rm *
124    \cp ../../tutorial_held_suarez_cs/input/grid* .
125  \cp ../input/* .  \cp ../input/* .
126  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
127  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 42  comparison output is in: Line 132  comparison output is in:
132  to use matlab to look at the output  to use matlab to look at the output
133  matlab  matlab
134    
135  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
136      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);           'surForcT','oceTAUX','oceTAUY','surForcS'}
137        tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
138      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
139  end  end
140    
141  heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
142  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
143  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]);
144  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]);
145  clf  clf
146  subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
147  subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
148  subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
149  subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
150    
151    
152  ##########################################################################  ##########################################################################
# Line 74  cd .. Line 165  cd ..
165  mkdir run  mkdir run
166  cd run  cd run
167  \rm *  \rm *
168    \cp ../../tutorial_held_suarez_cs/input/grid* .
169  \cp ../input/* .  \cp ../input/* .
170  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
171  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
172    
 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')  
   
173    
174  ##########################################################################  ##########################################################################
175  ##########################################################################  ##########################################################################
176  # 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
177    
178  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
179  \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 182  cd MITgcm/verification/global_ocean.cs32
182    
183  cd ../build  cd ../build
184  \rm *  \rm *
185  ../../../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
186  make depend  make depend
187  make -j  make -j
188    
# Line 119  cd .. Line 190  cd ..
190  mkdir run  mkdir run
191  cd run  cd run
192  \rm *  \rm *
193    \cp ../../tutorial_held_suarez_cs/input/grid* .
194  \cp ../input/* .  \cp ../input/* .
195  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
196  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
# Line 152  qsub job_altix92_54t Line 224  qsub job_altix92_54t
224    
225  ##########################################################################  ##########################################################################
226  ##########################################################################  ##########################################################################
227  # 510*510*6*50, 216-cpu cube sphere on altix with ifort  # 510*510*6*50, 1500-tile, 150-cpu, excludes land
228  # requires input files in sudirectories run_template and ncep_rgau  # uses s1500t_17x51 configuration
 # these can be obained from lou:/u/menemenl/cube  
229    
230  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
231  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
232  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
233  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_150 SIZE.h
234  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
235    
236  cd ../build  cd ../build
237  \rm *  \rm *
238  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
239  make depend  make depend
240  make -j 4  make -j
241    
242  cd ..  cd ..
243  mkdir run  mkdir run
# Line 176  cd run Line 247  cd run
247  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
248  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
249  \rm pickup*  \rm pickup*
250  ln -sf ../../../../run_template/pickup.0000316440.cube20 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
251  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube20 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
252    \cp ../build/mitgcmuv mitgcmuv150
253    qsub job_altix150
254    
255    
256    ##########################################################################
257    ##########################################################################
258    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
259    # uses s1500t_17x51 configuration
260    # example for running on c17-c20 using arrayd
261    
262    cd MITgcm/verification/global_ocean.cs32x15/code
263    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
264    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
265    \cp SIZE.h_375 SIZE.h
266    \cp packages.conf_hr packages.conf
267    
268    cd ../build
269    \rm *
270    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
271    make depend
272    make -j
273    
274    cd ..
275    mkdir run
276    cd run
277    \rm *
278    \cp ../input/* .
279    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
280    ln -sf ../../../../run_template/* .
281    \rm pickup*
282    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
283    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
284  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv .
285  qsub job_altix92  job_c20_375cpu < /dev/null >&! output.run &
286    
287    
288    ##########################################################################
289    ##########################################################################
290    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
291    # uses s1500t_17x51 configuration
292    # example for running on c17-c20 using arrayd
293    
294    cd MITgcm/verification/global_ocean.cs32x15/code
295    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
296    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
297    \cp SIZE.h_375 SIZE.h
298    \cp packages.conf_hr packages.conf
299    
300    cd ../build
301    \rm *
302    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
303    make depend
304    make -j
305    
306    cd ..
307    mkdir run
308    cd run
309    \rm *
310    \cp ../input/* .
311    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
312    ln -sf ../../../../run_template/* .
313    \rm pickup*
314    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
315    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
316    \cp ../build/mitgcmuv .
317    job_c20_375cpu < /dev/null >&! output.run &
318    
319    
320    ##########################################################################
321    ##########################################################################
322    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
323    # uses s1500t_17x51 configuration
324    # example for running on c17-c20 using arrayd
325    
326    cd MITgcm/verification/global_ocean.cs32x15/code
327    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
328    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
329    \cp SIZE.h_500 SIZE.h
330    \cp packages.conf_hr packages.conf
331    
332    cd ../build
333    \rm *
334    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
335    make depend
336    make -j
337    
338    cd ..
339    mkdir run
340    cd run
341    \rm *
342    \cp ../input/* .
343    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
344    ln -sf ../../../../run_template/* .
345    \rm pickup*
346    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
347    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
348    \cp ../build/mitgcmuv .
349    job_c19_500cpu < /dev/null >&! output.run &
350    
351    
352    ##########################################################################
353    ##########################################################################
354    # 510*510*6*50, 216-cpu cube sphere on cosmos
355    
356    cd MITgcm/verification/global_ocean.cs32x15/code
357    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
358    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
359    \cp SIZE.h_216 SIZE.h
360    \cp packages.conf_hr packages.conf
361    
362    module unload latest_intel80
363    module unload mpich-gm-intel80
364    module load latest_intel81
365    module load mpich-gm-intel81
366    
367    cd ../build
368    \rm *
369    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
370    make depend
371    make -j
372    
373    cd ..
374    mkdir run
375    cd run
376    \rm *
377    \cp ../input/* .
378    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
379    ln -sf ../../../../run_template/* .
380    \rm pickup*
381    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
382    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
383    \cp ../build/mitgcmuv .
384    bsub < job_cosmos
385    
386    
387  ##########################################################################  ##########################################################################
# Line 277  cd run Line 463  cd run
463  \cp ../input/* .  \cp ../input/* .
464  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
465  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  
   
   
   
   
   
   
 #!/bin/csh  
 \cp data.pkg_hr data.pkg  
 \cp data.seaice_hr data.seaice  
 \cp data.exf_clim_hr data.exf_clim  
   
 \cp data_hr92 data  
 ./modpickup  
 \cp data.exf_hr92 data.exf  
 /opt/sgi/mpt/1.11-85/bin/mpirun.real -v -a a2k c20 216 runon 221-436 mitgcmuv  
 mkdir out.1992  
 \mv STDOUT.0000 *.data pickup*.meta out.1992  
 \cp data* out.1992  
 \rm STD* *.meta  
   
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