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revision 1.55 by dimitri, Mon Feb 21 19:15:01 2005 UTC revision 1.91 by dimitri, Sat Apr 7 21:52:43 2007 UTC
# Line 1  Line 1 
1  daInstructions for setting up a cube-sphere integration with sea-ice.  !!!! Instructions in this file are obsolete and will eventually
2  Date last updated: February 17, 2005  !!!! be removed.  This file has been replaced by
3  Code and input used for integrating cube22.  !!!! MITgcm_contrib/high_res_cube/README.cs510
4    !!!! MITgcm_contrib/high_res_cube/README.cs32
5    
6    =================
7    
8    Instructions for setting up a cube-sphere integration with sea-ice.
9    
10    Forcing fields and other input files needed for the CS510
11    configuration can be obtained from
12    http://ecco2.org/products/model_setups/cs510.html
13    
14    =================
15    
16    UPDATES
17    
18    February 6, 2006: cube56, same as cube 50 with SEAICEuseFlooding
19    
20    February 1, 2006: back to cube50 default (bottomDragQuadratic = 0.002)
21                      removed UVEL and VVEL from diagnostics
22    
23    January 5, 2006: cube51, like cube50 but with bottomDragQuadratic = 0.0012
24    
25    January 5, 2006: cube50, like cube48 but with snow advection
26    
27    December 30, 2006: updates for cube49, the first
28    "blend" integration.
29    
30    December 11, 2006: preparing for cube47, same as cube43
31    but with Arctic monthly river runoff climatology.
32    
33    December 5, 2006: 216-CPU code for cube46
34    Changed diagnostics to accomodate JMCs latest and some
35    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
36    to speed up code.
37    
38    November 7, 2006: 216-CPU code for cube43
39    Bug fixes in growth.F routine and new set of diagnostics
40    
41    October 15, 2006: 216-CPU code for cube40
42    
43    September 28, 2006: 216-CPU code for cube38
44    
45    September 4, 2006
46    Modified 32*32*6*15 experiments to use grid_cs32.* files from
47     verification/tutorial_held_suarez_cs/input instead of
48     tile* files from verification/global_ocean.cs32x15/input
49    
50    August 8, 2006: 216-CPU code and input used for cube37
51    using "June 10, 2006" MITgcm code.
52    
53    for online T/S profile diagnostics all that is needed is
54      profiles_init_fixed
55      profiles_inloop
56    see pkg/ecco/ecco_cost_init_fixed.F
57        pkg/ecco/cost_averagesfields.F
58    
59    ##########################################################################
60    ##########################################################################
61    # Get forcing files, etc.
62    # Example below is for cube46 on /nobackup2a/menemenl
63    
64    cd /nobackup2a/menemenl
65    mkdir cube47
66    cd cube47
67    ln -sf ../run_template .
68    ln -sf ../ncep_rgau .
69    
70    
71  ##########################################################################  ##########################################################################
72  ##########################################################################  ##########################################################################
73  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
74    
75      bash or sh shell:
76        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
77        $ cvs login
78          ( enter the CVS password: "cvsanon" )
79    
80      tcsh or csh shell:
81        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
82        $ cvs login
83          ( enter the CVS password: "cvsanon" )
84    
85  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
86  cvs co MITgcm_contrib/high_res_cube/code-mods  cvs co MITgcm_contrib/high_res_cube/code-mods
87  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
88  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
89  cvs co MITgcm_code  cvs co MITgcm_code
90  cvs co MITgcm/verification/global_ocean.cs32x15  cvs co MITgcm/verification/global_ocean.cs32x15
91  cvs co MITgcm/verification/testreport  cvs co MITgcm/verification/tutorial_held_suarez_cs/input
92    
93    
94    ##########################################################################
95    ##########################################################################
96    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
97    
98    cd MITgcm/verification/global_ocean.cs32x15/code
99    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
100    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
101    \cp SIZE.h_216 SIZE.h
102    \cp packages.conf_hr packages.conf
103    
104    cd ../build
105    \rm *
106    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
107    make depend
108    make -j
109    
110    cd ..
111    mkdir run
112    cd run
113    \rm *
114    \cp ../input/* .
115    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
116    ln -sf ../../../../run_template/* .
117    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
118    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
119    ln -sf ../../../../run_template/pickup.0000000216.cube49 pickup.0000000216
120    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube48 pickup_seaice.0000000216
121    \cp ../build/mitgcmuv .
122    qsub job_altix
123    
124    
125  ##########################################################################  ##########################################################################
# Line 23  cvs co MITgcm/verification/testreport Line 129  cvs co MITgcm/verification/testreport
129  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
130  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
131  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
132    \rm CPP_EEOPTIONS.h
133  cd ../build  cd ../build
134  \rm *  \rm *
135  ../../../tools/genmake2 -mods=../code  ../../../tools/genmake2 -mods=../code
# Line 32  cd .. Line 139  cd ..
139  mkdir run  mkdir run
140  cd run  cd run
141  \rm *  \rm *
142    \cp ../../tutorial_held_suarez_cs/input/grid* .
143  \cp ../input/* .  \cp ../input/* .
