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revision 1.33 by dimitri, Tue Mar 16 17:20:07 2004 UTC revision 1.80 by dimitri, Wed Dec 6 01:07:44 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: March 9, 2004.  
3  Code and input used for integrating cube5.  =================
4    UPDATES
5    
6    December 5, 2006: 216-CPU code for cube46
7    Changed diagnostics to accomodate JMCs latest and some
8    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
9    to speed up code.
10    
11    November 7, 2006: 216-CPU code for cube43
12    Bug fixes in growth.F routine and new set of diagnostics
13    
14    October 15, 2006: 216-CPU code for cube40
15    
16    September 28, 2006: 216-CPU code for cube38
17    
18    September 4, 2006
19    Modified 32*32*6*15 experiments to use grid_cs32.* files from
20     verification/tutorial_held_suarez_cs/input instead of
21     tile* files from verification/global_ocean.cs32x15/input
22    
23    August 8, 2006: 216-CPU code and input used for cube37
24    using "June 10, 2006" MITgcm code.
25    
26    for online T/S profile diagnostics all that is needed is
27      profiles_init_fixed
28      profiles_inloop
29    see pkg/ecco/ecco_cost_init_fixed.F
30        pkg/ecco/cost_averagesfields.F
31    
32    ##########################################################################
33    ##########################################################################
34    # Get forcing files, etc.
35    # Example below is for cube46 on /nobackup2a/menemenl
36    
37    cd /nobackup2a/menemenl
38    mkdir cube46
39    cd cube46
40    ln -sf ../run_template .
41    ln -sf ../ncep_rgau .
42    
43    
44  ##########################################################################  ##########################################################################
45  ##########################################################################  ##########################################################################
46  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
47    
48  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack    bash or sh shell:
49  cvs login ( CVS password: cvsanon )      $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
50  cvs co -r hrcube5 MITgcm_contrib/high_res_cube/README_ice      $ cvs login
51  cvs co -r hrcube5 MITgcm_contrib/high_res_cube/code-mods        ( enter the CVS password: "cvsanon" )
52  cvs co -r hrcube5 MITgcm_contrib/high_res_cube/input  
53  cvs co -r hrcube5 MITgcm_contrib/high_res_cube/results    tcsh or csh shell:
54  cvs co -r hrcube5 MITgcm_code      $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
55  cvs co -r hrcube5 MITgcm/verification/global_ocean.cs32x15      $ cvs login
56          ( enter the CVS password: "cvsanon" )
57    
58    cvs co MITgcm_contrib/high_res_cube/README_ice
59    cvs co MITgcm_contrib/high_res_cube/code-mods
60    cvs co MITgcm_contrib/high_res_cube/input
61    cvs co MITgcm_contrib/high_res_cube/results
62    cvs co MITgcm_code
63    cvs co MITgcm/verification/global_ocean.cs32x15
64    cvs co MITgcm/verification/tutorial_held_suarez_cs/input
65    
66    
67    ##########################################################################
68    ##########################################################################
69    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
70    
71    cd MITgcm/verification/global_ocean.cs32x15/code
72    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
73    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
74    \cp SIZE.h_216 SIZE.h
75    \cp packages.conf_hr packages.conf
76    
77    cd ../build
78    \rm *
79    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
80    make depend
81    make -j
82    
83    cd ..
84    mkdir run
85    cd run
86    \rm *
87    \cp ../input/* .
88    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
89    ln -sf ../../../../run_template/* .
90    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
91    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
92    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
93    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38 pickup_seaice.0000000216
94    \cp ../build/mitgcmuv .
95    qsub job_altix
96    
97    
98  ##########################################################################  ##########################################################################
# Line 24  cvs co -r hrcube5 MITgcm/verification/gl Line 102  cvs co -r hrcube5 MITgcm/verification/gl
102  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
103  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
104  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
   
105  cd ../build  cd ../build
106    \rm *
107  ../../../tools/genmake2 -mods=../code  ../../../tools/genmake2 -mods=../code
108  make depend  make depend
 \rm getcon.F  
109  make  make
   
110  cd ..  cd ..
111  mkdir run  mkdir run
112  cd run  cd run
113    \rm *
114    \cp ../../tutorial_held_suarez_cs/input/grid* .
115  \cp ../input/* .  \cp ../input/* .
