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revision 1.58 by dimitri, Sun May 1 14:02:20 2005 UTC revision 1.83 by dimitri, Thu Dec 21 15:16:17 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.  Forcing fields and other input files needed for the CS510
4    configuration can be obtained from
5    http://ecco2.org/products/model_setups/cs510.html
6    
7    =================
8    UPDATES
9    
10    December 11, 2006: preparing for cube47, same as cube43
11    but with Arctic monthly river runoff climatology
12    
13    December 5, 2006: 216-CPU code for cube46
14    Changed diagnostics to accomodate JMCs latest and some
15    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
16    to speed up code.
17    
18    November 7, 2006: 216-CPU code for cube43
19    Bug fixes in growth.F routine and new set of diagnostics
20    
21    October 15, 2006: 216-CPU code for cube40
22    
23    September 28, 2006: 216-CPU code for cube38
24    
25    September 4, 2006
26    Modified 32*32*6*15 experiments to use grid_cs32.* files from
27     verification/tutorial_held_suarez_cs/input instead of
28     tile* files from verification/global_ocean.cs32x15/input
29    
30    August 8, 2006: 216-CPU code and input used for cube37
31    using "June 10, 2006" MITgcm code.
32    
33    for online T/S profile diagnostics all that is needed is
34      profiles_init_fixed
35      profiles_inloop
36    see pkg/ecco/ecco_cost_init_fixed.F
37        pkg/ecco/cost_averagesfields.F
38    
39    ##########################################################################
40    ##########################################################################
41    # Get forcing files, etc.
42    # Example below is for cube46 on /nobackup2a/menemenl
43    
44    cd /nobackup2a/menemenl
45    mkdir cube47
46    cd cube47
47    ln -sf ../run_template .
48    ln -sf ../ncep_rgau .
49    
50    
51  ##########################################################################  ##########################################################################
52  ##########################################################################  ##########################################################################
53  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
54    
55      bash or sh shell:
56        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
57        $ cvs login
58          ( enter the CVS password: "cvsanon" )
59    
60      tcsh or csh shell:
61        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
62        $ cvs login
63          ( enter the CVS password: "cvsanon" )
64    
65  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
66  cvs co MITgcm_contrib/high_res_cube/code-mods  cvs co MITgcm_contrib/high_res_cube/code-mods
67  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
68  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
69  cvs co MITgcm_code  cvs co MITgcm_code
70  cvs co MITgcm/verification/global_ocean.cs32x15  cvs co MITgcm/verification/global_ocean.cs32x15
71  cvs co MITgcm/verification/testreport  cvs co MITgcm/verification/tutorial_held_suarez_cs/input
72    
73    
74    ##########################################################################
75    ##########################################################################
76    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
77    
78    cd MITgcm/verification/global_ocean.cs32x15/code
79    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
80    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
81    \cp SIZE.h_216 SIZE.h
82    \cp packages.conf_hr packages.conf
83    
84    cd ../build
85    \rm *
86    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
87    make depend
88    make -j
89    
90    cd ..
91    mkdir run
92    cd run
93    \rm *
94    \cp ../input/* .
95    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
96    ln -sf ../../../../run_template/* .
97    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
98    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
99    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
100    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38 pickup_seaice.0000000216
101    \cp ../build/mitgcmuv .
102    qsub job_altix
103    
104    
105  ##########################################################################  ##########################################################################
# Line 32  cd .. Line 118  cd ..
118  mkdir run  mkdir run
119  cd run  cd run
120  \rm *  \rm *
121    \cp ../../tutorial_held_suarez_cs/input/grid* .
122  \cp ../input/* .  \cp ../input/* .
123  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
124  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 42  comparison output is in: Line 129  comparison output is in:
129  to use matlab to look at the output  to use matlab to look at the output
130  matlab  matlab
131    
132  for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
133           'QNETtave','FVtave','FUtave','EmPmRtave'}           'surForcT','oceTAUX','oceTAUY','surForcS'}
134      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]);
135      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
136  end  end
137    
138  heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
139  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
140  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]);
141  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]);
142  clf  clf
143  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
144  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
# Line 75  cd .. Line 162  cd ..
162  mkdir run  mkdir run
163  cd run  cd run
164  \rm *  \rm *
165    \cp ../../tutorial_held_suarez_cs/input/grid* .
166  \cp ../input/* .  \cp ../input/* .
167  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
168  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 99  cd .. Line 187  cd ..
187  mkdir run  mkdir run
188  cd run  cd run
189  \rm *  \rm *
190    \cp ../../tutorial_held_suarez_cs/input/grid* .
191  \cp ../input/* .  \cp ../input/* .
192  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
193  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
# Line 132  qsub job_altix92_54t Line 221  qsub job_altix92_54t
221    
222  ##########################################################################  ##########################################################################
223  ##########################################################################  ##########################################################################
224  # 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
225  # requires input files in sudirectories run_template and ncep_rgau  # uses s1500t_17x51 configuration
 # these can be obained from lou:/u/menemenl/cube  
226    
227  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
228  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
229  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
230  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_150 SIZE.h
231  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
232    
233  cd ../build  cd ../build
# Line 156  cd run Line 244  cd run
244  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
245  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
246  \rm pickup*  \rm pickup*
247  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
248  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
249  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv mitgcmuv150
250  qsub job_altix  qsub job_altix150
251    
252    
253  ##########################################################################  ##########################################################################
254  ##########################################################################  ##########################################################################
255  # 510*510*6*50, 1500-tile, 150-cpu, excludes land  # 510*510*6*50, 1500-tile, 375-cpu, excludes land
256  # uses s1500t_17x51 configuration  # uses s1500t_17x51 configuration
257    # example for running on c17-c20 using arrayd
258    
259  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
260  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
261  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
262  \cp SIZE.h_150 SIZE.h  \cp SIZE.h_375 SIZE.h
263  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
264    
265  cd ../build  cd ../build
# Line 186  cd run Line 276  cd run
276  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
277  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
278  \rm pickup*  \rm pickup*
279  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
280  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
281  \cp ../build/mitgcmuv mitgcmuv150  \cp ../build/mitgcmuv .
282  qsub job_altix150  job_c20_375cpu < /dev/null >&! output.run &
   
