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revision 1.1 by dimitri, Sat Apr 7 21:56:47 2007 UTC revision 1.5 by dimitri, Wed Apr 11 01:22:02 2007 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  This file has been replaced by  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    
3  Forcing fields and other input files needed for the CS510  Forcing fields and other input files needed for the CS510
# Line 15  http://ecco2.org/products/model_setups/c Line 8  http://ecco2.org/products/model_setups/c
8    
9  UPDATES  UPDATES
10    
11  February 6, 2006: cube56, same as cube 50 with SEAICEuseFlooding  April 10, 2007: preparing for cube65, Bryan and Lewis 1979 diffusivity
12    April 7 , 2007: preparing for cube64, era40_fullres forcing
 February 1, 2006: back to cube50 default (bottomDragQuadratic = 0.002)  
                   removed UVEL and VVEL from diagnostics  
   
 January 5, 2006: cube51, like cube50 but with bottomDragQuadratic = 0.0012  
   
 January 5, 2006: cube50, like cube48 but with snow advection  
   
 December 30, 2006: updates for cube49, the first  
 "blend" integration.  
   
 December 11, 2006: preparing for cube47, same as cube43  
 but with Arctic monthly river runoff climatology.  
   
 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.  
   
 November 7, 2006: 216-CPU code for cube43  
 Bug fixes in growth.F routine and new set of diagnostics  
13    
 October 15, 2006: 216-CPU code for cube40  
14    
 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  
   
 ##########################################################################  
15  ##########################################################################  ##########################################################################
16  # Get forcing files, etc.  # Get forcing files, etc.
17  # Example below is for cube46 on /nobackup2a/menemenl  # Example below is for cube46 on /nobackup2a/menemenl
18    
19  cd /nobackup2a/menemenl  cd /nobackup2a/menemenl
20  mkdir cube47  mkdir cube65
21  cd cube47  cd cube65
22  ln -sf ../run_template .  ln -sf ../run_template .
23  ln -sf ../ncep_rgau .  ln -sf ../ncep_rgau .
24    ln -sf ../era40_fullres .
25    
26    
27  ##########################################################################  ##########################################################################
 ##########################################################################  
28  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
29    
30    bash or sh shell:    bash or sh shell:
# Line 82  ln -sf ../ncep_rgau . Line 37  ln -sf ../ncep_rgau .
37      $ cvs login      $ cvs login
38        ( enter the CVS password: "cvsanon" )        ( enter the CVS password: "cvsanon" )
39    
40  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README.cs510
41  cvs co MITgcm_contrib/high_res_cube/code-mods  cvs co MITgcm_contrib/high_res_cube/code-mods
42  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
 cvs co MITgcm_contrib/high_res_cube/results  
43  cvs co MITgcm_code  cvs co MITgcm_code
 cvs co MITgcm/verification/global_ocean.cs32x15  
 cvs co MITgcm/verification/tutorial_held_suarez_cs/input  
   
   
 ##########################################################################  
 ##########################################################################  
 # 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  
   
 cd ..  
 mkdir run  
 cd run  
 \rm *  
 \cp ../input/* .  
 \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  
 ln -sf ../../../../run_template/* .  
 \rm pickup* eedata.mth data.pkg data.seaice data.exf_clim data.exf data.mnc data pr*  
 \rm bathy_Hmin50.bin *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t  
 ln -sf ../../../../run_template/pickup.0000000216.cube49 pickup.0000000216  
 ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube48 pickup_seaice.0000000216  
 \cp ../build/mitgcmuv .  
 qsub job_altix  
   
   
 ##########################################################################  
 ##########################################################################  
 # 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')  
44    
45    
46  ##########################################################################  ##########################################################################
47  ##########################################################################  # 510*510*6*50, 216-cpu cube sphere on altix with ifort
 # 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  
48    
49  cd ../build  cd MITgcm
50    mkdir build run
51    cd build
52  \rm *  \rm *
53  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas  \cp ../../MITgcm_contrib/high_res_cube/code-mods/* .
54  make depend  \cp ../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
 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/* .  
55  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_216 SIZE.h
56  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
57    ../tools/genmake2 -of ../../MITgcm_contrib/high_res_cube/code-mods/linux_ia64_ifort+mpi_altix_nas
 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  
58  make depend  make depend
59  make -j  make -j
60    cd ../run
 cd ..  
 mkdir run  
 cd run  
61  \rm *  \rm *
62  \cp ../input/* .  \cp ../../MITgcm_contrib/high_res_cube/input/* .
63  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  ln -sf ../../run_template/* .
64  ln -sf ../../../../run_template/* .  \rm pickup* data.pkg data.seaice data.exf_clim data.exf data *192_94* *.m LEV*JAN*
65  \rm pickup*  ln -sf ../../run_template/pickup.0000000216.cube49 pickup.0000000216
66  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216  ln -sf ../../run_template/pickup_seaice.0000000216.cube48 pickup_seaice.0000000216
 ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216  
67  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv .
68  bsub < job_cosmos  qsub job_altix
   
   
 ##########################################################################  
 ##########################################################################  
 # 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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