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revision 1.3 by dimitri, Mon Nov 24 01:04:28 2003 UTC revision 1.86 by dimitri, Fri Jan 5 20:56:00 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: cube50, same as cube48 but with snow advection
11    
12    December 30, 2006: updates for cube49, the first
13    "blend" integration.
14    
15    December 11, 2006: preparing for cube47, same as cube43
16    but with Arctic monthly river runoff climatology.
17    
18    December 5, 2006: 216-CPU code for cube46
19    Changed diagnostics to accomodate JMCs latest and some
20    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
21    to speed up code.
22    
23    November 7, 2006: 216-CPU code for cube43
24    Bug fixes in growth.F routine and new set of diagnostics
25    
26    October 15, 2006: 216-CPU code for cube40
27    
28    September 28, 2006: 216-CPU code for cube38
29    
30    September 4, 2006
31    Modified 32*32*6*15 experiments to use grid_cs32.* files from
32     verification/tutorial_held_suarez_cs/input instead of
33     tile* files from verification/global_ocean.cs32x15/input
34    
35    August 8, 2006: 216-CPU code and input used for cube37
36    using "June 10, 2006" MITgcm code.
37    
38    for online T/S profile diagnostics all that is needed is
39      profiles_init_fixed
40      profiles_inloop
41    see pkg/ecco/ecco_cost_init_fixed.F
42        pkg/ecco/cost_averagesfields.F
43    
44    ##########################################################################
45    ##########################################################################
46    # Get forcing files, etc.
47    # Example below is for cube46 on /nobackup2a/menemenl
48    
49    cd /nobackup2a/menemenl
50    mkdir cube47
51    cd cube47
52    ln -sf ../run_template .
53    ln -sf ../ncep_rgau .
54    
55    
56    ##########################################################################
57    ##########################################################################
58    # getting the code from anonymous CVS server
59    
60      bash or sh shell:
61        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
62        $ cvs login
63          ( enter the CVS password: "cvsanon" )
64    
65      tcsh or csh shell:
66        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
67        $ cvs login
68          ( enter the CVS password: "cvsanon" )
69    
70  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
71  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  
72  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
73  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
74    cvs co MITgcm_code
75    cvs co MITgcm/verification/global_ocean.cs32x15
76    cvs co MITgcm/verification/tutorial_held_suarez_cs/input
77    
78    
79  cvs co -r checkpoint52a_post MITgcm_code  ##########################################################################
80  cvs co -r checkpoint52a_post MITgcm/verification/global_ocean.cs32x15  ##########################################################################
81    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
82    
83  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
84  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
85  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
86  \rm mdsio_readfield.F  \cp SIZE.h_216 SIZE.h
87    \cp packages.conf_hr packages.conf
88    
89    cd ../build
90    \rm *
91    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
92    make depend
93    make -j
94    
95  cd ..  cd ..
96  mkdir build  mkdir run
97  cd build  cd run
98  ../code/genmake2 -mods=../code  \rm *
99    \cp ../input/* .
100    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
101    ln -sf ../../../../run_template/* .
102    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
103    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
104    ln -sf ../../../../run_template/pickup.0000000216.cube49 pickup.0000000216
105    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube48 pickup_seaice.0000000216
106    \cp ../build/mitgcmuv .
107    qsub job_altix
108    
109    
110    ##########################################################################
111    ##########################################################################
112    # 32*32*6*15, 1-cpu cube sphere
113    
114    cd MITgcm/verification/global_ocean.cs32x15/code
115    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
116    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
117    cd ../build
118    \rm *
119    ../../../tools/genmake2 -mods=../code
120  make depend  make depend
121  make  make
   
122  cd ..  cd ..
123  mkdir run  mkdir run
124  cd run  cd run
125  cp ../input/* .  \rm *
126  cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  \cp ../../tutorial_held_suarez_cs/input/grid* .
127  cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../input/* .
