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revision 1.3 by dimitri, Mon Nov 24 01:04:28 2003 UTC revision 1.65 by dimitri, Tue Sep 5 02:49:56 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  Last updated: September 4, 2006
4  cvs login ( CVS password: cvsanon )  Modified 32*32*6*15 experiments to use grid_cs32.* files from
5     verification/tutorial_held_suarez_cs/input instead of
6     tile* files from verification/global_ocean.cs32x15/input
7    
8    Updated: August 8, 2006
9    216-CPU code and input used for integrating cube37
10    using "June 10, 2006" MITgcm code.
11    
12    
13    ##########################################################################
14    ##########################################################################
15    # getting the code from anonymous CVS server
16    
17  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
18  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  
19  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
20  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
21    cvs co MITgcm_code
22    cvs co MITgcm/verification/global_ocean.cs32x15
23    cvs co MITgcm/verification/tutorial_held_suarez_cs/input
24    
 cvs co -r checkpoint52a_post MITgcm_code  
 cvs co -r checkpoint52a_post MITgcm/verification/global_ocean.cs32x15  
25    
26  cd MITgcm/verification/global_ocean.cs32x15/code  ##########################################################################
27  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  ##########################################################################
28  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  # 32*32*6*15, 1-cpu cube sphere
 \rm mdsio_readfield.F  
29    
30  cd ..  cd MITgcm/verification/global_ocean.cs32x15/code
31  mkdir build  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
32  cd build  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
33  ../code/genmake2 -mods=../code  cd ../build
34    \rm *
35    ../../../tools/genmake2 -mods=../code
36  make depend  make depend
37  make  make
   
38  cd ..  cd ..
39  mkdir run  mkdir run
40  cd run  cd run
41  cp ../input/* .  \rm *
42  cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  \cp ../../tutorial_held_suarez_cs/input/grid* .
43  cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../input/* .
44    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
45  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
46    
47  comparison output is in:  comparison output is in:
48  ../../../../MITgcm_contrib/high_res_cube/results/output.txt  ../../../../MITgcm_contrib/high_res_cube/results/output.txt
49    
   
50  to use matlab to look at the output  to use matlab to look at the output
51  matlab  matlab
52  eta=permute(readbin('Eta.0000072020.data',[32,6,32]),[1 3 2]);  
53  cx=[-1 1]; clf  for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...
54  subplot(3,4, 9);imagesc(flipud(eta(:,:,1)'));caxis(cx);colorbar           'QNETtave','FVtave','FUtave','EmPmRtave'}
55  subplot(3,4,10);imagesc(flipud(eta(:,:,2)'));caxis(cx);colorbar      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);
56  subplot(3,4, 6);imagesc(flipud(eta(:,:,3)'));caxis(cx);colorbar      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
57  subplot(3,4, 7);imagesc(flipud(eta(:,:,4)'));caxis(cx);colorbar  end
58  subplot(3,4, 3);imagesc(flipud(eta(:,:,5)'));caxis(cx);colorbar  
59  subplot(3,4, 4);imagesc(flipud(eta(:,:,6)'));caxis(cx);colorbar  heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);
60    mask=0*heff; mask(find(heff>.001))=1;
61    uice=mask.*permute(readbin(['UICEtave.0000000020.data'],[32,6,32]),[1 3 2]);
62    vice=mask.*permute(readbin(['VICEtave.0000000020.data'],[32,6,32]),[1 3 2]);
63    clf
64    subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
65    subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
66    subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
67    subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
68    
69    
70    ##########################################################################
71    ##########################################################################
72    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
73    
74    cd MITgcm/verification/global_ocean.cs32x15/code
75    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
76    \cp ../code_alt/code.176t_8x4/* .
77    cd ../build
78    \rm *
79    ../../../tools/genmake2 -mods=../code
80    make depend
81    make
82    cd ..
83    mkdir run
84    cd run
85    \rm *
86    \cp ../../tutorial_held_suarez_cs/input/grid* .
87    \cp ../input/* .
