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revision 1.57 by dimitri, Tue Feb 22 01:20:54 2005 UTC revision 1.80 by dimitri, Wed Dec 6 01:07:44 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 5, 2006: 216-CPU code for cube46
7    Changed diagnostics to accomodate JMCs latest and some
8    changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
9    to speed up code.
10    
11    November 7, 2006: 216-CPU code for cube43
12    Bug fixes in growth.F routine and new set of diagnostics
13    
14    October 15, 2006: 216-CPU code for cube40
15    
16    September 28, 2006: 216-CPU code for cube38
17    
18    September 4, 2006
19    Modified 32*32*6*15 experiments to use grid_cs32.* files from
20     verification/tutorial_held_suarez_cs/input instead of
21     tile* files from verification/global_ocean.cs32x15/input
22    
23    August 8, 2006: 216-CPU code and input used for cube37
24    using "June 10, 2006" MITgcm code.
25    
26    for online T/S profile diagnostics all that is needed is
27      profiles_init_fixed
28      profiles_inloop
29    see pkg/ecco/ecco_cost_init_fixed.F
30        pkg/ecco/cost_averagesfields.F
31    
32    ##########################################################################
33    ##########################################################################
34    # Get forcing files, etc.
35    # Example below is for cube46 on /nobackup2a/menemenl
36    
37    cd /nobackup2a/menemenl
38    mkdir cube46
39    cd cube46
40    ln -sf ../run_template .
41    ln -sf ../ncep_rgau .
42    
43    
44  ##########################################################################  ##########################################################################
45  ##########################################################################  ##########################################################################
46  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
47    
48      bash or sh shell:
49        $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
50        $ cvs login
51          ( enter the CVS password: "cvsanon" )
52    
53      tcsh or csh shell:
54        $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
55        $ cvs login
56          ( enter the CVS password: "cvsanon" )
57    
58  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README_ice
59  cvs co MITgcm_contrib/high_res_cube/code-mods  cvs co MITgcm_contrib/high_res_cube/code-mods
60  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
61  cvs co MITgcm_contrib/high_res_cube/results  cvs co MITgcm_contrib/high_res_cube/results
62  cvs co MITgcm_code  cvs co MITgcm_code
63  cvs co MITgcm/verification/global_ocean.cs32x15  cvs co MITgcm/verification/global_ocean.cs32x15
64  cvs co MITgcm/verification/testreport  cvs co MITgcm/verification/tutorial_held_suarez_cs/input
65    
66    
67    ##########################################################################
68    ##########################################################################
69    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
70    
71    cd MITgcm/verification/global_ocean.cs32x15/code
72    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
73    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
74    \cp SIZE.h_216 SIZE.h
75    \cp packages.conf_hr packages.conf
76    
77    cd ../build
78    \rm *
79    ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas
80    make depend
81    make -j
82    
83    cd ..
84    mkdir run
85    cd run
86    \rm *
87    \cp ../input/* .
88    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
89    ln -sf ../../../../run_template/* .
90    \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*
91    \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
92    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
93    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38 pickup_seaice.0000000216
94    \cp ../build/mitgcmuv .
95    qsub job_altix
96    
97    
98  ##########################################################################  ##########################################################################
# Line 32  cd .. Line 111  cd ..
111  mkdir run  mkdir run
112  cd run  cd run
113  \rm *  \rm *
114    \cp ../../tutorial_held_suarez_cs/input/grid* .
115  \cp ../input/* .  \cp ../input/* .
116  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
117  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 42  comparison output is in: Line 122  comparison output is in:
122  to use matlab to look at the output  to use matlab to look at the output
123  matlab  matlab
124    
125  for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...  for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...
126           'QNETtave','FVtave','FUtave','EmPmRtave'}           'surForcT','oceTAUX','oceTAUY','surForcS'}
127      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]);
128      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
129  end  end
130    
131  heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);
132  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
133  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]);
134  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]);
135  clf  clf
136  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
137  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
# Line 75  cd .. Line 155  cd ..
155  mkdir run  mkdir run
156  cd run  cd run
157  \rm *  \rm *
158    \cp ../../tutorial_held_suarez_cs/input/grid* .
159  \cp ../input/* .  \cp ../input/* .
160  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
161  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
# Line 99  cd .. Line 180  cd ..
180  mkdir run  mkdir run
181  cd run  cd run
182  \rm *  \rm *
183    \cp ../../tutorial_held_suarez_cs/input/grid* .
184  \cp ../input/* .  \cp ../input/* .
185  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
186  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
# Line 132  qsub job_altix92_54t Line 214  qsub job_altix92_54t
214    
215  ##########################################################################  ##########################################################################
216  ##########################################################################  ##########################################################################
217  # 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
218  # requires input files in sudirectories run_template and ncep_rgau  # uses s1500t_17x51 configuration
 # these can be obained from lou:/u/menemenl/cube  
219    
220  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
221  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
222  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
223  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_150 SIZE.h
224  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
225    
226  cd ../build  cd ../build
# Line 156  cd run Line 237  cd run
237  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
238  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
239  \rm pickup*  \rm pickup*
240  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
241  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
242  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv mitgcmuv150
243  qsub job_altix  qsub job_altix150
244    
245    
246  ##########################################################################  ##########################################################################
# Line 188  cd run Line 269  cd run
269  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
270  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
271  \rm pickup*  \rm pickup*
272  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
273  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
274  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv .
275  job_c20_375cpu < /dev/null >&! output.run &  job_c20_375cpu < /dev/null >&! output.run &
276    
277    
278  ##########################################################################  ##########################################################################
279  ##########################################################################  ##########################################################################
280  # 510*510*6*50, 1500-tile, 500-cpu, excludes land  # 510*510*6*50, 1500-tile, 375-cpu, excludes land
281  # uses s1500t_17x51 configuration  # uses s1500t_17x51 configuration
282  # example for running on c17-c20 using arrayd  # example for running on c17-c20 using arrayd
283    
284  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
285  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
286  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
287  \cp SIZE.h_500 SIZE.h  \cp SIZE.h_375 SIZE.h
288  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
289    
290  cd ../build  cd ../build
# Line 220  cd run Line 301  cd run
301  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
302  ln -sf ../../../../run_template/* .  ln -sf ../../../../run_template/* .
303  \rm pickup*  \rm pickup*
304  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216.data  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
305  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216.data  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
306  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv .
307  job_c19_500cpu < /dev/null >&! output.run &  job_c20_375cpu < /dev/null >&! output.run &
   
