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revision 1.3 by dimitri, Mon Nov 24 01:04:28 2003 UTC revision 1.77 by dimitri, Wed Nov 22 07:21:31 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.
 Date last tested: November 21, 2003.  
2    
3  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  =================
4  cvs login ( CVS password: cvsanon )  UPDATES
5    
6    November 22, 2006: 216-CPU code for cube44
7    Changed diagnostics, yet again.
8    
9    November 7, 2006: 216-CPU code for cube43
10    Bug fixes in growth.F routine and new set of diagnostics
11    
12    October 15, 2006: 216-CPU code for cube40
13    
14    September 28, 2006: 216-CPU code for cube38
15    
16    September 4, 2006
17    Modified 32*32*6*15 experiments to use grid_cs32.* files from
18     verification/tutorial_held_suarez_cs/input instead of
19     tile* files from verification/global_ocean.cs32x15/input
20    
21    August 8, 2006: 216-CPU code and input used for cube37
22    using "June 10, 2006" MITgcm code.
23    
24    for online T/S profile diagnostics all that is needed is
25      profiles_init_fixed
26      profiles_inloop
27    see pkg/ecco/ecco_cost_init_fixed.F
28        pkg/ecco/cost_averagesfields.F
29    
30    
31    ##########################################################################
32    ##########################################################################
33    # getting the code from anonymous CVS server
34    #
35    
36      bash or sh shell:
37        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
38        $ cvs login
39          ( enter the CVS password: "cvsanon" )
40    
41      tcsh or csh shell:
42        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
43        $ cvs login
44          ( enter the CVS password: "cvsanon" )
45    
46  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
47  cvs co MITgcm_contrib/high_res_cube/code-mods  cvs co MITgcm_contrib/high_res_cube/code-mods
 cvs co MITgcm_contrib/high_res_cube/matlab-grid-converter  
48  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
49  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
50    cvs co MITgcm_code
51    cvs co MITgcm/verification/global_ocean.cs32x15
52    cvs co MITgcm/verification/tutorial_held_suarez_cs/input
53    
54  cvs co -r checkpoint52a_post MITgcm_code  
55  cvs co -r checkpoint52a_post MITgcm/verification/global_ocean.cs32x15  ##########################################################################
56    ##########################################################################
57    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
58    # requires input files in sudirectories run_template and ncep_rgau
59    # these can be obained from lou:/u/menemenl/cube
60    
61  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
62  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
63  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
64  \rm mdsio_readfield.F  \cp SIZE.h_216 SIZE.h
65    \cp packages.conf_hr packages.conf
66    
67    cd ../build
68    \rm *
69    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
70    make depend
71    make -j
72    
73  cd ..  cd ..
74  mkdir build  mkdir run
75  cd build  cd run
76  ../code/genmake2 -mods=../code  \rm *
77    \cp ../input/* .
78    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
79    ln -sf ../../../../run_template/* .
80    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
81    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
82    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
83    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38 pickup_seaice.0000000216
84    \cp ../build/mitgcmuv .
85    qsub job_altix
86    
87    
88    ##########################################################################
89    ##########################################################################
90    # 32*32*6*15, 1-cpu cube sphere
91    
92    cd MITgcm/verification/global_ocean.cs32x15/code
93    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
94    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
95    cd ../build
96    \rm *
97    ../../../tools/genmake2 -mods=../code
98  make depend  make depend
99  make  make
   
100  cd ..  cd ..
101  mkdir run  mkdir run
102  cd run  cd run
103  cp ../input/* .  \rm *
104  cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  \cp ../../tutorial_held_suarez_cs/input/grid* .
105  cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../input/* .
