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revision 1.54 by dimitri, Sun Feb 20 20:39:43 2005 UTC revision 1.87 by dimitri, Sat Jan 6 07:09:50 2007 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.  Forcing fields and other input files needed for the CS510
4    configuration can be obtained from
5    http://ecco2.org/products/model_setups/cs510.html
6    
7    =================
8    UPDATES
9    
10    January 5, 2006: cube51, like cube50 but with bottomDragQuadratic = 0.0012
11    
12    January 5, 2006: cube50, like cube48 but with snow advection
13    
14    December 30, 2006: updates for cube49, the first
15    "blend" integration.
16    
17    December 11, 2006: preparing for cube47, same as cube43
18    but with Arctic monthly river runoff climatology.
19    
20    December 5, 2006: 216-CPU code for cube46
21    Changed diagnostics to accomodate JMCs latest and some
22    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
23    to speed up code.
24    
25    November 7, 2006: 216-CPU code for cube43
26    Bug fixes in growth.F routine and new set of diagnostics
27    
28    October 15, 2006: 216-CPU code for cube40
29    
30    September 28, 2006: 216-CPU code for cube38
31    
32    September 4, 2006
33    Modified 32*32*6*15 experiments to use grid_cs32.* files from
34     verification/tutorial_held_suarez_cs/input instead of
35     tile* files from verification/global_ocean.cs32x15/input
36    
37    August 8, 2006: 216-CPU code and input used for cube37
38    using "June 10, 2006" MITgcm code.
39    
40    for online T/S profile diagnostics all that is needed is
41      profiles_init_fixed
42      profiles_inloop
43    see pkg/ecco/ecco_cost_init_fixed.F
44        pkg/ecco/cost_averagesfields.F
45    
46    ##########################################################################
47    ##########################################################################
48    # Get forcing files, etc.
49    # Example below is for cube46 on /nobackup2a/menemenl
50    
51    cd /nobackup2a/menemenl
52    mkdir cube47
53    cd cube47
54    ln -sf ../run_template .
55    ln -sf ../ncep_rgau .
56    
57    
58  ##########################################################################  ##########################################################################
59  ##########################################################################  ##########################################################################
60  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
61    
62      bash or sh shell:
63        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
64        $ cvs login
65          ( enter the CVS password: "cvsanon" )
66    
67      tcsh or csh shell:
68        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
69        $ cvs login
70          ( enter the CVS password: "cvsanon" )
71    
72  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
73  cvs co MITgcm_contrib/high_res_cube/code-mods  cvs co MITgcm_contrib/high_res_cube/code-mods
74  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
75  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
76  cvs co MITgcm_code  cvs co MITgcm_code
77  cvs co MITgcm/verification/global_ocean.cs32x15  cvs co MITgcm/verification/global_ocean.cs32x15
78  cvs co MITgcm/verification/testreport  cvs co MITgcm/verification/tutorial_held_suarez_cs/input
79    
80    
81    ##########################################################################
82    ##########################################################################
83    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
84    
85    cd MITgcm/verification/global_ocean.cs32x15/code
86    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
87    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
88    \cp SIZE.h_216 SIZE.h
89    \cp packages.conf_hr packages.conf
90    
91    cd ../build
92    \rm *
93    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
94    make depend
95    make -j
96    
97    cd ..
98    mkdir run
99    cd run
100    \rm *
101    \cp ../input/* .
102    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
103    ln -sf ../../../../run_template/* .
104    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
105    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
106    ln -sf ../../../../run_template/pickup.0000000216.cube49 pickup.0000000216
107    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube48 pickup_seaice.0000000216
108    \cp ../build/mitgcmuv .
109    qsub job_altix
110    
111    
112  ##########################################################################  ##########################################################################
# Line 32  cd .. Line 125  cd ..
125  mkdir run  mkdir run
126  cd run  cd run
127  \rm *  \rm *
128    \cp ../../tutorial_held_suarez_cs/input/grid* .
129  \cp ../input/* .  \cp ../input/* .
130  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
131  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 42  comparison output is in: Line 136  comparison output is in:
136  to use matlab to look at the output  to use matlab to look at the output
137  matlab  matlab
138    
139  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
140      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);           'surForcT','oceTAUX','oceTAUY','surForcS'}
141        tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
142      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
143  end  end
144    
145  heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
146  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
147  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]);
148  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]);
149  clf  clf
150  subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
151  subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
152  subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
153  subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
154    
155    
156  ##########################################################################  ##########################################################################
# Line 74  cd .. Line 169  cd ..
169  mkdir run  mkdir run
170  cd run  cd run
171  \rm *  \rm *
172    \cp ../../tutorial_held_suarez_cs/input/grid* .