128    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
129  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
130    
131  comparison output is in:  comparison output is in:
132  ../../../../MITgcm_contrib/high_res_cube/results/output.txt  ../../../../MITgcm_contrib/high_res_cube/results/output.txt
133    
   
134  to use matlab to look at the output  to use matlab to look at the output
135  matlab  matlab
136  eta=permute(readbin('Eta.0000072020.data',[32,6,32]),[1 3 2]);  
137  cx=[-1 1]; clf  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
138  subplot(3,4, 9);imagesc(flipud(eta(:,:,1)'));caxis(cx);colorbar           'surForcT','oceTAUX','oceTAUY','surForcS'}
139  subplot(3,4,10);imagesc(flipud(eta(:,:,2)'));caxis(cx);colorbar      tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
140  subplot(3,4, 6);imagesc(flipud(eta(:,:,3)'));caxis(cx);colorbar      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
141  subplot(3,4, 7);imagesc(flipud(eta(:,:,4)'));caxis(cx);colorbar  end
142  subplot(3,4, 3);imagesc(flipud(eta(:,:,5)'));caxis(cx);colorbar  
143  subplot(3,4, 4);imagesc(flipud(eta(:,:,6)'));caxis(cx);colorbar  heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
144    mask=0*heff; mask(find(heff>.001))=1;
145    uice=mask.*permute(readbin(['SIuice.0000000072.data'],[32,6,32]),[1 3 2]);
146    vice=mask.*permute(readbin(['SIvice.0000000072.data'],[32,6,32]),[1 3 2]);
147    clf
148    subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
149    subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
150    subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
151    subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
152    
153    
154    ##########################################################################
155    ##########################################################################
156    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
157    
158    cd MITgcm/verification/global_ocean.cs32x15/code
159    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
160    \cp ../code_alt/code.176t_8x4/* .
161    cd ../build
162    \rm *
163    ../../../tools/genmake2 -mods=../code
164    make depend
165    make
166    cd ..
167    mkdir run
168    cd run
169    \rm *
170    \cp ../../tutorial_held_suarez_cs/input/grid* .
171    \cp ../input/* .
172    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
173    ../build/mitgcmuv >& output.txt
174    
175    
176    ##########################################################################
177    ##########################################################################
178    # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
179    
180    cd MITgcm/verification/global_ocean.cs32x15/code
181    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
182    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
183    \cp SIZE.h_mpi SIZE.h
184    
185    cd ../build
186    \rm *
187    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
188    make depend
189    make -j
190    
191    cd ..
192    mkdir run
193    cd run
194    \rm *
195    \cp ../../tutorial_held_suarez_cs/input/grid* .
196    \cp ../input/* .
197    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
198    mpirun -np 2 ../build/mitgcmuv
199    
200    
201    ##########################################################################
202    ##########################################################################
203    # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
204    # starting with pickup file from end of 1992
205    # requires input files in sudirectories run_template and ncep_rgau
206    
207    cd MITgcm/verification/global_ocean.cs32x15/code
208    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
209    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
210    \cp packages.conf_hr packages.conf
211    
212    cd ../build
213    \rm *
214    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
215    make depend
216    make -j
217    
218    cd ..
219    mkdir run
220    cd run
221    \rm *
222    \cp ../input/* .
223    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
224    qsub job_altix92_54t
225    
226    
227    ##########################################################################
228    ##########################################################################
229    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
230    # uses s1500t_17x51 configuration
231    
232    cd MITgcm/verification/global_ocean.cs32x15/code
233    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
234    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
235    \cp SIZE.h_150 SIZE.h
236    \cp packages.conf_hr packages.conf
237    
238    cd ../build
239    \rm *
240    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
241    make depend
242    make -j
243    
244    cd ..
245    mkdir run
246    cd run
247    \rm *
248    \cp ../input/* .
249    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
250    ln -sf ../../../../run_template/* .
251    \rm pickup*
252    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
253    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
254    \cp ../build/mitgcmuv mitgcmuv150
255    qsub job_altix150
256    
257    
258    ##########################################################################
259    ##########################################################################
260    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
261    # uses s1500t_17x51 configuration
262    # example for running on c17-c20 using arrayd
263    
264    cd MITgcm/verification/global_ocean.cs32x15/code
265    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
266    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
267    \cp SIZE.h_375 SIZE.h
268    \cp packages.conf_hr packages.conf
269    
270    cd ../build
271    \rm *
272    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
273    make depend
274    make -j
275    
276    cd ..
277    mkdir run
278    cd run
279    \rm *
280    \cp ../input/* .
281    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
282    ln -sf ../../../../run_template/* .
283    \rm pickup*
284    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
285    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
286    \cp ../build/mitgcmuv .
