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revision 1.7 by dimitri, Wed Dec 10 19:40:13 2003 UTC revision 1.80 by dimitri, Wed Dec 6 01:07:44 2006 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: December 6, 2003.  
2    
3  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  =================
4  cvs login ( CVS password: cvsanon )  UPDATES
5    
6  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/README_ice  December 5, 2006: 216-CPU code for cube46
7  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/code-mods  Changed diagnostics to accomodate JMCs latest and some
8  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/matlab-grid-converter  changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
9  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/input  to speed up code.
 cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/results  
10    
11  cvs co -r checkpoint52d_pre MITgcm_code  November 7, 2006: 216-CPU code for cube43
12  cvs co -r checkpoint52d_pre MITgcm/verification/global_ocean.cs32x15  Bug fixes in growth.F routine and new set of diagnostics
13    
14    October 15, 2006: 216-CPU code for cube40
15    
16    September 28, 2006: 216-CPU code for cube38
17    
18    September 4, 2006
19    Modified 32*32*6*15 experiments to use grid_cs32.* files from
20     verification/tutorial_held_suarez_cs/input instead of
21     tile* files from verification/global_ocean.cs32x15/input
22    
23    August 8, 2006: 216-CPU code and input used for cube37
24    using "June 10, 2006" MITgcm code.
25    
26    for online T/S profile diagnostics all that is needed is
27      profiles_init_fixed
28      profiles_inloop
29    see pkg/ecco/ecco_cost_init_fixed.F
30        pkg/ecco/cost_averagesfields.F
31    
32    ##########################################################################
33    ##########################################################################
34    # Get forcing files, etc.
35    # Example below is for cube46 on /nobackup2a/menemenl
36    
37    cd /nobackup2a/menemenl
38    mkdir cube46
39    cd cube46
40    ln -sf ../run_template .
41    ln -sf ../ncep_rgau .
42    
43    
44    ##########################################################################
45    ##########################################################################
46    # getting the code from anonymous CVS server
47    
48      bash or sh shell:
49        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
50        $ cvs login
51          ( enter the CVS password: "cvsanon" )
52    
53      tcsh or csh shell:
54        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
55        $ cvs login
56          ( enter the CVS password: "cvsanon" )
57    
58    cvs co MITgcm_contrib/high_res_cube/README_ice
59    cvs co MITgcm_contrib/high_res_cube/code-mods
60    cvs co MITgcm_contrib/high_res_cube/input
61    cvs co MITgcm_contrib/high_res_cube/results
62    cvs co MITgcm_code
63    cvs co MITgcm/verification/global_ocean.cs32x15
64    cvs co MITgcm/verification/tutorial_held_suarez_cs/input
65    
66    
67    ##########################################################################
68    ##########################################################################
69    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
70    
71  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
72  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
73  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
74  \rm mdsio_readfield.F  \cp SIZE.h_216 SIZE.h
75    \cp packages.conf_hr packages.conf
76    
77    cd ../build
78    \rm *
79    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
80    make depend
81    make -j
82    
83  cd ..  cd ..
84  mkdir build  mkdir run
85  cd build  cd run
86  ../code/genmake2 -mods=../code  \rm *
87    \cp ../input/* .
88    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
89    ln -sf ../../../../run_template/* .
90    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
91    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
92    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
93    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38 pickup_seaice.0000000216
94    \cp ../build/mitgcmuv .
95    qsub job_altix
96    
97    
98    ##########################################################################
99    ##########################################################################
100    # 32*32*6*15, 1-cpu cube sphere
101    
102    cd MITgcm/verification/global_ocean.cs32x15/code
103    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
104    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
105    cd ../build
106    \rm *
107    ../../../tools/genmake2 -mods=../code
108  make depend  make depend
109  make  make
   
110  cd ..  cd ..
111  mkdir run  mkdir run
112  cd run  cd run
113  cp ../inp_thsice/* .  \rm *
114  cp ../input/* .  \cp ../../tutorial_held_suarez_cs/input/grid* .
115  cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  \cp ../input/* .
