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revision 1.3 by dimitri, Mon Nov 24 01:04:28 2003 UTC revision 1.88 by dimitri, Wed Jan 31 01:57:41 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    January 5, 2006: cube51, like cube50 but with bottomDragQuadratic = 0.0012
12    
13    January 5, 2006: cube50, like cube48 but with snow advection
14    
15    December 30, 2006: updates for cube49, the first
16    "blend" integration.
17    
18    December 11, 2006: preparing for cube47, same as cube43
19    but with Arctic monthly river runoff climatology.
20    
21    December 5, 2006: 216-CPU code for cube46
22    Changed diagnostics to accomodate JMCs latest and some
23    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
24    to speed up code.
25    
26    November 7, 2006: 216-CPU code for cube43
27    Bug fixes in growth.F routine and new set of diagnostics
28    
29    October 15, 2006: 216-CPU code for cube40
30    
31    September 28, 2006: 216-CPU code for cube38
32    
33    September 4, 2006
34    Modified 32*32*6*15 experiments to use grid_cs32.* files from
35     verification/tutorial_held_suarez_cs/input instead of
36     tile* files from verification/global_ocean.cs32x15/input
37    
38    August 8, 2006: 216-CPU code and input used for cube37
39    using "June 10, 2006" MITgcm code.
40    
41    for online T/S profile diagnostics all that is needed is
42      profiles_init_fixed
43      profiles_inloop
44    see pkg/ecco/ecco_cost_init_fixed.F
45        pkg/ecco/cost_averagesfields.F
46    
47    ##########################################################################
48    ##########################################################################
49    # Get forcing files, etc.
50    # Example below is for cube46 on /nobackup2a/menemenl
51    
52    cd /nobackup2a/menemenl
53    mkdir cube47
54    cd cube47
55    ln -sf ../run_template .
56    ln -sf ../ncep_rgau .
57    
58    
59    ##########################################################################
60    ##########################################################################
61    # getting the code from anonymous CVS server
62    
63      bash or sh shell:
64        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
65        $ cvs login
66          ( enter the CVS password: "cvsanon" )
67    
68      tcsh or csh shell:
69        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
70        $ cvs login
71          ( enter the CVS password: "cvsanon" )
72    
73  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
74  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  
75  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
76  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
77    cvs co MITgcm_code
78    cvs co MITgcm/verification/global_ocean.cs32x15
79    cvs co MITgcm/verification/tutorial_held_suarez_cs/input
80    
81    
82  cvs co -r checkpoint52a_post MITgcm_code  ##########################################################################
83  cvs co -r checkpoint52a_post MITgcm/verification/global_ocean.cs32x15  ##########################################################################
84    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
85    
86  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
87  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
88  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
89  \rm mdsio_readfield.F  \cp SIZE.h_216 SIZE.h
90    \cp packages.conf_hr packages.conf
91    
92    cd ../build
93    \rm *
94    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
95    make depend
96    make -j
97    
98  cd ..  cd ..
99  mkdir build  mkdir run
100  cd build  cd run
101  ../code/genmake2 -mods=../code  \rm *
102    \cp ../input/* .
103    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
104    ln -sf ../../../../run_template/* .
105    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
106    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
107    ln -sf ../../../../run_template/pickup.0000000216.cube49 pickup.0000000216
108    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube48 pickup_seaice.0000000216
109    \cp ../build/mitgcmuv .
110    qsub job_altix
111    
112    
113    ##########################################################################
114    ##########################################################################
115    # 32*32*6*15, 1-cpu cube sphere
116    
117    cd MITgcm/verification/global_ocean.cs32x15/code
118    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
119    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
120    \rm CPP_EEOPTIONS.h
121    cd ../build
122    \rm *
123    ../../../tools/genmake2 -mods=../code
124  make depend  make depend
125  make  make
   
126  cd ..  cd ..
127  mkdir run  mkdir run
128  cd run  cd run
129  cp ../input/* .  \rm *
130  cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  \cp ../../tutorial_held_suarez_cs/input/grid* .
131  cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../input/* .
