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revision 1.52 by dimitri, Sat Feb 19 06:28:28 2005 UTC revision 1.77 by dimitri, Wed Nov 22 07:21:31 2006 UTC
# Line 1  Line 1 
1  daInstructions for setting up a cube-sphere integration with sea-ice.  Instructions for setting up a cube-sphere integration with sea-ice.
2  Date last updated: February 17, 2005  
3  Code and input used for integrating cube22.  =================
4    UPDATES
5    
6    November 22, 2006: 216-CPU code for cube44
7    Changed diagnostics, yet again.
8    
9    November 7, 2006: 216-CPU code for cube43
10    Bug fixes in growth.F routine and new set of diagnostics
11    
12    October 15, 2006: 216-CPU code for cube40
13    
14    September 28, 2006: 216-CPU code for cube38
15    
16    September 4, 2006
17    Modified 32*32*6*15 experiments to use grid_cs32.* files from
18     verification/tutorial_held_suarez_cs/input instead of
19     tile* files from verification/global_ocean.cs32x15/input
20    
21    August 8, 2006: 216-CPU code and input used for cube37
22    using "June 10, 2006" MITgcm code.
23    
24    for online T/S profile diagnostics all that is needed is
25      profiles_init_fixed
26      profiles_inloop
27    see pkg/ecco/ecco_cost_init_fixed.F
28        pkg/ecco/cost_averagesfields.F
29    
30    
31  ##########################################################################  ##########################################################################
32  ##########################################################################  ##########################################################################
33  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
34    #
35    
36      bash or sh shell:
37        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
38        $ cvs login
39          ( enter the CVS password: "cvsanon" )
40    
41      tcsh or csh shell:
42        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
43        $ cvs login
44          ( enter the CVS password: "cvsanon" )
45    
46  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
47  cvs co MITgcm_contrib/high_res_cube/code-mods  cvs co MITgcm_contrib/high_res_cube/code-mods
# Line 13  cvs co MITgcm_contrib/high_res_cube/inpu Line 49  cvs co MITgcm_contrib/high_res_cube/inpu
49  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
50  cvs co MITgcm_code  cvs co MITgcm_code
51  cvs co MITgcm/verification/global_ocean.cs32x15  cvs co MITgcm/verification/global_ocean.cs32x15
52  cvs co MITgcm/verification/testreport  cvs co MITgcm/verification/tutorial_held_suarez_cs/input
53    
54    
55    ##########################################################################
56    ##########################################################################
57    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
58    # requires input files in sudirectories run_template and ncep_rgau
59    # these can be obained from lou:/u/menemenl/cube
60    
61    cd MITgcm/verification/global_ocean.cs32x15/code
62    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
63    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
64    \cp SIZE.h_216 SIZE.h
65    \cp packages.conf_hr packages.conf
66    
67    cd ../build
68    \rm *
69    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
70    make depend
71    make -j
72    
73    cd ..
74    mkdir run
75    cd run
76    \rm *
77    \cp ../input/* .
78    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
79    ln -sf ../../../../run_template/* .
80    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
81    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
82    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
83    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38 pickup_seaice.0000000216
84    \cp ../build/mitgcmuv .
85    qsub job_altix
86    
87    
88  ##########################################################################  ##########################################################################
# Line 32  cd .. Line 101  cd ..
101  mkdir run  mkdir run
102  cd run  cd run
103  \rm *  \rm *
104    \cp ../../tutorial_held_suarez_cs/input/grid* .
105  \cp ../input/* .  \cp ../input/* .
106  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
107  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 42  comparison output is in: Line 112  comparison output is in:
112  to use matlab to look at the output  to use matlab to look at the output
113  matlab  matlab
114    
115  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
116      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);           'surForcT','oceTAUX','oceTAUY','surForcS'}
117        tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
118      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
119  end  end
120    
121  heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
122  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
123  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]);
124  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]);
125  clf  clf
126  subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
127  subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
128  subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
129  subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
130    
131    
132  ##########################################################################  ##########################################################################
# Line 74  cd .. Line 145  cd ..
145  mkdir run  mkdir run
146  cd run  cd run
147  \rm *  \rm *
148    \cp ../../tutorial_held_suarez_cs/input/grid* .
149  \cp ../input/* .  \cp ../input/* .
