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revision 1.3 by dimitri, Mon Nov 24 01:04:28 2003 UTC revision 1.87 by dimitri, Sat Jan 6 07:09:50 2007 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: November 21, 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    January 5, 2006: cube51, like cube50 but with bottomDragQuadratic = 0.0012
11    
12    January 5, 2006: cube50, like cube48 but with snow advection
13    
14    December 30, 2006: updates for cube49, the first
15    "blend" integration.
16    
17    December 11, 2006: preparing for cube47, same as cube43
18    but with Arctic monthly river runoff climatology.
19    
20    December 5, 2006: 216-CPU code for cube46
21    Changed diagnostics to accomodate JMCs latest and some
22    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
23    to speed up code.
24    
25    November 7, 2006: 216-CPU code for cube43
26    Bug fixes in growth.F routine and new set of diagnostics
27    
28    October 15, 2006: 216-CPU code for cube40
29    
30    September 28, 2006: 216-CPU code for cube38
31    
32    September 4, 2006
33    Modified 32*32*6*15 experiments to use grid_cs32.* files from
34     verification/tutorial_held_suarez_cs/input instead of
35     tile* files from verification/global_ocean.cs32x15/input
36    
37    August 8, 2006: 216-CPU code and input used for cube37
38    using "June 10, 2006" MITgcm code.
39    
40    for online T/S profile diagnostics all that is needed is
41      profiles_init_fixed
42      profiles_inloop
43    see pkg/ecco/ecco_cost_init_fixed.F
44        pkg/ecco/cost_averagesfields.F
45    
46    ##########################################################################
47    ##########################################################################
48    # Get forcing files, etc.
49    # Example below is for cube46 on /nobackup2a/menemenl
50    
51    cd /nobackup2a/menemenl
52    mkdir cube47
53    cd cube47
54    ln -sf ../run_template .
55    ln -sf ../ncep_rgau .
56    
57    
58    ##########################################################################
59    ##########################################################################
60    # getting the code from anonymous CVS server
61    
62      bash or sh shell:
63        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
64        $ cvs login
65          ( enter the CVS password: "cvsanon" )
66    
67      tcsh or csh shell:
68        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
69        $ cvs login
70          ( enter the CVS password: "cvsanon" )
71    
72  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
73  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  
74  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
75  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
76    cvs co MITgcm_code
77    cvs co MITgcm/verification/global_ocean.cs32x15
78    cvs co MITgcm/verification/tutorial_held_suarez_cs/input
79    
80  cvs co -r checkpoint52a_post MITgcm_code  
81  cvs co -r checkpoint52a_post MITgcm/verification/global_ocean.cs32x15  ##########################################################################
82    ##########################################################################
83    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
84    
85  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
86  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
87  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
88  \rm mdsio_readfield.F  \cp SIZE.h_216 SIZE.h
89    \cp packages.conf_hr packages.conf
90    
91    cd ../build
92    \rm *
93    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
94    make depend
95    make -j
96    
97  cd ..  cd ..
98  mkdir build  mkdir run
99  cd build  cd run
100  ../code/genmake2 -mods=../code  \rm *
101    \cp ../input/* .
102    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
103    ln -sf ../../../../run_template/* .
104    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
105    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
106    ln -sf ../../../../run_template/pickup.0000000216.cube49 pickup.0000000216
107    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube48 pickup_seaice.0000000216
108    \cp ../build/mitgcmuv .
109    qsub job_altix
110    
111    
112    ##########################################################################
113    ##########################################################################
114    # 32*32*6*15, 1-cpu cube sphere
115    
116    cd MITgcm/verification/global_ocean.cs32x15/code
117    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
118    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
119    cd ../build
120    \rm *
121    ../../../tools/genmake2 -mods=../code
122  make depend  make depend
123  make  make
   
124  cd ..  cd ..
125  mkdir run  mkdir run
126  cd run  cd run
127  cp ../input/* .  \rm *
128  cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  \cp ../../tutorial_held_suarez_cs/input/grid* .
129  cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../input/* .