116  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
117  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 44  comparison output is in: Line 122  comparison output is in:
122  to use matlab to look at the output  to use matlab to look at the output
123  matlab  matlab
124    
125  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
126      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);           'surForcT','oceTAUX','oceTAUY','surForcS'}
127        tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
128      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
129  end  end
130    
131  heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
132  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
133  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]);
134  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]);
135  clf  clf
136  subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
137  subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
138  subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
139  subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
140    
141    
142    ##########################################################################
143    ##########################################################################
144    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
145    
146    cd MITgcm/verification/global_ocean.cs32x15/code
147    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
148    \cp ../code_alt/code.176t_8x4/* .
149    cd ../build
150    \rm *
151    ../../../tools/genmake2 -mods=../code
152    make depend
153    make
154    cd ..
155    mkdir run
156    cd run
157    \rm *
158    \cp ../../tutorial_held_suarez_cs/input/grid* .
159    \cp ../input/* .
160    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
161    ../build/mitgcmuv >& output.txt
162    
163    
164  ##########################################################################  ##########################################################################
165  ##########################################################################  ##########################################################################
166  # 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
167    
168  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
169  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
# Line 71  cd MITgcm/verification/global_ocean.cs32 Line 172  cd MITgcm/verification/global_ocean.cs32
172    
173  cd ../build  cd ../build
174  \rm *  \rm *
175  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
176  make depend  make depend
177  \rm getcon.F  make -j
 make  
178    
179  cd ..  cd ..
180  mkdir run  mkdir run
181  cd run  cd run
182  \rm *  \rm *
183    \cp ../../tutorial_held_suarez_cs/input/grid* .
184  \cp ../input/* .  \cp ../input/* .
185  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
186  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
# Line 87  mpirun -np 2 ../build/mitgcmuv Line 188  mpirun -np 2 ../build/mitgcmuv
188    
189  ##########################################################################  ##########################################################################
190  ##########################################################################  ##########################################################################
191  # 510*510*6*50, 54-cpu cube sphere on the altices with efc  # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
192    # starting with pickup file from end of 1992
193    # requires input files in sudirectories run_template and ncep_rgau
194    
195    cd MITgcm/verification/global_ocean.cs32x15/code
196    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
197    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
198    \cp packages.conf_hr packages.conf
199    
200    cd ../build
201    \rm *
202    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
203    make depend
204    make -j
205    
206    cd ..
207    mkdir run
208    cd run
209    \rm *
210    \cp ../input/* .
211    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
212    qsub job_altix92_54t
213    
214    
215    ##########################################################################
216    ##########################################################################
217    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
218    # uses s1500t_17x51 configuration
219    
220    cd MITgcm/verification/global_ocean.cs32x15/code
221    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
222    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
223    \cp SIZE.h_150 SIZE.h
224    \cp packages.conf_hr packages.conf
225    
226    cd ../build
227    \rm *
228    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
229    make depend
230    make -j
231    
232    cd ..
233    mkdir run
234    cd run
235    \rm *
236    \cp ../input/* .
237    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
238    ln -sf ../../../../run_template/* .
239    \rm pickup*
240    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
241    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
242    \cp ../build/mitgcmuv mitgcmuv150
243    qsub job_altix150
244    
245    
246    ##########################################################################
247    ##########################################################################
248    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
249    # uses s1500t_17x51 configuration
250    # example for running on c17-c20 using arrayd
251    
252    cd MITgcm/verification/global_ocean.cs32x15/code
253    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
254    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
255    \cp SIZE.h_375 SIZE.h
256    \cp packages.conf_hr packages.conf
257    
258    cd ../build
259    \rm *
260    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
261    make depend
262    make -j
263    
264    cd ..
265    mkdir run
266    cd run
267    \rm *
268    \cp ../input/* .
269    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
270    ln -sf ../../../../run_template/* .
271    \rm pickup*
272    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
273    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
274    \cp ../build/mitgcmuv .
275    job_c20_375cpu < /dev/null >&! output.run &
276    
277    
278    ##########################################################################
279    ##########################################################################
280    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
281    # uses s1500t_17x51 configuration
282    # example for running on c17-c20 using arrayd
283    
284    cd MITgcm/verification/global_ocean.cs32x15/code
285    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
286    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
287    \cp SIZE.h_375 SIZE.h
288    \cp packages.conf_hr packages.conf
289    
290    cd ../build
291    \rm *
292    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
293    make depend
294    make -j
295    
296    cd ..