150  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
151  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
152    
 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')  
   
153    
154  ##########################################################################  ##########################################################################
155  ##########################################################################  ##########################################################################
156  # 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
157    
158  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
159  \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 162  cd MITgcm/verification/global_ocean.cs32
162    
163  cd ../build  cd ../build
164  \rm *  \rm *
165  ../../../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
166  make depend  make depend
167  make -j  make -j
168    
# Line 119  cd .. Line 170  cd ..
170  mkdir run  mkdir run
171  cd run  cd run
172  \rm *  \rm *
173    \cp ../../tutorial_held_suarez_cs/input/grid* .
174  \cp ../input/* .  \cp ../input/* .
175  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
176  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
# Line 152  qsub job_altix92_54t Line 204  qsub job_altix92_54t
204    
205  ##########################################################################  ##########################################################################
206  ##########################################################################  ##########################################################################
207  # 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
208  # requires input files in sudirectories run_template and ncep_rgau  # uses s1500t_17x51 configuration
 # these can be obained from lou:/u/menemenl/cube  
209    
210  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
211  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
212  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
213  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_150 SIZE.h
214  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
215    
216  cd ../build  cd ../build
# Line 176  cd run Line 227  cd run
227  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
228  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
229  \rm pickup*  \rm pickup*
230  ln -sf ../../../../run_template/pickup.0000316440.cube20 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
231  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube20 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
232  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv mitgcmuv150
233  qsub job_altix92  qsub job_altix150
234    
235    
236    ##########################################################################
237    ##########################################################################
238    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
239    # uses s1500t_17x51 configuration
240    # example for running on c17-c20 using arrayd
241    
242    cd MITgcm/verification/global_ocean.cs32x15/code
243    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
244    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
245    \cp SIZE.h_375 SIZE.h
246    \cp packages.conf_hr packages.conf
247    
248    cd ../build
249    \rm *
250    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
251    make depend
252    make -j
253    
254    cd ..
255    mkdir run
256    cd run
257    \rm *
258    \cp ../input/* .
259    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
260    ln -sf ../../../../run_template/* .
261    \rm pickup*
262    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
263    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
264    \cp ../build/mitgcmuv .
265    job_c20_375cpu < /dev/null >&! output.run &
266    
267    
268    ##########################################################################
269    ##########################################################################
270    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
271    # uses s1500t_17x51 configuration
272    # example for running on c17-c20 using arrayd
273    
274    cd MITgcm/verification/global_ocean.cs32x15/code
275    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
276    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
277    \cp SIZE.h_375 SIZE.h
278    \cp packages.conf_hr packages.conf
279    
280    cd ../build
281    \rm *
282    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
283    make depend
284    make -j
285    
286    cd ..
287    mkdir run
288    cd run
289    \rm *
290    \cp ../input/* .
291    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
292    ln -sf ../../../../run_template/* .
293    \rm pickup*
294    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
295    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
296    \cp ../build/mitgcmuv .
297    job_c20_375cpu < /dev/null >&! output.run &
298    
299    
300    ##########################################################################
301    ##########################################################################
302    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
303    # uses s1500t_17x51 configuration
304    # example for running on c17-c20 using arrayd
305    
306    cd MITgcm/verification/global_ocean.cs32x15/code
307    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
308    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
309    \cp SIZE.h_500 SIZE.h
310    \cp packages.conf_hr packages.conf
311    
312    cd ../build
313    \rm *
314    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
315    make depend
316    make -j
317    
318    cd ..
319    mkdir run
320    cd run
321    \rm *
322    \cp ../input/* .
323    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
324    ln -sf ../../../../run_template/* .
325    \rm pickup*
326    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
327    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
328    \cp ../build/mitgcmuv .
329    job_c19_500cpu < /dev/null >&! output.run &
330    
331    
332    ##########################################################################
333    ##########################################################################
334    # 510*510*6*50, 216-cpu cube sphere on cosmos
335    
336    cd MITgcm/verification/global_ocean.cs32x15/code
337    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
338    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
339    \cp SIZE.h_216 SIZE.h
340    \cp packages.conf_hr packages.conf
341    
342    module unload latest_intel80
343    module unload mpich-gm-intel80
344    module load latest_intel81
345    module load mpich-gm-intel81
346    
347    cd ../build
348    \rm *
349    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
350    make depend
351    make -j
352    
353    cd ..
354    mkdir run
355    cd run
356    \rm *
357    \cp ../input/* .
358    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
359    ln -sf ../../../../run_template/* .
360    \rm pickup*
361    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
362    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
363    \cp ../build/mitgcmuv .
364    bsub < job_cosmos
365    
366    
367  ##########################################################################  ##########################################################################
# Line 282  cd run Line 443  cd run
443  \cp ../input/* .  \cp ../input/* .
444  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
445  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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