   
   
   
   
   
   
   
   
   
   
308    
309    
310    ##########################################################################
311    ##########################################################################
312    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
313    # uses s1500t_17x51 configuration
314    # example for running on c17-c20 using arrayd
315    
316    cd MITgcm/verification/global_ocean.cs32x15/code
317    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
318    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
319    \cp SIZE.h_500 SIZE.h
320    \cp packages.conf_hr packages.conf
321    
322    cd ../build
323    \rm *
324    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
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    job_c19_500cpu < /dev/null >&! output.run &
340    
341    
342    ##########################################################################
343    ##########################################################################
344    # 510*510*6*50, 216-cpu cube sphere on cosmos
345    
346    cd MITgcm/verification/global_ocean.cs32x15/code
347    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
348    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
349    \cp SIZE.h_216 SIZE.h
350    \cp packages.conf_hr packages.conf
351    
352    module unload latest_intel80
353    module unload mpich-gm-intel80
354    module load latest_intel81
355    module load mpich-gm-intel81
356    
357    cd ../build
358    \rm *
359    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
360    make depend
361    make -j
362    
363    cd ..
364    mkdir run
365    cd run
366    \rm *
367    \cp ../input/* .
368    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
369    ln -sf ../../../../run_template/* .
370    \rm pickup*
371    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
372    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
373    \cp ../build/mitgcmuv .
374    bsub < job_cosmos
375    
376    
377  ##########################################################################  ##########################################################################
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