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revision 1.6 by dimitri, Sat Dec 6 22:04:19 2003 UTC revision 1.81 by dimitri, Tue Dec 12 04:20:42 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: December 6, 2003.  
2    
3  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  =================
4  cvs login ( CVS password: cvsanon )  UPDATES
5    
6    December 11, 2006: preparing for cube47, same as cube43
7    but with Arctic monthly river runoff climatology
8    
9    December 5, 2006: 216-CPU code for cube46
10    Changed diagnostics to accomodate JMCs latest and some
11    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
12    to speed up code.
13    
14    November 7, 2006: 216-CPU code for cube43
15    Bug fixes in growth.F routine and new set of diagnostics
16    
17    October 15, 2006: 216-CPU code for cube40
18    
19    September 28, 2006: 216-CPU code for cube38
20    
21    September 4, 2006
22    Modified 32*32*6*15 experiments to use grid_cs32.* files from
23     verification/tutorial_held_suarez_cs/input instead of
24     tile* files from verification/global_ocean.cs32x15/input
25    
26    August 8, 2006: 216-CPU code and input used for cube37
27    using "June 10, 2006" MITgcm code.
28    
29    for online T/S profile diagnostics all that is needed is
30      profiles_init_fixed
31      profiles_inloop
32    see pkg/ecco/ecco_cost_init_fixed.F
33        pkg/ecco/cost_averagesfields.F
34    
35    ##########################################################################
36    ##########################################################################
37    # Get forcing files, etc.
38    # Example below is for cube46 on /nobackup2a/menemenl
39    
40    cd /nobackup2a/menemenl
41    mkdir cube46
42    cd cube46
43    ln -sf ../run_template .
44    ln -sf ../ncep_rgau .
45    
46    
47    ##########################################################################
48    ##########################################################################
49    # getting the code from anonymous CVS server
50    
51      bash or sh shell:
52        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
53        $ cvs login
54          ( enter the CVS password: "cvsanon" )
55    
56      tcsh or csh shell:
57        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
58        $ cvs login
59          ( enter the CVS password: "cvsanon" )
60    
61  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
62  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  
63  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
64  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
65    cvs co MITgcm_code
66    cvs co MITgcm/verification/global_ocean.cs32x15
67    cvs co MITgcm/verification/tutorial_held_suarez_cs/input
68    
69  cvs co -r checkpoint52d_pre MITgcm_code  
70  cvs co -r checkpoint52d_pre MITgcm/verification/global_ocean.cs32x15  ##########################################################################
71    ##########################################################################
72    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
73    
74  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
75  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
76  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
77  \rm mdsio_readfield.F  \cp SIZE.h_216 SIZE.h
78    \cp packages.conf_hr packages.conf
79    
80    cd ../build
81    \rm *
82    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
83    make depend
84    make -j
85    
86  cd ..  cd ..
87  mkdir build  mkdir run
88  cd build  cd run
89  ../code/genmake2 -mods=../code  \rm *
90    \cp ../input/* .
91    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
92    ln -sf ../../../../run_template/* .
93    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
94    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
95    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
96    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38 pickup_seaice.0000000216
97    \cp ../build/mitgcmuv .
98    qsub job_altix
99    
100    
101    ##########################################################################
102    ##########################################################################
103    # 32*32*6*15, 1-cpu cube sphere
104    
105    cd MITgcm/verification/global_ocean.cs32x15/code
106    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
107    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
108    cd ../build
109    \rm *
110    ../../../tools/genmake2 -mods=../code
111  make depend  make depend
112  make  make
   
113  cd ..  cd ..
114  mkdir run  mkdir run
115  cd run  cd run
116  cp ../inp_thsice/* .  \rm *
117  cp ../input/* .  \cp ../../tutorial_held_suarez_cs/input/grid* .
118  cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  \cp ../input/* .
