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revision 1.1 by dimitri, Sat Apr 7 21:56:47 2007 UTC revision 1.49 by dimitri, Wed Jul 28 22:48:02 2010 UTC
# Line 1  Line 1 
 !!!! Instructions in this file are obsolete and will eventually  
 !!!! be removed.  This file has been replaced by  
 !!!! MITgcm_contrib/high_res_cube/README.cs510  
 !!!! MITgcm_contrib/high_res_cube/README.cs32  
   
 =================  
   
1  Instructions for setting up a cube-sphere integration with sea-ice.  Instructions for setting up a cube-sphere integration with sea-ice.
2    
 Forcing fields and other input files needed for the CS510  
 configuration can be obtained from  
 http://ecco2.org/products/model_setups/cs510.html  
   
3  =================  =================
4    
5  UPDATES  UPDATES
6    
7  February 6, 2006: cube56, same as cube 50 with SEAICEuseFlooding  July 27, 2010.  Cube88 on pleiades - same as cube84 but with:
8       1. JRA25 instead of cube84 blend forcing
9  February 1, 2006: back to cube50 default (bottomDragQuadratic = 0.002)     2. useSALT_PLUME  = .TRUE., (off in Southern Ocean)
10                    removed UVEL and VVEL from diagnostics     3. useDOWN_SLOPE  = .TRUE.,
11       4. split north/south data.sec17saice parameters from regional optimizations
12  January 5, 2006: cube51, like cube50 but with bottomDragQuadratic = 0.0012     5. initialize from T/S/U/V/ETAN and sea ice from cube78 Jan 1992 pickup
13       6. 3-day 3D diagnostics
14  January 5, 2006: cube50, like cube48 but with snow advection     7. SEAICE_no_slip = .TRUE. to keep code stable
15    
16  December 30, 2006: updates for cube49, the first  June 30, 2009.  Cube86 -same as cube85 but with:
17  "blend" integration.     1. updated Southern OCean Bathymetry
18       2. ice shelf cavities
19  December 11, 2006: preparing for cube47, same as cube43  
20  but with Arctic monthly river runoff climatology.  June 16, 2009. Cube85 -same as cube84 but with:
21       1. split north/south data.seaice parameters from regional optimizations
22       2. includes pkg/salt_plume in the Arctic and pkg/down_slope globally
23       3. initialize from T/S/U/V/ETAN and sea ice files
24       4. 3-day 3D diagnostics
25       5. SEAICE_no_slip=.TRUE. to keep code stable
26    
27    June 13, 2008. Cube 81 - same as cube79 but with
28       1. new values for data.seaice and data.exf
29       2. DIFFKR_2_20_1_lat6070_cube81, which has diffKrS/T=3.55e-7 in Arctic
30       3. GMRedi turned off
31    
32    December 22, 2007. Cube80 - same as cube79 but with
33       SEAICE_BREAKS_VERIFICATION (SST relaxation depends on SIarea)
34       ALLOW_CLIMSST_RELAXATION to Reynold's daily 1/4-deg AVHRR analysis
35       ALLOW_CLIMSST_RELAXATION to monthly 1-deg WOA05 analysis
36    December 2, 2007. Cube79 - same as cube78 (blend3) but with
37       useRelativeWind=.TRUE. and SEAICE_gamma_t=259200
38    November 22, 2007. Cube 78 - blend 3
39    November 6, 2007. Cube 77 - same as cube75 but with SEAICE_SALINITY
40                                and era40_ecmwf_blend/cube59_GPCP forcing
41    November 3, 2007. Cube 76 - same as cube77 but 1979-2006 integration
42    August 31, 2007.  Cube75 - the second blend.
43    August 9, 2007. Cube74
44    August 6, 2007. Cube73
45    July 24, 2007. Cube72
46    July 8, 2007. Cube66: SEAICE_MULTICATEGORY, SEAICE_VARIABLE_FREEZING_POINT,
47       rhonil=1027.5, [temp/salt]AdvScheme=7, convertFW2Salt=-1, LSR_ERROR=1e-6
48       useRealFreshWaterFlux=.TRUE., runoff_lat_inc=179*1, SEAICE_salinity=10
49       bathyFile=GEBCO_510x6x510_ver06_dig.bin, HeffFile=heff_file8
50       SEAICE_availHeatFrac=.5, useGMRedi=.TRUE.
51    April 24, 2007. Cube65: Bryan and Lewis 1979 diffusivity
52       (cube67, cube68, and cube69 were carried out with cube65 code)
53    April 7 , 2007. Cube64: era40_fullres forcing
54    
 December 5, 2006: 216-CPU code for cube46  
 Changed diagnostics to accomodate JMCs latest and some  
 changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h  
 to speed up code.  
55    
 November 7, 2006: 216-CPU code for cube43  
 Bug fixes in growth.F routine and new set of diagnostics  
   