   
   
   
   
   
   
   
   
   
   
   
   
283    
284    
285  ##########################################################################  ##########################################################################
# Line 231  cd run Line 308  cd run
308  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
309  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
310  \rm pickup*  \rm pickup*
311  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
312  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
313  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv .
314  job_c20_375cpu < /dev/null >&! output.run &  job_c20_375cpu < /dev/null >&! output.run &
315    
# Line 263  cd run Line 340  cd run
340  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
341  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
342  \rm pickup*  \rm pickup*
343  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
344  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
345  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv .
346  job_c19_500cpu < /dev/null >&! output.run &  job_c19_500cpu < /dev/null >&! output.run &
347    
348    
349    ##########################################################################
350    ##########################################################################
351    # 510*510*6*50, 216-cpu cube sphere on cosmos
352    
353    cd MITgcm/verification/global_ocean.cs32x15/code
354    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
355    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
356    \cp SIZE.h_216 SIZE.h
357    \cp packages.conf_hr packages.conf
358    
359    module unload latest_intel80
360    module unload mpich-gm-intel80
361    module load latest_intel81
362    module load mpich-gm-intel81
363    
364    cd ../build
365    \rm *
366    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
367    make depend
368    make -j
369    
370    cd ..
371    mkdir run
372    cd run
373    \rm *
374    \cp ../input/* .
375    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
376    ln -sf ../../../../run_template/* .
377    \rm pickup*
378    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
379    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
380    \cp ../build/mitgcmuv .
381    bsub < job_cosmos
   
   
   
   
382    
383    
384  ##########################################################################  ##########################################################################
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