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revision 1.4 by dimitri, Mon Nov 24 06:32:44 2003 UTC revision 1.89 by dimitri, Fri Feb 2 01:05:25 2007 UTC
# Line 1  Line 1 
1    
2  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.  
3    
4  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  Forcing fields and other input files needed for the CS510
5  cvs login ( CVS password: cvsanon )  configuration can be obtained from
6    http://ecco2.org/products/model_setups/cs510.html
7    
8    =================
9    UPDATES
10    
11    February 1, 2006: back to cube50 default (bottomDragQuadratic = 0.0012)
12                      removed UVEL and VVEL from diagnostics
13    
14    January 5, 2006: cube51, like cube50 but with bottomDragQuadratic = 0.0012
15    
16    January 5, 2006: cube50, like cube48 but with snow advection
17    
18    December 30, 2006: updates for cube49, the first
19    "blend" integration.
20    
21    December 11, 2006: preparing for cube47, same as cube43
22    but with Arctic monthly river runoff climatology.
23    
24    December 5, 2006: 216-CPU code for cube46
25    Changed diagnostics to accomodate JMCs latest and some
26    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
27    to speed up code.
28    
29    November 7, 2006: 216-CPU code for cube43
30    Bug fixes in growth.F routine and new set of diagnostics
31    
32    October 15, 2006: 216-CPU code for cube40
33    
34    September 28, 2006: 216-CPU code for cube38
35    
36    September 4, 2006
37    Modified 32*32*6*15 experiments to use grid_cs32.* files from
38     verification/tutorial_held_suarez_cs/input instead of
39     tile* files from verification/global_ocean.cs32x15/input
40    
41    August 8, 2006: 216-CPU code and input used for cube37
42    using "June 10, 2006" MITgcm code.
43    
44    for online T/S profile diagnostics all that is needed is
45      profiles_init_fixed
46      profiles_inloop
47    see pkg/ecco/ecco_cost_init_fixed.F
48        pkg/ecco/cost_averagesfields.F
49    
50    ##########################################################################
51    ##########################################################################
52    # Get forcing files, etc.
53    # Example below is for cube46 on /nobackup2a/menemenl
54    
55    cd /nobackup2a/menemenl
56    mkdir cube47
57    cd cube47
58    ln -sf ../run_template .
59    ln -sf ../ncep_rgau .
60    
61    
62    ##########################################################################
63    ##########################################################################
64    # getting the code from anonymous CVS server
65    
66      bash or sh shell:
67        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
68        $ cvs login
69          ( enter the CVS password: "cvsanon" )
70    
71      tcsh or csh shell:
72        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
73        $ cvs login
74          ( enter the CVS password: "cvsanon" )
75    
76  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
77  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  
78  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
79  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
80    cvs co MITgcm_code
81    cvs co MITgcm/verification/global_ocean.cs32x15
82    cvs co MITgcm/verification/tutorial_held_suarez_cs/input
83    
84    
85  cvs co -r checkpoint52b_post MITgcm_code  ##########################################################################
86  cvs co -r checkpoint52b_post MITgcm/verification/global_ocean.cs32x15  ##########################################################################
87    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
88    
89  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
90  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
91  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
92  \rm mdsio_readfield.F  \cp SIZE.h_216 SIZE.h
93    \cp packages.conf_hr packages.conf
94    
95    cd ../build
96    \rm *
97    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
98    make depend
99    make -j
100    
101  cd ..  cd ..
102  mkdir build  mkdir run
103  cd build  cd run
104  ../code/genmake2 -mods=../code  \rm *
105    \cp ../input/* .
106    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
107    ln -sf ../../../../run_template/* .
108    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
109    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
110    ln -sf ../../../../run_template/pickup.0000000216.cube49 pickup.0000000216
111    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube48 pickup_seaice.0000000216
112    \cp ../build/mitgcmuv .
113    qsub job_altix
114    
115    
116    ##########################################################################
117    ##########################################################################
118    # 32*32*6*15, 1-cpu cube sphere
119    
120    cd MITgcm/verification/global_ocean.cs32x15/code
121    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
122    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
123    \rm CPP_EEOPTIONS.h
124    cd ../build
125    \rm *
126    ../../../tools/genmake2 -mods=../code
127  make depend  make depend
128  make  make
   
129  cd ..  cd ..
130  mkdir run  mkdir run
131  cd run  cd run
132  cp ../inp_thsice/* .  \rm *
133  cp ../input/* .  \cp ../../tutorial_held_suarez_cs/input/grid* .
134  cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  \cp ../input/* .