116  cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
117  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
118    
119  comparison output is in:  comparison output is in:
# Line 39  comparison output is in: Line 121  comparison output is in:
121    
122  to use matlab to look at the output  to use matlab to look at the output
123  matlab  matlab
124  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  
125      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
126             'surForcT','oceTAUX','oceTAUY','surForcS'}
127        tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
128      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
129  end  end
130    
131    heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
132    mask=0*heff; mask(find(heff>.001))=1;
133    uice=mask.*permute(readbin(['SIuice.0000000072.data'],[32,6,32]),[1 3 2]);
134    vice=mask.*permute(readbin(['SIvice.0000000072.data'],[32,6,32]),[1 3 2]);
135    clf
136    subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
137    subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
138    subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
139    subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
140    
141    
142    ##########################################################################
143    ##########################################################################
144    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
145    
146    cd MITgcm/verification/global_ocean.cs32x15/code
147    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
148    \cp ../code_alt/code.176t_8x4/* .
149    cd ../build
150    \rm *
151    ../../../tools/genmake2 -mods=../code
152    make depend
153    make
154    cd ..
155    mkdir run
156    cd run
157    \rm *
158    \cp ../../tutorial_held_suarez_cs/input/grid* .
159    \cp ../input/* .
160    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
161    ../build/mitgcmuv >& output.txt
162    
163    
164    ##########################################################################
165    ##########################################################################
166    # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
167    
168    cd MITgcm/verification/global_ocean.cs32x15/code
169    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
170    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
171    \cp SIZE.h_mpi SIZE.h
172    
173    cd ../build
174    \rm *
175    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
176    make depend
177    make -j
178    
179    cd ..
180    mkdir run
181    cd run
182    \rm *
183    \cp ../../tutorial_held_suarez_cs/input/grid* .
184    \cp ../input/* .
185    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
186    mpirun -np 2 ../build/mitgcmuv
187    
188    
189    ##########################################################################
190    ##########################################################################
191    # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
192    # starting with pickup file from end of 1992
193    # requires input files in sudirectories run_template and ncep_rgau
194    
195    cd MITgcm/verification/global_ocean.cs32x15/code
196    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
197    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
198    \cp packages.conf_hr packages.conf
199    
200    cd ../build
201    \rm *
202    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
203    make depend
204    make -j
205    
206    cd ..
207    mkdir run
208    cd run
209    \rm *
210    \cp ../input/* .
211    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
212    qsub job_altix92_54t
213    
214    
215    ##########################################################################
216    ##########################################################################
217    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
218    # uses s1500t_17x51 configuration
219    
220    cd MITgcm/verification/global_ocean.cs32x15/code
221    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
222    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
223    \cp SIZE.h_150 SIZE.h
224    \cp packages.conf_hr packages.conf
225    
226    cd ../build
227    \rm *
228    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
229    make depend
230    make -j
231    
232    cd ..
233    mkdir run
234    cd run
235    \rm *
236    \cp ../input/* .
237    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
238    ln -sf ../../../../run_template/* .
239    \rm pickup*
240    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
241    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
242    \cp ../build/mitgcmuv mitgcmuv150
243    qsub job_altix150
244    
245    
246    ##########################################################################
247    ##########################################################################
248    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
249    # uses s1500t_17x51 configuration
250    # example for running on c17-c20 using arrayd
251    
252    cd MITgcm/verification/global_ocean.cs32x15/code
253    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
254    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
255    \cp SIZE.h_375 SIZE.h
256    \cp packages.conf_hr packages.conf
257    
258    cd ../build
259    \rm *
260    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
261    make depend
262    make -j
263    
264    cd ..
265    mkdir run
266    cd run
267    \rm *
268    \cp ../input/* .
269    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
270    ln -sf ../../../../run_template/* .
271    \rm pickup*
272    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
273    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
274    \cp ../build/mitgcmuv .
