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revision 1.1 by dimitri, Sun Nov 23 17:16:24 2003 UTC revision 1.90 by dimitri, Wed Feb 7 01:30:48 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  cvs co MITgcm_contrib/high_res_cube/code-mods  http://ecco2.org/products/model_setups/cs510.html
7  cvs co MITgcm_contrib/high_res_cube/matlab-grid-converter  
8    =================
9    UPDATES
10    
11    February 6, 2006: cube56, same as cube 50 with SEAICEuseFlooding
12    
13    February 1, 2006: back to cube50 default (bottomDragQuadratic = 0.002)
14                      removed UVEL and VVEL from diagnostics
15    
16    January 5, 2006: cube51, like cube50 but with bottomDragQuadratic = 0.0012
17    
18    January 5, 2006: cube50, like cube48 but with snow advection
19    
20    December 30, 2006: updates for cube49, the first
21    "blend" integration.
22    
23    December 11, 2006: preparing for cube47, same as cube43
24    but with Arctic monthly river runoff climatology.
25    
26    December 5, 2006: 216-CPU code for cube46
27    Changed diagnostics to accomodate JMCs latest and some
28    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
29    to speed up code.
30    
31    November 7, 2006: 216-CPU code for cube43
32    Bug fixes in growth.F routine and new set of diagnostics
33    
34    October 15, 2006: 216-CPU code for cube40
35    
36    September 28, 2006: 216-CPU code for cube38
37    
38    September 4, 2006
39    Modified 32*32*6*15 experiments to use grid_cs32.* files from
40     verification/tutorial_held_suarez_cs/input instead of
41     tile* files from verification/global_ocean.cs32x15/input
42    
43    August 8, 2006: 216-CPU code and input used for cube37
44    using "June 10, 2006" MITgcm code.
45    
46    for online T/S profile diagnostics all that is needed is
47      profiles_init_fixed
48      profiles_inloop
49    see pkg/ecco/ecco_cost_init_fixed.F
50        pkg/ecco/cost_averagesfields.F
51    
52    ##########################################################################
53    ##########################################################################
54    # Get forcing files, etc.
55    # Example below is for cube46 on /nobackup2a/menemenl
56    
57    cd /nobackup2a/menemenl
58    mkdir cube47
59    cd cube47
60    ln -sf ../run_template .
61    ln -sf ../ncep_rgau .
62    
63    
64    ##########################################################################
65    ##########################################################################
66    # getting the code from anonymous CVS server
67    
68      bash or sh shell:
69        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
70        $ cvs login
71          ( enter the CVS password: "cvsanon" )
72    
73      tcsh or csh shell:
74        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
75        $ cvs login
76          ( enter the CVS password: "cvsanon" )
77    
78  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
79  cvs co -r checkpoint52a_post MITgcm_code  cvs co MITgcm_contrib/high_res_cube/code-mods
80    cvs co MITgcm_contrib/high_res_cube/input
81    cvs co MITgcm_contrib/high_res_cube/results
82    cvs co MITgcm_code
83  cvs co MITgcm/verification/global_ocean.cs32x15  cvs co MITgcm/verification/global_ocean.cs32x15
84    cvs co MITgcm/verification/tutorial_held_suarez_cs/input
85    
86    
87    ##########################################################################
88    ##########################################################################
89    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
90    
91    cd MITgcm/verification/global_ocean.cs32x15/code
92    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
93    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
94    \cp SIZE.h_216 SIZE.h
95    \cp packages.conf_hr packages.conf
96    
97    cd ../build
98    \rm *
99    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
100    make depend
101    make -j
102    
103    cd ..
104    mkdir run
105    cd run
106    \rm *
107    \cp ../input/* .
108    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
109    ln -sf ../../../../run_template/* .
110    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
111    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
112    ln -sf ../../../../run_template/pickup.0000000216.cube49 pickup.0000000216
113    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube48 pickup_seaice.0000000216
114    \cp ../build/mitgcmuv .
115    qsub job_altix
116    
117    
118    ##########################################################################
119    ##########################################################################
120    # 32*32*6*15, 1-cpu cube sphere
121    
122    cd MITgcm/verification/global_ocean.cs32x15/code
123    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
124    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
125    \rm CPP_EEOPTIONS.h
126    cd ../build
127    \rm *
128    ../../../tools/genmake2 -mods=../code
129    make depend
130    make
131    cd ..