135  cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
136  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
137    
138  comparison output is in:  comparison output is in:
139  ../../../../MITgcm_contrib/high_res_cube/results/output.txt  ../../../../MITgcm_contrib/high_res_cube/results/output.txt
140    
   
141  to use matlab to look at the output  to use matlab to look at the output
142  matlab  matlab
143  % for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  
144  for fld={'Eta','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
145      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);           'surForcT','oceTAUX','oceTAUY','surForcS'}
146        tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
147      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
148  end  end
149    
150    heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
151    mask=0*heff; mask(find(heff>.001))=1;
152    uice=mask.*permute(readbin(['SIuice.0000000072.data'],[32,6,32]),[1 3 2]);
153    vice=mask.*permute(readbin(['SIvice.0000000072.data'],[32,6,32]),[1 3 2]);
154    clf
155    subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
156    subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
157    subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
158    subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
159    
160    
161    ##########################################################################
162    ##########################################################################
163    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
164    
165    cd MITgcm/verification/global_ocean.cs32x15/code
166    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
167    \cp ../code_alt/code.176t_8x4/* .
168    cd ../build
169    \rm *
170    ../../../tools/genmake2 -mods=../code
171    make depend
172    make
173    cd ..
174    mkdir run
175    cd run
176    \rm *
177    \cp ../../tutorial_held_suarez_cs/input/grid* .
178    \cp ../input/* .
179    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
180    ../build/mitgcmuv >& output.txt
181    
182    
183    ##########################################################################
184    ##########################################################################
185    # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
186    
187    cd MITgcm/verification/global_ocean.cs32x15/code
188    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
189    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
190    \cp SIZE.h_mpi SIZE.h
191    
192    cd ../build
193    \rm *
194    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
195    make depend
196    make -j
197    
198    cd ..
199    mkdir run
200    cd run
201    \rm *
202    \cp ../../tutorial_held_suarez_cs/input/grid* .
203    \cp ../input/* .
204    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
205    mpirun -np 2 ../build/mitgcmuv
206    
207    
208    ##########################################################################
209    ##########################################################################
210    # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
211    # starting with pickup file from end of 1992
212    # requires input files in sudirectories run_template and ncep_rgau
213    
214    cd MITgcm/verification/global_ocean.cs32x15/code
215    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
216    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
217    \cp packages.conf_hr packages.conf
218    
219    cd ../build
220    \rm *
221    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
222    make depend
223    make -j
224    
225    cd ..
226    mkdir run
227    cd run
228    \rm *
229    \cp ../input/* .
230    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
231    qsub job_altix92_54t
232    
233    
234    ##########################################################################
235    ##########################################################################
236    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
237    # uses s1500t_17x51 configuration
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_150 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 mitgcmuv150
262    qsub job_altix150
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, 375-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_375 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_c20_375cpu < /dev/null >&! output.run &
327    
328    
329    ##########################################################################
330    ##########################################################################
331    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
332    # uses s1500t_17x51 configuration
333    # example for running on c17-c20 using arrayd
334    
335    cd MITgcm/verification/global_ocean.cs32x15/code
336    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
337    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
338    \cp SIZE.h_500 SIZE.h
339    \cp packages.conf_hr packages.conf
340    
341    cd ../build
342    \rm *
343    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
344    make depend
345    make -j
346    
347    cd ..
348    mkdir run
349    cd run
350    \rm *
351    \cp ../input/* .
352    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
353    ln -sf ../../../../run_template/* .
354    \rm pickup*
355    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
356    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
357    \cp ../build/mitgcmuv .
358    job_c19_500cpu < /dev/null >&! output.run &
359    
360    
361    ##########################################################################
362    ##########################################################################
363    # 510*510*6*50, 216-cpu cube sphere on cosmos
364    
365    cd MITgcm/verification/global_ocean.cs32x15/code
366    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
367    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
368    \cp SIZE.h_216 SIZE.h
369    \cp packages.conf_hr packages.conf
370    
371    module unload latest_intel80
372    module unload mpich-gm-intel80
373    module load latest_intel81
374    module load mpich-gm-intel81
375    
376    cd ../build
377    \rm *
378    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
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    ln -sf ../../../../run_template/* .
389    \rm pickup*
390    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
391    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
392    \cp ../build/mitgcmuv .
393    bsub < job_cosmos
394    
395    
396    ##########################################################################
397    ##########################################################################
398    # 510*510*6*50, 216-tile, 54-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/s216t_85x85/* .
405    \cp SIZE.h_54 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_orion
421    
422    
423    ##########################################################################
424    ##########################################################################
425    # 510*510*6*50, 205-tile, 41-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/s205t_85x85/* .
432    \cp SIZE.h_41 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_orion41
448    
449    
450    ##########################################################################
451    ##########################################################################
452    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
453    # requires input files in sudirectories run_template and ncep_rgau
454    # presently residing under orion:/tmp1/dmenem/cube
455    
456    cd MITgcm/verification/global_ocean.cs32x15/code
457    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
458    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
459    \cp SIZE.h_50 SIZE.h
460    \cp packages.conf_hr packages.conf
461    
462    cd ../build
463    \rm *
464    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
465    make depend
466    make -j
467    
468    cd ..
469    mkdir run
470    cd run
471    \rm *
472    \cp ../input/* .
473    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
474    qsub job_orion
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