287    job_c20_375cpu < /dev/null >&! output.run &
288    
289    
290    ##########################################################################
291    ##########################################################################
292    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
293    # uses s1500t_17x51 configuration
294    # example for running on c17-c20 using arrayd
295    
296    cd MITgcm/verification/global_ocean.cs32x15/code
297    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
298    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
299    \cp SIZE.h_375 SIZE.h
300    \cp packages.conf_hr packages.conf
301    
302    cd ../build
303    \rm *
304    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
305    make depend
306    make -j
307    
308    cd ..
309    mkdir run
310    cd run
311    \rm *
312    \cp ../input/* .
313    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
314    ln -sf ../../../../run_template/* .
315    \rm pickup*
316    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
317    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
318    \cp ../build/mitgcmuv .
319    job_c20_375cpu < /dev/null >&! output.run &
320    
321    
322    ##########################################################################
323    ##########################################################################
324    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
325    # uses s1500t_17x51 configuration
326    # example for running on c17-c20 using arrayd
327    
328    cd MITgcm/verification/global_ocean.cs32x15/code
329    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
330    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
331    \cp SIZE.h_500 SIZE.h
332    \cp packages.conf_hr packages.conf
333    
334    cd ../build
335    \rm *
336    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
337    make depend
338    make -j
339    
340    cd ..
341    mkdir run
342    cd run
343    \rm *
344    \cp ../input/* .
345    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
346    ln -sf ../../../../run_template/* .
347    \rm pickup*
348    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
349    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
350    \cp ../build/mitgcmuv .
351    job_c19_500cpu < /dev/null >&! output.run &
352    
353    
354    ##########################################################################
355    ##########################################################################
356    # 510*510*6*50, 216-cpu cube sphere on cosmos
357    
358    cd MITgcm/verification/global_ocean.cs32x15/code
359    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
360    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
361    \cp SIZE.h_216 SIZE.h
362    \cp packages.conf_hr packages.conf
363    
364    module unload latest_intel80
365    module unload mpich-gm-intel80
366    module load latest_intel81
367    module load mpich-gm-intel81
368    
369    cd ../build
370    \rm *
371    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
372    make depend
373    make -j
374    
375    cd ..
376    mkdir run
377    cd run
378    \rm *
379    \cp ../input/* .
380    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
381    ln -sf ../../../../run_template/* .
382    \rm pickup*
383    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
384    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
385    \cp ../build/mitgcmuv .
386    bsub < job_cosmos
387    
388    
389    ##########################################################################
390    ##########################################################################
391    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
392    # requires input files in sudirectories run_template and ncep_rgau
393    # presently residing under orion:/tmp1/dmenem/cube
394    
395    cd MITgcm/verification/global_ocean.cs32x15/code
396    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
397    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
398    \cp SIZE.h_54 SIZE.h
399    \cp packages.conf_hr packages.conf
400    
401    cd ../build
402    \rm *
403    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
404    make depend
405    make -j
406    
407    cd ..
408    mkdir run
409    cd run
410    \rm *
411    \cp ../input/* .
412    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
413    qsub job_orion
414    
415    
416    ##########################################################################
417    ##########################################################################
418    # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
419    # requires input files in sudirectories run_template and ncep_rgau
420    # presently residing under orion:/tmp1/dmenem/cube
421    
422    cd MITgcm/verification/global_ocean.cs32x15/code
423    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
424    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
425    \cp SIZE.h_41 SIZE.h
426    \cp packages.conf_hr packages.conf
427    
428    cd ../build
429    \rm *
430    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
431    make depend
432    make -j
433    
434    cd ..
435    mkdir run
436    cd run
437    \rm *
438    \cp ../input/* .
439    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
440    qsub job_orion41
441    
442    
443    ##########################################################################
444    ##########################################################################
445    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
446    # requires input files in sudirectories run_template and ncep_rgau
447    # presently residing under orion:/tmp1/dmenem/cube
448    
449    cd MITgcm/verification/global_ocean.cs32x15/code
450    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
451    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
452    \cp SIZE.h_50 SIZE.h
453    \cp packages.conf_hr packages.conf
454    
455    cd ../build
456    \rm *
457    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
458    make depend
459    make -j
460    
461    cd ..
462    mkdir run
463    cd run
464    \rm *
465    \cp ../input/* .
466    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
467    qsub job_orion
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