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revision 1.3 by dimitri, Mon Nov 24 01:04:28 2003 UTC revision 1.67 by dimitri, Wed Oct 4 17:47:26 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  September 28, 2006: 216-CPU code for cube38
4  cvs login ( CVS password: cvsanon )  
5    September 4, 2006
6    Modified 32*32*6*15 experiments to use grid_cs32.* files from
7     verification/tutorial_held_suarez_cs/input instead of
8     tile* files from verification/global_ocean.cs32x15/input
9    
10    August 8, 2006
11    216-CPU code and input used for integrating cube37
12    using "June 10, 2006" MITgcm code.
13    
14    for online T/S profile diagnostics all that is needed is
15      profiles_init_fixed
16      profiles_inloop
17    see pkg/ecco/ecco_cost_init_fixed.F
18        pkg/ecco/cost_averagesfields.F
19    
20    
21    ##########################################################################
22    ##########################################################################
23    # getting the code from anonymous CVS server
24    
25  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
26  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  
27  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
28  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
29    cvs co MITgcm_code
30    cvs co MITgcm/verification/global_ocean.cs32x15
31    cvs co MITgcm/verification/tutorial_held_suarez_cs/input
32    
 cvs co -r checkpoint52a_post MITgcm_code  
 cvs co -r checkpoint52a_post MITgcm/verification/global_ocean.cs32x15  
33    
34  cd MITgcm/verification/global_ocean.cs32x15/code  ##########################################################################
35  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  ##########################################################################
36  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  # 32*32*6*15, 1-cpu cube sphere
 \rm mdsio_readfield.F  
37    
38  cd ..  cd MITgcm/verification/global_ocean.cs32x15/code
39  mkdir build  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
40  cd build  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
41  ../code/genmake2 -mods=../code  cd ../build
42    \rm *
43    ../../../tools/genmake2 -mods=../code
44  make depend  make depend
45  make  make
   
46  cd ..  cd ..
47  mkdir run  mkdir run
48  cd run  cd run
49  cp ../input/* .  \rm *
50  cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  \cp ../../tutorial_held_suarez_cs/input/grid* .
51  cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../input/* .
52    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
53  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
54    
55  comparison output is in:  comparison output is in:
56  ../../../../MITgcm_contrib/high_res_cube/results/output.txt  ../../../../MITgcm_contrib/high_res_cube/results/output.txt
57    
   
58  to use matlab to look at the output  to use matlab to look at the output
59  matlab  matlab
60  eta=permute(readbin('Eta.0000072020.data',[32,6,32]),[1 3 2]);  
61  cx=[-1 1]; clf  for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...
62  subplot(3,4, 9);imagesc(flipud(eta(:,:,1)'));caxis(cx);colorbar           'QNETtave','FVtave','FUtave','EmPmRtave'}
63  subplot(3,4,10);imagesc(flipud(eta(:,:,2)'));caxis(cx);colorbar      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);
64  subplot(3,4, 6);imagesc(flipud(eta(:,:,3)'));caxis(cx);colorbar      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
65  subplot(3,4, 7);imagesc(flipud(eta(:,:,4)'));caxis(cx);colorbar  end
66  subplot(3,4, 3);imagesc(flipud(eta(:,:,5)'));caxis(cx);colorbar  
67  subplot(3,4, 4);imagesc(flipud(eta(:,:,6)'));caxis(cx);colorbar  heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);
68    mask=0*heff; mask(find(heff>.001))=1;
69    uice=mask.*permute(readbin(['UICEtave.0000000020.data'],[32,6,32]),[1 3 2]);
70    vice=mask.*permute(readbin(['VICEtave.0000000020.data'],[32,6,32]),[1 3 2]);
71    clf
72    subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
73    subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
74    subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
75    subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
76    
77    
78    ##########################################################################
79    ##########################################################################
80    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
81    # requires input files in sudirectories run_template and ncep_rgau
82    # these can be obained from lou:/u/menemenl/cube
83    
84    cd MITgcm/verification/global_ocean.cs32x15/code
85    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
86    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
87    \cp SIZE.h_216 SIZE.h
88    \cp packages.conf_hr packages.conf
89    
90    cd ../build
91    \rm *
92    ../../../tools/genmake2 -mods=../code -of
93    ../../../tools/build_options/linux_ia\
94    64_ifort+mpi_altix_nas
95    make depend
96    make -j
97    
98    cd ..
99    mkdir run
100    cd run
101    \rm *
102    \cp ../input/* .
103    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
104    ln -sf ../../../../run_template/* .
105    \rm pickup* data.pkg data.seaice data.exf_clim data.exf data bathy_Hmin50.bin
106    \rm *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
107    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
108    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38
109    pickup_seaice.\
110    0000000216
111    \cp ../build/mitgcmuv .
112    qsub job_altix
113    
114    
115    ##########################################################################
116    ##########################################################################
117    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
118    
119    cd MITgcm/verification/global_ocean.cs32x15/code
120    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
121    \cp ../code_alt/code.176t_8x4/* .
122    cd ../build
123    \rm *
124    ../../../tools/genmake2 -mods=../code
125    make depend
126    make
127    cd ..
128    mkdir run
129    cd run
130    \rm *
131    \cp ../../tutorial_held_suarez_cs/input/grid* .
132    \cp ../input/* .
