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revision 1.51 by dimitri, Thu Feb 10 20:47:06 2005 UTC revision 1.67 by dimitri, Wed Oct 4 17:47:26 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.  September 28, 2006: 216-CPU code for cube38
4    
5    September 4, 2006
6    Modified 32*32*6*15 experiments to use grid_cs32.* files from
7     verification/tutorial_held_suarez_cs/input instead of
8     tile* files from verification/global_ocean.cs32x15/input
9    
10    August 8, 2006
11    216-CPU code and input used for integrating cube37
12    using "June 10, 2006" MITgcm code.
13    
14    for online T/S profile diagnostics all that is needed is
15      profiles_init_fixed
16      profiles_inloop
17    see pkg/ecco/ecco_cost_init_fixed.F
18        pkg/ecco/cost_averagesfields.F
19    
20    
21  ##########################################################################  ##########################################################################
# Line 13  cvs co MITgcm_contrib/high_res_cube/inpu Line 28  cvs co MITgcm_contrib/high_res_cube/inpu
28  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
29  cvs co MITgcm_code  cvs co MITgcm_code
30  cvs co MITgcm/verification/global_ocean.cs32x15  cvs co MITgcm/verification/global_ocean.cs32x15
31  cvs co MITgcm/verification/testreport  cvs co MITgcm/verification/tutorial_held_suarez_cs/input
32    
33    
34  ##########################################################################  ##########################################################################
# Line 32  cd .. Line 47  cd ..
47  mkdir run  mkdir run
48  cd run  cd run
49  \rm *  \rm *
50    \cp ../../tutorial_held_suarez_cs/input/grid* .
51  \cp ../input/* .  \cp ../input/* .
52  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
53  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 42  comparison output is in: Line 58  comparison output is in:
58  to use matlab to look at the output  to use matlab to look at the output
59  matlab  matlab
60    
61  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...
62             'QNETtave','FVtave','FUtave','EmPmRtave'}
63      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);
64      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
65  end  end
66    
67  heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);
68  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
69  uice=mask.*permute(readbin(['UICE.0000000020.data'],[32,6,32]),[1 3 2]);  uice=mask.*permute(readbin(['UICEtave.0000000020.data'],[32,6,32]),[1 3 2]);
70  vice=mask.*permute(readbin(['VICE.0000000020.data'],[32,6,32]),[1 3 2]);  vice=mask.*permute(readbin(['VICEtave.0000000020.data'],[32,6,32]),[1 3 2]);
71  clf  clf
72  subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
73  subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
74  subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
75  subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
76    
77    
78    ##########################################################################
79    ##########################################################################
80    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
81    # requires input files in sudirectories run_template and ncep_rgau
82    # these can be obained from lou:/u/menemenl/cube
83    
84    cd MITgcm/verification/global_ocean.cs32x15/code
85    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
86    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
87    \cp SIZE.h_216 SIZE.h
88    \cp packages.conf_hr packages.conf
89    
90    cd ../build
91    \rm *
92    ../../../tools/genmake2 -mods=../code -of
93    ../../../tools/build_options/linux_ia\
94    64_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* data.pkg data.seaice data.exf_clim data.exf data bathy_Hmin50.bin
106    \rm *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
107    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
108    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38
109    pickup_seaice.\
110    0000000216
111    \cp ../build/mitgcmuv .
112    qsub job_altix
113    
114    
115  ##########################################################################  ##########################################################################
# Line 74  cd .. Line 128  cd ..
128  mkdir run  mkdir run
129  cd run  cd run
130  \rm *  \rm *
131    \cp ../../tutorial_held_suarez_cs/input/grid* .
132  \cp ../input/* .  \cp ../input/* .
133  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
134  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
135    
 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')  
   