130    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
131  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
132    
133  comparison output is in:  comparison output is in:
134  ../../../../MITgcm_contrib/high_res_cube/results/output.txt  ../../../../MITgcm_contrib/high_res_cube/results/output.txt
135    
   
136  to use matlab to look at the output  to use matlab to look at the output
137  matlab  matlab
138  eta=permute(readbin('Eta.0000072020.data',[32,6,32]),[1 3 2]);  
139  cx=[-1 1]; clf  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
140  subplot(3,4, 9);imagesc(flipud(eta(:,:,1)'));caxis(cx);colorbar           'surForcT','oceTAUX','oceTAUY','surForcS'}
141  subplot(3,4,10);imagesc(flipud(eta(:,:,2)'));caxis(cx);colorbar      tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
142  subplot(3,4, 6);imagesc(flipud(eta(:,:,3)'));caxis(cx);colorbar      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
143  subplot(3,4, 7);imagesc(flipud(eta(:,:,4)'));caxis(cx);colorbar  end
144  subplot(3,4, 3);imagesc(flipud(eta(:,:,5)'));caxis(cx);colorbar  
145  subplot(3,4, 4);imagesc(flipud(eta(:,:,6)'));caxis(cx);colorbar  heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
146    mask=0*heff; mask(find(heff>.001))=1;
147    uice=mask.*permute(readbin(['SIuice.0000000072.data'],[32,6,32]),[1 3 2]);
148    vice=mask.*permute(readbin(['SIvice.0000000072.data'],[32,6,32]),[1 3 2]);
149    clf
150    subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
151    subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
152    subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
153    subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
154    
155    
156    ##########################################################################
157    ##########################################################################
158    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
159    
160    cd MITgcm/verification/global_ocean.cs32x15/code
161    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
162    \cp ../code_alt/code.176t_8x4/* .
163    cd ../build
164    \rm *
165    ../../../tools/genmake2 -mods=../code
166    make depend
167    make
168    cd ..
169    mkdir run
170    cd run
171    \rm *
172    \cp ../../tutorial_held_suarez_cs/input/grid* .
173    \cp ../input/* .
174    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
175    ../build/mitgcmuv >& output.txt
176    
177    
178    ##########################################################################
179    ##########################################################################
180    # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
181    
182    cd MITgcm/verification/global_ocean.cs32x15/code
183    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
184    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
185    \cp SIZE.h_mpi SIZE.h
186    
187    cd ../build
188    \rm *
189    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
190    make depend
191    make -j
192    
193    cd ..
194    mkdir run
195    cd run
196    \rm *
197    \cp ../../tutorial_held_suarez_cs/input/grid* .
198    \cp ../input/* .
199    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
200    mpirun -np 2 ../build/mitgcmuv
201    
202    
203    ##########################################################################
204    ##########################################################################
205    # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
206    # starting with pickup file from end of 1992
207    # requires input files in sudirectories run_template and ncep_rgau
208    
209    cd MITgcm/verification/global_ocean.cs32x15/code
210    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
211    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
212    \cp packages.conf_hr packages.conf
213    
214    cd ../build
215    \rm *
216    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
217    make depend
218    make -j
219    
220    cd ..
221    mkdir run
222    cd run
223    \rm *
224    \cp ../input/* .
225    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
226    qsub job_altix92_54t
227    
228    
229    ##########################################################################
230    ##########################################################################
231    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
232    # uses s1500t_17x51 configuration
233    
234    cd MITgcm/verification/global_ocean.cs32x15/code
235    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
236    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
237    \cp SIZE.h_150 SIZE.h
238    \cp packages.conf_hr packages.conf
239    
240    cd ../build
241    \rm *
242    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
243    make depend
244    make -j
245    
246    cd ..
247    mkdir run
248    cd run
249    \rm *
250    \cp ../input/* .
251    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
252    ln -sf ../../../../run_template/* .
253    \rm pickup*
254    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
255    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
256    \cp ../build/mitgcmuv mitgcmuv150
257    qsub job_altix150
258    
259    
260    ##########################################################################
261    ##########################################################################
262    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
263    # uses s1500t_17x51 configuration
264    # example for running on c17-c20 using arrayd
265    
266    cd MITgcm/verification/global_ocean.cs32x15/code
267    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
268    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
269    \cp SIZE.h_375 SIZE.h
270    \cp packages.conf_hr packages.conf
271    
272    cd ../build
273    \rm *
274    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
275    make depend
276    make -j
277    
278    cd ..
279    mkdir run
280    cd run
281    \rm *
282    \cp ../input/* .
283    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
284    ln -sf ../../../../run_template/* .
285    \rm pickup*
286    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
287    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
288    \cp ../build/mitgcmuv .
