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revision 1.5 by dimitri, Tue Nov 25 05:41:28 2003 UTC revision 1.68 by dimitri, Mon Oct 9 21:56:42 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: November 21, 2003.  
2    
3  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  September 28, 2006: 216-CPU code for cube38
4  cvs login ( CVS password: cvsanon )  
5    September 4, 2006
6    Modified 32*32*6*15 experiments to use grid_cs32.* files from
7     verification/tutorial_held_suarez_cs/input instead of
8     tile* files from verification/global_ocean.cs32x15/input
9    
10    August 8, 2006
11    216-CPU code and input used for integrating cube37
12    using "June 10, 2006" MITgcm code.
13    
14    for online T/S profile diagnostics all that is needed is
15      profiles_init_fixed
16      profiles_inloop
17    see pkg/ecco/ecco_cost_init_fixed.F
18        pkg/ecco/cost_averagesfields.F
19    
20    
21    ##########################################################################
22    ##########################################################################
23    # getting the code from anonymous CVS server
24    #
25    
26      bash or sh shell:
27        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
28        $ cvs login
29          ( enter the CVS password: "cvsanon" )
30    
31      tcsh or csh shell:
32        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
33        $ cvs login
34          ( enter the CVS password: "cvsanon" )
35    
36  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
37  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  
38  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
39  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
40    cvs co MITgcm_code
41    cvs co MITgcm/verification/global_ocean.cs32x15
42    cvs co MITgcm/verification/tutorial_held_suarez_cs/input
43    
 cvs co -r checkpoint52b_post MITgcm_code  
 cvs co -r checkpoint52b_post MITgcm/verification/global_ocean.cs32x15  
44    
45  cd MITgcm/verification/global_ocean.cs32x15/code  ##########################################################################
46  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  ##########################################################################
47  cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  # 32*32*6*15, 1-cpu cube sphere
 \rm mdsio_readfield.F  
48    
49  cd ..  cd MITgcm/verification/global_ocean.cs32x15/code
50  mkdir build  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
51  cd build  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
52  ../code/genmake2 -mods=../code  cd ../build
53    \rm *
54    ../../../tools/genmake2 -mods=../code
55  make depend  make depend
56  make  make
   
57  cd ..  cd ..
58  mkdir run  mkdir run
59  cd run  cd run
60  cp ../inp_thsice/* .  \rm *
61  cp ../input/* .  \cp ../../tutorial_held_suarez_cs/input/grid* .
62  cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  \cp ../input/* .
63  cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
64  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
65    
66  comparison output is in:  comparison output is in:
67  ../../../../MITgcm_contrib/high_res_cube/results/output.txt  ../../../../MITgcm_contrib/high_res_cube/results/output.txt
68    
   
69  to use matlab to look at the output  to use matlab to look at the output
70  matlab  matlab
71  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  
72    for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...
73             'QNETtave','FVtave','FUtave','EmPmRtave'}
74      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);
75      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
76  end  end
77    
78    heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);
79    mask=0*heff; mask(find(heff>.001))=1;
80    uice=mask.*permute(readbin(['UICEtave.0000000020.data'],[32,6,32]),[1 3 2]);
81    vice=mask.*permute(readbin(['VICEtave.0000000020.data'],[32,6,32]),[1 3 2]);
82    clf
83    subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
84    subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
85    subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
86    subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
87    
88    
89    ##########################################################################
90    ##########################################################################
91    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
92    # requires input files in sudirectories run_template and ncep_rgau
93    # these can be obained from lou:/u/menemenl/cube
94    
95    cd MITgcm/verification/global_ocean.cs32x15/code
96    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
97    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
98    \cp SIZE.h_216 SIZE.h
99    \cp packages.conf_hr packages.conf
100    
101    cd ../build
102    \rm *
103    ../../../tools/genmake2 -mods=../code -of
104    ../../../tools/build_options/linux_ia\
105    64_ifort+mpi_altix_nas
106    make depend
107    make -j
108    
109    cd ..
110    mkdir run
111    cd run
112    \rm *
113    \cp ../input/* .
114    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
115    ln -sf ../../../../run_template/* .
116    \rm pickup* data.pkg data.seaice data.exf_clim data.exf data bathy_Hmin50.bin
117    \rm *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
118    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
119    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38
120    pickup_seaice.\
121    0000000216
122    \cp ../build/mitgcmuv .
123    qsub job_altix
124    
125    
126    ##########################################################################
127    ##########################################################################
128    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
129    
130    cd MITgcm/verification/global_ocean.cs32x15/code
131    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
132    \cp ../code_alt/code.176t_8x4/* .
133    cd ../build
134    \rm *
135    ../../../tools/genmake2 -mods=../code
136    make depend
137    make
138    cd ..