132    mkdir run
133    cd run
134    \rm *
135    \cp ../../tutorial_held_suarez_cs/input/grid* .
136    \cp ../input/* .
137    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
138    ../build/mitgcmuv >& output.txt
139    
140    comparison output is in:
141    ../../../../MITgcm_contrib/high_res_cube/results/output.txt
142    
143    to use matlab to look at the output
144    matlab
145    
146    for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
147             'surForcT','oceTAUX','oceTAUY','surForcS'}
148        tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
149        cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
150    end
151    
152    heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
153    mask=0*heff; mask(find(heff>.001))=1;
154    uice=mask.*permute(readbin(['SIuice.0000000072.data'],[32,6,32]),[1 3 2]);
155    vice=mask.*permute(readbin(['SIvice.0000000072.data'],[32,6,32]),[1 3 2]);
156    clf
157    subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
158    subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
159    subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
160    subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
161    
162    
163    ##########################################################################
164    ##########################################################################
165    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
166    
167  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
168  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
169  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../code_alt/code.176t_8x4/* .
 \rm mdsio_readfield.F  
170  cd ../build  cd ../build
171    \rm *
172  ../../../tools/genmake2 -mods=../code  ../../../tools/genmake2 -mods=../code
173  make depend  make depend
174  make  make
175  cd ..  cd ..
176  mkdir run  mkdir run
177  cd run  cd run
178  cp ../input/* .  \rm *
179  cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  \cp ../../tutorial_held_suarez_cs/input/grid* .
180  cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../input/* .
181  ../build/mitgcmuv >& output  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
182    ../build/mitgcmuv >& output.txt
183    
184    
185    ##########################################################################
186    ##########################################################################
187    # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
188    
189    cd MITgcm/verification/global_ocean.cs32x15/code
190    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
191    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
192    \cp SIZE.h_mpi SIZE.h
193    
194    cd ../build
195    \rm *
196    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
197    make depend
198    make -j
199    
200    cd ..
201    mkdir run
202    cd run
203    \rm *
204    \cp ../../tutorial_held_suarez_cs/input/grid* .
205    \cp ../input/* .
206    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
207    mpirun -np 2 ../build/mitgcmuv
208    
209    
210    ##########################################################################
211    ##########################################################################
212    # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
213    # starting with pickup file from end of 1992
214    # requires input files in sudirectories run_template and ncep_rgau
215    
216    cd MITgcm/verification/global_ocean.cs32x15/code
217    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
218    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
219    \cp packages.conf_hr packages.conf
220    
221    cd ../build
222    \rm *
223    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
224    make depend
225    make -j
226    
227    cd ..
228    mkdir run
229    cd run
230    \rm *
231    \cp ../input/* .
232    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
233    qsub job_altix92_54t
234    
235    
236    ##########################################################################
237    ##########################################################################
238    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
239    # uses s1500t_17x51 configuration
240    
241    cd MITgcm/verification/global_ocean.cs32x15/code
242    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
243    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
244    \cp SIZE.h_150 SIZE.h
245    \cp packages.conf_hr packages.conf
246    
247    cd ../build
248    \rm *
249    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
250    make depend
251    make -j
252    
253    cd ..
254    mkdir run
255    cd run
256    \rm *
257    \cp ../input/* .
258    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
259    ln -sf ../../../../run_template/* .
260    \rm pickup*
261    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
262    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
263    \cp ../build/mitgcmuv mitgcmuv150
264    qsub job_altix150
265    
266    
267    ##########################################################################
268    ##########################################################################
269    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
270    # uses s1500t_17x51 configuration
271    # example for running on c17-c20 using arrayd
272    
273    cd MITgcm/verification/global_ocean.cs32x15/code
274    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
275    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
276    \cp SIZE.h_375 SIZE.h
277    \cp packages.conf_hr packages.conf
278    
279    cd ../build
280    \rm *
281    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
282    make depend
283    make -j
284    
285    cd ..
286    mkdir run
287    cd run
288    \rm *
289    \cp ../input/* .
290    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
291    ln -sf ../../../../run_template/* .
292    \rm pickup*
293    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
294    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
295    \cp ../build/mitgcmuv .