289    job_c20_375cpu < /dev/null >&! output.run &
290    
291    
292    ##########################################################################
293    ##########################################################################
294    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
295    # uses s1500t_17x51 configuration
296    # example for running on c17-c20 using arrayd
297    
298    cd MITgcm/verification/global_ocean.cs32x15/code
299    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
300    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
301    \cp SIZE.h_375 SIZE.h
302    \cp packages.conf_hr packages.conf
303    
304    cd ../build
305    \rm *
306    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
307    make depend
308    make -j
309    
310    cd ..
311    mkdir run
312    cd run
313    \rm *
314    \cp ../input/* .
315    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
316    ln -sf ../../../../run_template/* .
317    \rm pickup*
318    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
319    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
320    \cp ../build/mitgcmuv .
321    job_c20_375cpu < /dev/null >&! output.run &
322    
323    
324    ##########################################################################
325    ##########################################################################
326    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
327    # uses s1500t_17x51 configuration
328    # example for running on c17-c20 using arrayd
329    
330    cd MITgcm/verification/global_ocean.cs32x15/code
331    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
332    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
333    \cp SIZE.h_500 SIZE.h
334    \cp packages.conf_hr packages.conf
335    
336    cd ../build
337    \rm *
338    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
339    make depend
340    make -j
341    
342    cd ..
343    mkdir run
344    cd run
345    \rm *
346    \cp ../input/* .
347    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
348    ln -sf ../../../../run_template/* .
349    \rm pickup*
350    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
351    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
352    \cp ../build/mitgcmuv .
353    job_c19_500cpu < /dev/null >&! output.run &
354    
355    
356    ##########################################################################
357    ##########################################################################
358    # 510*510*6*50, 216-cpu cube sphere on cosmos
359    
360    cd MITgcm/verification/global_ocean.cs32x15/code
361    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
362    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
363    \cp SIZE.h_216 SIZE.h
364    \cp packages.conf_hr packages.conf
365    
366    module unload latest_intel80
367    module unload mpich-gm-intel80
368    module load latest_intel81
369    module load mpich-gm-intel81
370    
371    cd ../build
372    \rm *
373    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
374    make depend
375    make -j
376    
377    cd ..
378    mkdir run
379    cd run
380    \rm *
381    \cp ../input/* .
382    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
383    ln -sf ../../../../run_template/* .
384    \rm pickup*
385    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
386    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
387    \cp ../build/mitgcmuv .
388    bsub < job_cosmos
389    
390    
391    ##########################################################################
392    ##########################################################################
393    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
394    # requires input files in sudirectories run_template and ncep_rgau
395    # presently residing under orion:/tmp1/dmenem/cube
396    
397    cd MITgcm/verification/global_ocean.cs32x15/code
398    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
399    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
400    \cp SIZE.h_54 SIZE.h
401    \cp packages.conf_hr packages.conf
402    
403    cd ../build
404    \rm *
405    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
406    make depend
407    make -j
408    
409    cd ..
410    mkdir run
411    cd run
412    \rm *
413    \cp ../input/* .
414    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
415    qsub job_orion
416    
417    
418    ##########################################################################
419    ##########################################################################
420    # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
421    # requires input files in sudirectories run_template and ncep_rgau
422    # presently residing under orion:/tmp1/dmenem/cube
423    
424    cd MITgcm/verification/global_ocean.cs32x15/code
425    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
426    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
427    \cp SIZE.h_41 SIZE.h
428    \cp packages.conf_hr packages.conf
429    
430    cd ../build
431    \rm *
432    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
433    make depend
434    make -j
435    
436    cd ..
437    mkdir run
438    cd run
439    \rm *
440    \cp ../input/* .
441    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
442    qsub job_orion41
443    
444    
445    ##########################################################################
446    ##########################################################################
447    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
448    # requires input files in sudirectories run_template and ncep_rgau
449    # presently residing under orion:/tmp1/dmenem/cube
450    
451    cd MITgcm/verification/global_ocean.cs32x15/code
452    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
453    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
454    \cp SIZE.h_50 SIZE.h
455    \cp packages.conf_hr packages.conf
456    
457    cd ../build
458    \rm *
459    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
460    make depend
461    make -j
462    
463    cd ..
464    mkdir run
465    cd run
466    \rm *
467    \cp ../input/* .
468    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
469    qsub job_orion
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