 October 15, 2006: 216-CPU code for cube40  
   
 September 28, 2006: 216-CPU code for cube38  
   
 September 4, 2006  
 Modified 32*32*6*15 experiments to use grid_cs32.* files from  
  verification/tutorial_held_suarez_cs/input instead of  
  tile* files from verification/global_ocean.cs32x15/input  
   
 August 8, 2006: 216-CPU code and input used for cube37  
 using "June 10, 2006" MITgcm code.  
   
 for online T/S profile diagnostics all that is needed is  
   profiles_init_fixed  
   profiles_inloop  
 see pkg/ecco/ecco_cost_init_fixed.F  
     pkg/ecco/cost_averagesfields.F  
   
 ##########################################################################  
56  ##########################################################################  ##########################################################################
57  # Get forcing files, etc.  # Get forcing files, etc.
58  # Example below is for cube46 on /nobackup2a/menemenl  # Example below is for cube88 on pleiades
59    
60  cd /nobackup2a/menemenl  mkdir cube88
61  mkdir cube47  cd cube88
62  cd cube47  ln -sf /nobackupp10/hzhang1/cs510/run_template .
63  ln -sf ../run_template .  ln -sf /nobackupp10/hzhang1/forcing/jra25 .
64  ln -sf ../ncep_rgau .  ln -sf /nobackupp10/hzhang1/forcing/cube78_forcing .
65    
66    
67  ##########################################################################  ##########################################################################
 ##########################################################################  
68  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
69    
70    bash or sh shell:  cvs co MITgcm_contrib/high_res_cube/README.cs510
     $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'  
     $ cvs login  
       ( enter the CVS password: "cvsanon" )  
   
   tcsh or csh shell:  
     $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'  
     $ cvs login  
       ( enter the CVS password: "cvsanon" )  
   
 cvs co MITgcm_contrib/high_res_cube/README_ice  
71  cvs co MITgcm_contrib/high_res_cube/code-mods  cvs co MITgcm_contrib/high_res_cube/code-mods
72  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
 cvs co MITgcm_contrib/high_res_cube/results  
73  cvs co MITgcm_code  cvs co MITgcm_code
 cvs co MITgcm/verification/global_ocean.cs32x15  
 cvs co MITgcm/verification/tutorial_held_suarez_cs/input  
74    
75    
76  ##########################################################################  ##########################################################################
77  ##########################################################################  # 510*510*6*50, 450-cpu cube sphere on pleiades with ifort
 # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics  
   
 cd MITgcm/verification/global_ocean.cs32x15/code  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  
 \cp SIZE.h_216 SIZE.h  
 \cp packages.conf_hr packages.conf  
   
 cd ../build  
 \rm *  
 ../../../tools/genmake2 -mods=../code -of ../code/linux_ia64_ifort+mpi_altix_nas  
 make depend  
 make -j  
78    
79  cd ..  cd MITgcm
80  mkdir run  mkdir build run
81  cd run  cd build
82  \rm *  \rm *
83  \cp ../input/* .  \cp ../../MITgcm_contrib/high_res_cube/code-mods/* .
84  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../MITgcm_contrib/high_res_cube/code-mods/s450t_34x102/SIZE.h .
85  ln -sf ../../../../run_template/* .  \rm README SIZE.h_mpi rotate_en_to_uv.F
86  \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*  ../tools/genmake2 -of ../tools/build_options/linux_amd64_ifort+mpi_ice_nas
87  \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t  make depend
88  ln -sf ../../../../run_template/pickup.0000000216.cube49 pickup.0000000216  make -j 16
89  ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube48 pickup_seaice.0000000216  cd ../run
90    \rm *
91    \cp ../../MITgcm_contrib/high_res_cube/input/*data* .
92    \cp ../../MITgcm_contrib/high_res_cube/input/modpickup .
93    \cp ../../MITgcm_contrib/high_res_cube/input/job* .
94    \mv data.seaice_hr data.seaice
95    \mv data.exf_hr data.exf
96    \mv data_hr data
97    \ln -sf ../../run_template/tile* .
98    \ln -sf ../../run_template/G*dig* .
99    \ln -sf ../../run_template/*Init.cube78 .
100  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv .
101  qsub job_altix  qsub job_cs510_pleiades450
   
