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revision 1.52 by dimitri, Sat Feb 19 06:28:28 2005 UTC revision 1.73 by dimitri, Sun Oct 15 18:23:06 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    October 15, 2006: 216-CPU code for cube40
7    
8    September 28, 2006: 216-CPU code for cube38
9    
10    September 4, 2006
11    Modified 32*32*6*15 experiments to use grid_cs32.* files from
12     verification/tutorial_held_suarez_cs/input instead of
13     tile* files from verification/global_ocean.cs32x15/input
14    
15    August 8, 2006: 216-CPU code and input used for cube37
16    using "June 10, 2006" MITgcm code.
17    
18    for online T/S profile diagnostics all that is needed is
19      profiles_init_fixed
20      profiles_inloop
21    see pkg/ecco/ecco_cost_init_fixed.F
22        pkg/ecco/cost_averagesfields.F
23    
24    
25  ##########################################################################  ##########################################################################
26  ##########################################################################  ##########################################################################
27  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
28    #
29    
30      bash or sh shell:
31        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
32        $ cvs login
33          ( enter the CVS password: "cvsanon" )
34    
35      tcsh or csh shell:
36        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
37        $ cvs login
38          ( enter the CVS password: "cvsanon" )
39    
40  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
41  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 43  cvs co MITgcm_contrib/high_res_cube/inpu
43  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
44  cvs co MITgcm_code  cvs co MITgcm_code
45  cvs co MITgcm/verification/global_ocean.cs32x15  cvs co MITgcm/verification/global_ocean.cs32x15
46  cvs co MITgcm/verification/testreport  cvs co MITgcm/verification/tutorial_held_suarez_cs/input
47    
48    
49    ##########################################################################
50    ##########################################################################
51    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
52    # requires input files in sudirectories run_template and ncep_rgau
53    # these can be obained from lou:/u/menemenl/cube
54    
55    cd MITgcm/verification/global_ocean.cs32x15/code
56    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
57    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
58    \cp SIZE.h_216 SIZE.h
59    \cp packages.conf_hr packages.conf
60    
61    cd ../build
62    \rm *
63    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
64    make depend
65    make -j
66    
67    cd ..
68    mkdir run
69    cd run
70    \rm *
71    \cp ../input/* .
72    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
73    ln -sf ../../../../run_template/* .
74    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
75    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
76    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
77    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38 pickup_seaice.0000000216
78    \cp ../build/mitgcmuv .
79    qsub job_altix
80    
81    
82  ##########################################################################  ##########################################################################
# Line 32  cd .. Line 95  cd ..
95  mkdir run  mkdir run
96  cd run  cd run
97  \rm *  \rm *
98    \cp ../../tutorial_held_suarez_cs/input/grid* .
99  \cp ../input/* .  \cp ../input/* .
100  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
101  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 42  comparison output is in: Line 106  comparison output is in:
106  to use matlab to look at the output  to use matlab to look at the output
107  matlab  matlab
108    
109  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...
110             'QNETtave','FVtave','FUtave','EmPmRtave'}
111      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]);
112      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
113  end  end
114    
115  heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);
116  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
117  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]);
118  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]);
119  clf  clf
120  subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
121  subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
122  subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
123  subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
124    
125    
126  ##########################################################################  ##########################################################################
# Line 74  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
146    
 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')  
   
147    
148  ##########################################################################  ##########################################################################
149  ##########################################################################  ##########################################################################
150  # 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
151    
152  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
153  \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 156  cd MITgcm/verification/global_ocean.cs32
156    
157  cd ../build  cd ../build
158  \rm *  \rm *
159  ../../../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
160  make depend  make depend
161  make -j  make -j
162    
# Line 119  cd .. Line 164  cd ..
164  mkdir run  mkdir run
165  cd run  cd run
166  \rm *  \rm *
167    \cp ../../tutorial_held_suarez_cs/input/grid* .
168  \cp ../input/* .  \cp ../input/* .
