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revision 1.4 by dimitri, Mon Nov 24 06:32:44 2003 UTC revision 1.91 by dimitri, Sat Apr 7 21:52:43 2007 UTC
# Line 1  Line 1 
1    !!!! Instructions in this file are obsolete and will eventually
2    !!!! be removed.  This file has been replaced by
3    !!!! MITgcm_contrib/high_res_cube/README.cs510
4    !!!! MITgcm_contrib/high_res_cube/README.cs32
5    
6    =================
7    
8  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.  
9    
10  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  Forcing fields and other input files needed for the CS510
11  cvs login ( CVS password: cvsanon )  configuration can be obtained from
12    http://ecco2.org/products/model_setups/cs510.html
13    
14    =================
15    
16    UPDATES
17    
18    February 6, 2006: cube56, same as cube 50 with SEAICEuseFlooding
19    
20    February 1, 2006: back to cube50 default (bottomDragQuadratic = 0.002)
21                      removed UVEL and VVEL from diagnostics
22    
23    January 5, 2006: cube51, like cube50 but with bottomDragQuadratic = 0.0012
24    
25    January 5, 2006: cube50, like cube48 but with snow advection
26    
27    December 30, 2006: updates for cube49, the first
28    "blend" integration.
29    
30    December 11, 2006: preparing for cube47, same as cube43
31    but with Arctic monthly river runoff climatology.
32    
33    December 5, 2006: 216-CPU code for cube46
34    Changed diagnostics to accomodate JMCs latest and some
35    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
36    to speed up code.
37    
38    November 7, 2006: 216-CPU code for cube43
39    Bug fixes in growth.F routine and new set of diagnostics
40    
41    October 15, 2006: 216-CPU code for cube40
42    
43    September 28, 2006: 216-CPU code for cube38
44    
45    September 4, 2006
46    Modified 32*32*6*15 experiments to use grid_cs32.* files from
47     verification/tutorial_held_suarez_cs/input instead of
48     tile* files from verification/global_ocean.cs32x15/input
49    
50    August 8, 2006: 216-CPU code and input used for cube37
51    using "June 10, 2006" MITgcm code.
52    
53    for online T/S profile diagnostics all that is needed is
54      profiles_init_fixed
55      profiles_inloop
56    see pkg/ecco/ecco_cost_init_fixed.F
57        pkg/ecco/cost_averagesfields.F
58    
59    ##########################################################################
60    ##########################################################################
61    # Get forcing files, etc.
62    # Example below is for cube46 on /nobackup2a/menemenl
63    
64    cd /nobackup2a/menemenl
65    mkdir cube47
66    cd cube47
67    ln -sf ../run_template .
68    ln -sf ../ncep_rgau .
69    
70    
71    ##########################################################################
72    ##########################################################################
73    # getting the code from anonymous CVS server
74    
75      bash or sh shell:
76        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
77        $ cvs login
78          ( enter the CVS password: "cvsanon" )
79    
80      tcsh or csh shell:
81        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
82        $ cvs login
83          ( enter the CVS password: "cvsanon" )
84    
85  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
86  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  
87  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
88  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
89    cvs co MITgcm_code
90    cvs co MITgcm/verification/global_ocean.cs32x15
91    cvs co MITgcm/verification/tutorial_held_suarez_cs/input
92    
93    
94  cvs co -r checkpoint52b_post MITgcm_code  ##########################################################################
95  cvs co -r checkpoint52b_post MITgcm/verification/global_ocean.cs32x15  ##########################################################################
96    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
97    
98  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
99  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
100  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
101  \rm mdsio_readfield.F  \cp SIZE.h_216 SIZE.h
102    \cp packages.conf_hr packages.conf
103    
104    cd ../build
105    \rm *
106    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
107    make depend
108    make -j
109    
110  cd ..  cd ..
111  mkdir build  mkdir run
112  cd build  cd run
113  ../code/genmake2 -mods=../code  \rm *
114    \cp ../input/* .
115    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
116    ln -sf ../../../../run_template/* .
117    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
118    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
119    ln -sf ../../../../run_template/pickup.0000000216.cube49 pickup.0000000216
120    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube48 pickup_seaice.0000000216
121    \cp ../build/mitgcmuv .
