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revision 1.13 by dimitri, Sat Jan 10 00:50:25 2004 UTC revision 1.63 by dimitri, Sat Jun 10 15:47:23 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.
2  Date last tested: December 11, 2003.  Date last updated: June 10, 2006
3    216-CPU code and input used for integrating cube37.
4    
5    
6  ##########################################################################  ##########################################################################
7  ##########################################################################  ##########################################################################
8  # 32*32*6*15, 1-cpu cube sphere  # getting the code from anonymous CVS server
9    
10    cvs co MITgcm_contrib/high_res_cube/README_ice
11    cvs co MITgcm_contrib/high_res_cube/code-mods
12    cvs co MITgcm_contrib/high_res_cube/input
13    cvs co MITgcm_contrib/high_res_cube/results
14    cvs co MITgcm_code
15    cvs co MITgcm/verification/global_ocean.cs32x15
16    
17  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  
18  cvs login ( CVS password: cvsanon )  ##########################################################################
19  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/README_ice  ##########################################################################
20  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/code-mods  # 32*32*6*15, 1-cpu cube sphere
 cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/matlab-grid-converter  
 cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/input  
 cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/results  
 cvs co -r checkpoint52d_pre MITgcm_code  
 cvs co -r checkpoint52d_pre MITgcm/verification/global_ocean.cs32x15  
21    
22  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
23  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
24  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
25  \rm mdsio_readfield.F  cd ../build
26    \rm *
 cd ..  
 mkdir build  
 cd build  
27  ../../../tools/genmake2 -mods=../code  ../../../tools/genmake2 -mods=../code
28  make depend  make depend
29  make  make
   
30  cd ..  cd ..
31  mkdir run  mkdir run
32  cd run  cd run
33    \rm *
34  \cp ../input/* .  \cp ../input/* .
 \cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  
35  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
36  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
37    
# Line 41  comparison output is in: Line 40  comparison output is in:
40    
41  to use matlab to look at the output  to use matlab to look at the output
42  matlab  matlab
43  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  
44    for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...
45             'QNETtave','FVtave','FUtave','EmPmRtave'}
46      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]);
47      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
48  end  end
49    
50    heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);
51    mask=0*heff; mask(find(heff>.001))=1;
52    uice=mask.*permute(readbin(['UICEtave.0000000020.data'],[32,6,32]),[1 3 2]);
53    vice=mask.*permute(readbin(['VICEtave.0000000020.data'],[32,6,32]),[1 3 2]);
54    clf
55    subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
56    subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
57    subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
58    subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
59    
60    
61  ##########################################################################  ##########################################################################
62  ##########################################################################  ##########################################################################
63  # 32*32*6*15, 2-cpu cube sphere on the altices with efc  # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
64    
65    cd MITgcm/verification/global_ocean.cs32x15/code
66    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
67    \cp ../code_alt/code.176t_8x4/* .
68    cd ../build
69    \rm *
70    ../../../tools/genmake2 -mods=../code
71    make depend
72    make
73    cd ..
74    mkdir run
75    cd run
76    \rm *
77    \cp ../input/* .
78    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
79    ../build/mitgcmuv >& output.txt
80    
81  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  
82  cvs login ( CVS password: cvsanon )  ##########################################################################
83  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/README_ice  ##########################################################################
84  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/code-mods  # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
 cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/matlab-grid-converter  
 cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/input  
 cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/results  
 cvs co -r checkpoint52d_pre MITgcm_code  
 cvs co -r checkpoint52d_pre MITgcm/verification/global_ocean.cs32x15  
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 ../../../utils/exch2/code-mods/s12t_16x32/* .
89  \cp SIZE.h_mpi SIZE.h  \cp SIZE.h_mpi SIZE.h
 \cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h  
 \rm mdsio_readfield.F  
90    
91  cd ..  cd ../build
92  mkdir build  \rm *
93  cd build  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
 ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi  
94  make depend  make depend
95  make  make -j
96    
97  cd ..  cd ..
98  mkdir run  mkdir run
99  cd run  cd run
100    \rm *
101  \cp ../input/* .  \cp ../input/* .
