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revision 1.42 by dimitri, Fri Jul 9 23:58:24 2004 UTC revision 1.86 by dimitri, Fri Jan 5 20:56:00 2007 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    January 5, 2006: cube50, same as cube48 but with snow advection
11    
12    December 30, 2006: updates for cube49, the first
13    "blend" integration.
14    
15    December 11, 2006: preparing for cube47, same as cube43
16    but with Arctic monthly river runoff climatology.
17    
18    December 5, 2006: 216-CPU code for cube46
19    Changed diagnostics to accomodate JMCs latest and some
20    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
21    to speed up code.
22    
23    November 7, 2006: 216-CPU code for cube43
24    Bug fixes in growth.F routine and new set of diagnostics
25    
26    October 15, 2006: 216-CPU code for cube40
27    
28    September 28, 2006: 216-CPU code for cube38
29    
30    September 4, 2006
31    Modified 32*32*6*15 experiments to use grid_cs32.* files from
32     verification/tutorial_held_suarez_cs/input instead of
33     tile* files from verification/global_ocean.cs32x15/input
34    
35    August 8, 2006: 216-CPU code and input used for cube37
36    using "June 10, 2006" MITgcm code.
37    
38    for online T/S profile diagnostics all that is needed is
39      profiles_init_fixed
40      profiles_inloop
41    see pkg/ecco/ecco_cost_init_fixed.F
42        pkg/ecco/cost_averagesfields.F
43    
44    ##########################################################################
45    ##########################################################################
46    # Get forcing files, etc.
47    # Example below is for cube46 on /nobackup2a/menemenl
48    
49    cd /nobackup2a/menemenl
50    mkdir cube47
51    cd cube47
52    ln -sf ../run_template .
53    ln -sf ../ncep_rgau .
54    
55    
56  ##########################################################################  ##########################################################################
57  ##########################################################################  ##########################################################################
58  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
59    
60      bash or sh shell:
61        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
62        $ cvs login
63          ( enter the CVS password: "cvsanon" )
64    
65      tcsh or csh shell:
66        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
67        $ cvs login
68          ( enter the CVS password: "cvsanon" )
69    
70  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
71  cvs co MITgcm_contrib/high_res_cube/code-mods  cvs co MITgcm_contrib/high_res_cube/code-mods
72  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
73  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
74  cvs co MITgcm_contrib/edge_problem  cvs co MITgcm_code
75  cvs co -r checkpoint54b_post MITgcm_code  cvs co MITgcm/verification/global_ocean.cs32x15
76  cvs co -r checkpoint54b_post MITgcm/verification/global_ocean.cs32x15  cvs co MITgcm/verification/tutorial_held_suarez_cs/input
77  cvs co -r checkpoint54b_post MITgcm/verification/testreport  
78    
79    ##########################################################################
80    ##########################################################################
81    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
82    
83    cd MITgcm/verification/global_ocean.cs32x15/code
84    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
85    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
86    \cp SIZE.h_216 SIZE.h
87    \cp packages.conf_hr packages.conf
88    
89    cd ../build
90    \rm *
91    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
92    make depend
93    make -j
94    
95    cd ..
96    mkdir run
97    cd run
98    \rm *
99    \cp ../input/* .
100    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
101    ln -sf ../../../../run_template/* .
102    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
103    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
104    ln -sf ../../../../run_template/pickup.0000000216.cube49 pickup.0000000216
105    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube48 pickup_seaice.0000000216
106    \cp ../build/mitgcmuv .
107    qsub job_altix
108    
109    
110  ##########################################################################  ##########################################################################
# Line 33  cd .. Line 123  cd ..
123  mkdir run  mkdir run
124  cd run  cd run
125  \rm *  \rm *
126    \cp ../../tutorial_held_suarez_cs/input/grid* .
127  \cp ../input/* .  \cp ../input/* .
128  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
129  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 43  comparison output is in: Line 134  comparison output is in:
134  to use matlab to look at the output  to use matlab to look at the output
135  matlab  matlab
136    
137  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
138      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);           'surForcT','oceTAUX','oceTAUY','surForcS'}
139        tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
140      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
141  end  end
142    
143  heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
144  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
145  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]);
146  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]);
147  clf  clf
148  subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
149  subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
150  subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
151  subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
152    
153    
154  ##########################################################################  ##########################################################################
# Line 75  cd .. Line 167  cd ..
167  mkdir run  mkdir run
168  cd run  cd run
169  \rm *  \rm *
170    \cp ../../tutorial_held_suarez_cs/input/grid* .
171  \cp ../input/* .  \cp ../input/* .
