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revision 1.52 by dimitri, Sat Feb 19 06:28:28 2005 UTC revision 1.89 by dimitri, Fri Feb 2 01:05:25 2007 UTC
# Line 1  Line 1 
1  daInstructions for setting up a cube-sphere integration with sea-ice.  
2  Date last updated: February 17, 2005  Instructions for setting up a cube-sphere integration with sea-ice.
3  Code and input used for integrating cube22.  
4    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 1, 2006: back to cube50 default (bottomDragQuadratic = 0.0012)
12                      removed UVEL and VVEL from diagnostics
13    
14    January 5, 2006: cube51, like cube50 but with bottomDragQuadratic = 0.0012
15    
16    January 5, 2006: cube50, like cube48 but with snow advection
17    
18    December 30, 2006: updates for cube49, the first
19    "blend" integration.
20    
21    December 11, 2006: preparing for cube47, same as cube43
22    but with Arctic monthly river runoff climatology.
23    
24    December 5, 2006: 216-CPU code for cube46
25    Changed diagnostics to accomodate JMCs latest and some
26    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
27    to speed up code.
28    
29    November 7, 2006: 216-CPU code for cube43
30    Bug fixes in growth.F routine and new set of diagnostics
31    
32    October 15, 2006: 216-CPU code for cube40
33    
34    September 28, 2006: 216-CPU code for cube38
35    
36    September 4, 2006
37    Modified 32*32*6*15 experiments to use grid_cs32.* files from
38     verification/tutorial_held_suarez_cs/input instead of
39     tile* files from verification/global_ocean.cs32x15/input
40    
41    August 8, 2006: 216-CPU code and input used for cube37
42    using "June 10, 2006" MITgcm code.
43    
44    for online T/S profile diagnostics all that is needed is
45      profiles_init_fixed
46      profiles_inloop
47    see pkg/ecco/ecco_cost_init_fixed.F
48        pkg/ecco/cost_averagesfields.F
49    
50    ##########################################################################
51    ##########################################################################
52    # Get forcing files, etc.
53    # Example below is for cube46 on /nobackup2a/menemenl
54    
55    cd /nobackup2a/menemenl
56    mkdir cube47
57    cd cube47
58    ln -sf ../run_template .
59    ln -sf ../ncep_rgau .
60    
61    
62  ##########################################################################  ##########################################################################
63  ##########################################################################  ##########################################################################
64  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
65    
66      bash or sh shell:
67        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
68        $ cvs login
69          ( enter the CVS password: "cvsanon" )
70    
71      tcsh or csh shell:
72        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
73        $ cvs login
74          ( enter the CVS password: "cvsanon" )
75    
76  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
77  cvs co MITgcm_contrib/high_res_cube/code-mods  cvs co MITgcm_contrib/high_res_cube/code-mods
78  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
79  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
80  cvs co MITgcm_code  cvs co MITgcm_code
81  cvs co MITgcm/verification/global_ocean.cs32x15  cvs co MITgcm/verification/global_ocean.cs32x15
82  cvs co MITgcm/verification/testreport  cvs co MITgcm/verification/tutorial_held_suarez_cs/input
83    
84    
85    ##########################################################################
86    ##########################################################################
87    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
88    
89    cd MITgcm/verification/global_ocean.cs32x15/code
90    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
91    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
92    \cp SIZE.h_216 SIZE.h
93    \cp packages.conf_hr packages.conf
94    
95    cd ../build
96    \rm *
97    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
98    make depend
99    make -j
100    
101    cd ..
102    mkdir run
103    cd run
104    \rm *
105    \cp ../input/* .
106    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
107    ln -sf ../../../../run_template/* .
108    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
109    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
110    ln -sf ../../../../run_template/pickup.0000000216.cube49 pickup.0000000216
111    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube48 pickup_seaice.0000000216
112    \cp ../build/mitgcmuv .
113    qsub job_altix
114    
115    
116  ##########################################################################  ##########################################################################
# Line 23  cvs co MITgcm/verification/testreport Line 120  cvs co MITgcm/verification/testreport
120  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
121  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
122  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
123    \rm CPP_EEOPTIONS.h
124  cd ../build  cd ../build
125  \rm *  \rm *
126  ../../../tools/genmake2 -mods=../code  ../../../tools/genmake2 -mods=../code
# Line 32  cd .. Line 130  cd ..
130  mkdir run  mkdir run
131  cd run  cd run
132  \rm *  \rm *
133    \cp ../../tutorial_held_suarez_cs/input/grid* .
134  \cp ../input/* .  \cp ../input/* .
135  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
136  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 42  comparison output is in: Line 141  comparison output is in:
141  to use matlab to look at the output  to use matlab to look at the output
142  matlab  matlab
143    
144  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
145      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);           'surForcT','oceTAUX','oceTAUY','surForcS'}
146        tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
147      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
148  end  end
149    
150  heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
151  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
152  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]);
153  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]);
154  clf  clf
155  subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
156  subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
157  subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
158  subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
159    
160    
161  ##########################################################################  ##########################################################################
# Line 74  cd .. Line 174  cd ..
174  mkdir run  mkdir run
175  cd run  cd run
176  \rm *  \rm *
177    \cp ../../tutorial_held_suarez_cs/input/grid* .
