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revision 1.6 by dimitri, Sat Dec 6 22:04:19 2003 UTC revision 1.84 by dimitri, Sat Dec 30 18:23:24 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: December 6, 2003.  
2    
3  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  Forcing fields and other input files needed for the CS510
4  cvs login ( CVS password: cvsanon )  configuration can be obtained from
5    http://ecco2.org/products/model_setups/cs510.html
6    
7    =================
8    UPDATES
9    
10    December 30, 2006: updates for cube49, the first
11    "blend" integration.
12    
13    December 11, 2006: preparing for cube47, same as cube43
14    but with Arctic monthly river runoff climatology.
15    
16    December 5, 2006: 216-CPU code for cube46
17    Changed diagnostics to accomodate JMCs latest and some
18    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
19    to speed up code.
20    
21    November 7, 2006: 216-CPU code for cube43
22    Bug fixes in growth.F routine and new set of diagnostics
23    
24    October 15, 2006: 216-CPU code for cube40
25    
26    September 28, 2006: 216-CPU code for cube38
27    
28    September 4, 2006
29    Modified 32*32*6*15 experiments to use grid_cs32.* files from
30     verification/tutorial_held_suarez_cs/input instead of
31     tile* files from verification/global_ocean.cs32x15/input
32    
33    August 8, 2006: 216-CPU code and input used for cube37
34    using "June 10, 2006" MITgcm code.
35    
36    for online T/S profile diagnostics all that is needed is
37      profiles_init_fixed
38      profiles_inloop
39    see pkg/ecco/ecco_cost_init_fixed.F
40        pkg/ecco/cost_averagesfields.F
41    
42    ##########################################################################
43    ##########################################################################
44    # Get forcing files, etc.
45    # Example below is for cube46 on /nobackup2a/menemenl
46    
47    cd /nobackup2a/menemenl
48    mkdir cube47
49    cd cube47
50    ln -sf ../run_template .
51    ln -sf ../ncep_rgau .
52    
53    
54    ##########################################################################
55    ##########################################################################
56    # getting the code from anonymous CVS server
57    
58      bash or sh shell:
59        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
60        $ cvs login
61          ( enter the CVS password: "cvsanon" )
62    
63      tcsh or csh shell:
64        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
65        $ cvs login
66          ( enter the CVS password: "cvsanon" )
67    
68  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
69  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  
70  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
71  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
72    cvs co MITgcm_code
73    cvs co MITgcm/verification/global_ocean.cs32x15
74    cvs co MITgcm/verification/tutorial_held_suarez_cs/input
75    
76  cvs co -r checkpoint52d_pre MITgcm_code  
77  cvs co -r checkpoint52d_pre MITgcm/verification/global_ocean.cs32x15  ##########################################################################
78    ##########################################################################
79    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
80    
81  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
82  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
83  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
84  \rm mdsio_readfield.F  \cp SIZE.h_216 SIZE.h
85    \cp packages.conf_hr packages.conf
86    
87    cd ../build
88    \rm *
89    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
90    make depend
91    make -j
92    
93  cd ..  cd ..
94  mkdir build  mkdir run
95  cd build  cd run
96  ../code/genmake2 -mods=../code  \rm *
97    \cp ../input/* .
98    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
99    ln -sf ../../../../run_template/* .
100    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
101    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
102    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
103    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38 pickup_seaice.0000000216
104    \cp ../build/mitgcmuv .
105    qsub job_altix
106    
107    
108    ##########################################################################
109    ##########################################################################
110    # 32*32*6*15, 1-cpu cube sphere
111    
112    cd MITgcm/verification/global_ocean.cs32x15/code
113    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
114    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
115    cd ../build
116    \rm *
117    ../../../tools/genmake2 -mods=../code
118  make depend  make depend
119  make  make
   
120  cd ..  cd ..
121  mkdir run  mkdir run
122  cd run  cd run
123  cp ../inp_thsice/* .  \rm *
124  cp ../input/* .  \cp ../../tutorial_held_suarez_cs/input/grid* .
125  cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  \cp ../input/* .