 \cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  
102  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
103  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
104    
105    
106  ##########################################################################  ##########################################################################
107  ##########################################################################  ##########################################################################
108  # 510*510*6*50, 54-cpu cube sphere on the altices with efc  # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
109    # starting with pickup file from end of 1992
110    # requires input files in sudirectories run_template and ncep_rgau
111    
112  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  cd MITgcm/verification/global_ocean.cs32x15/code
113  cvs login ( CVS password: cvsanon )  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
114  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/README_ice  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
115  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/code-mods  \cp packages.conf_hr packages.conf
116  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/matlab-grid-converter  
117  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/input  cd ../build
118  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/results  \rm *
119  cvs co -r checkpoint52d_pre MITgcm_code  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
120  cvs co -r checkpoint52d_pre MITgcm/verification/global_ocean.cs32x15  make depend
121    make -j
122    
123    cd ..
124    mkdir run
125    cd run
126    \rm *
127    \cp ../input/* .
128    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
129    qsub job_altix92_54t
130    
131    
132    ##########################################################################
133    ##########################################################################
134    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
135    # requires input files in sudirectories run_template and ncep_rgau
136    # these can be obained from lou:/u/menemenl/cube
137    
138  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
139  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
140  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
141  \cp SIZE.h_54 SIZE.h  \cp SIZE.h_216 SIZE.h
 \cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h  
142  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
143  \cp mom_vi_hdissip.F_hr mom_vi_hdissip.F  
144  \rm mdsio_readfield.F  cd ../build
145    \rm *
146    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
147    make depend
148    make -j
149    
150  cd ..  cd ..
151  mkdir build  mkdir run
152  cd build  cd run
153  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi  \rm *
154    \cp ../input/* .
155    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
156    ln -sf ../../../../run_template/* .
157    \rm pickup* data.pkg data.seaice data.exf_clim data.exf data
158    \rm *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
159    ln -sf ../../../../run_template/pickup.0000000216.cube27 pickup.0000000216
160    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube27 pickup_seaice.0000000216
161    \cp ../build/mitgcmuv .
162    qsub job_altix
163    
164    
165    ##########################################################################
166    ##########################################################################
167    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
168    # uses s1500t_17x51 configuration
169    
170    cd MITgcm/verification/global_ocean.cs32x15/code
171    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
172    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
173    \cp SIZE.h_150 SIZE.h
174    \cp packages.conf_hr packages.conf
175    
176    cd ../build
177    \rm *
178    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
179  make depend  make depend
180  make  make -j
181    
182  cd ..  cd ..
183  mkdir run  mkdir run
184  cd run  cd run
185    \rm *
186  \cp ../input/* .  \cp ../input/* .
187  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
188  \cp data_hr data  ln -sf ../../../../run_template/* .
189  \cp data.pkg_hr data.pkg  \rm pickup*
190  \ln -sf ../../../../run_template/tile00* .  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
191  \ln -sf ../../../../run_template/LEV* .  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
192  \ln -sf ../../../../run_template/BATHY_18360x85_filled.bin .  \cp ../build/mitgcmuv mitgcmuv150
193  qsub job_orion  qsub job_altix150
194    
195    
196    
197    
198  ##########################################################################  ##########################################################################
199  ##########################################################################  ##########################################################################
200  # 510*510*6*50, 216-cpu cube sphere on altix with efc  # 510*510*6*50, 1500-tile, 375-cpu, excludes land
201    # uses s1500t_17x51 configuration
202    # example for running on c17-c20 using arrayd
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_375 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 .
227    job_c20_375cpu < /dev/null >&! output.run &
228    
229    
230    
231    
232    
233    
234  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  
235  cvs login ( CVS password: cvsanon )  
236  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/README_ice  
237  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/code-mods  
238  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/matlab-grid-converter  
239  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/input  
240  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/results  ##########################################################################
241  cvs co -r checkpoint52d_pre MITgcm_code  ##########################################################################
242  cvs co -r checkpoint52d_pre MITgcm/verification/global_ocean.cs32x15  # 510*510*6*50, 1500-tile, 375-cpu, excludes land
243    # uses s1500t_17x51 configuration
244    # example for running on c17-c20 using arrayd
245    
246    cd MITgcm/verification/global_ocean.cs32x15/code
247    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
248    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
249    \cp SIZE.h_375 SIZE.h
250    \cp packages.conf_hr packages.conf
251    
252    cd ../build
253    \rm *
254    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
255    make depend
256    make -j
257    
258    cd ..
