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revision 1.52 by dimitri, Sat Feb 19 06:28:28 2005 UTC revision 1.88 by dimitri, Wed Jan 31 01:57:41 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    January 5, 2006: cube51, like cube50 but with bottomDragQuadratic = 0.0012
12    
13    January 5, 2006: cube50, like cube48 but with snow advection
14    
15    December 30, 2006: updates for cube49, the first
16    "blend" integration.
17    
18    December 11, 2006: preparing for cube47, same as cube43
19    but with Arctic monthly river runoff climatology.
20    
21    December 5, 2006: 216-CPU code for cube46
22    Changed diagnostics to accomodate JMCs latest and some
23    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
24    to speed up code.
25    
26    November 7, 2006: 216-CPU code for cube43
27    Bug fixes in growth.F routine and new set of diagnostics
28    
29    October 15, 2006: 216-CPU code for cube40
30    
31    September 28, 2006: 216-CPU code for cube38
32    
33    September 4, 2006
34    Modified 32*32*6*15 experiments to use grid_cs32.* files from
35     verification/tutorial_held_suarez_cs/input instead of
36     tile* files from verification/global_ocean.cs32x15/input
37    
38    August 8, 2006: 216-CPU code and input used for cube37
39    using "June 10, 2006" MITgcm code.
40    
41    for online T/S profile diagnostics all that is needed is
42      profiles_init_fixed
43      profiles_inloop
44    see pkg/ecco/ecco_cost_init_fixed.F
45        pkg/ecco/cost_averagesfields.F
46    
47    ##########################################################################
48    ##########################################################################
49    # Get forcing files, etc.
50    # Example below is for cube46 on /nobackup2a/menemenl
51    
52    cd /nobackup2a/menemenl
53    mkdir cube47
54    cd cube47
55    ln -sf ../run_template .
56    ln -sf ../ncep_rgau .
57    
58    
59  ##########################################################################  ##########################################################################
60  ##########################################################################  ##########################################################################
61  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
62    
63      bash or sh shell:
64        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
65        $ cvs login
66          ( enter the CVS password: "cvsanon" )
67    
68      tcsh or csh shell:
69        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
70        $ cvs login
71          ( enter the CVS password: "cvsanon" )
72    
73  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
74  cvs co MITgcm_contrib/high_res_cube/code-mods  cvs co MITgcm_contrib/high_res_cube/code-mods
75  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
76  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
77  cvs co MITgcm_code  cvs co MITgcm_code
78  cvs co MITgcm/verification/global_ocean.cs32x15  cvs co MITgcm/verification/global_ocean.cs32x15
79  cvs co MITgcm/verification/testreport  cvs co MITgcm/verification/tutorial_held_suarez_cs/input
80    
81    
82    ##########################################################################
83    ##########################################################################
84    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
85    
86    cd MITgcm/verification/global_ocean.cs32x15/code
87    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
88    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
89    \cp SIZE.h_216 SIZE.h
90    \cp packages.conf_hr packages.conf
91    
92    cd ../build
93    \rm *
94    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
95    make depend
96    make -j
97    
98    cd ..
99    mkdir run
100    cd run
101    \rm *
102    \cp ../input/* .
103    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
104    ln -sf ../../../../run_template/* .
105    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
106    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
107    ln -sf ../../../../run_template/pickup.0000000216.cube49 pickup.0000000216
108    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube48 pickup_seaice.0000000216
109    \cp ../build/mitgcmuv .
110    qsub job_altix
111    
112    
113  ##########################################################################  ##########################################################################
# Line 23  cvs co MITgcm/verification/testreport Line 117  cvs co MITgcm/verification/testreport
117  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
118  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
119  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
120    \rm CPP_EEOPTIONS.h
121  cd ../build  cd ../build
122  \rm *  \rm *
123  ../../../tools/genmake2 -mods=../code  ../../../tools/genmake2 -mods=../code
# Line 32  cd .. Line 127  cd ..
127  mkdir run  mkdir run
128  cd run  cd run
129  \rm *  \rm *
130    \cp ../../tutorial_held_suarez_cs/input/grid* .
131  \cp ../input/* .  \cp ../input/* .
132  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
133  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 42  comparison output is in: Line 138  comparison output is in:
138  to use matlab to look at the output  to use matlab to look at the output
139  matlab  matlab
140    
141  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
142      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);           'surForcT','oceTAUX','oceTAUY','surForcS'}
143        tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
144      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
145  end  end
146    
147  heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
148  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
149  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]);
150  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]);
151  clf  clf
152  subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
153  subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
154  subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
155  subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
156    
157    
158  ##########################################################################  ##########################################################################
# Line 74  cd .. Line 171  cd ..
171  mkdir run  mkdir run
172  cd run  cd run
173  \rm *  \rm *
174    \cp ../../tutorial_held_suarez_cs/input/grid* .