297    mkdir run
298    cd run
299    \rm *
300    \cp ../input/* .
301    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
302    ln -sf ../../../../run_template/* .
303    \rm pickup*
304    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
305    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
306    \cp ../build/mitgcmuv .
307    job_c20_375cpu < /dev/null >&! output.run &
308    
309    
310    ##########################################################################
311    ##########################################################################
312    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
313    # uses s1500t_17x51 configuration
314    # example for running on c17-c20 using arrayd
315    
316    cd MITgcm/verification/global_ocean.cs32x15/code
317    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
318    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
319    \cp SIZE.h_500 SIZE.h
320    \cp packages.conf_hr packages.conf
321    
322    cd ../build
323    \rm *
324    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
325    make depend
326    make -j
327    
328    cd ..
329    mkdir run
330    cd run
331    \rm *
332    \cp ../input/* .
333    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
334    ln -sf ../../../../run_template/* .
335    \rm pickup*
336    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
337    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
338    \cp ../build/mitgcmuv .
339    job_c19_500cpu < /dev/null >&! output.run &
340    
341    
342    ##########################################################################
343    ##########################################################################
344    # 510*510*6*50, 216-cpu cube sphere on cosmos
345    
346    cd MITgcm/verification/global_ocean.cs32x15/code
347    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
348    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
349    \cp SIZE.h_216 SIZE.h
350    \cp packages.conf_hr packages.conf
351    
352    module unload latest_intel80
353    module unload mpich-gm-intel80
354    module load latest_intel81
355    module load mpich-gm-intel81
356    
357    cd ../build
358    \rm *
359    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
360    make depend
361    make -j
362    
363    cd ..
364    mkdir run
365    cd run
366    \rm *
367    \cp ../input/* .
368    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
369    ln -sf ../../../../run_template/* .
370    \rm pickup*
371    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
372    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
373    \cp ../build/mitgcmuv .
374    bsub < job_cosmos
375    
376    
377    ##########################################################################
378    ##########################################################################
379    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
380  # requires input files in sudirectories run_template and ncep_rgau  # requires input files in sudirectories run_template and ncep_rgau
381  # presently residing under orion:/tmp1/dmenem/cube  # presently residing under orion:/tmp1/dmenem/cube
382    
# Line 99  cd MITgcm/verification/global_ocean.cs32 Line 388  cd MITgcm/verification/global_ocean.cs32
388    
389  cd ../build  cd ../build
390  \rm *  \rm *
391  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
392  make depend  make depend
393  \rm getcon.F  make -j
 make  
394    
395  cd ..  cd ..
396  mkdir run  mkdir run
# Line 127  cd MITgcm/verification/global_ocean.cs32 Line 415  cd MITgcm/verification/global_ocean.cs32
415    
416  cd ../build  cd ../build
417  \rm *  \rm *
418  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
419  make depend  make depend
420  \rm getcon.F  make -j
 make  
421    
422  cd ..  cd ..
423  mkdir run  mkdir run
# Line 143  qsub job_orion41 Line 430  qsub job_orion41
430    
431  ##########################################################################  ##########################################################################
432  ##########################################################################  ##########################################################################
433  # 510*510*6*50, 216-cpu cube sphere on altix with efc  # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
434  # requires input files in sudirectories run_template and ncep_rgau  # requires input files in sudirectories run_template and ncep_rgau
435  # these can be obained from lou:/u/menemenl/cube  # presently residing under orion:/tmp1/dmenem/cube
436    
437  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
438  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
439  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
440  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_50 SIZE.h
441  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
442    
443  cd ../build  cd ../build
444  \rm *  \rm *
445  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
446  make depend  make depend
447  \rm getcon.F  make -j
 make  
448    
449  cd ..  cd ..
450  mkdir run  mkdir run
# Line 166  cd run Line 452  cd run
452  \rm *  \rm *
453  \cp ../input/* .  \cp ../input/* .
454  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
455  qsub job_altix  qsub job_orion
   
   
 ##########################################################################  
 ##########################################################################  
 # matlab script for generating pChkptFreq  
   
 nTimeSteps=26352;  
 for niter0=216:26352:(26352*11)  
  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  
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