259    mkdir run
260    cd run
261    \rm *
262    \cp ../input/* .
263    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
264    ln -sf ../../../../run_template/* .
265    \rm pickup*
266    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
267    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
268    \cp ../build/mitgcmuv .
269    job_c20_375cpu < /dev/null >&! output.run &
270    
271    
272    ##########################################################################
273    ##########################################################################
274    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
275    # uses s1500t_17x51 configuration
276    # example for running on c17-c20 using arrayd
277    
278    cd MITgcm/verification/global_ocean.cs32x15/code
279    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
280    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
281    \cp SIZE.h_500 SIZE.h
282    \cp packages.conf_hr packages.conf
283    
284    cd ../build
285    \rm *
286    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
287    make depend
288    make -j
289    
290    cd ..
291    mkdir run
292    cd run
293    \rm *
294    \cp ../input/* .
295    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
296    ln -sf ../../../../run_template/* .
297    \rm pickup*
298    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
299    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
300    \cp ../build/mitgcmuv .
301    job_c19_500cpu < /dev/null >&! output.run &
302    
303    
304    
305    
306    
307    ##########################################################################
308    ##########################################################################
309    # 510*510*6*50, 216-cpu cube sphere on cosmos
310    
311  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
312  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
313  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
314  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_216 SIZE.h
 \cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h  
315  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
316  \cp mom_vi_hdissip.F_hr mom_vi_hdissip.F  
317  \rm mdsio_readfield.F  module unload latest_intel80
318    module unload mpich-gm-intel80
319    module load latest_intel81
320    module load mpich-gm-intel81
321    
322    cd ../build
323    \rm *
324    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
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    bsub < job_cosmos
340    
341    
342    
343    
344    
345    
346    
347    
348    
349    
350    
351    
352    
353    
354    
355    
356    
357    
358    
359    
360    ##########################################################################
361    ##########################################################################
362    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
363    # requires input files in sudirectories run_template and ncep_rgau
364    # presently residing under orion:/tmp1/dmenem/cube
365    
366    cd MITgcm/verification/global_ocean.cs32x15/code
367    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
368    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
369    \cp SIZE.h_54 SIZE.h
370    \cp packages.conf_hr packages.conf
371    
372    cd ../build
373    \rm *
374    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
375    make depend
376    make -j
377    
378    cd ..
379    mkdir run
380    cd run
381    \rm *
382    \cp ../input/* .
383    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
384    qsub job_orion
385    
386    
387    ##########################################################################
388    ##########################################################################
389    # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
390    # requires input files in sudirectories run_template and ncep_rgau
391    # presently residing under orion:/tmp1/dmenem/cube
392    
393    cd MITgcm/verification/global_ocean.cs32x15/code
394    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
395    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
396    \cp SIZE.h_41 SIZE.h
397    \cp packages.conf_hr packages.conf
398    
399    cd ../build
400    \rm *
401    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
402    make depend
403    make -j
404    
405  cd ..  cd ..
406  mkdir build  mkdir run
407  cd build  cd run
408    \rm *
409    \cp ../input/* .
410    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
411    qsub job_orion41
412    
413    
414    ##########################################################################
415    ##########################################################################
416    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
417    # requires input files in sudirectories run_template and ncep_rgau
418    # presently residing under orion:/tmp1/dmenem/cube
419    
420    cd MITgcm/verification/global_ocean.cs32x15/code
421    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
422    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
423    \cp SIZE.h_50 SIZE.h
424    \cp packages.conf_hr packages.conf
425    
426    cd ../build
427    \rm *
428  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
429  make depend  make depend
430  make  make -j
431    
432  cd ..  cd ..
433  mkdir run  mkdir run
434  cd run  cd run
435  qsub job_altix  \rm *
436    \cp ../input/* .
437    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
438    qsub job_orion
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