132    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
133  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
134    
135  comparison output is in:  comparison output is in:
136  ../../../../MITgcm_contrib/high_res_cube/results/output.txt  ../../../../MITgcm_contrib/high_res_cube/results/output.txt
137    
   
138  to use matlab to look at the output  to use matlab to look at the output
139  matlab  matlab
140  eta=permute(readbin('Eta.0000072020.data',[32,6,32]),[1 3 2]);  
141  cx=[-1 1]; clf  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
142  subplot(3,4, 9);imagesc(flipud(eta(:,:,1)'));caxis(cx);colorbar           'surForcT','oceTAUX','oceTAUY','surForcS'}
143  subplot(3,4,10);imagesc(flipud(eta(:,:,2)'));caxis(cx);colorbar      tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
144  subplot(3,4, 6);imagesc(flipud(eta(:,:,3)'));caxis(cx);colorbar      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
145  subplot(3,4, 7);imagesc(flipud(eta(:,:,4)'));caxis(cx);colorbar  end
146  subplot(3,4, 3);imagesc(flipud(eta(:,:,5)'));caxis(cx);colorbar  
147  subplot(3,4, 4);imagesc(flipud(eta(:,:,6)'));caxis(cx);colorbar  heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
148    mask=0*heff; mask(find(heff>.001))=1;
149    uice=mask.*permute(readbin(['SIuice.0000000072.data'],[32,6,32]),[1 3 2]);
150    vice=mask.*permute(readbin(['SIvice.0000000072.data'],[32,6,32]),[1 3 2]);
151    clf
152    subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
153    subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
154    subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
155    subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
156    
157    
158    ##########################################################################
159    ##########################################################################
160    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
161    
162    cd MITgcm/verification/global_ocean.cs32x15/code
163    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
164    \cp ../code_alt/code.176t_8x4/* .
165    cd ../build
166    \rm *
167    ../../../tools/genmake2 -mods=../code
168    make depend
169    make
170    cd ..
171    mkdir run
172    cd run
173    \rm *
174    \cp ../../tutorial_held_suarez_cs/input/grid* .
175    \cp ../input/* .
176    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
177    ../build/mitgcmuv >& output.txt
178    
179    
180    ##########################################################################
181    ##########################################################################
182    # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
183    
184    cd MITgcm/verification/global_ocean.cs32x15/code
185    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
186    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
187    \cp SIZE.h_mpi SIZE.h
188    
189    cd ../build
190    \rm *
191    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
192    make depend
193    make -j
194    
195    cd ..
196    mkdir run
197    cd run
198    \rm *
199    \cp ../../tutorial_held_suarez_cs/input/grid* .
200    \cp ../input/* .
201    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
202    mpirun -np 2 ../build/mitgcmuv
203    
204    
205    ##########################################################################
206    ##########################################################################
207    # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
208    # starting with pickup file from end of 1992
209    # requires input files in sudirectories run_template and ncep_rgau
210    
211    cd MITgcm/verification/global_ocean.cs32x15/code
212    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
213    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
214    \cp packages.conf_hr packages.conf
215    
216    cd ../build
217    \rm *
218    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
219    make depend
220    make -j
221    
222    cd ..
223    mkdir run
224    cd run
225    \rm *
226    \cp ../input/* .
227    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
228    qsub job_altix92_54t
229    
230    
231    ##########################################################################
232    ##########################################################################
233    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
234    # uses s1500t_17x51 configuration
235    
236    cd MITgcm/verification/global_ocean.cs32x15/code
237    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
238    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
239    \cp SIZE.h_150 SIZE.h
240    \cp packages.conf_hr packages.conf
241    
242    cd ../build
243    \rm *
244    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
245    make depend
246    make -j
247    
248    cd ..
249    mkdir run
250    cd run
251    \rm *
252    \cp ../input/* .
253    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
254    ln -sf ../../../../run_template/* .
255    \rm pickup*
256    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
257    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
258    \cp ../build/mitgcmuv mitgcmuv150
259    qsub job_altix150
260    
261    
262    ##########################################################################
263    ##########################################################################
264    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
265    # uses s1500t_17x51 configuration
266    # example for running on c17-c20 using arrayd
267    
268    cd MITgcm/verification/global_ocean.cs32x15/code
269    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
270    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
271    \cp SIZE.h_375 SIZE.h
272    \cp packages.conf_hr packages.conf
273    
274    cd ../build
275    \rm *
276    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
277    make depend
278    make -j
279    
280    cd ..
281    mkdir run
282    cd run
283    \rm *
284    \cp ../input/* .
285    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
286    ln -sf ../../../../run_template/* .
287    \rm pickup*
288    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
289    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
290    \cp ../build/mitgcmuv .
