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revision 1.3 by dimitri, Mon Nov 24 01:04:28 2003 UTC revision 1.70 by dimitri, Thu Oct 12 05:45:52 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    
26      bash or sh shell:
27        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
28        $ cvs login
29          ( enter the CVS password: "cvsanon" )
30    
31      tcsh or csh shell:
32        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
33        $ cvs login
34          ( enter the CVS password: "cvsanon" )
35    
36  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
37  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  
38  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
39  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
40    cvs co MITgcm_code
41    cvs co MITgcm/verification/global_ocean.cs32x15
42    cvs co MITgcm/verification/tutorial_held_suarez_cs/input
43    
 cvs co -r checkpoint52a_post MITgcm_code  
 cvs co -r checkpoint52a_post MITgcm/verification/global_ocean.cs32x15  
44    
45  cd MITgcm/verification/global_ocean.cs32x15/code  ##########################################################################
46  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  ##########################################################################
47  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  # 32*32*6*15, 1-cpu cube sphere
 \rm mdsio_readfield.F  
48    
49  cd ..  cd MITgcm/verification/global_ocean.cs32x15/code
50  mkdir build  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
51  cd build  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
52  ../code/genmake2 -mods=../code  cd ../build
53    \rm *
54    ../../../tools/genmake2 -mods=../code
55  make depend  make depend
56  make  make
   
57  cd ..  cd ..
58  mkdir run  mkdir run
59  cd run  cd run
60  cp ../input/* .  \rm *
61  cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  \cp ../../tutorial_held_suarez_cs/input/grid* .
62  cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../input/* .
63    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
64  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
65    
66  comparison output is in:  comparison output is in:
67  ../../../../MITgcm_contrib/high_res_cube/results/output.txt  ../../../../MITgcm_contrib/high_res_cube/results/output.txt
68    
   
69  to use matlab to look at the output  to use matlab to look at the output
70  matlab  matlab
71  eta=permute(readbin('Eta.0000072020.data',[32,6,32]),[1 3 2]);  
72  cx=[-1 1]; clf  for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...
73  subplot(3,4, 9);imagesc(flipud(eta(:,:,1)'));caxis(cx);colorbar           'QNETtave','FVtave','FUtave','EmPmRtave'}
74  subplot(3,4,10);imagesc(flipud(eta(:,:,2)'));caxis(cx);colorbar      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);
75  subplot(3,4, 6);imagesc(flipud(eta(:,:,3)'));caxis(cx);colorbar      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
76  subplot(3,4, 7);imagesc(flipud(eta(:,:,4)'));caxis(cx);colorbar  end
77  subplot(3,4, 3);imagesc(flipud(eta(:,:,5)'));caxis(cx);colorbar  
78  subplot(3,4, 4);imagesc(flipud(eta(:,:,6)'));caxis(cx);colorbar  heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);
79    mask=0*heff; mask(find(heff>.001))=1;
80    uice=mask.*permute(readbin(['UICEtave.0000000020.data'],[32,6,32]),[1 3 2]);
81    vice=mask.*permute(readbin(['VICEtave.0000000020.data'],[32,6,32]),[1 3 2]);
82    clf
83    subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
84    subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
85    subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
86    subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
87    
88    
89    ##########################################################################
90    ##########################################################################
91    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
92    # requires input files in sudirectories run_template and ncep_rgau
93    # these can be obained from lou:/u/menemenl/cube
94    
95    cd MITgcm/verification/global_ocean.cs32x15/code
96    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
97    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
98    \cp SIZE.h_216 SIZE.h
99    \cp packages.conf_hr packages.conf
100    
101    cd ../build
102    \rm *
103    ../../../tools/genmake2 -mods=../code -of
104    ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
105    make depend
106    make -j
107    
108    cd ..
109    mkdir run
110    cd run
111    \rm *
112    \cp ../input/* .
