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revision 1.8 by dimitri, Fri Dec 12 10:20:05 2003 UTC revision 1.74 by dimitri, Thu Nov 2 06:05:17 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.  
3    =================
4    UPDATES
5    
6    November 1, 2006: 216-CPU code for cube43
7    Martin's growth.F routine and Patrick's pkg/seaice diagnostics
8    
9    October 15, 2006: 216-CPU code for cube40
10    
11    September 28, 2006: 216-CPU code for cube38
12    
13    September 4, 2006
14    Modified 32*32*6*15 experiments to use grid_cs32.* files from
15     verification/tutorial_held_suarez_cs/input instead of
16     tile* files from verification/global_ocean.cs32x15/input
17    
18    August 8, 2006: 216-CPU code and input used for cube37
19    using "June 10, 2006" MITgcm code.
20    
21    for online T/S profile diagnostics all that is needed is
22      profiles_init_fixed
23      profiles_inloop
24    see pkg/ecco/ecco_cost_init_fixed.F
25        pkg/ecco/cost_averagesfields.F
26    
27    
28  ##########################################################################  ##########################################################################
29  ##########################################################################  ##########################################################################
30  # 32*32*6*15, 1-cpu cube sphere  # getting the code from anonymous CVS server
31    #
32    
33      bash or sh shell:
34        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
35        $ cvs login
36          ( enter the CVS password: "cvsanon" )
37    
38      tcsh or csh shell:
39        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
40        $ cvs login
41          ( enter the CVS password: "cvsanon" )
42    
43    cvs co MITgcm_contrib/high_res_cube/README_ice
44    cvs co MITgcm_contrib/high_res_cube/code-mods
45    cvs co MITgcm_contrib/high_res_cube/input
46    cvs co MITgcm_contrib/high_res_cube/results
47    cvs co MITgcm_code
48    cvs co MITgcm/verification/global_ocean.cs32x15
49    cvs co MITgcm/verification/tutorial_held_suarez_cs/input
50    
51  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  
52  cvs login ( CVS password: cvsanon )  ##########################################################################
53  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/README_ice  ##########################################################################
54  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/code-mods  # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
55  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/matlab-grid-converter  # requires input files in sudirectories run_template and ncep_rgau
56  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/input  # these can be obained from lou:/u/menemenl/cube
 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  
57    
58  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
59  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
60  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
61  \rm mdsio_readfield.F  \cp SIZE.h_216 SIZE.h
62    \cp packages.conf_hr packages.conf
63    
64    cd ../build
65    \rm *
66    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
67    make depend
68    make -j
69    
70  cd ..  cd ..
71  mkdir build  mkdir run
72  cd build  cd run
73  ../code/genmake2 -mods=../code  \rm *
74    \cp ../input/* .
75    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
76    ln -sf ../../../../run_template/* .
77    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
78    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
79    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
80    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38 pickup_seaice.0000000216
81    \cp ../build/mitgcmuv .
82    qsub job_altix
83    
84    
85    ##########################################################################
86    ##########################################################################
87    # 32*32*6*15, 1-cpu cube sphere
88    
89    cd MITgcm/verification/global_ocean.cs32x15/code
90    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
91    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
92    cd ../build
93    \rm *
94    ../../../tools/genmake2 -mods=../code
95  make depend  make depend
96  make  make
   
97  cd ..  cd ..
98  mkdir run  mkdir run
99  cd run  cd run
100  \cp ../inp_thsice/* .  \rm *
101    \cp ../../tutorial_held_suarez_cs/input/grid* .
102  \cp ../input/* .  \cp ../input/* .
 \cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  
103  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
104  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
105    
# Line 42  comparison output is in: Line 108  comparison output is in:
108    
109  to use matlab to look at the output  to use matlab to look at the output
110  matlab  matlab
111  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  
112    for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...
113             'QNETtave','FVtave','FUtave','EmPmRtave'}
114      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]);
115      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
116  end  end
117    
118    heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);
119    mask=0*heff; mask(find(heff>.001))=1;
120    uice=mask.*permute(readbin(['UICEtave.0000000020.data'],[32,6,32]),[1 3 2]);
121    vice=mask.*permute(readbin(['VICEtave.0000000020.data'],[32,6,32]),[1 3 2]);
122    clf
123    subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
124    subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
125    subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
126    subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
127    
128    
129  ##########################################################################  ##########################################################################
130  ##########################################################################  ##########################################################################
131  # 32*32*6*15, 2-cpu cube sphere on the altices with efc  # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
132    
133    cd MITgcm/verification/global_ocean.cs32x15/code
134    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
135    \cp ../code_alt/code.176t_8x4/* .