122    qsub job_altix
123    
124    
125    ##########################################################################
126    ##########################################################################
127    # 32*32*6*15, 1-cpu cube sphere
128    
129    cd MITgcm/verification/global_ocean.cs32x15/code
130    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
131    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
132    \rm CPP_EEOPTIONS.h
133    cd ../build
134    \rm *
135    ../../../tools/genmake2 -mods=../code
136  make depend  make depend
137  make  make
   
138  cd ..  cd ..
139  mkdir run  mkdir run
140  cd run  cd run
141  cp ../inp_thsice/* .  \rm *
142  cp ../input/* .  \cp ../../tutorial_held_suarez_cs/input/grid* .
143  cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  \cp ../input/* .
144  cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
145  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
146    
147  comparison output is in:  comparison output is in:
148  ../../../../MITgcm_contrib/high_res_cube/results/output.txt  ../../../../MITgcm_contrib/high_res_cube/results/output.txt
149    
   
150  to use matlab to look at the output  to use matlab to look at the output
151  matlab  matlab
152  % for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  
153  for fld={'Eta','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
154      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);           'surForcT','oceTAUX','oceTAUY','surForcS'}
155        tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
156      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
157  end  end
158    
159    heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
160    mask=0*heff; mask(find(heff>.001))=1;
161    uice=mask.*permute(readbin(['SIuice.0000000072.data'],[32,6,32]),[1 3 2]);
162    vice=mask.*permute(readbin(['SIvice.0000000072.data'],[32,6,32]),[1 3 2]);
163    clf
164    subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
165    subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
166    subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
167    subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
168    
169    
170    ##########################################################################
171    ##########################################################################
172    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
173    
174    cd MITgcm/verification/global_ocean.cs32x15/code
175    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
176    \cp ../code_alt/code.176t_8x4/* .
177    cd ../build
178    \rm *
179    ../../../tools/genmake2 -mods=../code
180    make depend
181    make
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    ../build/mitgcmuv >& output.txt
190    
191    
192    ##########################################################################
193    ##########################################################################
194    # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
195    
196    cd MITgcm/verification/global_ocean.cs32x15/code
197    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
198    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
199    \cp SIZE.h_mpi SIZE.h
200    
201    cd ../build
202    \rm *
203    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
204    make depend
205    make -j
206    
207    cd ..
208    mkdir run
209    cd run
210    \rm *
211    \cp ../../tutorial_held_suarez_cs/input/grid* .
212    \cp ../input/* .
213    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
214    mpirun -np 2 ../build/mitgcmuv
215    
216    
217    ##########################################################################
218    ##########################################################################
219    # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
220    # starting with pickup file from end of 1992
221    # requires input files in sudirectories run_template and ncep_rgau
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/s54t_170x170/* .
226    \cp packages.conf_hr packages.conf
227    
228    cd ../build
229    \rm *
230    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
231    make depend
232    make -j
233    
234    cd ..
235    mkdir run
236    cd run
237    \rm *
238    \cp ../input/* .
239    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
240    qsub job_altix92_54t
241    
242    
243    ##########################################################################
244    ##########################################################################
245    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
246    # uses s1500t_17x51 configuration
247    
248    cd MITgcm/verification/global_ocean.cs32x15/code
249    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
250    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
251    \cp SIZE.h_150 SIZE.h
252    \cp packages.conf_hr packages.conf
253    
254    cd ../build
255    \rm *
256    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
257    make depend
258    make -j
259    
260    cd ..
261    mkdir run
262    cd run
263    \rm *
264    \cp ../input/* .
265    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
266    ln -sf ../../../../run_template/* .
267    \rm pickup*
268    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
269    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
270    \cp ../build/mitgcmuv mitgcmuv150
271    qsub job_altix150
272    
273    
274    ##########################################################################
275    ##########################################################################
276    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
277    # uses s1500t_17x51 configuration
278    # example for running on c17-c20 using arrayd
279    
280    cd MITgcm/verification/global_ocean.cs32x15/code
281    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
282    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
283    \cp SIZE.h_375 SIZE.h
284    \cp packages.conf_hr packages.conf
285    
286    cd ../build
287    \rm *
288    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
289    make depend
290    make -j
291    
292    cd ..
293    mkdir run
294    cd run
295    \rm *
296    \cp ../input/* .
297    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
298    ln -sf ../../../../run_template/* .
299    \rm pickup*
300    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
301    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
302    \cp ../build/mitgcmuv .