178  \cp ../input/* .  \cp ../input/* .
179  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
180  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
181    
 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')  
   
182    
183  ##########################################################################  ##########################################################################
184  ##########################################################################  ##########################################################################
185  # 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
186    
187  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
188  \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 191  cd MITgcm/verification/global_ocean.cs32
191    
192  cd ../build  cd ../build
193  \rm *  \rm *
194  ../../../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
195  make depend  make depend
196  make -j  make -j
197    
# Line 119  cd .. Line 199  cd ..
199  mkdir run  mkdir run
200  cd run  cd run
201  \rm *  \rm *
202    \cp ../../tutorial_held_suarez_cs/input/grid* .
203  \cp ../input/* .  \cp ../input/* .
204  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
205  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
# Line 152  qsub job_altix92_54t Line 233  qsub job_altix92_54t
233    
234  ##########################################################################  ##########################################################################
235  ##########################################################################  ##########################################################################
236  # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics  # 510*510*6*50, 1500-tile, 150-cpu, excludes land
237  # requires input files in sudirectories run_template and ncep_rgau  # uses s1500t_17x51 configuration
 # these can be obained from lou:/u/menemenl/cube  
238    
239  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
240  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
241  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
242  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_150 SIZE.h
243  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
244    
245  cd ../build  cd ../build
# Line 176  cd run Line 256  cd run
256  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
257  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
258  \rm pickup*  \rm pickup*
259  ln -sf ../../../../run_template/pickup.0000316440.cube20 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
260  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube20 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
261  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv mitgcmuv150
262  qsub job_altix92  qsub job_altix150
263    
264    
265    ##########################################################################
266    ##########################################################################
267    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
268    # uses s1500t_17x51 configuration
269    # example for running on c17-c20 using arrayd
270    
271    cd MITgcm/verification/global_ocean.cs32x15/code
272    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
273    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
274    \cp SIZE.h_375 SIZE.h
275    \cp packages.conf_hr packages.conf
276    
277    cd ../build
278    \rm *
279    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
280    make depend
281    make -j
282    
283    cd ..
284    mkdir run
285    cd run
286    \rm *
287    \cp ../input/* .
288    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
289    ln -sf ../../../../run_template/* .
290    \rm pickup*
291    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
292    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
293    \cp ../build/mitgcmuv .
294    job_c20_375cpu < /dev/null >&! output.run &
295    
296    
297    ##########################################################################
298    ##########################################################################
299    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
300    # uses s1500t_17x51 configuration
301    # example for running on c17-c20 using arrayd
302    
303    cd MITgcm/verification/global_ocean.cs32x15/code
304    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
305    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
306    \cp SIZE.h_375 SIZE.h
307    \cp packages.conf_hr packages.conf
308    
309    cd ../build
310    \rm *
311    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
312    make depend
313    make -j
314    
315    cd ..
316    mkdir run
317    cd run
318    \rm *
319    \cp ../input/* .
320    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
321    ln -sf ../../../../run_template/* .
322    \rm pickup*
323    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
324    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
325    \cp ../build/mitgcmuv .
326    job_c20_375cpu < /dev/null >&! output.run &
327    
328    
329    ##########################################################################
330    ##########################################################################
331    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
332    # uses s1500t_17x51 configuration
333    # example for running on c17-c20 using arrayd
334    
335    cd MITgcm/verification/global_ocean.cs32x15/code
336    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
337    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
338    \cp SIZE.h_500 SIZE.h
339    \cp packages.conf_hr packages.conf
340    
341    cd ../build
342    \rm *
343    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
344    make depend
345    make -j
346    
347    cd ..
348    mkdir run
349    cd run
350    \rm *
351    \cp ../input/* .
352    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
353    ln -sf ../../../../run_template/* .
354    \rm pickup*
355    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
356    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
357    \cp ../build/mitgcmuv .
358    job_c19_500cpu < /dev/null >&! output.run &
359    
360    
361    ##########################################################################
362    ##########################################################################
363    # 510*510*6*50, 216-cpu cube sphere on cosmos
364    
365    cd MITgcm/verification/global_ocean.cs32x15/code
366    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
367    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
368    \cp SIZE.h_216 SIZE.h
369    \cp packages.conf_hr packages.conf
370    
371    module unload latest_intel80
372    module unload mpich-gm-intel80
373    module load latest_intel81
374    module load mpich-gm-intel81
375    
376    cd ../build
377    \rm *
378    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
379    make depend
380    make -j
381    
382    cd ..
383    mkdir run
384    cd run
385    \rm *
386    \cp ../input/* .
387    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
388    ln -sf ../../../../run_template/* .
389    \rm pickup*
390    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
391    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
392    \cp ../build/mitgcmuv .
393    bsub < job_cosmos
394    
395    
396  ##########################################################################  ##########################################################################
# Line 282  cd run Line 472  cd run
472  \cp ../input/* .  \cp ../input/* .
473  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
474  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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