88    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
89    ../build/mitgcmuv >& output.txt
90    
91    
92    ##########################################################################
93    ##########################################################################
94    # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
95    
96    cd MITgcm/verification/global_ocean.cs32x15/code
97    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
98    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
99    \cp SIZE.h_mpi SIZE.h
100    
101    cd ../build
102    \rm *
103    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
104    make depend
105    make -j
106    
107    cd ..
108    mkdir run
109    cd run
110    \rm *
111    \cp ../../tutorial_held_suarez_cs/input/grid* .
112    \cp ../input/* .
113    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
114    mpirun -np 2 ../build/mitgcmuv
115    
116    
117    ##########################################################################
118    ##########################################################################
119    # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
120    # starting with pickup file from end of 1992
121    # requires input files in sudirectories run_template and ncep_rgau
122    
123    cd MITgcm/verification/global_ocean.cs32x15/code
124    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
125    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
126    \cp packages.conf_hr packages.conf
127    
128    cd ../build
129    \rm *
130    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
131    make depend
132    make -j
133    
134    cd ..
135    mkdir run
136    cd run
137    \rm *
138    \cp ../input/* .
139    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
140    qsub job_altix92_54t
141    
142    
143    ##########################################################################
144    ##########################################################################
145    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
146    # requires input files in sudirectories run_template and ncep_rgau
147    # these can be obained from lou:/u/menemenl/cube
148    
149    cd MITgcm/verification/global_ocean.cs32x15/code
150    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
151    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
152    \cp SIZE.h_216 SIZE.h
153    \cp packages.conf_hr packages.conf
154    
155    cd ../build
156    \rm *
157    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
158    make depend
159    make -j
160    
161    cd ..
162    mkdir run
163    cd run
164    \rm *
165    \cp ../input/* .
166    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
167    ln -sf ../../../../run_template/* .
168    \rm pickup* data.pkg data.seaice data.exf_clim data.exf data
169    \rm *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
170    ln -sf ../../../../run_template/pickup.0000000216.cube27 pickup.0000000216
171    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube27 pickup_seaice.0000000216
172    \cp ../build/mitgcmuv .
173    qsub job_altix
174    
175    
176    ##########################################################################
177    ##########################################################################
178    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
179    # uses s1500t_17x51 configuration
180    
181    cd MITgcm/verification/global_ocean.cs32x15/code
182    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
183    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
184    \cp SIZE.h_150 SIZE.h
185    \cp packages.conf_hr packages.conf
186    
187    cd ../build
188    \rm *
189    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
190    make depend
191    make -j
192    
193    cd ..
194    mkdir run
195    cd run
196    \rm *
197    \cp ../input/* .
198    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
199    ln -sf ../../../../run_template/* .
200    \rm pickup*
201    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
202    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
203    \cp ../build/mitgcmuv mitgcmuv150
204    qsub job_altix150
205    
206    
207    
208    
209    ##########################################################################
210    ##########################################################################
211    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
212    # uses s1500t_17x51 configuration
213    # example for running on c17-c20 using arrayd
214    
215    cd MITgcm/verification/global_ocean.cs32x15/code
216    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
217    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
218    \cp SIZE.h_375 SIZE.h
219    \cp packages.conf_hr packages.conf
220    
221    cd ../build
222    \rm *
223    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
224    make depend
225    make -j
226    
227    cd ..
228    mkdir run
229    cd run
230    \rm *
231    \cp ../input/* .
232    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
233    ln -sf ../../../../run_template/* .
234    \rm pickup*
235    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
236    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
237    \cp ../build/mitgcmuv .
238    job_c20_375cpu < /dev/null >&! output.run &
239    
240    
241    
242    
243    
244    
245    
246    
247    
248    
249    
250    
251    ##########################################################################
252    ##########################################################################
253    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
254    # uses s1500t_17x51 configuration
255    # example for running on c17-c20 using arrayd
256    
257    cd MITgcm/verification/global_ocean.cs32x15/code
258    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
259    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
260    \cp SIZE.h_375 SIZE.h
261    \cp packages.conf_hr packages.conf
262    
263    cd ../build
264    \rm *
265    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
266    make depend
267    make -j
268    
269    cd ..