133    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
134    ../build/mitgcmuv >& output.txt
135    
136    
137    ##########################################################################
138    ##########################################################################
139    # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
140    
141    cd MITgcm/verification/global_ocean.cs32x15/code
142    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
143    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
144    \cp SIZE.h_mpi SIZE.h
145    
146    cd ../build
147    \rm *
148    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
149    make depend
150    make -j
151    
152    cd ..
153    mkdir run
154    cd run
155    \rm *
156    \cp ../../tutorial_held_suarez_cs/input/grid* .
157    \cp ../input/* .
158    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
159    mpirun -np 2 ../build/mitgcmuv
160    
161    
162    ##########################################################################
163    ##########################################################################
164    # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
165    # starting with pickup file from end of 1992
166    # requires input files in sudirectories run_template and ncep_rgau
167    
168    cd MITgcm/verification/global_ocean.cs32x15/code
169    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
170    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
171    \cp packages.conf_hr packages.conf
172    
173    cd ../build
174    \rm *
175    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
176    make depend
177    make -j
178    
179    cd ..
180    mkdir run
181    cd run
182    \rm *
183    \cp ../input/* .
184    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
185    qsub job_altix92_54t
186    
187    
188    ##########################################################################
189    ##########################################################################
190    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
191    # uses s1500t_17x51 configuration
192    
193    cd MITgcm/verification/global_ocean.cs32x15/code
194    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
195    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
196    \cp SIZE.h_150 SIZE.h
197    \cp packages.conf_hr packages.conf
198    
199    cd ../build
200    \rm *
201    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
202    make depend
203    make -j
204    
205    cd ..
206    mkdir run
207    cd run
208    \rm *
209    \cp ../input/* .
210    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
211    ln -sf ../../../../run_template/* .
212    \rm pickup*
213    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
214    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
215    \cp ../build/mitgcmuv mitgcmuv150
216    qsub job_altix150
217    
218    
219    ##########################################################################
220    ##########################################################################
221    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
222    # uses s1500t_17x51 configuration
223    # example for running on c17-c20 using arrayd
224    
225    cd MITgcm/verification/global_ocean.cs32x15/code
226    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
227    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
228    \cp SIZE.h_375 SIZE.h
229    \cp packages.conf_hr packages.conf
230    
231    cd ../build
232    \rm *
233    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
234    make depend
235    make -j
236    
237    cd ..
238    mkdir run
239    cd run
240    \rm *
241    \cp ../input/* .
242    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
243    ln -sf ../../../../run_template/* .
244    \rm pickup*
245    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
246    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
247    \cp ../build/mitgcmuv .
248    job_c20_375cpu < /dev/null >&! output.run &
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    # 510*510*6*50, 216-cpu cube sphere on cosmos
318    
319    cd MITgcm/verification/global_ocean.cs32x15/code
320    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
321    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
322    \cp SIZE.h_216 SIZE.h
323    \cp packages.conf_hr packages.conf
324    
325    module unload latest_intel80
326    module unload mpich-gm-intel80
327    module load latest_intel81
328    module load mpich-gm-intel81
329    
330    cd ../build
331    \rm *
332    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
333    make depend
334    make -j
335    
336    cd ..
337    mkdir run
338    cd run
339    \rm *
340    \cp ../input/* .
341    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
342    ln -sf ../../../../run_template/* .
343    \rm pickup*
344    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
345    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
346    \cp ../build/mitgcmuv .
347    bsub < job_cosmos
348    
349    
350    ##########################################################################
351    ##########################################################################
352    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
353    # requires input files in sudirectories run_template and ncep_rgau
354    # presently residing under orion:/tmp1/dmenem/cube
355    
356    cd MITgcm/verification/global_ocean.cs32x15/code
357    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
358    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
359    \cp SIZE.h_54 SIZE.h
360    \cp packages.conf_hr packages.conf
361    
362    cd ../build
363    \rm *
364    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
365    make depend
366    make -j
367    
368    cd ..
369    mkdir run
370    cd run
371    \rm *
372    \cp ../input/* .
373    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
374    qsub job_orion
375    
376    
377    ##########################################################################
378    ##########################################################################
379    # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
380    # requires input files in sudirectories run_template and ncep_rgau
381    # presently residing under orion:/tmp1/dmenem/cube
382    
383    cd MITgcm/verification/global_ocean.cs32x15/code
384    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
385    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
386    \cp SIZE.h_41 SIZE.h
387    \cp packages.conf_hr packages.conf
388    
389    cd ../build
390    \rm *
391    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
392    make depend
393    make -j
394    
395    cd ..
396    mkdir run
397    cd run
398    \rm *
399    \cp ../input/* .
400    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
401    qsub job_orion41
402    
403    
404    ##########################################################################
405    ##########################################################################
406    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
407    # requires input files in sudirectories run_template and ncep_rgau
408    # presently residing under orion:/tmp1/dmenem/cube
409    
410    cd MITgcm/verification/global_ocean.cs32x15/code
411    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
412    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
413    \cp SIZE.h_50 SIZE.h
414    \cp packages.conf_hr packages.conf
415    
416    cd ../build
417    \rm *
418    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
419    make depend
420    make -j
421    
422    cd ..
423    mkdir run
424    cd run
425    \rm *
426    \cp ../input/* .
427    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
428    qsub job_orion
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