136    cd ../build
137    \rm *
138    ../../../tools/genmake2 -mods=../code
139    make depend
140    make
141    cd ..
142    mkdir run
143    cd run
144    \rm *
145    \cp ../../tutorial_held_suarez_cs/input/grid* .
146    \cp ../input/* .
147    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
148    ../build/mitgcmuv >& output.txt
149    
150  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  
151  cvs login ( CVS password: cvsanon )  ##########################################################################
152  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/README_ice  ##########################################################################
153  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  
154    
155  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
156  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
157  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
158  \cp SIZE.h_mpi SIZE.h  \cp SIZE.h_mpi SIZE.h
 \cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h  
 \rm mdsio_readfield.F  
159    
160  cd ..  cd ../build
161  mkdir build  \rm *
162  cd build  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
 ../code/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi  
163  make depend  make depend
164  make  make -j
165    
166  cd ..  cd ..
167  mkdir run  mkdir run
168  cd run  cd run
169  \cp ../inp_thsice/* .  \rm *
170    \cp ../../tutorial_held_suarez_cs/input/grid* .
171  \cp ../input/* .  \cp ../input/* .
 \cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  
172  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
173  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
174    
175    
176  ##########################################################################  ##########################################################################
177  ##########################################################################  ##########################################################################
178  # 32*32*6*15, 2-cpu cube sphere on the altices with efc  # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
179    # starting with pickup file from end of 1992
180    # requires input files in sudirectories run_template and ncep_rgau
181    
182    cd MITgcm/verification/global_ocean.cs32x15/code
183    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
184    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
185    \cp packages.conf_hr packages.conf
186    
187    cd ../build
188    \rm *
189    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
190    make depend
191    make -j
192    
193    cd ..
194    mkdir run
195    cd run
196    \rm *
197    \cp ../input/* .
198    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
199    qsub job_altix92_54t
200    
201    
202    ##########################################################################
203    ##########################################################################
204    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
205    # uses s1500t_17x51 configuration
206    
207    cd MITgcm/verification/global_ocean.cs32x15/code
208    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
209    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
210    \cp SIZE.h_150 SIZE.h
211    \cp packages.conf_hr packages.conf
212    
213    cd ../build
214    \rm *
215    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
216    make depend
217    make -j
218    
219    cd ..
220    mkdir run
221    cd run
222    \rm *
223    \cp ../input/* .
224    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
225    ln -sf ../../../../run_template/* .
226    \rm pickup*
227    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
228    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
229    \cp ../build/mitgcmuv mitgcmuv150
230    qsub job_altix150
231    
232  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  
233  cvs login ( CVS password: cvsanon )  ##########################################################################
234  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/README_ice  ##########################################################################
235  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/code-mods  # 510*510*6*50, 1500-tile, 375-cpu, excludes land
236  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/matlab-grid-converter  # uses s1500t_17x51 configuration
237  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/input  # example for running on c17-c20 using arrayd
238  cvs co -r checkpoint52d_pre MITgcm_contrib/high_res_cube/results  
239  cvs co -r checkpoint52d_pre MITgcm_code  cd MITgcm/verification/global_ocean.cs32x15/code
240  cvs co -r checkpoint52d_pre MITgcm/verification/global_ocean.cs32x15  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
241    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
242    \cp SIZE.h_375 SIZE.h
243    \cp packages.conf_hr packages.conf
244    
245    cd ../build
246    \rm *
247    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
248    make depend
249    make -j
250    
251    cd ..
252    mkdir run
253    cd run
254    \rm *
255    \cp ../input/* .
256    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
257    ln -sf ../../../../run_template/* .
258    \rm pickup*
259    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
260    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
261    \cp ../build/mitgcmuv .
262    job_c20_375cpu < /dev/null >&! output.run &
263    
264    
265    ##########################################################################
266    ##########################################################################
267    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
268    # uses s1500t_17x51 configuration
269    # example for running on c17-c20 using arrayd
270    
271    cd MITgcm/verification/global_ocean.cs32x15/code
272    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
273    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
274    \cp SIZE.h_375 SIZE.h
275    \cp packages.conf_hr packages.conf
276    
277    cd ../build
278    \rm *
279    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
280    make depend
281    make -j
282    
283    cd ..