270    mkdir run
271    cd run
272    \rm *
273    \cp ../input/* .
274    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
275    ln -sf ../../../../run_template/* .
276    \rm pickup*
277    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
278    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
279    \cp ../build/mitgcmuv .
280    job_c20_375cpu < /dev/null >&! output.run &
281    
282    
283    ##########################################################################
284    ##########################################################################
285    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
286    # uses s1500t_17x51 configuration
287    # example for running on c17-c20 using arrayd
288    
289    cd MITgcm/verification/global_ocean.cs32x15/code
290    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
291    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
292    \cp SIZE.h_500 SIZE.h
293    \cp packages.conf_hr packages.conf
294    
295    cd ../build
296    \rm *
297    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
298    make depend
299    make -j
300    
301    cd ..
302    mkdir run
303    cd run
304    \rm *
305    \cp ../input/* .
306    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
307    ln -sf ../../../../run_template/* .
308    \rm pickup*
309    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
310    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
311    \cp ../build/mitgcmuv .
312    job_c19_500cpu < /dev/null >&! output.run &
313    
314    
315    
316    
317    
318    ##########################################################################
319    ##########################################################################
320    # 510*510*6*50, 216-cpu cube sphere on cosmos
321    
322    cd MITgcm/verification/global_ocean.cs32x15/code
323    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
324    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
325    \cp SIZE.h_216 SIZE.h
326    \cp packages.conf_hr packages.conf
327    
328    module unload latest_intel80
329    module unload mpich-gm-intel80
330    module load latest_intel81
331    module load mpich-gm-intel81
332    
333    cd ../build
334    \rm *
335    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
336    make depend
337    make -j
338    
339    cd ..
340    mkdir run
341    cd run
342    \rm *
343    \cp ../input/* .
344    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
345    ln -sf ../../../../run_template/* .
346    \rm pickup*
347    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
348    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
349    \cp ../build/mitgcmuv .
350    bsub < job_cosmos
351    
352    
353    
354    
355    
356    
357    
358    
359    
360    
361    
362    
363    
364    
365    
366    
367    
368    
369    
370    
371    ##########################################################################
372    ##########################################################################
373    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
374    # requires input files in sudirectories run_template and ncep_rgau
375    # presently residing under orion:/tmp1/dmenem/cube
376    
377    cd MITgcm/verification/global_ocean.cs32x15/code
378    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
379    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
380    \cp SIZE.h_54 SIZE.h
381    \cp packages.conf_hr packages.conf
382    
383    cd ../build
384    \rm *
385    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
386    make depend
387    make -j
388    
389    cd ..
390    mkdir run
391    cd run
392    \rm *
393    \cp ../input/* .
394    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
395    qsub job_orion
396    
397    
398    ##########################################################################
399    ##########################################################################
400    # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
401    # requires input files in sudirectories run_template and ncep_rgau
402    # presently residing under orion:/tmp1/dmenem/cube
403    
404    cd MITgcm/verification/global_ocean.cs32x15/code
405    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
406    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
407    \cp SIZE.h_41 SIZE.h
408    \cp packages.conf_hr packages.conf
409    
410    cd ../build
411    \rm *
412    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
413    make depend
414    make -j
415    
416    cd ..
417    mkdir run
418    cd run
419    \rm *
420    \cp ../input/* .
421    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
422    qsub job_orion41
423    
424    
425    ##########################################################################
426    ##########################################################################
427    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
428    # requires input files in sudirectories run_template and ncep_rgau
429    # presently residing under orion:/tmp1/dmenem/cube
430    
431    cd MITgcm/verification/global_ocean.cs32x15/code
432    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
433    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
434    \cp SIZE.h_50 SIZE.h
435    \cp packages.conf_hr packages.conf
436    
437    cd ../build
438    \rm *
439    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
440    make depend
441    make -j
442    
443    cd ..
444    mkdir run
445    cd run
446    \rm *
447    \cp ../input/* .
448    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
449    qsub job_orion
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