172  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
173  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
174    
 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')  
   
175    
176  ##########################################################################  ##########################################################################
177  ##########################################################################  ##########################################################################
178  # 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
179    
180  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
181  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
# Line 112  cd MITgcm/verification/global_ocean.cs32 Line 184  cd MITgcm/verification/global_ocean.cs32
184    
185  cd ../build  cd ../build
186  \rm *  \rm *
187  ../../../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
188  make depend  make depend
189  make -j  make -j
190    
# Line 120  cd .. Line 192  cd ..
192  mkdir run  mkdir run
193  cd run  cd run
194  \rm *  \rm *
195    \cp ../../tutorial_held_suarez_cs/input/grid* .
196  \cp ../input/* .  \cp ../input/* .
197  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
198  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
# Line 153  qsub job_altix92_54t Line 226  qsub job_altix92_54t
226    
227  ##########################################################################  ##########################################################################
228  ##########################################################################  ##########################################################################
229  # 510*510*6*50, 216-cpu cube sphere on altix with efc  # 510*510*6*50, 1500-tile, 150-cpu, excludes land
230  # requires input files in sudirectories run_template and ncep_rgau  # uses s1500t_17x51 configuration
 # these can be obained from lou:/u/menemenl/cube  
231    
232  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
233  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
234  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
235  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_150 SIZE.h
236  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
237    
238  cd ../build  cd ../build
239  \rm *  \rm *
240  ../../../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
241    make depend
242    make -j
243    
244    cd ..
245    mkdir run
246    cd run
247    \rm *
248    \cp ../input/* .
249    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
250    ln -sf ../../../../run_template/* .
251    \rm pickup*
252    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
253    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
254    \cp ../build/mitgcmuv mitgcmuv150
255    qsub job_altix150
256    
257    
258    ##########################################################################
259    ##########################################################################
260    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
261    # uses s1500t_17x51 configuration
262    # example for running on c17-c20 using arrayd
263    
264    cd MITgcm/verification/global_ocean.cs32x15/code
265    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
266    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
267    \cp SIZE.h_375 SIZE.h
268    \cp packages.conf_hr packages.conf
269    
270    cd ../build
271    \rm *
272    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
273  make depend  make depend
274  make -j  make -j
275    
# Line 175  cd run Line 279  cd run
279  \rm *  \rm *
280  \cp ../input/* .  \cp ../input/* .
281  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
282  qsub job_altix92  ln -sf ../../../../run_template/* .
283    \rm pickup*
284    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
285    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
286    \cp ../build/mitgcmuv .
287    job_c20_375cpu < /dev/null >&! output.run &
288    
289    
290    ##########################################################################
291    ##########################################################################
292    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
293    # uses s1500t_17x51 configuration
294    # example for running on c17-c20 using arrayd
295    
296    cd MITgcm/verification/global_ocean.cs32x15/code
297    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
298    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
299    \cp SIZE.h_375 SIZE.h
300    \cp packages.conf_hr packages.conf
301    
302    cd ../build
303    \rm *
304    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
305    make depend
306    make -j
307    
308    cd ..
309    mkdir run
310    cd run
311    \rm *
312    \cp ../input/* .
313    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
314    ln -sf ../../../../run_template/* .
315    \rm pickup*
316    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
317    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
318    \cp ../build/mitgcmuv .
319    job_c20_375cpu < /dev/null >&! output.run &
320    
321    
322    ##########################################################################
323    ##########################################################################
324    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
325    # uses s1500t_17x51 configuration
326    # example for running on c17-c20 using arrayd
327    
328    cd MITgcm/verification/global_ocean.cs32x15/code
329    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
330    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
331    \cp SIZE.h_500 SIZE.h
332    \cp packages.conf_hr packages.conf
333    
334    cd ../build
335    \rm *
336    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
337    make depend
338    make -j
339    
340    cd ..
341    mkdir run
342    cd run
343    \rm *
344    \cp ../input/* .
345    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
346    ln -sf ../../../../run_template/* .
347    \rm pickup*
348    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
349    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
350    \cp ../build/mitgcmuv .
351    job_c19_500cpu < /dev/null >&! output.run &
352    
353    
354    ##########################################################################
355    ##########################################################################
356    # 510*510*6*50, 216-cpu cube sphere on cosmos
357    
358    cd MITgcm/verification/global_ocean.cs32x15/code
359    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
360    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
361    \cp SIZE.h_216 SIZE.h
362    \cp packages.conf_hr packages.conf
363    
364    module unload latest_intel80
365    module unload mpich-gm-intel80
366    module load latest_intel81
367    module load mpich-gm-intel81
368    
369    cd ../build
370    \rm *
371    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
372    make depend
373    make -j
374    
375    cd ..
376    mkdir run
377    cd run
378    \rm *
379    \cp ../input/* .
380    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
381    ln -sf ../../../../run_template/* .
382    \rm pickup*
383    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
384    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
385    \cp ../build/mitgcmuv .
386    bsub < job_cosmos
387    
388    
389  ##########################################################################  ##########################################################################
# Line 273  cd run Line 465  cd run
465  \cp ../input/* .  \cp ../input/* .
466  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
467  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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