144  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
145  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 42  comparison output is in: Line 150  comparison output is in:
150  to use matlab to look at the output  to use matlab to look at the output
151  matlab  matlab
152    
153  for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
154           'QNETtave','FVtave','FUtave','EmPmRtave'}           'surForcT','oceTAUX','oceTAUY','surForcS'}
155      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]);
156      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
157  end  end
158    
159  heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
160  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
161  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]);
162  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]);
163  clf  clf
164  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
165  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
# Line 75  cd .. Line 183  cd ..
183  mkdir run  mkdir run
184  cd run  cd run
185  \rm *  \rm *
186    \cp ../../tutorial_held_suarez_cs/input/grid* .
187  \cp ../input/* .  \cp ../input/* .
188  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
189  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 82  cd run Line 191  cd run
191    
192  ##########################################################################  ##########################################################################
193  ##########################################################################  ##########################################################################
194  # 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
195    
196  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
197  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
# Line 99  cd .. Line 208  cd ..
208  mkdir run  mkdir run
209  cd run  cd run
210  \rm *  \rm *
211    \cp ../../tutorial_held_suarez_cs/input/grid* .
212  \cp ../input/* .  \cp ../input/* .
213  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
214  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
# Line 132  qsub job_altix92_54t Line 242  qsub job_altix92_54t
242    
243  ##########################################################################  ##########################################################################
244  ##########################################################################  ##########################################################################
245  # 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
246  # requires input files in sudirectories run_template and ncep_rgau  # uses s1500t_17x51 configuration
 # these can be obained from lou:/u/menemenl/cube  
247    
248  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
249  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
250  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
251  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_150 SIZE.h
252  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
253    
254  cd ../build  cd ../build
# Line 156  cd run Line 265  cd run
265  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
266  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
267  \rm pickup*  \rm pickup*
268  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
269  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
270  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv mitgcmuv150
271  qsub job_altix92  qsub job_altix150
272    
273    
274    ##########################################################################
275    ##########################################################################
276    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
277    # uses s1500t_17x51 configuration
278    # example for running on c17-c20 using arrayd
279    
280    cd MITgcm/verification/global_ocean.cs32x15/code
281    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
282    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
283    \cp SIZE.h_375 SIZE.h
284    \cp packages.conf_hr packages.conf
285    
286    cd ../build
287    \rm *
288    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
289    make depend
290    make -j
291    
292    cd ..
293    mkdir run
294    cd run
295    \rm *
296    \cp ../input/* .
297    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
298    ln -sf ../../../../run_template/* .
299    \rm pickup*
300    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
301    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
302    \cp ../build/mitgcmuv .
303    job_c20_375cpu < /dev/null >&! output.run &
304    
305    
306    ##########################################################################
307    ##########################################################################
308    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
309    # uses s1500t_17x51 configuration
310    # example for running on c17-c20 using arrayd
311    
312    cd MITgcm/verification/global_ocean.cs32x15/code
313    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
314    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
315    \cp SIZE.h_375 SIZE.h
316    \cp packages.conf_hr packages.conf
317    
318    cd ../build
319    \rm *
320    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
321    make depend
322    make -j
323    
324    cd ..
325    mkdir run
326    cd run
327    \rm *
328    \cp ../input/* .
329    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
330    ln -sf ../../../../run_template/* .
331    \rm pickup*
332    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
333    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
334    \cp ../build/mitgcmuv .
335    job_c20_375cpu < /dev/null >&! output.run &
336    
337    
338    ##########################################################################
339    ##########################################################################
340    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
341    # uses s1500t_17x51 configuration
342    # example for running on c17-c20 using arrayd
343    
344    cd MITgcm/verification/global_ocean.cs32x15/code
345    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
346    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
347    \cp SIZE.h_500 SIZE.h
348    \cp packages.conf_hr packages.conf
349    
350    cd ../build
351    \rm *
352    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
353    make depend
354    make -j
355    
356    cd ..
357    mkdir run
358    cd run
359    \rm *
360    \cp ../input/* .
361    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
362    ln -sf ../../../../run_template/* .
363    \rm pickup*
364    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
365    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
366    \cp ../build/mitgcmuv .
367    job_c19_500cpu < /dev/null >&! output.run &
368    
369    
370    ##########################################################################
371    ##########################################################################
372    # 510*510*6*50, 216-cpu cube sphere on cosmos
373    
374    cd MITgcm/verification/global_ocean.cs32x15/code
375    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
376    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
377    \cp SIZE.h_216 SIZE.h
378    \cp packages.conf_hr packages.conf
379    
380    module unload latest_intel80
381    module unload mpich-gm-intel80
382    module load latest_intel81
383    module load mpich-gm-intel81
384    
385    cd ../build
386    \rm *
387    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
388    make depend
389    make -j
390    
391    cd ..
392    mkdir run
393    cd run
394    \rm *
395    \cp ../input/* .
396    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
397    ln -sf ../../../../run_template/* .
398    \rm pickup*
399    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
400    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
401    \cp ../build/mitgcmuv .
402    bsub < job_cosmos
403    
404    
405  ##########################################################################  ##########################################################################
# Line 262  cd run Line 481  cd run
481  \cp ../input/* .  \cp ../input/* .
482  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
483  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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