139    mkdir run
140    cd run
141    \rm *
142    \cp ../../tutorial_held_suarez_cs/input/grid* .
143    \cp ../input/* .
144    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
145    ../build/mitgcmuv >& output.txt
146    
147    
148    ##########################################################################
149    ##########################################################################
150    # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
151    
152    cd MITgcm/verification/global_ocean.cs32x15/code
153    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
154    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
155    \cp SIZE.h_mpi SIZE.h
156    
157    cd ../build
158    \rm *
159    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
160    make depend
161    make -j
162    
163    cd ..
164    mkdir run
165    cd run
166    \rm *
167    \cp ../../tutorial_held_suarez_cs/input/grid* .
168    \cp ../input/* .
169    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
170    mpirun -np 2 ../build/mitgcmuv
171    
172    
173    ##########################################################################
174    ##########################################################################
175    # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
176    # starting with pickup file from end of 1992
177    # requires input files in sudirectories run_template and ncep_rgau
178    
179    cd MITgcm/verification/global_ocean.cs32x15/code
180    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
181    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
182    \cp packages.conf_hr packages.conf
183    
184    cd ../build
185    \rm *
186    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
187    make depend
188    make -j
189    
190    cd ..
191    mkdir run
192    cd run
193    \rm *
194    \cp ../input/* .
195    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
196    qsub job_altix92_54t
197    
198    
199    ##########################################################################
200    ##########################################################################
201    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
202    # uses s1500t_17x51 configuration
203    
204    cd MITgcm/verification/global_ocean.cs32x15/code
205    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
206    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
207    \cp SIZE.h_150 SIZE.h
208    \cp packages.conf_hr packages.conf
209    
210    cd ../build
211    \rm *
212    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
213    make depend
214    make -j
215    
216    cd ..
217    mkdir run
218    cd run
219    \rm *
220    \cp ../input/* .
221    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
222    ln -sf ../../../../run_template/* .
223    \rm pickup*
224    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
225    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
226    \cp ../build/mitgcmuv mitgcmuv150
227    qsub job_altix150
228    
229    
230    ##########################################################################
231    ##########################################################################
232    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
233    # uses s1500t_17x51 configuration
234    # example for running on c17-c20 using arrayd
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_375 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 .
259    job_c20_375cpu < /dev/null >&! output.run &
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, 500-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_500 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_c19_500cpu < /dev/null >&! output.run &
324    
325    
326    ##########################################################################
327    ##########################################################################
328    # 510*510*6*50, 216-cpu cube sphere on cosmos
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/s216t_85x85/* .
333    \cp SIZE.h_216 SIZE.h
334    \cp packages.conf_hr packages.conf
335    
336    module unload latest_intel80
337    module unload mpich-gm-intel80
338    module load latest_intel81
339    module load mpich-gm-intel81
340    
341    cd ../build
342    \rm *
343    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
344    make depend
345    make -j
346    
347    cd ..
348    mkdir run
349    cd run
350    \rm *
351    \cp ../input/* .
352    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
353    ln -sf ../../../../run_template/* .
354    \rm pickup*
355    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
356    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
357    \cp ../build/mitgcmuv .
358    bsub < job_cosmos
359    
360    
361    ##########################################################################
362    ##########################################################################
363    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
364    # requires input files in sudirectories run_template and ncep_rgau
365    # presently residing under orion:/tmp1/dmenem/cube
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_54 SIZE.h
371    \cp packages.conf_hr packages.conf
372    
373    cd ../build
374    \rm *
375    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
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    qsub job_orion
386    
387    
388    ##########################################################################
389    ##########################################################################
390    # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
391    # requires input files in sudirectories run_template and ncep_rgau
392    # presently residing under orion:/tmp1/dmenem/cube
393    
394    cd MITgcm/verification/global_ocean.cs32x15/code
395    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
396    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
397    \cp SIZE.h_41 SIZE.h
398    \cp packages.conf_hr packages.conf
399    
400    cd ../build
401    \rm *
402    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
403    make depend
404    make -j
405    
406    cd ..
407    mkdir run
408    cd run
409    \rm *
410    \cp ../input/* .
411    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
412    qsub job_orion41
413    
414    
415    ##########################################################################
416    ##########################################################################
417    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
418    # requires input files in sudirectories run_template and ncep_rgau
419    # presently residing under orion:/tmp1/dmenem/cube
420    
421    cd MITgcm/verification/global_ocean.cs32x15/code
422    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
423    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
424    \cp SIZE.h_50 SIZE.h
425    \cp packages.conf_hr packages.conf
426    
427    cd ../build
428    \rm *
429    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
430    make depend
431    make -j
432    
433    cd ..
434    mkdir run
435    cd run
436    \rm *
437    \cp ../input/* .
438    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
439    qsub job_orion
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