119  cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
120  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
121    
122  comparison output is in:  comparison output is in:
123  ../../../../MITgcm_contrib/high_res_cube/results/output.txt  ../../../../MITgcm_contrib/high_res_cube/results/output.txt
124    
   
125  to use matlab to look at the output  to use matlab to look at the output
126  matlab  matlab
127  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  
128      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
129             'surForcT','oceTAUX','oceTAUY','surForcS'}
130        tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
131      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
132  end  end
133    
134    heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
135    mask=0*heff; mask(find(heff>.001))=1;
136    uice=mask.*permute(readbin(['SIuice.0000000072.data'],[32,6,32]),[1 3 2]);
137    vice=mask.*permute(readbin(['SIvice.0000000072.data'],[32,6,32]),[1 3 2]);
138    clf
139    subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
140    subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
141    subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
142    subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
143    
144    
145    ##########################################################################
146    ##########################################################################
147    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
148    
149    cd MITgcm/verification/global_ocean.cs32x15/code
150    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
151    \cp ../code_alt/code.176t_8x4/* .
152    cd ../build
153    \rm *
154    ../../../tools/genmake2 -mods=../code
155    make depend
156    make
157    cd ..
158    mkdir run
159    cd run
160    \rm *
161    \cp ../../tutorial_held_suarez_cs/input/grid* .
162    \cp ../input/* .
163    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
164    ../build/mitgcmuv >& output.txt
165    
166    
167    ##########################################################################
168    ##########################################################################
169    # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
170    
171    cd MITgcm/verification/global_ocean.cs32x15/code
172    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
173    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
174    \cp SIZE.h_mpi SIZE.h
175    
176    cd ../build
177    \rm *
178    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
179    make depend
180    make -j
181    
182    cd ..
183    mkdir run
184    cd run
185    \rm *
186    \cp ../../tutorial_held_suarez_cs/input/grid* .
187    \cp ../input/* .
188    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
189    mpirun -np 2 ../build/mitgcmuv
190    
191    
192    ##########################################################################
193    ##########################################################################
194    # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
195    # starting with pickup file from end of 1992
196    # requires input files in sudirectories run_template and ncep_rgau
197    
198    cd MITgcm/verification/global_ocean.cs32x15/code
199    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
200    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
201    \cp packages.conf_hr packages.conf
202    
203    cd ../build
204    \rm *
205    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
206    make depend
207    make -j
208    
209    cd ..
210    mkdir run
211    cd run
212    \rm *
213    \cp ../input/* .
214    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
215    qsub job_altix92_54t
216    
217    
218    ##########################################################################
219    ##########################################################################
220    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
221    # uses s1500t_17x51 configuration
222    
223    cd MITgcm/verification/global_ocean.cs32x15/code
224    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
225    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
226    \cp SIZE.h_150 SIZE.h
227    \cp packages.conf_hr packages.conf
228    
229    cd ../build
230    \rm *
231    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
232    make depend
233    make -j
234    
235    cd ..
236    mkdir run
237    cd run
238    \rm *
239    \cp ../input/* .
240    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
241    ln -sf ../../../../run_template/* .
242    \rm pickup*
243    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
244    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
245    \cp ../build/mitgcmuv mitgcmuv150
246    qsub job_altix150
247    
248    
249    ##########################################################################
250    ##########################################################################
251    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
252    # uses s1500t_17x51 configuration
253    # example for running on c17-c20 using arrayd
254    
255    cd MITgcm/verification/global_ocean.cs32x15/code
256    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
257    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
258    \cp SIZE.h_375 SIZE.h
259    \cp packages.conf_hr packages.conf
260    
261    cd ../build
262    \rm *
263    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
264    make depend
265    make -j
266    
267    cd ..
268    mkdir run
269    cd run
270    \rm *
271    \cp ../input/* .
272    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
273    ln -sf ../../../../run_template/* .
274    \rm pickup*
275    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
276    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
277    \cp ../build/mitgcmuv .
