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revision 1.51 by dimitri, Thu Feb 10 20:47:06 2005 UTC revision 1.65 by dimitri, Tue Sep 5 02:49:56 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.  Last updated: September 4, 2006
4    Modified 32*32*6*15 experiments to use grid_cs32.* files from
5     verification/tutorial_held_suarez_cs/input instead of
6     tile* files from verification/global_ocean.cs32x15/input
7    
8    Updated: August 8, 2006
9    216-CPU code and input used for integrating cube37
10    using "June 10, 2006" MITgcm code.
11    
12    
13  ##########################################################################  ##########################################################################
# Line 13  cvs co MITgcm_contrib/high_res_cube/inpu Line 20  cvs co MITgcm_contrib/high_res_cube/inpu
20  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
21  cvs co MITgcm_code  cvs co MITgcm_code
22  cvs co MITgcm/verification/global_ocean.cs32x15  cvs co MITgcm/verification/global_ocean.cs32x15
23  cvs co MITgcm/verification/testreport  cvs co MITgcm/verification/tutorial_held_suarez_cs/input
24    
25    
26  ##########################################################################  ##########################################################################
# Line 32  cd .. Line 39  cd ..
39  mkdir run  mkdir run
40  cd run  cd run
41  \rm *  \rm *
42    \cp ../../tutorial_held_suarez_cs/input/grid* .
43  \cp ../input/* .  \cp ../input/* .
44  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
45  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 42  comparison output is in: Line 50  comparison output is in:
50  to use matlab to look at the output  to use matlab to look at the output
51  matlab  matlab
52    
53  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...
54             'QNETtave','FVtave','FUtave','EmPmRtave'}
55      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]);
56      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
57  end  end
58    
59  heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);
60  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
61  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]);
62  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]);
63  clf  clf
64  subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
65  subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
66  subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
67  subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
68    
69    
70  ##########################################################################  ##########################################################################
# Line 74  cd .. Line 83  cd ..
83  mkdir run  mkdir run
84  cd run  cd run
85  \rm *  \rm *
86    \cp ../../tutorial_held_suarez_cs/input/grid* .
87  \cp ../input/* .  \cp ../input/* .
88  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
89  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
90    
 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')  
   
91    
92  ##########################################################################  ##########################################################################
93  ##########################################################################  ##########################################################################
94  # 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
95    
96  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
97  \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 100  cd MITgcm/verification/global_ocean.cs32
100    
101  cd ../build  cd ../build
102  \rm *  \rm *
103  ../../../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
104  make depend  make depend
105  make -j  make -j
106    
# Line 119  cd .. Line 108  cd ..
108  mkdir run  mkdir run
109  cd run  cd run
110  \rm *  \rm *
111    \cp ../../tutorial_held_suarez_cs/input/grid* .
112  \cp ../input/* .  \cp ../input/* .
113  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
114  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
# Line 152  qsub job_altix92_54t Line 142  qsub job_altix92_54t
142    
143  ##########################################################################  ##########################################################################
144  ##########################################################################  ##########################################################################
145  # 510*510*6*50, 216-cpu cube sphere on altix with ifort  # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
146  # requires input files in sudirectories run_template and ncep_rgau  # requires input files in sudirectories run_template and ncep_rgau
147  # these can be obained from lou:/u/menemenl/cube  # these can be obained from lou:/u/menemenl/cube
148    
# Line 166  cd ../build Line 156  cd ../build
156  \rm *  \rm *
157  ../../../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
158  make depend  make depend
159  make -j 4  make -j
160    
161    cd ..
162    mkdir run
163    cd run
164    \rm *
165    \cp ../input/* .
166    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
167    ln -sf ../../../../run_template/* .
168    \rm pickup* data.pkg data.seaice data.exf_clim data.exf data
169    \rm *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
170    ln -sf ../../../../run_template/pickup.0000000216.cube27 pickup.0000000216
171    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube27 pickup_seaice.0000000216
172    \cp ../build/mitgcmuv .
173    qsub job_altix
174    
175    
176    ##########################################################################
177    ##########################################################################
178    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
179    # uses s1500t_17x51 configuration
180    
181    cd MITgcm/verification/global_ocean.cs32x15/code
182    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
183    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
184    \cp SIZE.h_150 SIZE.h
185    \cp packages.conf_hr packages.conf
186    
187    cd ../build
188    \rm *
189    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
190    make depend
191    make -j
192    
193  cd ..  cd ..
194  mkdir run  mkdir run
# Line 176  cd run Line 198  cd run
198  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
199  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
200  \rm pickup*  \rm pickup*
201  ln -sf ../../../../run_template/pickup.0000316440.cube20 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
202  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube20 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
203    \cp ../build/mitgcmuv mitgcmuv150
204    qsub job_altix150
205    
206    
207    
208    
209    ##########################################################################
210    ##########################################################################
211    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
212    # uses s1500t_17x51 configuration
213    # example for running on c17-c20 using arrayd
214    
215    cd MITgcm/verification/global_ocean.cs32x15/code
216    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
217    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
218    \cp SIZE.h_375 SIZE.h
219    \cp packages.conf_hr packages.conf
220    
221    cd ../build
222    \rm *
223    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
224    make depend
225    make -j
226    
227    cd ..
228    mkdir run
229    cd run
230    \rm *
231    \cp ../input/* .
232    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
233    ln -sf ../../../../run_template/* .
234    \rm pickup*
235    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
236    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
237  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv .
238  qsub job_altix92  job_c20_375cpu < /dev/null >&! output.run &
239    
240    
241    
242    
243    
244    
245    
246    
247    
# Line 188  qsub job_altix92 Line 250  qsub job_altix92
250    
251  ##########################################################################  ##########################################################################
252  ##########################################################################  ##########################################################################
253  # 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
254  # requires input files in sudirectories run_template and ncep_rgau  # uses s1500t_17x51 configuration
255  # these can be obained from lou:/u/menemenl/cube  # 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    
318    ##########################################################################
319    ##########################################################################
320    # 510*510*6*50, 216-cpu cube sphere on cosmos
321    
322  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
323  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
324  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
325  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_216 SIZE.h
326  \cp packages.conf_diagnostics packages.conf  \cp packages.conf_hr packages.conf
327    
328    module unload latest_intel80
329    module unload mpich-gm-intel80
330    module load latest_intel81
331    module load mpich-gm-intel81
332    
333  cd ../build  cd ../build
334  \rm *  \rm *
335  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
336  make depend  make depend
337  make -j 4  make -j
338    
339  cd ..  cd ..
340  mkdir run  mkdir run
# Line 212  cd run Line 344  cd run
344  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
345  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
346  \rm pickup*  \rm pickup*
347  ln -sf ../../../../run_template/pickup.0000316440.cube20 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
348  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube20 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
349  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv .
350  qsub job_altix92  bsub < job_cosmos
351    
352    
353    
354    
355    
# Line 313  cd run Line 447  cd run
447  \cp ../input/* .  \cp ../input/* .
448  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
449  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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