275    job_c20_375cpu < /dev/null >&! output.run &
276    
277    
278    ##########################################################################
279    ##########################################################################
280    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
281    # uses s1500t_17x51 configuration
282    # example for running on c17-c20 using arrayd
283    
284    cd MITgcm/verification/global_ocean.cs32x15/code
285    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
286    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
287    \cp SIZE.h_375 SIZE.h
288    \cp packages.conf_hr packages.conf
289    
290    cd ../build
291    \rm *
292    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
293    make depend
294    make -j
295    
296    cd ..
297    mkdir run
298    cd run
299    \rm *
300    \cp ../input/* .
301    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
302    ln -sf ../../../../run_template/* .
303    \rm pickup*
304    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
305    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
306    \cp ../build/mitgcmuv .
307    job_c20_375cpu < /dev/null >&! output.run &
308    
309    
310    ##########################################################################
311    ##########################################################################
312    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
313    # uses s1500t_17x51 configuration
314    # example for running on c17-c20 using arrayd
315    
316    cd MITgcm/verification/global_ocean.cs32x15/code
317    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
318    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
319    \cp SIZE.h_500 SIZE.h
320    \cp packages.conf_hr packages.conf
321    
322    cd ../build
323    \rm *
324    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
325    make depend
326    make -j
327    
328    cd ..
329    mkdir run
330    cd run
331    \rm *
332    \cp ../input/* .
333    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
334    ln -sf ../../../../run_template/* .
335    \rm pickup*
336    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
337    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
338    \cp ../build/mitgcmuv .
339    job_c19_500cpu < /dev/null >&! output.run &
340    
341    
342    ##########################################################################
343    ##########################################################################
344    # 510*510*6*50, 216-cpu cube sphere on cosmos
345    
346    cd MITgcm/verification/global_ocean.cs32x15/code
347    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
348    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
349    \cp SIZE.h_216 SIZE.h
350    \cp packages.conf_hr packages.conf
351    
352    module unload latest_intel80
353    module unload mpich-gm-intel80
354    module load latest_intel81
355    module load mpich-gm-intel81
356    
357    cd ../build
358    \rm *
359    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
360    make depend
361    make -j
362    
363    cd ..
364    mkdir run
365    cd run
366    \rm *
367    \cp ../input/* .
368    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
369    ln -sf ../../../../run_template/* .
370    \rm pickup*
371    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
372    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
373    \cp ../build/mitgcmuv .
374    bsub < job_cosmos
375    
376    
377    ##########################################################################
378    ##########################################################################
379    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
380    # requires input files in sudirectories run_template and ncep_rgau
381    # presently residing under orion:/tmp1/dmenem/cube
382    
383    cd MITgcm/verification/global_ocean.cs32x15/code
384    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
385    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
386    \cp SIZE.h_54 SIZE.h
387    \cp packages.conf_hr packages.conf
388    
389    cd ../build
390    \rm *
391    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
392    make depend
393    make -j
394    
395    cd ..
396    mkdir run
397    cd run
398    \rm *
399    \cp ../input/* .
400    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
401    qsub job_orion
402    
403    
404    ##########################################################################
405    ##########################################################################
406    # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
407    # requires input files in sudirectories run_template and ncep_rgau
408    # presently residing under orion:/tmp1/dmenem/cube
409    
410    cd MITgcm/verification/global_ocean.cs32x15/code
411    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
412    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
413    \cp SIZE.h_41 SIZE.h
414    \cp packages.conf_hr packages.conf
415    
416    cd ../build
417    \rm *
418    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
419    make depend
420    make -j
421    
422    cd ..
423    mkdir run
424    cd run
425    \rm *
426    \cp ../input/* .
427    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
428    qsub job_orion41
429    
430    
431    ##########################################################################
432    ##########################################################################
433    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
434    # requires input files in sudirectories run_template and ncep_rgau
435    # presently residing under orion:/tmp1/dmenem/cube
436    
437    cd MITgcm/verification/global_ocean.cs32x15/code
438    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
439    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
440    \cp SIZE.h_50 SIZE.h
441    \cp packages.conf_hr packages.conf
442    
443    cd ../build
444    \rm *
445    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
446    make depend
447    make -j
448    
449    cd ..
450    mkdir run
451    cd run
452    \rm *
453    \cp ../input/* .
454    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
455    qsub job_orion
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