   
 ##########################################################################  
 ##########################################################################  
 # 32*32*6*15, 1-cpu cube sphere  
   
 cd MITgcm/verification/global_ocean.cs32x15/code  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  
 \cp ../../../utils/exch2/code-mods/s12t_16x32/* .  
 \rm CPP_EEOPTIONS.h  
 cd ../build  
 \rm *  
 ../../../tools/genmake2 -mods=../code  
 make depend  
 make  
 cd ..  
 mkdir run  
 cd run  
 \rm *  
 \cp ../../tutorial_held_suarez_cs/input/grid* .  
 \cp ../input/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  
 ../build/mitgcmuv >& output.txt  
   
 comparison output is in:  
 ../../../../MITgcm_contrib/high_res_cube/results/output.txt  
   
 to use matlab to look at the output  
 matlab  
   
 for fld={'SIuice','SIvice','SIheff','SIarea','oceQsw', ...  
          'surForcT','oceTAUX','oceTAUY','surForcS'}  
     tmp=permute(readbin([fld{1} '.0000000072.data'],[32,6,32]),[1 3 2]);  
     cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause  
 end  
   
 heff=permute(readbin(['SIheff.0000000072.data'],[32,6,32]),[1 3 2]);  
 mask=0*heff; mask(find(heff>.001))=1;  
 uice=mask.*permute(readbin(['SIuice.0000000072.data'],[32,6,32]),[1 3 2]);  
 vice=mask.*permute(readbin(['SIvice.0000000072.data'],[32,6,32]),[1 3 2]);  
 clf  
 subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')  
 subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')  
 subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')  
 subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')  
   
   
 ##########################################################################  
 ##########################################################################  
 # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment  
   
 cd MITgcm/verification/global_ocean.cs32x15/code  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  
 \cp ../code_alt/code.176t_8x4/* .  
 cd ../build  
 \rm *  
 ../../../tools/genmake2 -mods=../code  
 make depend  
 make  
 cd ..  
 mkdir run  
 cd run  
 \rm *  
 \cp ../../tutorial_held_suarez_cs/input/grid* .  
 \cp ../input/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  
 ../build/mitgcmuv >& output.txt  
   
   
 ##########################################################################  
 ##########################################################################  
 # 32*32*6*15, 2-cpu cube sphere on the altices with ifort  
   
 cd MITgcm/verification/global_ocean.cs32x15/code  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  
 \cp ../../../utils/exch2/code-mods/s12t_16x32/* .  
 \cp SIZE.h_mpi SIZE.h  
   
 cd ../build  
 \rm *  
 ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas  
 make depend  
 make -j  
   
 cd ..  
 mkdir run  
 cd run  
 \rm *  
 \cp ../../tutorial_held_suarez_cs/input/grid* .  
 \cp ../input/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  
 mpirun -np 2 ../build/mitgcmuv  
   
   
 ##########################################################################  
 ##########################################################################  
 # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc  
 # starting with pickup file from end of 1992  
 # requires input files in sudirectories run_template and ncep_rgau  
   
 cd MITgcm/verification/global_ocean.cs32x15/code  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .  
 \cp packages.conf_hr packages.conf  
   
 cd ../build  
 \rm *  
 ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix  
 make depend  
 make -j  
   
 cd ..  
 mkdir run  
 cd run  
 \rm *  
 \cp ../input/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  
 qsub job_altix92_54t  
   
   
 ##########################################################################  
 ##########################################################################  
 # 510*510*6*50, 1500-tile, 150-cpu, excludes land  
 # uses s1500t_17x51 configuration  
   
 cd MITgcm/verification/global_ocean.cs32x15/code  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .  
 \cp SIZE.h_150 SIZE.h  
 \cp packages.conf_hr packages.conf  
   
 cd ../build  
 \rm *  
 ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas  
 make depend  
 make -j  
   
 cd ..  
 mkdir run  
 cd run  
 \rm *  
 \cp ../input/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  
 ln -sf ../../../../run_template/* .  
 \rm pickup*  
 ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216  
 ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216  
 \cp ../build/mitgcmuv mitgcmuv150  
 qsub job_altix150  
   
   
 ##########################################################################  
 ##########################################################################  
 # 510*510*6*50, 1500-tile, 375-cpu, excludes land  
 # uses s1500t_17x51 configuration  
 # example for running on c17-c20 using arrayd  
   
 cd MITgcm/verification/global_ocean.cs32x15/code  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .  
 \cp SIZE.h_375 SIZE.h  
 \cp packages.conf_hr packages.conf  
   
 cd ../build  
 \rm *  
 ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas  
 make depend  
 make -j  
   
 cd ..  
 mkdir run  
 cd run  
 \rm *  
 \cp ../input/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  
 ln -sf ../../../../run_template/* .  
 \rm pickup*  
 ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216  
 ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216  
 \cp ../build/mitgcmuv .  
 job_c20_375cpu < /dev/null >&! output.run &  
   
