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revision 1.57 by dimitri, Tue Feb 22 01:20:54 2005 UTC revision 1.81 by dimitri, Tue Dec 12 04:20:42 2006 UTC
# Line 1  Line 1 
1  daInstructions for setting up a cube-sphere integration with sea-ice.  Instructions for setting up a cube-sphere integration with sea-ice.
2  Date last updated: February 17, 2005  
3  Code and input used for integrating cube22.  =================
4    UPDATES
5    
6    December 11, 2006: preparing for cube47, same as cube43
7    but with Arctic monthly river runoff climatology
8    
9    December 5, 2006: 216-CPU code for cube46
10    Changed diagnostics to accomodate JMCs latest and some
11    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
12    to speed up code.
13    
14    November 7, 2006: 216-CPU code for cube43
15    Bug fixes in growth.F routine and new set of diagnostics
16    
17    October 15, 2006: 216-CPU code for cube40
18    
19    September 28, 2006: 216-CPU code for cube38
20    
21    September 4, 2006
22    Modified 32*32*6*15 experiments to use grid_cs32.* files from
23     verification/tutorial_held_suarez_cs/input instead of
24     tile* files from verification/global_ocean.cs32x15/input
25    
26    August 8, 2006: 216-CPU code and input used for cube37
27    using "June 10, 2006" MITgcm code.
28    
29    for online T/S profile diagnostics all that is needed is
30      profiles_init_fixed
31      profiles_inloop
32    see pkg/ecco/ecco_cost_init_fixed.F
33        pkg/ecco/cost_averagesfields.F
34    
35    ##########################################################################
36    ##########################################################################
37    # Get forcing files, etc.
38    # Example below is for cube46 on /nobackup2a/menemenl
39    
40    cd /nobackup2a/menemenl
41    mkdir cube46
42    cd cube46
43    ln -sf ../run_template .
44    ln -sf ../ncep_rgau .
45    
46    
47  ##########################################################################  ##########################################################################
48  ##########################################################################  ##########################################################################
49  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
50    
51      bash or sh shell:
52        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
53        $ cvs login
54          ( enter the CVS password: "cvsanon" )
55    
56      tcsh or csh shell:
57        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
58        $ cvs login
59          ( enter the CVS password: "cvsanon" )
60    
61  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
62  cvs co MITgcm_contrib/high_res_cube/code-mods  cvs co MITgcm_contrib/high_res_cube/code-mods
63  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
64  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
65  cvs co MITgcm_code  cvs co MITgcm_code
66  cvs co MITgcm/verification/global_ocean.cs32x15  cvs co MITgcm/verification/global_ocean.cs32x15
67  cvs co MITgcm/verification/testreport  cvs co MITgcm/verification/tutorial_held_suarez_cs/input
68    
69    
70    ##########################################################################
71    ##########################################################################
72    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
73    
74    cd MITgcm/verification/global_ocean.cs32x15/code
75    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
76    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
77    \cp SIZE.h_216 SIZE.h
78    \cp packages.conf_hr packages.conf
79    
80    cd ../build
81    \rm *
82    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
83    make depend
84    make -j
85    
86    cd ..
87    mkdir run
88    cd run
89    \rm *
90    \cp ../input/* .
91    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
92    ln -sf ../../../../run_template/* .
93    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
94    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
95    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
96    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38 pickup_seaice.0000000216
97    \cp ../build/mitgcmuv .
98    qsub job_altix
99    
100    
101  ##########################################################################  ##########################################################################
# Line 32  cd .. Line 114  cd ..
114  mkdir run  mkdir run
115  cd run  cd run
116  \rm *  \rm *
117    \cp ../../tutorial_held_suarez_cs/input/grid* .
118  \cp ../input/* .  \cp ../input/* .
119  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
120  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 42  comparison output is in: Line 125  comparison output is in:
125  to use matlab to look at the output  to use matlab to look at the output
126  matlab  matlab
127    
128  for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
129           'QNETtave','FVtave','FUtave','EmPmRtave'}           'surForcT','oceTAUX','oceTAUY','surForcS'}
130      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);      tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);
131      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
132  end  end
133    
134  heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
135  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
136  uice=mask.*permute(readbin(['UICEtave.0000000020.data'],[32,6,32]),[1 3 2]);  uice=mask.*permute(readbin(['SIuice.0000000072.data'],[32,6,32]),[1 3 2]);
137  vice=mask.*permute(readbin(['VICEtave.0000000020.data'],[32,6,32]),[1 3 2]);  vice=mask.*permute(readbin(['SIvice.0000000072.data'],[32,6,32]),[1 3 2]);
138  clf  clf
139  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
140  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
# Line 75  cd .. Line 158  cd ..
158  mkdir run  mkdir run
159  cd run  cd run
160  \rm *  \rm *
161    \cp ../../tutorial_held_suarez_cs/input/grid* .
162  \cp ../input/* .  \cp ../input/* .
163  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
164  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 99  cd .. Line 183  cd ..
183  mkdir run  mkdir run
184  cd run  cd run
185  \rm *  \rm *
186    \cp ../../tutorial_held_suarez_cs/input/grid* .
187  \cp ../input/* .  \cp ../input/* .
188  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
189  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
# Line 132  qsub job_altix92_54t Line 217  qsub job_altix92_54t
217    
218  ##########################################################################  ##########################################################################
219  ##########################################################################  ##########################################################################
220  # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics  # 510*510*6*50, 1500-tile, 150-cpu, excludes land
221  # requires input files in sudirectories run_template and ncep_rgau  # uses s1500t_17x51 configuration
 # these can be obained from lou:/u/menemenl/cube  
222    
223  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
224  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
225  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
226  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_150 SIZE.h
227  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
228    
229  cd ../build  cd ../build
# Line 156  cd run Line 240  cd run
240  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
241  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
242  \rm pickup*  \rm pickup*
243  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
244  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
245  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv mitgcmuv150
246  qsub job_altix  qsub job_altix150
247    
248    
249  ##########################################################################  ##########################################################################
# Line 188  cd run Line 272  cd run
272  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
273  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
274  \rm pickup*  \rm pickup*
275  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
276  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
277  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv .
278  job_c20_375cpu < /dev/null >&! output.run &  job_c20_375cpu < /dev/null >&! output.run &
279    
280    
281  ##########################################################################  ##########################################################################
282  ##########################################################################  ##########################################################################
283  # 510*510*6*50, 1500-tile, 500-cpu, excludes land  # 510*510*6*50, 1500-tile, 375-cpu, excludes land
284  # uses s1500t_17x51 configuration  # uses s1500t_17x51 configuration
285  # example for running on c17-c20 using arrayd  # example for running on c17-c20 using arrayd
286    
287  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
288  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
289  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
290  \cp SIZE.h_500 SIZE.h  \cp SIZE.h_375 SIZE.h
291  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
292    
293  cd ../build  cd ../build
# Line 220  cd run Line 304  cd run
304  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
305  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
306  \rm pickup*  \rm pickup*
307  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
308  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
309  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv .
310  job_c19_500cpu < /dev/null >&! output.run &  job_c20_375cpu < /dev/null >&! output.run &
   