284    mkdir run
285    cd run
286    \rm *
287    \cp ../input/* .
288    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
289    ln -sf ../../../../run_template/* .
290    \rm pickup*
291    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
292    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
293    \cp ../build/mitgcmuv .
294    job_c20_375cpu < /dev/null >&! output.run &
295    
296    
297    ##########################################################################
298    ##########################################################################
299    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
300    # uses s1500t_17x51 configuration
301    # example for running on c17-c20 using arrayd
302    
303    cd MITgcm/verification/global_ocean.cs32x15/code
304    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
305    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
306    \cp SIZE.h_500 SIZE.h
307    \cp packages.conf_hr packages.conf
308    
309    cd ../build
310    \rm *
311    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
312    make depend
313    make -j
314    
315    cd ..
316    mkdir run
317    cd run
318    \rm *
319    \cp ../input/* .
320    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
321    ln -sf ../../../../run_template/* .
322    \rm pickup*
323    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
324    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
325    \cp ../build/mitgcmuv .
326    job_c19_500cpu < /dev/null >&! output.run &
327    
328    
329    ##########################################################################
330    ##########################################################################
331    # 510*510*6*50, 216-cpu cube sphere on cosmos
332    
333    cd MITgcm/verification/global_ocean.cs32x15/code
334    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
335    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
336    \cp SIZE.h_216 SIZE.h
337    \cp packages.conf_hr packages.conf
338    
339    module unload latest_intel80
340    module unload mpich-gm-intel80
341    module load latest_intel81
342    module load mpich-gm-intel81
343    
344    cd ../build
345    \rm *
346    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
347    make depend
348    make -j
349    
350    cd ..
351    mkdir run
352    cd run
353    \rm *
354    \cp ../input/* .
355    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
356    ln -sf ../../../../run_template/* .
357    \rm pickup*
358    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
359    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
360    \cp ../build/mitgcmuv .
361    bsub < job_cosmos
362    
363    
364    ##########################################################################
365    ##########################################################################
366    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
367    # requires input files in sudirectories run_template and ncep_rgau
368    # presently residing under orion:/tmp1/dmenem/cube
369    
370  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
371  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
372  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
373  \cp SIZE.h_54 SIZE.h  \cp SIZE.h_54 SIZE.h
374  \cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h  \cp packages.conf_hr packages.conf
375  \rm mdsio_readfield.F  
376    cd ../build
377    \rm *
378    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
379    make depend
380    make -j
381    
382    cd ..
383    mkdir run
384    cd run
385    \rm *
386    \cp ../input/* .
387    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
388    qsub job_orion
389    
390    
391    ##########################################################################
392    ##########################################################################
393    # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
394    # requires input files in sudirectories run_template and ncep_rgau
395    # presently residing under orion:/tmp1/dmenem/cube
396    
397    cd MITgcm/verification/global_ocean.cs32x15/code
398    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
399    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
400    \cp SIZE.h_41 SIZE.h
401    \cp packages.conf_hr packages.conf
402    
403    cd ../build
404    \rm *
405    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
406    make depend
407    make -j
408    
409  cd ..  cd ..
410  mkdir build  mkdir run
411  cd build  cd run
412  ../code/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi  \rm *
413    \cp ../input/* .
414    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
415    qsub job_orion41
416    
417    
418    ##########################################################################
419    ##########################################################################
420    # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
421    # requires input files in sudirectories run_template and ncep_rgau
422    # presently residing under orion:/tmp1/dmenem/cube
423    
424    cd MITgcm/verification/global_ocean.cs32x15/code
425    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
426    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
427    \cp SIZE.h_50 SIZE.h
428    \cp packages.conf_hr packages.conf
429    
430    cd ../build
431    \rm *
432    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
433  make depend  make depend
434  make  make -j
435    
436  cd ..  cd ..
437  mkdir run  mkdir run
438  cd run  cd run
439  \cp ../inp_thsice/* .  \rm *
440  \cp ../input/* .  \cp ../input/* .
441  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
 \cp data_hr data  
 \ln -sf ../../../../run_template/tile00* .  
 \ln -sf ../../../../run_template/LEV* .  
 \ln -sf ../../../../run_template/BATHY_18360x85_filled.bin .  
442  qsub job_orion  qsub job_orion
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