106    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
107  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
108    
109  comparison output is in:  comparison output is in:
110  ../../../../MITgcm_contrib/high_res_cube/results/output.txt  ../../../../MITgcm_contrib/high_res_cube/results/output.txt
111    
   
112  to use matlab to look at the output  to use matlab to look at the output
113  matlab  matlab
114  eta=permute(readbin('Eta.0000072020.data',[32,6,32]),[1 3 2]);  
115  cx=[-1 1]; clf  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
116  subplot(3,4, 9);imagesc(flipud(eta(:,:,1)'));caxis(cx);colorbar           'surForcT','oceTAUX','oceTAUY','surForcS'}
117  subplot(3,4,10);imagesc(flipud(eta(:,:,2)'));caxis(cx);colorbar      tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
118  subplot(3,4, 6);imagesc(flipud(eta(:,:,3)'));caxis(cx);colorbar      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
119  subplot(3,4, 7);imagesc(flipud(eta(:,:,4)'));caxis(cx);colorbar  end
120  subplot(3,4, 3);imagesc(flipud(eta(:,:,5)'));caxis(cx);colorbar  
121  subplot(3,4, 4);imagesc(flipud(eta(:,:,6)'));caxis(cx);colorbar  heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
122    mask=0*heff; mask(find(heff>.001))=1;
123    uice=mask.*permute(readbin(['SIuice.0000000072.data'],[32,6,32]),[1 3 2]);
124    vice=mask.*permute(readbin(['SIvice.0000000072.data'],[32,6,32]),[1 3 2]);
125    clf
126    subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
127    subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
128    subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
129    subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
130    
131    
132    ##########################################################################
133    ##########################################################################
134    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
135    
136    cd MITgcm/verification/global_ocean.cs32x15/code
137    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
138    \cp ../code_alt/code.176t_8x4/* .
139    cd ../build
140    \rm *
141    ../../../tools/genmake2 -mods=../code
142    make depend
143    make
144    cd ..
145    mkdir run
146    cd run
147    \rm *
148    \cp ../../tutorial_held_suarez_cs/input/grid* .
149    \cp ../input/* .
150    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
151    ../build/mitgcmuv >& output.txt
152    
153    
154    ##########################################################################
155    ##########################################################################
156    # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
157    
158    cd MITgcm/verification/global_ocean.cs32x15/code
159    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
160    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
161    \cp SIZE.h_mpi SIZE.h
162    
163    cd ../build
164    \rm *
165    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
166    make depend
167    make -j
168    
169    cd ..
170    mkdir run
171    cd run
172    \rm *
173    \cp ../../tutorial_held_suarez_cs/input/grid* .
174    \cp ../input/* .
175    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
176    mpirun -np 2 ../build/mitgcmuv
177    
178    
179    ##########################################################################
180    ##########################################################################
181    # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
182    # starting with pickup file from end of 1992
183    # requires input files in sudirectories run_template and ncep_rgau
184    
185    cd MITgcm/verification/global_ocean.cs32x15/code
186    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
187    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
188    \cp packages.conf_hr packages.conf
189    
190    cd ../build
191    \rm *
192    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
193    make depend
194    make -j
195    
196    cd ..
197    mkdir run
198    cd run
199    \rm *
200    \cp ../input/* .
201    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
202    qsub job_altix92_54t
203    
204    
205    ##########################################################################
206    ##########################################################################
207    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
208    # uses s1500t_17x51 configuration
209    
210    cd MITgcm/verification/global_ocean.cs32x15/code
211    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
212    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
213    \cp SIZE.h_150 SIZE.h
214    \cp packages.conf_hr packages.conf
215    
216    cd ../build
217    \rm *
218    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
219    make depend
220    make -j
221    
222    cd ..
223    mkdir run
224    cd run
225    \rm *
226    \cp ../input/* .
227    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
228    ln -sf ../../../../run_template/* .
229    \rm pickup*
230    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
231    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
232    \cp ../build/mitgcmuv mitgcmuv150
233    qsub job_altix150
234    
235    
236    ##########################################################################
237    ##########################################################################
238    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
239    # uses s1500t_17x51 configuration
240    # example for running on c17-c20 using arrayd
241    
242    cd MITgcm/verification/global_ocean.cs32x15/code
243    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
244    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
245    \cp SIZE.h_375 SIZE.h
246    \cp packages.conf_hr packages.conf
247    
248    cd ../build
249    \rm *
250    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
251    make depend
252    make -j
253    
254    cd ..
255    mkdir run
256    cd run
257    \rm *
258    \cp ../input/* .
259    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
260    ln -sf ../../../../run_template/* .
261    \rm pickup*
262    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
263    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
264    \cp ../build/mitgcmuv .