291    job_c20_375cpu < /dev/null >&! output.run &
292    
293    
294    ##########################################################################
295    ##########################################################################
296    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
297    # uses s1500t_17x51 configuration
298    # example for running on c17-c20 using arrayd
299    
300    cd MITgcm/verification/global_ocean.cs32x15/code
301    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
302    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
303    \cp SIZE.h_375 SIZE.h
304    \cp packages.conf_hr packages.conf
305    
306    cd ../build
307    \rm *
308    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
309    make depend
310    make -j
311    
312    cd ..
313    mkdir run
314    cd run
315    \rm *
316    \cp ../input/* .
317    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
318    ln -sf ../../../../run_template/* .
319    \rm pickup*
320    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
321    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
322    \cp ../build/mitgcmuv .
323    job_c20_375cpu < /dev/null >&! output.run &
324    
325    
326    ##########################################################################
327    ##########################################################################
328    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
329    # uses s1500t_17x51 configuration
330    # example for running on c17-c20 using arrayd
331    
332    cd MITgcm/verification/global_ocean.cs32x15/code
333    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
334    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
335    \cp SIZE.h_500 SIZE.h
336    \cp packages.conf_hr packages.conf
337    
338    cd ../build
339    \rm *
340    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
341    make depend
342    make -j
343    
344    cd ..
345    mkdir run
346    cd run
347    \rm *
348    \cp ../input/* .
349    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
350    ln -sf ../../../../run_template/* .
351    \rm pickup*
352    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
353    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
354    \cp ../build/mitgcmuv .
355    job_c19_500cpu < /dev/null >&! output.run &
356    
357    
358    ##########################################################################
359    ##########################################################################
360    # 510*510*6*50, 216-cpu cube sphere on cosmos
361    
362    cd MITgcm/verification/global_ocean.cs32x15/code
363    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
364    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
365    \cp SIZE.h_216 SIZE.h
366    \cp packages.conf_hr packages.conf
367    
368    module unload latest_intel80
369    module unload mpich-gm-intel80
370    module load latest_intel81
371    module load mpich-gm-intel81
372    
373    cd ../build
374    \rm *
375    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
376    make depend
377    make -j
378    
379    cd ..
380    mkdir run
381    cd run
382    \rm *
383    \cp ../input/* .
384    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
385    ln -sf ../../../../run_template/* .
386    \rm pickup*
387    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
388    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
389    \cp ../build/mitgcmuv .
390    bsub < job_cosmos
391    
392    
393    ##########################################################################
394    ##########################################################################
395    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
396    # requires input files in sudirectories run_template and ncep_rgau
397    # presently residing under orion:/tmp1/dmenem/cube
398    
399    cd MITgcm/verification/global_ocean.cs32x15/code
400    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
401    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
402    \cp SIZE.h_54 SIZE.h
403    \cp packages.conf_hr packages.conf
404    
405    cd ../build
406    \rm *
407    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
408    make depend
409    make -j
410    
411    cd ..
412    mkdir run
413    cd run
414    \rm *
415    \cp ../input/* .
416    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
417    qsub job_orion
418    
419    
420    ##########################################################################
421    ##########################################################################
422    # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
423    # requires input files in sudirectories run_template and ncep_rgau
424    # presently residing under orion:/tmp1/dmenem/cube
425    
426    cd MITgcm/verification/global_ocean.cs32x15/code
427    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
428    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
429    \cp SIZE.h_41 SIZE.h
430    \cp packages.conf_hr packages.conf
431    
432    cd ../build
433    \rm *
434    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
435    make depend
436    make -j
437    
438    cd ..
439    mkdir run
440    cd run
441    \rm *
442    \cp ../input/* .
443    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
444    qsub job_orion41
445    
446    
447    ##########################################################################
448    ##########################################################################
449    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
450    # requires input files in sudirectories run_template and ncep_rgau
451    # presently residing under orion:/tmp1/dmenem/cube
452    
453    cd MITgcm/verification/global_ocean.cs32x15/code
454    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
455    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
456    \cp SIZE.h_50 SIZE.h
457    \cp packages.conf_hr packages.conf
458    
459    cd ../build
460    \rm *
461    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
462    make depend
463    make -j
464    
465    cd ..
466    mkdir run
467    cd run
468    \rm *
469    \cp ../input/* .
470    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
471    qsub job_orion
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