296    job_c20_375cpu < /dev/null >&! output.run &
297    
298    
299    ##########################################################################
300    ##########################################################################
301    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
302    # uses s1500t_17x51 configuration
303    # example for running on c17-c20 using arrayd
304    
305    cd MITgcm/verification/global_ocean.cs32x15/code
306    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
307    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
308    \cp SIZE.h_375 SIZE.h
309    \cp packages.conf_hr packages.conf
310    
311    cd ../build
312    \rm *
313    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
314    make depend
315    make -j
316    
317    cd ..
318    mkdir run
319    cd run
320    \rm *
321    \cp ../input/* .
322    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
323    ln -sf ../../../../run_template/* .
324    \rm pickup*
325    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
326    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
327    \cp ../build/mitgcmuv .
328    job_c20_375cpu < /dev/null >&! output.run &
329    
330    
331    ##########################################################################
332    ##########################################################################
333    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
334    # uses s1500t_17x51 configuration
335    # example for running on c17-c20 using arrayd
336    
337    cd MITgcm/verification/global_ocean.cs32x15/code
338    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
339    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
340    \cp SIZE.h_500 SIZE.h
341    \cp packages.conf_hr packages.conf
342    
343    cd ../build
344    \rm *
345    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
346    make depend
347    make -j
348    
349    cd ..
350    mkdir run
351    cd run
352    \rm *
353    \cp ../input/* .
354    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
355    ln -sf ../../../../run_template/* .
356    \rm pickup*
357    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
358    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
359    \cp ../build/mitgcmuv .
360    job_c19_500cpu < /dev/null >&! output.run &
361    
362    
363    ##########################################################################
364    ##########################################################################
365    # 510*510*6*50, 216-cpu cube sphere on cosmos
366    
367    cd MITgcm/verification/global_ocean.cs32x15/code
368    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
369    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
370    \cp SIZE.h_216 SIZE.h
371    \cp packages.conf_hr packages.conf
372    
373    module unload latest_intel80
374    module unload mpich-gm-intel80
375    module load latest_intel81
376    module load mpich-gm-intel81
377    
378    cd ../build
379    \rm *
380    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
381    make depend
382    make -j
383    
384    cd ..
385    mkdir run
386    cd run
387    \rm *
388    \cp ../input/* .
389    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
390    ln -sf ../../../../run_template/* .
391    \rm pickup*
392    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
393    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
394    \cp ../build/mitgcmuv .
395    bsub < job_cosmos
396    
397    
398    ##########################################################################
399    ##########################################################################
400    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
401    # requires input files in sudirectories run_template and ncep_rgau
402    # presently residing under orion:/tmp1/dmenem/cube
403    
404    cd MITgcm/verification/global_ocean.cs32x15/code
405    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
406    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
407    \cp SIZE.h_54 SIZE.h
408    \cp packages.conf_hr packages.conf
409    
410    cd ../build
411    \rm *
412    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
413    make depend
414    make -j
415    
416    cd ..
417    mkdir run
418    cd run
419    \rm *
420    \cp ../input/* .
421    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
422    qsub job_orion
423    
424    
425    ##########################################################################
426    ##########################################################################
427    # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
428    # requires input files in sudirectories run_template and ncep_rgau
429    # presently residing under orion:/tmp1/dmenem/cube
430    
431    cd MITgcm/verification/global_ocean.cs32x15/code
432    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
433    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
434    \cp SIZE.h_41 SIZE.h
435    \cp packages.conf_hr packages.conf
436    
437    cd ../build
438    \rm *
439    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
440    make depend
441    make -j
442    
443    cd ..
444    mkdir run
445    cd run
446    \rm *
447    \cp ../input/* .
448    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
449    qsub job_orion41
450    
451    
452    ##########################################################################
453    ##########################################################################
454    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
455    # requires input files in sudirectories run_template and ncep_rgau
456    # presently residing under orion:/tmp1/dmenem/cube
457    
458    cd MITgcm/verification/global_ocean.cs32x15/code
459    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
460    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
461    \cp SIZE.h_50 SIZE.h
462    \cp packages.conf_hr packages.conf
463    
464    cd ../build
465    \rm *
466    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
467    make depend
468    make -j
469    
470    cd ..
471    mkdir run
472    cd run
473    \rm *
474    \cp ../input/* .
475    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
476    qsub job_orion
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