136    
137  ##########################################################################  ##########################################################################
138  ##########################################################################  ##########################################################################
139  # 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
140    
141  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
142  \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 145  cd MITgcm/verification/global_ocean.cs32
145    
146  cd ../build  cd ../build
147  \rm *  \rm *
148  ../../../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
149  make depend  make depend
150  make -j  make -j
151    
# Line 119  cd .. Line 153  cd ..
153  mkdir run  mkdir run
154  cd run  cd run
155  \rm *  \rm *
156    \cp ../../tutorial_held_suarez_cs/input/grid* .
157  \cp ../input/* .  \cp ../input/* .
158  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
159  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
# Line 152  qsub job_altix92_54t Line 187  qsub job_altix92_54t
187    
188  ##########################################################################  ##########################################################################
189  ##########################################################################  ##########################################################################
190  # 510*510*6*50, 216-cpu cube sphere on altix with ifort  # 510*510*6*50, 1500-tile, 150-cpu, excludes land
191  # requires input files in sudirectories run_template and ncep_rgau  # uses s1500t_17x51 configuration
 # these can be obained from lou:/u/menemenl/cube  
192    
193  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
194  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
195  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
196  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_150 SIZE.h
197  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
198    
199  cd ../build  cd ../build
200  \rm *  \rm *
201  ../../../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
202  make depend  make depend
203  make -j 4  make -j
204    
205  cd ..  cd ..
206  mkdir run  mkdir run
# Line 176  cd run Line 210  cd run
210  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
211  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
212  \rm pickup*  \rm pickup*
213  ln -sf ../../../../run_template/pickup.0000316440.cube20 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
214  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube20 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
215  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv mitgcmuv150
216  qsub job_altix92  qsub job_altix150
   
   
   
   
217    
218    
219  ##########################################################################  ##########################################################################
220  ##########################################################################  ##########################################################################
221  # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics  # 510*510*6*50, 1500-tile, 375-cpu, excludes land
222  # requires input files in sudirectories run_template and ncep_rgau  # uses s1500t_17x51 configuration
223  # these can be obained from lou:/u/menemenl/cube  # example for running on c17-c20 using arrayd
224    
225  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
226  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
227  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
228  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_375 SIZE.h
229  \cp packages.conf_diagnostics packages.conf  \cp packages.conf_hr packages.conf
230    
231  cd ../build  cd ../build
232  \rm *  \rm *
233  ../../../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
234  make depend  make depend
235  make -j 4  make -j
236    
237  cd ..  cd ..
238  mkdir run  mkdir run
# Line 212  cd run Line 242  cd run
242  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
243  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
244  \rm pickup*  \rm pickup*
245  ln -sf ../../../../run_template/pickup.0000316440.cube20 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
246  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube20 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
247  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv .
248  qsub job_altix92  job_c20_375cpu < /dev/null >&! output.run &
249    
250    
251    ##########################################################################
252    ##########################################################################
253    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
254    # uses s1500t_17x51 configuration
255    # example for running on c17-c20 using arrayd
256    
257    cd MITgcm/verification/global_ocean.cs32x15/code
258    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
259    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
260    \cp SIZE.h_375 SIZE.h
261    \cp packages.conf_hr packages.conf
262    
263    cd ../build
264    \rm *
265    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
266    make depend
267    make -j
268    
269    cd ..
270    mkdir run
271    cd run
272    \rm *
273    \cp ../input/* .
274    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
275    ln -sf ../../../../run_template/* .
276    \rm pickup*
277    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
278    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
279    \cp ../build/mitgcmuv .
280    job_c20_375cpu < /dev/null >&! output.run &
281    
282    
283    ##########################################################################
284    ##########################################################################
285    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
286    # uses s1500t_17x51 configuration
287    # example for running on c17-c20 using arrayd
288    
289    cd MITgcm/verification/global_ocean.cs32x15/code
290    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
291    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
292    \cp SIZE.h_500 SIZE.h
293    \cp packages.conf_hr packages.conf
294    
295    cd ../build
296    \rm *
297    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
298    make depend
299    make -j
300    
301    cd ..
302    mkdir run
303    cd run
304    \rm *
305    \cp ../input/* .
306    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
307    ln -sf ../../../../run_template/* .
308    \rm pickup*
309    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
310    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
311    \cp ../build/mitgcmuv .
312    job_c19_500cpu < /dev/null >&! output.run &
313    
314    
315    ##########################################################################
316    ##########################################################################
317    # 510*510*6*50, 216-cpu cube sphere on cosmos
318    
319    cd MITgcm/verification/global_ocean.cs32x15/code
320    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
321    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
322    \cp SIZE.h_216 SIZE.h
323    \cp packages.conf_hr packages.conf
324    
325    module unload latest_intel80
326    module unload mpich-gm-intel80
327    module load latest_intel81
328    module load mpich-gm-intel81
329    
330    cd ../build
331    \rm *
332    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
333    make depend
334    make -j
335    
336    cd ..
337    mkdir run
338    cd run
339    \rm *
340    \cp ../input/* .
341    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
342    ln -sf ../../../../run_template/* .
343    \rm pickup*
344    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
345    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
346    \cp ../build/mitgcmuv .
347    bsub < job_cosmos
348    
349    
350  ##########################################################################  ##########################################################################
# Line 313  cd run Line 426  cd run
426  \cp ../input/* .  \cp ../input/* .
427  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
428  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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