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revision 1.4 by dimitri, Mon Nov 24 06:32:44 2003 UTC revision 1.71 by dimitri, Thu Oct 12 06:09:38 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={'Eta','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  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 ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
104    make depend
105    make -j
106    
107    cd ..
108    mkdir run
109    cd run
110    \rm *
111    \cp ../input/* .
112    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
113    ln -sf ../../../../run_template/* .
114    \rm pickup* data.pkg data.seaice data.exf_clim data.exf data bathy_Hmin50.bin
115    \rm *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
116    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
117    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38 pickup_seaice.0000000216
118    \cp ../build/mitgcmuv .
119    qsub job_altix
120    
121    
122    ##########################################################################
123    ##########################################################################
124    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
125    
126    cd MITgcm/verification/global_ocean.cs32x15/code
127    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
128    \cp ../code_alt/code.176t_8x4/* .
129    cd ../build
130    \rm *
131    ../../../tools/genmake2 -mods=../code
132    make depend
133    make
134    cd ..
135    mkdir run
136    cd run
137    \rm *
138    \cp ../../tutorial_held_suarez_cs/input/grid* .
139    \cp ../input/* .
140    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
141    ../build/mitgcmuv >& output.txt
142    
143    
144    ##########################################################################
145    ##########################################################################
146    # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
147    
148    cd MITgcm/verification/global_ocean.cs32x15/code
149    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
150    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
151    \cp SIZE.h_mpi SIZE.h
152    
153    cd ../build
154    \rm *
155    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
156    make depend
157    make -j
158    
159    cd ..
160    mkdir run
161    cd run
162    \rm *
163    \cp ../../tutorial_held_suarez_cs/input/grid* .
164    \cp ../input/* .
165    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
166    mpirun -np 2 ../build/mitgcmuv
167    
168    
169    ##########################################################################
170    ##########################################################################
171    # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
172    # starting with pickup file from end of 1992
173    # requires input files in sudirectories run_template and ncep_rgau
174    
175    cd MITgcm/verification/global_ocean.cs32x15/code
176    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
177    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
178    \cp packages.conf_hr packages.conf
179    
180    cd ../build
181    \rm *
182    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
183    make depend
184    make -j
185    
186    cd ..
187    mkdir run
188    cd run
189    \rm *
190    \cp ../input/* .
191    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
192    qsub job_altix92_54t
193    
194    
195    ##########################################################################
196    ##########################################################################
197    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
198    # uses s1500t_17x51 configuration
199    
200    cd MITgcm/verification/global_ocean.cs32x15/code
201    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
202    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
203    \cp SIZE.h_150 SIZE.h
204    \cp packages.conf_hr packages.conf
205    
206    cd ../build
207    \rm *
208    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
209    make depend
210    make -j
211    
212    cd ..
213    mkdir run
214    cd run
215    \rm *
216    \cp ../input/* .
217    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
218    ln -sf ../../../../run_template/* .
219    \rm pickup*
220    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
221    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
222    \cp ../build/mitgcmuv mitgcmuv150
223    qsub job_altix150
224    
225    
226    ##########################################################################
227    ##########################################################################
228    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
229    # uses s1500t_17x51 configuration
230    # example for running on c17-c20 using arrayd
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_375 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 .
255    job_c20_375cpu < /dev/null >&! output.run &
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, 500-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_500 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_c19_500cpu < /dev/null >&! output.run &
320    
321    
322    ##########################################################################
323    ##########################################################################
324    # 510*510*6*50, 216-cpu cube sphere on cosmos
325    
326    cd MITgcm/verification/global_ocean.cs32x15/code
327    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
328    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
329    \cp SIZE.h_216 SIZE.h
330    \cp packages.conf_hr packages.conf
331    
332    module unload latest_intel80
333    module unload mpich-gm-intel80
334    module load latest_intel81
335    module load mpich-gm-intel81
336    
337    cd ../build
338    \rm *
339    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
340    make depend
341    make -j
342    
343    cd ..
344    mkdir run
345    cd run
346    \rm *
347    \cp ../input/* .
348    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
349    ln -sf ../../../../run_template/* .
350    \rm pickup*
351    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
352    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
353    \cp ../build/mitgcmuv .
354    bsub < job_cosmos
355    
356    
357    ##########################################################################
358    ##########################################################################
359    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
360    # requires input files in sudirectories run_template and ncep_rgau
361    # presently residing under orion:/tmp1/dmenem/cube
362    
363    cd MITgcm/verification/global_ocean.cs32x15/code
364    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
365    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
366    \cp SIZE.h_54 SIZE.h
367    \cp packages.conf_hr packages.conf
368    
369    cd ../build
370    \rm *
371    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
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    qsub job_orion
382    
383    
384    ##########################################################################
385    ##########################################################################
386    # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
387    # requires input files in sudirectories run_template and ncep_rgau
388    # presently residing under orion:/tmp1/dmenem/cube
389    
390    cd MITgcm/verification/global_ocean.cs32x15/code
391    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
392    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
393    \cp SIZE.h_41 SIZE.h
394    \cp packages.conf_hr packages.conf
395    
396    cd ../build
397    \rm *
398    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
399    make depend
400    make -j
401    
402    cd ..
403    mkdir run
404    cd run
405    \rm *
406    \cp ../input/* .
407    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
408    qsub job_orion41
409    
410    
411    ##########################################################################
412    ##########################################################################
413    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
414    # requires input files in sudirectories run_template and ncep_rgau
415    # presently residing under orion:/tmp1/dmenem/cube
416    
417    cd MITgcm/verification/global_ocean.cs32x15/code
418    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
419    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
420    \cp SIZE.h_50 SIZE.h
421    \cp packages.conf_hr packages.conf
422    
423    cd ../build
424    \rm *
425    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
426    make depend
427    make -j
428    
429    cd ..
430    mkdir run
431    cd run
432    \rm *
433    \cp ../input/* .
434    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
435    qsub job_orion
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