173  \cp ../input/* .  \cp ../input/* .
174  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
175  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
176    
 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')  
   
177    
178  ##########################################################################  ##########################################################################
179  ##########################################################################  ##########################################################################
180  # 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
181    
182  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
183  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
# Line 119  cd .. Line 194  cd ..
194  mkdir run  mkdir run
195  cd run  cd run
196  \rm *  \rm *
197    \cp ../../tutorial_held_suarez_cs/input/grid* .
198  \cp ../input/* .  \cp ../input/* .
199  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
200  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
# Line 152  qsub job_altix92_54t Line 228  qsub job_altix92_54t
228    
229  ##########################################################################  ##########################################################################
230  ##########################################################################  ##########################################################################
231  # 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
232  # requires input files in sudirectories run_template and ncep_rgau  # uses s1500t_17x51 configuration
 # these can be obained from lou:/u/menemenl/cube  
233    
234  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
235  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
236  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
237  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_150 SIZE.h
238  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
239    
240  cd ../build  cd ../build
# Line 176  cd run Line 251  cd run
251  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
252  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
253  \rm pickup*  \rm pickup*
254  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
255  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
256  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv mitgcmuv150
257  qsub job_altix92  qsub job_altix150
258    
259    
260    ##########################################################################
261    ##########################################################################
262    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
263    # uses s1500t_17x51 configuration
264    # example for running on c17-c20 using arrayd
265    
266    cd MITgcm/verification/global_ocean.cs32x15/code
267    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
268    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
269    \cp SIZE.h_375 SIZE.h
270    \cp packages.conf_hr packages.conf
271    
272    cd ../build
273    \rm *
274    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
275    make depend
276    make -j
277    
278    cd ..
279    mkdir run
280    cd run
281    \rm *
282    \cp ../input/* .
283    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
284    ln -sf ../../../../run_template/* .
285    \rm pickup*
286    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
287    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
288    \cp ../build/mitgcmuv .
289    job_c20_375cpu < /dev/null >&! output.run &
290    
291    
292    ##########################################################################
293    ##########################################################################
294    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
295    # uses s1500t_17x51 configuration
296    # example for running on c17-c20 using arrayd
297    
298    cd MITgcm/verification/global_ocean.cs32x15/code
299    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
300    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
301    \cp SIZE.h_375 SIZE.h
302    \cp packages.conf_hr packages.conf
303    
304    cd ../build
305    \rm *
306    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
307    make depend
308    make -j
309    
310    cd ..
311    mkdir run
312    cd run
313    \rm *
314    \cp ../input/* .
315    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
316    ln -sf ../../../../run_template/* .
317    \rm pickup*
318    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
319    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
320    \cp ../build/mitgcmuv .
321    job_c20_375cpu < /dev/null >&! output.run &
322    
323    
324    ##########################################################################
325    ##########################################################################
326    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
327    # uses s1500t_17x51 configuration
328    # example for running on c17-c20 using arrayd
329    
330    cd MITgcm/verification/global_ocean.cs32x15/code
331    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
332    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
333    \cp SIZE.h_500 SIZE.h
334    \cp packages.conf_hr packages.conf
335    
336    cd ../build
337    \rm *
338    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
339    make depend
340    make -j
341    
342    cd ..
343    mkdir run
344    cd run
345    \rm *
346    \cp ../input/* .
347    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
348    ln -sf ../../../../run_template/* .
349    \rm pickup*
350    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
351    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
352    \cp ../build/mitgcmuv .
353    job_c19_500cpu < /dev/null >&! output.run &
354    
355    
356    ##########################################################################
357    ##########################################################################
358    # 510*510*6*50, 216-cpu cube sphere on cosmos
359    
360    cd MITgcm/verification/global_ocean.cs32x15/code
361    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
362    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
363    \cp SIZE.h_216 SIZE.h
364    \cp packages.conf_hr packages.conf
365    
366    module unload latest_intel80
367    module unload mpich-gm-intel80
368    module load latest_intel81
369    module load mpich-gm-intel81
370    
371    cd ../build
372    \rm *
373    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
374    make depend
375    make -j
376    
377    cd ..
378    mkdir run
379    cd run
380    \rm *
381    \cp ../input/* .
382    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
383    ln -sf ../../../../run_template/* .
384    \rm pickup*
385    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
386    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
387    \cp ../build/mitgcmuv .
388    bsub < job_cosmos
389    
390    
391  ##########################################################################  ##########################################################################
# Line 282  cd run Line 467  cd run
467  \cp ../input/* .  \cp ../input/* .
468  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
469  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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