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revision 1.3 by dimitri, Mon Nov 24 01:04:28 2003 UTC revision 1.78 by dimitri, Tue Dec 5 20:46:48 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    December 5, 2006: 216-CPU code for cube46
7    Changed diagnostics to accomodate JMCs latest and some
8    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
9    to speed up code.
10    
11    November 7, 2006: 216-CPU code for cube43
12    Bug fixes in growth.F routine and new set of diagnostics
13    
14    October 15, 2006: 216-CPU code for cube40
15    
16    September 28, 2006: 216-CPU code for cube38
17    
18    September 4, 2006
19    Modified 32*32*6*15 experiments to use grid_cs32.* files from
20     verification/tutorial_held_suarez_cs/input instead of
21     tile* files from verification/global_ocean.cs32x15/input
22    
23    August 8, 2006: 216-CPU code and input used for cube37
24    using "June 10, 2006" MITgcm code.
25    
26    for online T/S profile diagnostics all that is needed is
27      profiles_init_fixed
28      profiles_inloop
29    see pkg/ecco/ecco_cost_init_fixed.F
30        pkg/ecco/cost_averagesfields.F
31    
32    
33    ##########################################################################
34    ##########################################################################
35    # getting the code from anonymous CVS server
36    #
37    
38      bash or sh shell:
39        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
40        $ cvs login
41          ( enter the CVS password: "cvsanon" )
42    
43      tcsh or csh shell:
44        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
45        $ cvs login
46          ( enter the CVS password: "cvsanon" )
47    
48  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
49  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  
50  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
51  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
52    cvs co MITgcm_code
53    cvs co MITgcm/verification/global_ocean.cs32x15
54    cvs co MITgcm/verification/tutorial_held_suarez_cs/input
55    
56  cvs co -r checkpoint52a_post MITgcm_code  
57  cvs co -r checkpoint52a_post MITgcm/verification/global_ocean.cs32x15  ##########################################################################
58    ##########################################################################
59    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
60    # requires input files in sudirectories run_template and ncep_rgau
61    # these can be obained from lou:/u/menemenl/cube
62    
63  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
64  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
65  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
66  \rm mdsio_readfield.F  \cp SIZE.h_216 SIZE.h
67    \cp packages.conf_hr packages.conf
68    
69    cd ../build
70    \rm *
71    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
72    make depend
73    make -j
74    
75  cd ..  cd ..
76  mkdir build  mkdir run
77  cd build  cd run
78  ../code/genmake2 -mods=../code  \rm *
79    \cp ../input/* .
80    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
81    ln -sf ../../../../run_template/* .
82    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
83    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
84    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
85    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38 pickup_seaice.0000000216
86    \cp ../build/mitgcmuv .
87    qsub job_altix
88    
89    
90    ##########################################################################
91    ##########################################################################
92    # 32*32*6*15, 1-cpu cube sphere
93    
94    cd MITgcm/verification/global_ocean.cs32x15/code
95    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
96    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
97    cd ../build
98    \rm *
99    ../../../tools/genmake2 -mods=../code
100  make depend  make depend
101  make  make
   
102  cd ..  cd ..
103  mkdir run  mkdir run
104  cd run  cd run
105  cp ../input/* .  \rm *
106  cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  \cp ../../tutorial_held_suarez_cs/input/grid* .
107  cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../input/* .