   
   
   
   
   
   
   
   
   
   
311    
312    
313    ##########################################################################
314    ##########################################################################
315    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
316    # uses s1500t_17x51 configuration
317    # example for running on c17-c20 using arrayd
318    
319    cd MITgcm/verification/global_ocean.cs32x15/code
320    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
321    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
322    \cp SIZE.h_500 SIZE.h
323    \cp packages.conf_hr packages.conf
324    
325    cd ../build
326    \rm *
327    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
328    make depend
329    make -j
330    
331    cd ..
332    mkdir run
333    cd run
334    \rm *
335    \cp ../input/* .
336    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
337    ln -sf ../../../../run_template/* .
338    \rm pickup*
339    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
340    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
341    \cp ../build/mitgcmuv .
342    job_c19_500cpu < /dev/null >&! output.run &
343    
344    
345    ##########################################################################
346    ##########################################################################
347    # 510*510*6*50, 216-cpu cube sphere on cosmos
348    
349    cd MITgcm/verification/global_ocean.cs32x15/code
350    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
351    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
352    \cp SIZE.h_216 SIZE.h
353    \cp packages.conf_hr packages.conf
354    
355    module unload latest_intel80
356    module unload mpich-gm-intel80
357    module load latest_intel81
358    module load mpich-gm-intel81
359    
360    cd ../build
361    \rm *
362    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
363    make depend
364    make -j
365    
366    cd ..
367    mkdir run
368    cd run
369    \rm *
370    \cp ../input/* .
371    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
372    ln -sf ../../../../run_template/* .
373    \rm pickup*
374    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
375    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
376    \cp ../build/mitgcmuv .
377    bsub < job_cosmos
378    
379    
380  ##########################################################################  ##########################################################################
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