113    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
114    ln -sf ../../../../run_template/* .
115    \rm pickup* data.pkg data.seaice data.exf_clim data.exf data bathy_Hmin50.bin
116    \rm *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
117    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
118    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38 pickup_seaice.0000000216
119    \cp ../build/mitgcmuv .
120    qsub job_altix
121    
122    
123    ##########################################################################
124    ##########################################################################
125    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
126    
127    cd MITgcm/verification/global_ocean.cs32x15/code
128    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
129    \cp ../code_alt/code.176t_8x4/* .
130    cd ../build
131    \rm *
132    ../../../tools/genmake2 -mods=../code
133    make depend
134    make
135    cd ..
136    mkdir run
137    cd run
138    \rm *
139    \cp ../../tutorial_held_suarez_cs/input/grid* .
140    \cp ../input/* .
141    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
142    ../build/mitgcmuv >& output.txt
143    
144    
145    ##########################################################################
146    ##########################################################################
147    # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
148    
149    cd MITgcm/verification/global_ocean.cs32x15/code
150    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
151    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
152    \cp SIZE.h_mpi SIZE.h
153    
154    cd ../build
155    \rm *
156    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
157    make depend
158    make -j
159    
160    cd ..
161    mkdir run
162    cd run
163    \rm *
164    \cp ../../tutorial_held_suarez_cs/input/grid* .
165    \cp ../input/* .
166    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
167    mpirun -np 2 ../build/mitgcmuv
168    
169    
170    ##########################################################################
171    ##########################################################################
172    # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
173    # starting with pickup file from end of 1992
174    # requires input files in sudirectories run_template and ncep_rgau
175    
176    cd MITgcm/verification/global_ocean.cs32x15/code
177    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
178    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
179    \cp packages.conf_hr packages.conf
180    
181    cd ../build
182    \rm *
183    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
184    make depend
185    make -j
186    
187    cd ..
188    mkdir run
189    cd run
190    \rm *
191    \cp ../input/* .
192    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
193    qsub job_altix92_54t
194    
195    
196    ##########################################################################
197    ##########################################################################
198    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
199    # uses s1500t_17x51 configuration
200    
201    cd MITgcm/verification/global_ocean.cs32x15/code
202    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
203    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
204    \cp SIZE.h_150 SIZE.h
205    \cp packages.conf_hr packages.conf
206    
207    cd ../build
208    \rm *
209    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
210    make depend
211    make -j
212    
213    cd ..
214    mkdir run
215    cd run
216    \rm *
217    \cp ../input/* .
218    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
219    ln -sf ../../../../run_template/* .
220    \rm pickup*
221    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
222    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
223    \cp ../build/mitgcmuv mitgcmuv150
224    qsub job_altix150
225    
226    
227    ##########################################################################
228    ##########################################################################
229    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
230    # uses s1500t_17x51 configuration
231    # example for running on c17-c20 using arrayd
232    
233    cd MITgcm/verification/global_ocean.cs32x15/code
234    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
235    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
236    \cp SIZE.h_375 SIZE.h
237    \cp packages.conf_hr packages.conf
238    
239    cd ../build
240    \rm *
241    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
242    make depend
243    make -j
244    
245    cd ..
246    mkdir run
247    cd run
248    \rm *
249    \cp ../input/* .
250    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
251    ln -sf ../../../../run_template/* .
252    \rm pickup*
253    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
254    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
255    \cp ../build/mitgcmuv .
256    job_c20_375cpu < /dev/null >&! output.run &
257    
258    
259    ##########################################################################
260    ##########################################################################
261    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
262    # uses s1500t_17x51 configuration
263    # example for running on c17-c20 using arrayd
264    
265    cd MITgcm/verification/global_ocean.cs32x15/code
266    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
267    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
268    \cp SIZE.h_375 SIZE.h
269    \cp packages.conf_hr packages.conf
270    
271    cd ../build
272    \rm *
273    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
274    make depend
275    make -j
276    
277    cd ..