108    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
109  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
110    
111  comparison output is in:  comparison output is in:
112  ../../../../MITgcm_contrib/high_res_cube/results/output.txt  ../../../../MITgcm_contrib/high_res_cube/results/output.txt
113    
   
114  to use matlab to look at the output  to use matlab to look at the output
115  matlab  matlab
116  eta=permute(readbin('Eta.0000072020.data',[32,6,32]),[1 3 2]);  
117  cx=[-1 1]; clf  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
118  subplot(3,4, 9);imagesc(flipud(eta(:,:,1)'));caxis(cx);colorbar           'surForcT','oceTAUX','oceTAUY','surForcS'}
119  subplot(3,4,10);imagesc(flipud(eta(:,:,2)'));caxis(cx);colorbar      tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
120  subplot(3,4, 6);imagesc(flipud(eta(:,:,3)'));caxis(cx);colorbar      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
121  subplot(3,4, 7);imagesc(flipud(eta(:,:,4)'));caxis(cx);colorbar  end
122  subplot(3,4, 3);imagesc(flipud(eta(:,:,5)'));caxis(cx);colorbar  
123  subplot(3,4, 4);imagesc(flipud(eta(:,:,6)'));caxis(cx);colorbar  heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
124    mask=0*heff; mask(find(heff>.001))=1;
125    uice=mask.*permute(readbin(['SIuice.0000000072.data'],[32,6,32]),[1 3 2]);
126    vice=mask.*permute(readbin(['SIvice.0000000072.data'],[32,6,32]),[1 3 2]);
127    clf
128    subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
129    subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
130    subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
131    subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
132    
133    
134    ##########################################################################
135    ##########################################################################
136    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
137    
138    cd MITgcm/verification/global_ocean.cs32x15/code
139    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
140    \cp ../code_alt/code.176t_8x4/* .
141    cd ../build
142    \rm *
143    ../../../tools/genmake2 -mods=../code
144    make depend
145    make
146    cd ..
147    mkdir run
148    cd run
149    \rm *
150    \cp ../../tutorial_held_suarez_cs/input/grid* .
151    \cp ../input/* .
152    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
153    ../build/mitgcmuv >& output.txt
154    
155    
156    ##########################################################################
157    ##########################################################################
158    # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
159    
160    cd MITgcm/verification/global_ocean.cs32x15/code
161    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
162    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
163    \cp SIZE.h_mpi SIZE.h
164    
165    cd ../build
166    \rm *
167    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
168    make depend
169    make -j
170    
171    cd ..
172    mkdir run
173    cd run
174    \rm *
175    \cp ../../tutorial_held_suarez_cs/input/grid* .
176    \cp ../input/* .
177    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
178    mpirun -np 2 ../build/mitgcmuv
179    
180    
181    ##########################################################################
182    ##########################################################################
183    # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
184    # starting with pickup file from end of 1992
185    # requires input files in sudirectories run_template and ncep_rgau
186    
187    cd MITgcm/verification/global_ocean.cs32x15/code
188    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
189    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
190    \cp packages.conf_hr packages.conf
191    
192    cd ../build
193    \rm *
194    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
195    make depend
196    make -j
197    
198    cd ..
199    mkdir run
200    cd run
201    \rm *
202    \cp ../input/* .
203    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
204    qsub job_altix92_54t
205    
206    
207    ##########################################################################
208    ##########################################################################
209    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
210    # uses s1500t_17x51 configuration
211    
212    cd MITgcm/verification/global_ocean.cs32x15/code
213    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
214    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
215    \cp SIZE.h_150 SIZE.h
216    \cp packages.conf_hr packages.conf
217    
218    cd ../build
219    \rm *
220    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
221    make depend
222    make -j
223    
224    cd ..
225    mkdir run
226    cd run
227    \rm *
228    \cp ../input/* .
229    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
230    ln -sf ../../../../run_template/* .
231    \rm pickup*
232    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
233    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
234    \cp ../build/mitgcmuv mitgcmuv150
235    qsub job_altix150
236    
237    
238    ##########################################################################
239    ##########################################################################
240    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
241    # uses s1500t_17x51 configuration
242    # example for running on c17-c20 using arrayd
243    
244    cd MITgcm/verification/global_ocean.cs32x15/code
245    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
246    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
247    \cp SIZE.h_375 SIZE.h
248    \cp packages.conf_hr packages.conf
249    
250    cd ../build
251    \rm *
252    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
253    make depend
254    make -j
255    
256    cd ..
257    mkdir run
258    cd run
259    \rm *
260    \cp ../input/* .
261    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
262    ln -sf ../../../../run_template/* .
263    \rm pickup*
264    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
265    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
266    \cp ../build/mitgcmuv .
