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revision 1.2 by dimitri, Sun Nov 23 20:11:39 2003 UTC revision 1.75 by dimitri, Fri Nov 3 23:17:42 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  cvs co MITgcm_contrib/high_res_cube/code-mods  
6  cvs co MITgcm_contrib/high_res_cube/matlab-grid-converter  November 3, 2006: 216-CPU code for cube43
7    Martin's growth.F routine and Patrick's pkg/seaice diagnostics
8    
9    October 15, 2006: 216-CPU code for cube40
10    
11    September 28, 2006: 216-CPU code for cube38
12    
13    September 4, 2006
14    Modified 32*32*6*15 experiments to use grid_cs32.* files from
15     verification/tutorial_held_suarez_cs/input instead of
16     tile* files from verification/global_ocean.cs32x15/input
17    
18    August 8, 2006: 216-CPU code and input used for cube37
19    using "June 10, 2006" MITgcm code.
20    
21    for online T/S profile diagnostics all that is needed is
22      profiles_init_fixed
23      profiles_inloop
24    see pkg/ecco/ecco_cost_init_fixed.F
25        pkg/ecco/cost_averagesfields.F
26    
27    
28    ##########################################################################
29    ##########################################################################
30    # getting the code from anonymous CVS server
31    #
32    
33      bash or sh shell:
34        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
35        $ cvs login
36          ( enter the CVS password: "cvsanon" )
37    
38      tcsh or csh shell:
39        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
40        $ cvs login
41          ( enter the CVS password: "cvsanon" )
42    
43  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
44  cvs co -r checkpoint52a_post MITgcm_code  cvs co MITgcm_contrib/high_res_cube/code-mods
45    cvs co MITgcm_contrib/high_res_cube/input
46    cvs co MITgcm_contrib/high_res_cube/results
47    cvs co MITgcm_code
48  cvs co MITgcm/verification/global_ocean.cs32x15  cvs co MITgcm/verification/global_ocean.cs32x15
49    cvs co MITgcm/verification/tutorial_held_suarez_cs/input
50    
51    
52    ##########################################################################
53    ##########################################################################
54    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
55    # requires input files in sudirectories run_template and ncep_rgau
56    # these can be obained from lou:/u/menemenl/cube
57    
58    cd MITgcm/verification/global_ocean.cs32x15/code
59    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
60    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
61    \cp SIZE.h_216 SIZE.h
62    \cp packages.conf_hr packages.conf
63    
64    cd ../build
65    \rm *
66    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
67    make depend
68    make -j
69    
70    cd ..
71    mkdir run
72    cd run
73    \rm *
74    \cp ../input/* .
75    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
76    ln -sf ../../../../run_template/* .
77    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
78    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
79    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
80    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38 pickup_seaice.0000000216
81    \cp ../build/mitgcmuv .
82    qsub job_altix
83    
84    
85    ##########################################################################
86    ##########################################################################
87    # 32*32*6*15, 1-cpu cube sphere
88    
89    cd MITgcm/verification/global_ocean.cs32x15/code
90    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
91    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
92    cd ../build
93    \rm *
94    ../../../tools/genmake2 -mods=../code
95    make depend
96    make
97    cd ..
98    mkdir run
99    cd run
100    \rm *
101    \cp ../../tutorial_held_suarez_cs/input/grid* .
102    \cp ../input/* .
103    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
104    ../build/mitgcmuv >& output.txt
105    
106    comparison output is in:
107    ../../../../MITgcm_contrib/high_res_cube/results/output.txt
108    
109    to use matlab to look at the output
110    matlab
111    
112    for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...
113             'QNETtave','FVtave','FUtave','EmPmRtave'}
114        tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);
115        cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
116    end
117    
118    heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);
119    mask=0*heff; mask(find(heff>.001))=1;
120    uice=mask.*permute(readbin(['UICEtave.0000000020.data'],[32,6,32]),[1 3 2]);
121    vice=mask.*permute(readbin(['VICEtave.0000000020.data'],[32,6,32]),[1 3 2]);
122    clf
123    subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
124    subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
125    subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
126    subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
127    
128    
129    ##########################################################################
130    ##########################################################################
131    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
132    
133  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
134  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
135  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../code_alt/code.176t_8x4/* .
136  \rm mdsio_readfield.F  cd ../build
137  cd ..  \rm *
138  mkdir build  ../../../tools/genmake2 -mods=../code
 cd build  
 ../code/genmake2 -mods=../code  
139  make depend  make depend
140  make  make
141  cd ..  cd ..
142  mkdir run  mkdir run
143  cd run  cd run
144  cp ../input/* .  \rm *
145  cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  \cp ../../tutorial_held_suarez_cs/input/grid* .
146  cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../input/* .
147  ../build/mitgcmuv >& output  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
148    ../build/mitgcmuv >& output.txt
149    
150    
151    ##########################################################################
152    ##########################################################################
153    # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
154    
155    cd MITgcm/verification/global_ocean.cs32x15/code
156    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
157    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
158    \cp SIZE.h_mpi SIZE.h
159    
160    cd ../build
161    \rm *
162    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
163    make depend
164    make -j
165    
166    cd ..
167    mkdir run
168    cd run
169    \rm *
170    \cp ../../tutorial_held_suarez_cs/input/grid* .
171    \cp ../input/* .