175  \cp ../input/* .  \cp ../input/* .
176  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
177  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
178    
 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')  
   
179    
180  ##########################################################################  ##########################################################################
181  ##########################################################################  ##########################################################################
182  # 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
183    
184  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
185  \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 188  cd MITgcm/verification/global_ocean.cs32
188    
189  cd ../build  cd ../build
190  \rm *  \rm *
191  ../../../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
192  make depend  make depend
193  make -j  make -j
194    
# Line 119  cd .. Line 196  cd ..
196  mkdir run  mkdir run
197  cd run  cd run
198  \rm *  \rm *
199    \cp ../../tutorial_held_suarez_cs/input/grid* .
200  \cp ../input/* .  \cp ../input/* .
201  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
202  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
# Line 152  qsub job_altix92_54t Line 230  qsub job_altix92_54t
230    
231  ##########################################################################  ##########################################################################
232  ##########################################################################  ##########################################################################
233  # 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
234  # requires input files in sudirectories run_template and ncep_rgau  # uses s1500t_17x51 configuration
 # these can be obained from lou:/u/menemenl/cube  
235    
236  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
237  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
238  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
239  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_150 SIZE.h
240  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
241    
242  cd ../build  cd ../build
# Line 176  cd run Line 253  cd run
253  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
254  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
255  \rm pickup*  \rm pickup*
256  ln -sf ../../../../run_template/pickup.0000316440.cube20 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
257  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube20 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
258  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv mitgcmuv150
259  qsub job_altix92  qsub job_altix150
260    
261    
262    ##########################################################################
263    ##########################################################################
264    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
265    # uses s1500t_17x51 configuration
266    # example for running on c17-c20 using arrayd
267    
268    cd MITgcm/verification/global_ocean.cs32x15/code
269    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
270    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
271    \cp SIZE.h_375 SIZE.h
272    \cp packages.conf_hr packages.conf
273    
274    cd ../build
275    \rm *
276    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
277    make depend
278    make -j
279    
280    cd ..
281    mkdir run
282    cd run
283    \rm *
284    \cp ../input/* .
285    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
286    ln -sf ../../../../run_template/* .
287    \rm pickup*
288    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
289    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
290    \cp ../build/mitgcmuv .
291    job_c20_375cpu < /dev/null >&! output.run &
292    
293    
294    ##########################################################################
295    ##########################################################################
296    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
297    # uses s1500t_17x51 configuration
298    # example for running on c17-c20 using arrayd
299    
300    cd MITgcm/verification/global_ocean.cs32x15/code
301    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
302    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
303    \cp SIZE.h_375 SIZE.h
304    \cp packages.conf_hr packages.conf
305    
306    cd ../build
307    \rm *
308    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
309    make depend
310    make -j
311    
312    cd ..
313    mkdir run
314    cd run
315    \rm *
316    \cp ../input/* .
317    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
318    ln -sf ../../../../run_template/* .
319    \rm pickup*
320    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
321    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
322    \cp ../build/mitgcmuv .
323    job_c20_375cpu < /dev/null >&! output.run &
324    
325    
326    ##########################################################################
327    ##########################################################################
328    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
329    # uses s1500t_17x51 configuration
330    # example for running on c17-c20 using arrayd
331    
332    cd MITgcm/verification/global_ocean.cs32x15/code
333    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
334    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
335    \cp SIZE.h_500 SIZE.h
336    \cp packages.conf_hr packages.conf
337    
338    cd ../build
339    \rm *
340    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
341    make depend
342    make -j
343    
344    cd ..
345    mkdir run
346    cd run
347    \rm *
348    \cp ../input/* .
349    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
350    ln -sf ../../../../run_template/* .
351    \rm pickup*
352    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
353    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
354    \cp ../build/mitgcmuv .
355    job_c19_500cpu < /dev/null >&! output.run &
356    
357    
358    ##########################################################################
359    ##########################################################################
360    # 510*510*6*50, 216-cpu cube sphere on cosmos
361    
362    cd MITgcm/verification/global_ocean.cs32x15/code
363    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
364    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
365    \cp SIZE.h_216 SIZE.h
366    \cp packages.conf_hr packages.conf
367    
368    module unload latest_intel80
369    module unload mpich-gm-intel80
370    module load latest_intel81
371    module load mpich-gm-intel81
372    
373    cd ../build
374    \rm *
375    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
376    make depend
377    make -j
378    
379    cd ..
380    mkdir run
381    cd run
382    \rm *
383    \cp ../input/* .
384    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
385    ln -sf ../../../../run_template/* .
386    \rm pickup*
387    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
388    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
389    \cp ../build/mitgcmuv .
390    bsub < job_cosmos
391    
392    
393  ##########################################################################  ##########################################################################
# Line 282  cd run Line 469  cd run
469  \cp ../input/* .  \cp ../input/* .
470  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
471  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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