126  cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
127  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
128    
129  comparison output is in:  comparison output is in:
130  ../../../../MITgcm_contrib/high_res_cube/results/output.txt  ../../../../MITgcm_contrib/high_res_cube/results/output.txt
131    
   
132  to use matlab to look at the output  to use matlab to look at the output
133  matlab  matlab
134  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  
135      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
136             'surForcT','oceTAUX','oceTAUY','surForcS'}
137        tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
138      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
139  end  end
140    
141    heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
142    mask=0*heff; mask(find(heff>.001))=1;
143    uice=mask.*permute(readbin(['SIuice.0000000072.data'],[32,6,32]),[1 3 2]);
144    vice=mask.*permute(readbin(['SIvice.0000000072.data'],[32,6,32]),[1 3 2]);
145    clf
146    subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
147    subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
148    subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
149    subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
150    
151    
152    ##########################################################################
153    ##########################################################################
154    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
155    
156    cd MITgcm/verification/global_ocean.cs32x15/code
157    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
158    \cp ../code_alt/code.176t_8x4/* .
159    cd ../build
160    \rm *
161    ../../../tools/genmake2 -mods=../code
162    make depend
163    make
164    cd ..
165    mkdir run
166    cd run
167    \rm *
168    \cp ../../tutorial_held_suarez_cs/input/grid* .
169    \cp ../input/* .
170    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
171    ../build/mitgcmuv >& output.txt
172    
173    
174    ##########################################################################
175    ##########################################################################
176    # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
177    
178    cd MITgcm/verification/global_ocean.cs32x15/code
179    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
180    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
181    \cp SIZE.h_mpi SIZE.h
182    
183    cd ../build
184    \rm *
185    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
186    make depend
187    make -j
188    
189    cd ..
190    mkdir run
191    cd run
192    \rm *
193    \cp ../../tutorial_held_suarez_cs/input/grid* .
194    \cp ../input/* .
195    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
196    mpirun -np 2 ../build/mitgcmuv
197    
198    
199    ##########################################################################
200    ##########################################################################
201    # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
202    # starting with pickup file from end of 1992
203    # requires input files in sudirectories run_template and ncep_rgau
204    
205    cd MITgcm/verification/global_ocean.cs32x15/code
206    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
207    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
208    \cp packages.conf_hr packages.conf
209    
210    cd ../build
211    \rm *
212    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
213    make depend
214    make -j
215    
216    cd ..
217    mkdir run
218    cd run
219    \rm *
220    \cp ../input/* .
221    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
222    qsub job_altix92_54t
223    
224    
225    ##########################################################################
226    ##########################################################################
227    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
228    # uses s1500t_17x51 configuration
229    
230    cd MITgcm/verification/global_ocean.cs32x15/code
231    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
232    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
233    \cp SIZE.h_150 SIZE.h
234    \cp packages.conf_hr packages.conf
235    
236    cd ../build
237    \rm *
238    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
239    make depend
240    make -j
241    
242    cd ..
243    mkdir run
244    cd run
245    \rm *
246    \cp ../input/* .
247    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
248    ln -sf ../../../../run_template/* .
249    \rm pickup*
250    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
251    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
252    \cp ../build/mitgcmuv mitgcmuv150
253    qsub job_altix150
254    
255    
256    ##########################################################################
257    ##########################################################################
258    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
259    # uses s1500t_17x51 configuration
260    # example for running on c17-c20 using arrayd
261    
262    cd MITgcm/verification/global_ocean.cs32x15/code
263    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
264    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
265    \cp SIZE.h_375 SIZE.h
266    \cp packages.conf_hr packages.conf
267    
268    cd ../build
269    \rm *
270    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
271    make depend
272    make -j
273    
274    cd ..
275    mkdir run
276    cd run
277    \rm *
278    \cp ../input/* .
279    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
280    ln -sf ../../../../run_template/* .
281    \rm pickup*
282    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
283    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
284    \cp ../build/mitgcmuv .