303    job_c20_375cpu < /dev/null >&! output.run &
304    
305    
306    ##########################################################################
307    ##########################################################################
308    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
309    # uses s1500t_17x51 configuration
310    # example for running on c17-c20 using arrayd
311    
312    cd MITgcm/verification/global_ocean.cs32x15/code
313    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
314    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
315    \cp SIZE.h_375 SIZE.h
316    \cp packages.conf_hr packages.conf
317    
318    cd ../build
319    \rm *
320    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
321    make depend
322    make -j
323    
324    cd ..
325    mkdir run
326    cd run
327    \rm *
328    \cp ../input/* .
329    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
330    ln -sf ../../../../run_template/* .
331    \rm pickup*
332    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
333    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
334    \cp ../build/mitgcmuv .
335    job_c20_375cpu < /dev/null >&! output.run &
336    
337    
338    ##########################################################################
339    ##########################################################################
340    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
341    # uses s1500t_17x51 configuration
342    # example for running on c17-c20 using arrayd
343    
344    cd MITgcm/verification/global_ocean.cs32x15/code
345    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
346    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
347    \cp SIZE.h_500 SIZE.h
348    \cp packages.conf_hr packages.conf
349    
350    cd ../build
351    \rm *
352    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
353    make depend
354    make -j
355    
356    cd ..
357    mkdir run
358    cd run
359    \rm *
360    \cp ../input/* .
361    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
362    ln -sf ../../../../run_template/* .
363    \rm pickup*
364    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
365    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
366    \cp ../build/mitgcmuv .
367    job_c19_500cpu < /dev/null >&! output.run &
368    
369    
370    ##########################################################################
371    ##########################################################################
372    # 510*510*6*50, 216-cpu cube sphere on cosmos
373    
374    cd MITgcm/verification/global_ocean.cs32x15/code
375    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
376    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
377    \cp SIZE.h_216 SIZE.h
378    \cp packages.conf_hr packages.conf
379    
380    module unload latest_intel80
381    module unload mpich-gm-intel80
382    module load latest_intel81
383    module load mpich-gm-intel81
384    
385    cd ../build
386    \rm *
387    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
388    make depend
389    make -j
390    
391    cd ..
392    mkdir run
393    cd run
394    \rm *
395    \cp ../input/* .
396    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
397    ln -sf ../../../../run_template/* .
398    \rm pickup*
399    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
400    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
401    \cp ../build/mitgcmuv .
402    bsub < job_cosmos
403    
404    
405    ##########################################################################
406    ##########################################################################
407    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
408    # requires input files in sudirectories run_template and ncep_rgau
409    # presently residing under orion:/tmp1/dmenem/cube
410    
411    cd MITgcm/verification/global_ocean.cs32x15/code
412    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
413    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
414    \cp SIZE.h_54 SIZE.h
415    \cp packages.conf_hr packages.conf
416    
417    cd ../build
418    \rm *
419    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
420    make depend
421    make -j
422    
423    cd ..
424    mkdir run
425    cd run
426    \rm *
427    \cp ../input/* .
428    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
429    qsub job_orion
430    
431    
432    ##########################################################################
433    ##########################################################################
434    # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
435    # requires input files in sudirectories run_template and ncep_rgau
436    # presently residing under orion:/tmp1/dmenem/cube
437    
438    cd MITgcm/verification/global_ocean.cs32x15/code
439    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
440    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
441    \cp SIZE.h_41 SIZE.h
442    \cp packages.conf_hr packages.conf
443    
444    cd ../build
445    \rm *
446    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
447    make depend
448    make -j
449    
450    cd ..
451    mkdir run
452    cd run
453    \rm *
454    \cp ../input/* .
455    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
456    qsub job_orion41
457    
458    
459    ##########################################################################
460    ##########################################################################
461    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
462    # requires input files in sudirectories run_template and ncep_rgau
463    # presently residing under orion:/tmp1/dmenem/cube
464    
465    cd MITgcm/verification/global_ocean.cs32x15/code
466    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
467    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
468    \cp SIZE.h_50 SIZE.h
469    \cp packages.conf_hr packages.conf
470    
471    cd ../build
472    \rm *
473    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
474    make depend
475    make -j
476    
477    cd ..
478    mkdir run
479    cd run
480    \rm *
481    \cp ../input/* .
482    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
483    qsub job_orion
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