265    job_c20_375cpu < /dev/null >&! output.run &
266    
267    
268    ##########################################################################
269    ##########################################################################
270    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
271    # uses s1500t_17x51 configuration
272    # example for running on c17-c20 using arrayd
273    
274    cd MITgcm/verification/global_ocean.cs32x15/code
275    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
276    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
277    \cp SIZE.h_375 SIZE.h
278    \cp packages.conf_hr packages.conf
279    
280    cd ../build
281    \rm *
282    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
283    make depend
284    make -j
285    
286    cd ..
287    mkdir run
288    cd run
289    \rm *
290    \cp ../input/* .
291    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
292    ln -sf ../../../../run_template/* .
293    \rm pickup*
294    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
295    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
296    \cp ../build/mitgcmuv .
297    job_c20_375cpu < /dev/null >&! output.run &
298    
299    
300    ##########################################################################
301    ##########################################################################
302    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
303    # uses s1500t_17x51 configuration
304    # example for running on c17-c20 using arrayd
305    
306    cd MITgcm/verification/global_ocean.cs32x15/code
307    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
308    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
309    \cp SIZE.h_500 SIZE.h
310    \cp packages.conf_hr packages.conf
311    
312    cd ../build
313    \rm *
314    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
315    make depend
316    make -j
317    
318    cd ..
319    mkdir run
320    cd run
321    \rm *
322    \cp ../input/* .
323    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
324    ln -sf ../../../../run_template/* .
325    \rm pickup*
326    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
327    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
328    \cp ../build/mitgcmuv .
329    job_c19_500cpu < /dev/null >&! output.run &
330    
331    
332    ##########################################################################
333    ##########################################################################
334    # 510*510*6*50, 216-cpu cube sphere on cosmos
335    
336    cd MITgcm/verification/global_ocean.cs32x15/code
337    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
338    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
339    \cp SIZE.h_216 SIZE.h
340    \cp packages.conf_hr packages.conf
341    
342    module unload latest_intel80
343    module unload mpich-gm-intel80
344    module load latest_intel81
345    module load mpich-gm-intel81
346    
347    cd ../build
348    \rm *
349    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
350    make depend
351    make -j
352    
353    cd ..
354    mkdir run
355    cd run
356    \rm *
357    \cp ../input/* .
358    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
359    ln -sf ../../../../run_template/* .
360    \rm pickup*
361    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
362    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
363    \cp ../build/mitgcmuv .
364    bsub < job_cosmos
365    
366    
367    ##########################################################################
368    ##########################################################################
369    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
370    # requires input files in sudirectories run_template and ncep_rgau
371    # presently residing under orion:/tmp1/dmenem/cube
372    
373    cd MITgcm/verification/global_ocean.cs32x15/code
374    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
375    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
376    \cp SIZE.h_54 SIZE.h
377    \cp packages.conf_hr packages.conf
378    
379    cd ../build
380    \rm *
381    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
382    make depend
383    make -j
384    
385    cd ..
386    mkdir run
387    cd run
388    \rm *
389    \cp ../input/* .
390    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
391    qsub job_orion
392    
393    
394    ##########################################################################
395    ##########################################################################
396    # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
397    # requires input files in sudirectories run_template and ncep_rgau
398    # presently residing under orion:/tmp1/dmenem/cube
399    
400    cd MITgcm/verification/global_ocean.cs32x15/code
401    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
402    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
403    \cp SIZE.h_41 SIZE.h
404    \cp packages.conf_hr packages.conf
405    
406    cd ../build
407    \rm *
408    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
409    make depend
410    make -j
411    
412    cd ..
413    mkdir run
414    cd run
415    \rm *
416    \cp ../input/* .
417    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
418    qsub job_orion41
419    
420    
421    ##########################################################################
422    ##########################################################################
423    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
424    # requires input files in sudirectories run_template and ncep_rgau
425    # presently residing under orion:/tmp1/dmenem/cube
426    
427    cd MITgcm/verification/global_ocean.cs32x15/code
428    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
429    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
430    \cp SIZE.h_50 SIZE.h
431    \cp packages.conf_hr packages.conf
432    
433    cd ../build
434    \rm *
435    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
436    make depend
437    make -j
438    
439    cd ..
440    mkdir run
441    cd run
442    \rm *
443    \cp ../input/* .
444    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
445    qsub job_orion
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