172    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
173    mpirun -np 2 ../build/mitgcmuv
174    
175    
176    ##########################################################################
177    ##########################################################################
178    # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
179    # starting with pickup file from end of 1992
180    # requires input files in sudirectories run_template and ncep_rgau
181    
182    cd MITgcm/verification/global_ocean.cs32x15/code
183    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
184    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
185    \cp packages.conf_hr packages.conf
186    
187    cd ../build
188    \rm *
189    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
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    qsub job_altix92_54t
200    
201    
202    ##########################################################################
203    ##########################################################################
204    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
205    # uses s1500t_17x51 configuration
206    
207    cd MITgcm/verification/global_ocean.cs32x15/code
208    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
209    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
210    \cp SIZE.h_150 SIZE.h
211    \cp packages.conf_hr packages.conf
212    
213    cd ../build
214    \rm *
215    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
216    make depend
217    make -j
218    
219    cd ..
220    mkdir run
221    cd run
222    \rm *
223    \cp ../input/* .
224    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
225    ln -sf ../../../../run_template/* .
226    \rm pickup*
227    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
228    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
229    \cp ../build/mitgcmuv mitgcmuv150
230    qsub job_altix150
231    
232    
233    ##########################################################################
234    ##########################################################################
235    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
236    # uses s1500t_17x51 configuration
237    # example for running on c17-c20 using arrayd
238    
239    cd MITgcm/verification/global_ocean.cs32x15/code
240    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
241    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
242    \cp SIZE.h_375 SIZE.h
243    \cp packages.conf_hr packages.conf
244    
245    cd ../build
246    \rm *
247    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
248    make depend
249    make -j
250    
251    cd ..
252    mkdir run
253    cd run
254    \rm *
255    \cp ../input/* .
256    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
257    ln -sf ../../../../run_template/* .
258    \rm pickup*
259    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
260    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
261    \cp ../build/mitgcmuv .
262    job_c20_375cpu < /dev/null >&! output.run &
263    
264    
265    ##########################################################################
266    ##########################################################################
267    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
268    # uses s1500t_17x51 configuration
269    # example for running on c17-c20 using arrayd
270    
271    cd MITgcm/verification/global_ocean.cs32x15/code
272    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
273    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
274    \cp SIZE.h_375 SIZE.h
275    \cp packages.conf_hr packages.conf
276    
277    cd ../build
278    \rm *
279    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
280    make depend
281    make -j
282    
283    cd ..
284    mkdir run
285    cd run
286    \rm *
287    \cp ../input/* .
288    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
289    ln -sf ../../../../run_template/* .
290    \rm pickup*
291    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
292    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
293    \cp ../build/mitgcmuv .
294    job_c20_375cpu < /dev/null >&! output.run &
295    
296    
297    ##########################################################################
298    ##########################################################################
299    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
300    # uses s1500t_17x51 configuration
301    # example for running on c17-c20 using arrayd
302    
303    cd MITgcm/verification/global_ocean.cs32x15/code
304    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
305    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
306    \cp SIZE.h_500 SIZE.h
307    \cp packages.conf_hr packages.conf
308    
309    cd ../build
310    \rm *
311    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
312    make depend
313    make -j
314    
315    cd ..
316    mkdir run
317    cd run
318    \rm *
319    \cp ../input/* .
320    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
321    ln -sf ../../../../run_template/* .
322    \rm pickup*
323    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
324    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
325    \cp ../build/mitgcmuv .
326    job_c19_500cpu < /dev/null >&! output.run &
327    
328    
329    ##########################################################################
330    ##########################################################################
331    # 510*510*6*50, 216-cpu cube sphere on cosmos
332    
333    cd MITgcm/verification/global_ocean.cs32x15/code
334    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
335    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
336    \cp SIZE.h_216 SIZE.h
337    \cp packages.conf_hr packages.conf
338    
339    module unload latest_intel80
340    module unload mpich-gm-intel80
341    module load latest_intel81
342    module load mpich-gm-intel81
343    
344    cd ../build
345    \rm *
346    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
347    make depend
348    make -j
349    
350    cd ..
351    mkdir run
352    cd run
353    \rm *
354    \cp ../input/* .
355    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
356    ln -sf ../../../../run_template/* .
357    \rm pickup*
358    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
359    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
360    \cp ../build/mitgcmuv .
361    bsub < job_cosmos
362    
363    
364    ##########################################################################
365    ##########################################################################
366    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
367    # requires input files in sudirectories run_template and ncep_rgau
368    # presently residing under orion:/tmp1/dmenem/cube
369    
370    cd MITgcm/verification/global_ocean.cs32x15/code
371    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
372    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
373    \cp SIZE.h_54 SIZE.h
374    \cp packages.conf_hr packages.conf
375    
376    cd ../build
377    \rm *
378    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
379    make depend
380    make -j
381    
382    cd ..
383    mkdir run
384    cd run
385    \rm *
386    \cp ../input/* .
387    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
388    qsub job_orion
389    
390    
391    ##########################################################################
392    ##########################################################################
393    # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
394    # requires input files in sudirectories run_template and ncep_rgau
395    # presently residing under orion:/tmp1/dmenem/cube
396    
397    cd MITgcm/verification/global_ocean.cs32x15/code
398    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
399    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
400    \cp SIZE.h_41 SIZE.h
401    \cp packages.conf_hr packages.conf
402    
403    cd ../build
404    \rm *
405    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
406    make depend
407    make -j
408    
409    cd ..
410    mkdir run
411    cd run
412    \rm *
413    \cp ../input/* .
414    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
415    qsub job_orion41
416    
417    
418    ##########################################################################
419    ##########################################################################
420    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
421    # requires input files in sudirectories run_template and ncep_rgau
422    # presently residing under orion:/tmp1/dmenem/cube
423    
424    cd MITgcm/verification/global_ocean.cs32x15/code
425    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
426    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
427    \cp SIZE.h_50 SIZE.h
428    \cp packages.conf_hr packages.conf
429    
430    cd ../build
431    \rm *
432    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
433    make depend
434    make -j
435    
436    cd ..
437    mkdir run
438    cd run
439    \rm *
440    \cp ../input/* .
441    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
442    qsub job_orion
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