278    mkdir run
279    cd run
280    \rm *
281    \cp ../input/* .
282    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
283    ln -sf ../../../../run_template/* .
284    \rm pickup*
285    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
286    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
287    \cp ../build/mitgcmuv .
288    job_c20_375cpu < /dev/null >&! output.run &
289    
290    
291    ##########################################################################
292    ##########################################################################
293    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
294    # uses s1500t_17x51 configuration
295    # example for running on c17-c20 using arrayd
296    
297    cd MITgcm/verification/global_ocean.cs32x15/code
298    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
299    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
300    \cp SIZE.h_500 SIZE.h
301    \cp packages.conf_hr packages.conf
302    
303    cd ../build
304    \rm *
305    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
306    make depend
307    make -j
308    
309    cd ..
310    mkdir run
311    cd run
312    \rm *
313    \cp ../input/* .
314    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
315    ln -sf ../../../../run_template/* .
316    \rm pickup*
317    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
318    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
319    \cp ../build/mitgcmuv .
320    job_c19_500cpu < /dev/null >&! output.run &
321    
322    
323    ##########################################################################
324    ##########################################################################
325    # 510*510*6*50, 216-cpu cube sphere on cosmos
326    
327    cd MITgcm/verification/global_ocean.cs32x15/code
328    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
329    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
330    \cp SIZE.h_216 SIZE.h
331    \cp packages.conf_hr packages.conf
332    
333    module unload latest_intel80
334    module unload mpich-gm-intel80
335    module load latest_intel81
336    module load mpich-gm-intel81
337    
338    cd ../build
339    \rm *
340    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
341    make depend
342    make -j
343    
344    cd ..
345    mkdir run
346    cd run
347    \rm *
348    \cp ../input/* .
349    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
350    ln -sf ../../../../run_template/* .
351    \rm pickup*
352    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
353    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
354    \cp ../build/mitgcmuv .
355    bsub < job_cosmos
356    
357    
358    ##########################################################################
359    ##########################################################################
360    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
361    # requires input files in sudirectories run_template and ncep_rgau
362    # presently residing under orion:/tmp1/dmenem/cube
363    
364    cd MITgcm/verification/global_ocean.cs32x15/code
365    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
366    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
367    \cp SIZE.h_54 SIZE.h
368    \cp packages.conf_hr packages.conf
369    
370    cd ../build
371    \rm *
372    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
373    make depend
374    make -j
375    
376    cd ..
377    mkdir run
378    cd run
379    \rm *
380    \cp ../input/* .
381    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
382    qsub job_orion
383    
384    
385    ##########################################################################
386    ##########################################################################
387    # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
388    # requires input files in sudirectories run_template and ncep_rgau
389    # presently residing under orion:/tmp1/dmenem/cube
390    
391    cd MITgcm/verification/global_ocean.cs32x15/code
392    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
393    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
394    \cp SIZE.h_41 SIZE.h
395    \cp packages.conf_hr packages.conf
396    
397    cd ../build
398    \rm *
399    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
400    make depend
401    make -j
402    
403    cd ..
404    mkdir run
405    cd run
406    \rm *
407    \cp ../input/* .
408    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
409    qsub job_orion41
410    
411    
412    ##########################################################################
413    ##########################################################################
414    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
415    # requires input files in sudirectories run_template and ncep_rgau
416    # presently residing under orion:/tmp1/dmenem/cube
417    
418    cd MITgcm/verification/global_ocean.cs32x15/code
419    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
420    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
421    \cp SIZE.h_50 SIZE.h
422    \cp packages.conf_hr packages.conf
423    
424    cd ../build
425    \rm *
426    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
427    make depend
428    make -j
429    
430    cd ..
431    mkdir run
432    cd run
433    \rm *
434    \cp ../input/* .
435    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
436    qsub job_orion
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