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revision 1.55 by dimitri, Mon Feb 21 19:15:01 2005 UTC revision 1.78 by dimitri, Tue Dec 5 20:46:48 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    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  ##########################################################################  ##########################################################################
35  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
36    #
37    
38      bash or sh shell:
39        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
40        $ cvs login
41          ( enter the CVS password: "cvsanon" )
42    
43      tcsh or csh shell:
44        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
45        $ cvs login
46          ( enter the CVS password: "cvsanon" )
47    
48  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
49  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 51  cvs co MITgcm_contrib/high_res_cube/inpu
51  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
52  cvs co MITgcm_code  cvs co MITgcm_code
53  cvs co MITgcm/verification/global_ocean.cs32x15  cvs co MITgcm/verification/global_ocean.cs32x15
54  cvs co MITgcm/verification/testreport  cvs co MITgcm/verification/tutorial_held_suarez_cs/input
55    
56    
57    ##########################################################################
58    ##########################################################################
59    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
60    # requires input files in sudirectories run_template and ncep_rgau
61    # these can be obained from lou:/u/menemenl/cube
62    
63    cd MITgcm/verification/global_ocean.cs32x15/code
64    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
65    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
66    \cp SIZE.h_216 SIZE.h
67    \cp packages.conf_hr packages.conf
68    
69    cd ../build
70    \rm *
71    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
72    make depend
73    make -j
74    
75    cd ..
76    mkdir run
77    cd run
78    \rm *
79    \cp ../input/* .
80    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
81    ln -sf ../../../../run_template/* .
82    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
83    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
84    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
85    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38 pickup_seaice.0000000216
86    \cp ../build/mitgcmuv .
87    qsub job_altix
88    
89    
90  ##########################################################################  ##########################################################################
# Line 32  cd .. Line 103  cd ..
103  mkdir run  mkdir run
104  cd run  cd run
105  \rm *  \rm *
106    \cp ../../tutorial_held_suarez_cs/input/grid* .
107  \cp ../input/* .  \cp ../input/* .
108  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
109  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 42  comparison output is in: Line 114  comparison output is in:
114  to use matlab to look at the output  to use matlab to look at the output
115  matlab  matlab
116    
117  for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
118           'QNETtave','FVtave','FUtave','EmPmRtave'}           'surForcT','oceTAUX','oceTAUY','surForcS'}
119      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);      tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
120      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
121  end  end
122    
123  heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
124  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
125  uice=mask.*permute(readbin(['UICEtave.0000000020.data'],[32,6,32]),[1 3 2]);  uice=mask.*permute(readbin(['SIuice.0000000072.data'],[32,6,32]),[1 3 2]);
126  vice=mask.*permute(readbin(['VICEtave.0000000020.data'],[32,6,32]),[1 3 2]);  vice=mask.*permute(readbin(['SIvice.0000000072.data'],[32,6,32]),[1 3 2]);
127  clf  clf
128  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
129  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
# Line 75  cd .. Line 147  cd ..
147  mkdir run  mkdir run
148  cd run  cd run
149  \rm *  \rm *
150    \cp ../../tutorial_held_suarez_cs/input/grid* .
151  \cp ../input/* .  \cp ../input/* .
152  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
153  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 82  cd run Line 155  cd run
155    
156  ##########################################################################  ##########################################################################
157  ##########################################################################  ##########################################################################
158  # 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
159    
160  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
161  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
# Line 99  cd .. Line 172  cd ..
172  mkdir run  mkdir run
173  cd run  cd run
174  \rm *  \rm *
175    \cp ../../tutorial_held_suarez_cs/input/grid* .
176  \cp ../input/* .  \cp ../input/* .
177  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
178  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
# Line 132  qsub job_altix92_54t Line 206  qsub job_altix92_54t
206    
207  ##########################################################################  ##########################################################################
208  ##########################################################################  ##########################################################################
209  # 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
210  # requires input files in sudirectories run_template and ncep_rgau  # uses s1500t_17x51 configuration
 # these can be obained from lou:/u/menemenl/cube  
211    
212  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
213  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
214  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
215  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_150 SIZE.h
216  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
217    
218  cd ../build  cd ../build
# Line 156  cd run Line 229  cd run
229  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
230  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
231  \rm pickup*  \rm pickup*
232  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
233  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
234  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv mitgcmuv150
235  qsub job_altix92  qsub job_altix150
236    
237    
238    ##########################################################################
239    ##########################################################################
240    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
241    # uses s1500t_17x51 configuration
242    # example for running on c17-c20 using arrayd
243    
244    cd MITgcm/verification/global_ocean.cs32x15/code
245    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
246    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
247    \cp SIZE.h_375 SIZE.h
248    \cp packages.conf_hr packages.conf
249    
250    cd ../build
251    \rm *
252    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
253    make depend
254    make -j
255    
256    cd ..
257    mkdir run
258    cd run
259    \rm *
260    \cp ../input/* .
261    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
262    ln -sf ../../../../run_template/* .
263    \rm pickup*
264    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
265    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
266    \cp ../build/mitgcmuv .
267    job_c20_375cpu < /dev/null >&! output.run &
268    
269    
270    ##########################################################################
271    ##########################################################################
272    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
273    # uses s1500t_17x51 configuration
274    # example for running on c17-c20 using arrayd
275    
276    cd MITgcm/verification/global_ocean.cs32x15/code
277    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
278    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
279    \cp SIZE.h_375 SIZE.h
280    \cp packages.conf_hr packages.conf
281    
282    cd ../build
283    \rm *
284    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
285    make depend
286    make -j
287    
288    cd ..
289    mkdir run
290    cd run
291    \rm *
292    \cp ../input/* .
293    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
294    ln -sf ../../../../run_template/* .
295    \rm pickup*
296    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
297    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
298    \cp ../build/mitgcmuv .
299    job_c20_375cpu < /dev/null >&! output.run &
300    
301    
302    ##########################################################################
303    ##########################################################################
304    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
305    # uses s1500t_17x51 configuration
306    # example for running on c17-c20 using arrayd
307    
308    cd MITgcm/verification/global_ocean.cs32x15/code
309    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
310    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
311    \cp SIZE.h_500 SIZE.h
312    \cp packages.conf_hr packages.conf
313    
314    cd ../build
315    \rm *
316    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
317    make depend
318    make -j
319    
320    cd ..
321    mkdir run
322    cd run
323    \rm *
324    \cp ../input/* .
325    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
326    ln -sf ../../../../run_template/* .
327    \rm pickup*
328    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
329    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
330    \cp ../build/mitgcmuv .
331    job_c19_500cpu < /dev/null >&! output.run &
332    
333    
334    ##########################################################################
335    ##########################################################################
336    # 510*510*6*50, 216-cpu cube sphere on cosmos
337    
338    cd MITgcm/verification/global_ocean.cs32x15/code
339    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
340    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
341    \cp SIZE.h_216 SIZE.h
342    \cp packages.conf_hr packages.conf
343    
344    module unload latest_intel80
345    module unload mpich-gm-intel80
346    module load latest_intel81
347    module load mpich-gm-intel81
348    
349    cd ../build
350    \rm *
351    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
352    make depend
353    make -j
354    
355    cd ..
356    mkdir run
357    cd run
358    \rm *
359    \cp ../input/* .
360    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
361    ln -sf ../../../../run_template/* .
362    \rm pickup*
363    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
364    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
365    \cp ../build/mitgcmuv .
366    bsub < job_cosmos
367    
368    
369  ##########################################################################  ##########################################################################
# Line 262  cd run Line 445  cd run
445  \cp ../input/* .  \cp ../input/* .
446  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
447  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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