169  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
170  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
# Line 152  qsub job_altix92_54t Line 198  qsub job_altix92_54t
198    
199  ##########################################################################  ##########################################################################
200  ##########################################################################  ##########################################################################
201  # 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
202  # requires input files in sudirectories run_template and ncep_rgau  # uses s1500t_17x51 configuration
 # these can be obained from lou:/u/menemenl/cube  
203    
204  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
205  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
206  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
207  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_150 SIZE.h
208  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
209    
210  cd ../build  cd ../build
# Line 176  cd run Line 221  cd run
221  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
222  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
223  \rm pickup*  \rm pickup*
224  ln -sf ../../../../run_template/pickup.0000316440.cube20 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
225  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube20 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
226  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv mitgcmuv150
227  qsub job_altix92  qsub job_altix150
228    
229    
230    ##########################################################################
231    ##########################################################################
232    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
233    # uses s1500t_17x51 configuration
234    # example for running on c17-c20 using arrayd
235    
236    cd MITgcm/verification/global_ocean.cs32x15/code
237    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
238    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
239    \cp SIZE.h_375 SIZE.h
240    \cp packages.conf_hr packages.conf
241    
242    cd ../build
243    \rm *
244    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
245    make depend
246    make -j
247    
248    cd ..
249    mkdir run
250    cd run
251    \rm *
252    \cp ../input/* .
253    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
254    ln -sf ../../../../run_template/* .
255    \rm pickup*
256    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
257    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
258    \cp ../build/mitgcmuv .
259    job_c20_375cpu < /dev/null >&! output.run &
260    
261    
262    ##########################################################################
263    ##########################################################################
264    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
265    # uses s1500t_17x51 configuration
266    # example for running on c17-c20 using arrayd
267    
268    cd MITgcm/verification/global_ocean.cs32x15/code
269    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
270    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
271    \cp SIZE.h_375 SIZE.h
272    \cp packages.conf_hr packages.conf
273    
274    cd ../build
275    \rm *
276    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
277    make depend
278    make -j
279    
280    cd ..
281    mkdir run
282    cd run
283    \rm *
284    \cp ../input/* .
285    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
286    ln -sf ../../../../run_template/* .
287    \rm pickup*
288    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
289    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
290    \cp ../build/mitgcmuv .
291    job_c20_375cpu < /dev/null >&! output.run &
292    
293    
294    ##########################################################################
295    ##########################################################################
296    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
297    # uses s1500t_17x51 configuration
298    # example for running on c17-c20 using arrayd
299    
300    cd MITgcm/verification/global_ocean.cs32x15/code
301    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
302    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
303    \cp SIZE.h_500 SIZE.h
304    \cp packages.conf_hr packages.conf
305    
306    cd ../build
307    \rm *
308    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
309    make depend
310    make -j
311    
312    cd ..
313    mkdir run
314    cd run
315    \rm *
316    \cp ../input/* .
317    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
318    ln -sf ../../../../run_template/* .
319    \rm pickup*
320    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
321    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
322    \cp ../build/mitgcmuv .
323    job_c19_500cpu < /dev/null >&! output.run &
324    
325    
326    ##########################################################################
327    ##########################################################################
328    # 510*510*6*50, 216-cpu cube sphere on cosmos
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/s216t_85x85/* .
333    \cp SIZE.h_216 SIZE.h
334    \cp packages.conf_hr packages.conf
335    
336    module unload latest_intel80
337    module unload mpich-gm-intel80
338    module load latest_intel81
339    module load mpich-gm-intel81
340    
341    cd ../build
342    \rm *
343    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
344    make depend
345    make -j
346    
347    cd ..
348    mkdir run
349    cd run
350    \rm *
351    \cp ../input/* .
352    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
353    ln -sf ../../../../run_template/* .
354    \rm pickup*
355    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
356    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
357    \cp ../build/mitgcmuv .
358    bsub < job_cosmos
359    
360    
361  ##########################################################################  ##########################################################################
# Line 282  cd run Line 437  cd run
437  \cp ../input/* .  \cp ../input/* .
438  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
439  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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