278    job_c20_375cpu < /dev/null >&! output.run &
279    
280    
281    ##########################################################################
282    ##########################################################################
283    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
284    # uses s1500t_17x51 configuration
285    # example for running on c17-c20 using arrayd
286    
287    cd MITgcm/verification/global_ocean.cs32x15/code
288    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
289    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
290    \cp SIZE.h_375 SIZE.h
291    \cp packages.conf_hr packages.conf
292    
293    cd ../build
294    \rm *
295    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
296    make depend
297    make -j
298    
299    cd ..
300    mkdir run
301    cd run
302    \rm *
303    \cp ../input/* .
304    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
305    ln -sf ../../../../run_template/* .
306    \rm pickup*
307    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
308    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
309    \cp ../build/mitgcmuv .
310    job_c20_375cpu < /dev/null >&! output.run &
311    
312    
313    ##########################################################################
314    ##########################################################################
315    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
316    # uses s1500t_17x51 configuration
317    # example for running on c17-c20 using arrayd
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/s1500t_17x51/* .
322    \cp SIZE.h_500 SIZE.h
323    \cp packages.conf_hr packages.conf
324    
325    cd ../build
326    \rm *
327    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
328    make depend
329    make -j
330    
331    cd ..
332    mkdir run
333    cd run
334    \rm *
335    \cp ../input/* .
336    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
337    ln -sf ../../../../run_template/* .
338    \rm pickup*
339    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
340    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
341    \cp ../build/mitgcmuv .
342    job_c19_500cpu < /dev/null >&! output.run &
343    
344    
345    ##########################################################################
346    ##########################################################################
347    # 510*510*6*50, 216-cpu cube sphere on cosmos
348    
349    cd MITgcm/verification/global_ocean.cs32x15/code
350    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
351    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
352    \cp SIZE.h_216 SIZE.h
353    \cp packages.conf_hr packages.conf
354    
355    module unload latest_intel80
356    module unload mpich-gm-intel80
357    module load latest_intel81
358    module load mpich-gm-intel81
359    
360    cd ../build
361    \rm *
362    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
363    make depend
364    make -j
365    
366    cd ..
367    mkdir run
368    cd run
369    \rm *
370    \cp ../input/* .
371    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
372    ln -sf ../../../../run_template/* .
373    \rm pickup*
374    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
375    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
376    \cp ../build/mitgcmuv .
377    bsub < job_cosmos
378    
379    
380    ##########################################################################
381    ##########################################################################
382    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
383    # requires input files in sudirectories run_template and ncep_rgau
384    # presently residing under orion:/tmp1/dmenem/cube
385    
386    cd MITgcm/verification/global_ocean.cs32x15/code
387    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
388    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
389    \cp SIZE.h_54 SIZE.h
390    \cp packages.conf_hr packages.conf
391    
392    cd ../build
393    \rm *
394    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
395    make depend
396    make -j
397    
398    cd ..
399    mkdir run
400    cd run
401    \rm *
402    \cp ../input/* .
403    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
404    qsub job_orion
405    
406    
407    ##########################################################################
408    ##########################################################################
409    # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
410    # requires input files in sudirectories run_template and ncep_rgau
411    # presently residing under orion:/tmp1/dmenem/cube
412    
413    cd MITgcm/verification/global_ocean.cs32x15/code
414    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
415    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
416    \cp SIZE.h_41 SIZE.h
417    \cp packages.conf_hr packages.conf
418    
419    cd ../build
420    \rm *
421    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
422    make depend
423    make -j
424    
425    cd ..
426    mkdir run
427    cd run
428    \rm *
429    \cp ../input/* .
430    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
431    qsub job_orion41
432    
433    
434    ##########################################################################
435    ##########################################################################
436    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
437    # requires input files in sudirectories run_template and ncep_rgau
438    # presently residing under orion:/tmp1/dmenem/cube
439    
440    cd MITgcm/verification/global_ocean.cs32x15/code
441    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
442    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
443    \cp SIZE.h_50 SIZE.h
444    \cp packages.conf_hr packages.conf
445    
446    cd ../build
447    \rm *
448    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
449    make depend
450    make -j
451    
452    cd ..
453    mkdir run
454    cd run
455    \rm *
456    \cp ../input/* .
457    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
458    qsub job_orion
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