267    job_c20_375cpu < /dev/null >&! output.run &
268    
269    
270    ##########################################################################
271    ##########################################################################
272    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
273    # uses s1500t_17x51 configuration
274    # example for running on c17-c20 using arrayd
275    
276    cd MITgcm/verification/global_ocean.cs32x15/code
277    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
278    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
279    \cp SIZE.h_375 SIZE.h
280    \cp packages.conf_hr packages.conf
281    
282    cd ../build
283    \rm *
284    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
285    make depend
286    make -j
287    
288    cd ..
289    mkdir run
290    cd run
291    \rm *
292    \cp ../input/* .
293    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
294    ln -sf ../../../../run_template/* .
295    \rm pickup*
296    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
297    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
298    \cp ../build/mitgcmuv .
299    job_c20_375cpu < /dev/null >&! output.run &
300    
301    
302    ##########################################################################
303    ##########################################################################
304    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
305    # uses s1500t_17x51 configuration
306    # example for running on c17-c20 using arrayd
307    
308    cd MITgcm/verification/global_ocean.cs32x15/code
309    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
310    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
311    \cp SIZE.h_500 SIZE.h
312    \cp packages.conf_hr packages.conf
313    
314    cd ../build
315    \rm *
316    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
317    make depend
318    make -j
319    
320    cd ..
321    mkdir run
322    cd run
323    \rm *
324    \cp ../input/* .
325    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
326    ln -sf ../../../../run_template/* .
327    \rm pickup*
328    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
329    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
330    \cp ../build/mitgcmuv .
331    job_c19_500cpu < /dev/null >&! output.run &
332    
333    
334    ##########################################################################
335    ##########################################################################
336    # 510*510*6*50, 216-cpu cube sphere on cosmos
337    
338    cd MITgcm/verification/global_ocean.cs32x15/code
339    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
340    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
341    \cp SIZE.h_216 SIZE.h
342    \cp packages.conf_hr packages.conf
343    
344    module unload latest_intel80
345    module unload mpich-gm-intel80
346    module load latest_intel81
347    module load mpich-gm-intel81
348    
349    cd ../build
350    \rm *
351    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
352    make depend
353    make -j
354    
355    cd ..
356    mkdir run
357    cd run
358    \rm *
359    \cp ../input/* .
360    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
361    ln -sf ../../../../run_template/* .
362    \rm pickup*
363    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
364    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
365    \cp ../build/mitgcmuv .
366    bsub < job_cosmos
367    
368    
369    ##########################################################################
370    ##########################################################################
371    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
372    # requires input files in sudirectories run_template and ncep_rgau
373    # presently residing under orion:/tmp1/dmenem/cube
374    
375    cd MITgcm/verification/global_ocean.cs32x15/code
376    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
377    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
378    \cp SIZE.h_54 SIZE.h
379    \cp packages.conf_hr packages.conf
380    
381    cd ../build
382    \rm *
383    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
384    make depend
385    make -j
386    
387    cd ..
388    mkdir run
389    cd run
390    \rm *
391    \cp ../input/* .
392    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
393    qsub job_orion
394    
395    
396    ##########################################################################
397    ##########################################################################
398    # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
399    # requires input files in sudirectories run_template and ncep_rgau
400    # presently residing under orion:/tmp1/dmenem/cube
401    
402    cd MITgcm/verification/global_ocean.cs32x15/code
403    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
404    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
405    \cp SIZE.h_41 SIZE.h
406    \cp packages.conf_hr packages.conf
407    
408    cd ../build
409    \rm *
410    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
411    make depend
412    make -j
413    
414    cd ..
415    mkdir run
416    cd run
417    \rm *
418    \cp ../input/* .
419    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
420    qsub job_orion41
421    
422    
423    ##########################################################################
424    ##########################################################################
425    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
426    # requires input files in sudirectories run_template and ncep_rgau
427    # presently residing under orion:/tmp1/dmenem/cube
428    
429    cd MITgcm/verification/global_ocean.cs32x15/code
430    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
431    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
432    \cp SIZE.h_50 SIZE.h
433    \cp packages.conf_hr packages.conf
434    
435    cd ../build
436    \rm *
437    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
438    make depend
439    make -j
440    
441    cd ..
442    mkdir run
443    cd run
444    \rm *
445    \cp ../input/* .
446    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
447    qsub job_orion
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