   
 ##########################################################################  
 ##########################################################################  
 # 510*510*6*50, 1500-tile, 375-cpu, excludes land  
 # uses s1500t_17x51 configuration  
 # example for running on c17-c20 using arrayd  
   
 cd MITgcm/verification/global_ocean.cs32x15/code  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .  
 \cp SIZE.h_375 SIZE.h  
 \cp packages.conf_hr packages.conf  
   
 cd ../build  
 \rm *  
 ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas  
 make depend  
 make -j  
   
 cd ..  
 mkdir run  
 cd run  
 \rm *  
 \cp ../input/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  
 ln -sf ../../../../run_template/* .  
 \rm pickup*  
 ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216  
 ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216  
 \cp ../build/mitgcmuv .  
 job_c20_375cpu < /dev/null >&! output.run &  
   
   
 ##########################################################################  
 ##########################################################################  
 # 510*510*6*50, 1500-tile, 500-cpu, excludes land  
 # uses s1500t_17x51 configuration  
 # example for running on c17-c20 using arrayd  
   
 cd MITgcm/verification/global_ocean.cs32x15/code  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .  
 \cp SIZE.h_500 SIZE.h  
 \cp packages.conf_hr packages.conf  
   
 cd ../build  
 \rm *  
 ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas  
 make depend  
 make -j  
   
 cd ..  
 mkdir run  
 cd run  
 \rm *  
 \cp ../input/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  
 ln -sf ../../../../run_template/* .  
 \rm pickup*  
 ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216  
 ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216  
 \cp ../build/mitgcmuv .  
 job_c19_500cpu < /dev/null >&! output.run &  
   
   
 ##########################################################################  
 ##########################################################################  
 # 510*510*6*50, 216-cpu cube sphere on cosmos  
   
 cd MITgcm/verification/global_ocean.cs32x15/code  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  
 \cp SIZE.h_216 SIZE.h  
 \cp packages.conf_hr packages.conf  
   
 module unload latest_intel80  
 module unload mpich-gm-intel80  
 module load latest_intel81  
 module load mpich-gm-intel81  
   
 cd ../build  
 \rm *  
 ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos  
 make depend  
 make -j  
   
 cd ..  
 mkdir run  
 cd run  
 \rm *  
 \cp ../input/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  
 ln -sf ../../../../run_template/* .  
 \rm pickup*  
 ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216  
 ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216  
 \cp ../build/mitgcmuv .  
 bsub < job_cosmos  
   
   
 ##########################################################################  
 ##########################################################################  
 # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc  
 # requires input files in sudirectories run_template and ncep_rgau  
 # presently residing under orion:/tmp1/dmenem/cube  
   
 cd MITgcm/verification/global_ocean.cs32x15/code  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  
 \cp SIZE.h_54 SIZE.h  
 \cp packages.conf_hr packages.conf  
   
 cd ../build  
 \rm *  
 ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix  
 make depend  
 make -j  
   
 cd ..  
 mkdir run  
 cd run  
 \rm *  
 \cp ../input/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  
 qsub job_orion  
   
   
 ##########################################################################  
 ##########################################################################  
 # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc  
 # requires input files in sudirectories run_template and ncep_rgau  
 # presently residing under orion:/tmp1/dmenem/cube  
   
 cd MITgcm/verification/global_ocean.cs32x15/code  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .  
 \cp SIZE.h_41 SIZE.h  
 \cp packages.conf_hr packages.conf  
   
 cd ../build  
 \rm *  
 ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix  
 make depend  
 make -j  
   
 cd ..  
 mkdir run  
 cd run  
 \rm *  
 \cp ../input/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  
 qsub job_orion41  
   
   
 ##########################################################################  
 ##########################################################################  
 # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc  
 # requires input files in sudirectories run_template and ncep_rgau  
 # presently residing under orion:/tmp1/dmenem/cube  
   
 cd MITgcm/verification/global_ocean.cs32x15/code  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .  
 \cp SIZE.h_50 SIZE.h  
 \cp packages.conf_hr packages.conf  
   
 cd ../build  
 \rm *  
 ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix  
 make depend  
 make -j  
   
 cd ..  
 mkdir run  
 cd run  
 \rm *  
 \cp ../input/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  
 qsub job_orion  
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