285    job_c20_375cpu < /dev/null >&! output.run &
286    
287    
288    ##########################################################################
289    ##########################################################################
290    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
291    # uses s1500t_17x51 configuration
292    # example for running on c17-c20 using arrayd
293    
294    cd MITgcm/verification/global_ocean.cs32x15/code
295    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
296    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
297    \cp SIZE.h_375 SIZE.h
298    \cp packages.conf_hr packages.conf
299    
300    cd ../build
301    \rm *
302    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
303    make depend
304    make -j
305    
306    cd ..
307    mkdir run
308    cd run
309    \rm *
310    \cp ../input/* .
311    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
312    ln -sf ../../../../run_template/* .
313    \rm pickup*
314    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
315    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
316    \cp ../build/mitgcmuv .
317    job_c20_375cpu < /dev/null >&! output.run &
318    
319    
320    ##########################################################################
321    ##########################################################################
322    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
323    # uses s1500t_17x51 configuration
324    # example for running on c17-c20 using arrayd
325    
326    cd MITgcm/verification/global_ocean.cs32x15/code
327    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
328    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
329    \cp SIZE.h_500 SIZE.h
330    \cp packages.conf_hr packages.conf
331    
332    cd ../build
333    \rm *
334    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
335    make depend
336    make -j
337    
338    cd ..
339    mkdir run
340    cd run
341    \rm *
342    \cp ../input/* .
343    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
344    ln -sf ../../../../run_template/* .
345    \rm pickup*
346    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
347    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
348    \cp ../build/mitgcmuv .
349    job_c19_500cpu < /dev/null >&! output.run &
350    
351    
352    ##########################################################################
353    ##########################################################################
354    # 510*510*6*50, 216-cpu cube sphere on cosmos
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_216 SIZE.h
360    \cp packages.conf_hr packages.conf
361    
362    module unload latest_intel80
363    module unload mpich-gm-intel80
364    module load latest_intel81
365    module load mpich-gm-intel81
366    
367    cd ../build
368    \rm *
369    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
370    make depend
371    make -j
372    
373    cd ..
374    mkdir run
375    cd run
376    \rm *
377    \cp ../input/* .
378    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
379    ln -sf ../../../../run_template/* .
380    \rm pickup*
381    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
382    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
383    \cp ../build/mitgcmuv .
384    bsub < job_cosmos
385    
386    
387    ##########################################################################
388    ##########################################################################
389    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
390    # requires input files in sudirectories run_template and ncep_rgau
391    # presently residing under orion:/tmp1/dmenem/cube
392    
393    cd MITgcm/verification/global_ocean.cs32x15/code
394    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
395    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
396    \cp SIZE.h_54 SIZE.h
397    \cp packages.conf_hr packages.conf
398    
399    cd ../build
400    \rm *
401    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
402    make depend
403    make -j
404    
405    cd ..
406    mkdir run
407    cd run
408    \rm *
409    \cp ../input/* .
410    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
411    qsub job_orion
412    
413    
414    ##########################################################################
415    ##########################################################################
416    # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
417    # requires input files in sudirectories run_template and ncep_rgau
418    # presently residing under orion:/tmp1/dmenem/cube
419    
420    cd MITgcm/verification/global_ocean.cs32x15/code
421    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
422    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
423    \cp SIZE.h_41 SIZE.h
424    \cp packages.conf_hr packages.conf
425    
426    cd ../build
427    \rm *
428    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
429    make depend
430    make -j
431    
432    cd ..
433    mkdir run
434    cd run
435    \rm *
436    \cp ../input/* .
437    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
438    qsub job_orion41
439    
440    
441    ##########################################################################
442    ##########################################################################
443    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
444    # requires input files in sudirectories run_template and ncep_rgau
445    # presently residing under orion:/tmp1/dmenem/cube
446    
447    cd MITgcm/verification/global_ocean.cs32x15/code
448    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
449    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
450    \cp SIZE.h_50 SIZE.h
451    \cp packages.conf_hr packages.conf
452    
453    cd ../build
454    \rm *
455    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
456    make depend
457    make -j
458    
459    cd ..
460    mkdir run
461    cd run
462    \rm *
463    \cp ../input/* .
464    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
465    qsub job_orion
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