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revision 1.1 by dimitri, Sat Apr 7 21:56:47 2007 UTC revision 1.38 by dimitri, Fri Jun 13 18:58:39 2008 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  This file has been replaced by  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  June 13, 2008. Cube 81 - same as cube79 but with
12       1. salt plume package turned on
13  February 1, 2006: back to cube50 default (bottomDragQuadratic = 0.002)     2. new values for data.seaice and data.exf
14                    removed UVEL and VVEL from diagnostics     3. DIFFKR_2_20_1_lat6070_cube81, which has diffKrS/T=3.55e-7 in Arctic
15       4. GMRedi turned off
16  January 5, 2006: cube51, like cube50 but with bottomDragQuadratic = 0.0012  
17    December 22, 2007. Cube80 - same as cube79 but with
18  January 5, 2006: cube50, like cube48 but with snow advection     SEAICE_BREAKS_VERIFICATION (SST relaxation depends on SIarea)
19       ALLOW_CLIMSST_RELAXATION to Reynold's daily 1/4-deg AVHRR analysis
20  December 30, 2006: updates for cube49, the first     ALLOW_CLIMSST_RELAXATION to monthly 1-deg WOA05 analysis
21  "blend" integration.  December 2, 2007. Cube79 - same as cube78 (blend3) but with
22       useRelativeWind=.TRUE. and SEAICE_gamma_t=259200
23  December 11, 2006: preparing for cube47, same as cube43  November 22, 2007. Cube 78 - blend 3
24  but with Arctic monthly river runoff climatology.  November 6, 2007. Cube 77 - same as cube75 but with SEAICE_SALINITY
25                                and era40_ecmwf_blend/cube59_GPCP forcing
26  December 5, 2006: 216-CPU code for cube46  November 3, 2007. Cube 76 - same as cube77 but 1979-2006 integration
27  Changed diagnostics to accomodate JMCs latest and some  August 31, 2007.  Cube75 - the second blend.
28  changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h  August 9, 2007. Cube74
29  to speed up code.  August 6, 2007. Cube73
30    July 24, 2007. Cube72
31    July 8, 2007. Cube66: SEAICE_MULTICATEGORY, SEAICE_VARIABLE_FREEZING_POINT,
32       rhonil=1027.5, [temp/salt]AdvScheme=7, convertFW2Salt=-1, LSR_ERROR=1e-6
33       useRealFreshWaterFlux=.TRUE., runoff_lat_inc=179*1, SEAICE_salinity=10
34       bathyFile=GEBCO_510x6x510_ver06_dig.bin, HeffFile=heff_file8
35       SEAICE_availHeatFrac=.5, useGMRedi=.TRUE.
36    April 24, 2007. Cube65: Bryan and Lewis 1979 diffusivity
37       (cube67, cube68, and cube69 were carried out with cube65 code)
38    April 7 , 2007. Cube64: era40_fullres forcing
39    
 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  
40    
41  ##########################################################################  ##########################################################################
 ##########################################################################  
42  # Get forcing files, etc.  # Get forcing files, etc.
43  # Example below is for cube46 on /nobackup2a/menemenl  # Example below is for cube81 on /nobackup2a/menemenl
44    
45  cd /nobackup2a/menemenl  cd /nobackup2a/menemenl
46  mkdir cube47  mkdir cube81
47  cd cube47  cd cube81
48  ln -sf ../run_template .  ln -sf ../run_template .
49  ln -sf ../ncep_rgau .  ln -sf ../cube78_forcing .
50    ln -sf ../ncep_rgau/ .
51    
52    
53  ##########################################################################  ##########################################################################
 ##########################################################################  
54  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
55    
56    bash or sh shell:    bash or sh shell:
# Line 82  ln -sf ../ncep_rgau . Line 63  ln -sf ../ncep_rgau .
63      $ cvs login      $ cvs login
64        ( enter the CVS password: "cvsanon" )        ( enter the CVS password: "cvsanon" )
65    
66  cvs co MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/README.cs510
67  cvs co MITgcm_contrib/high_res_cube/code-mods  cvs co MITgcm_contrib/high_res_cube/code-mods
68  cvs co MITgcm_contrib/high_res_cube/input  cvs co MITgcm_contrib/high_res_cube/input
 cvs co MITgcm_contrib/high_res_cube/results  
69  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')  
   
   
 ##########################################################################  
 ##########################################################################  
 # 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  
70    
71    
72  ##########################################################################  ##########################################################################
73  ##########################################################################  # 510*510*6*50, 216-cpu cube sphere on altix with ifort
 # 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  
74    
75  cd ..  cd MITgcm
76  mkdir run  mkdir build run
77  cd run  cd build
78  \rm *  \rm *
79  \cp ../input/* .  \cp ../../MITgcm_contrib/high_res_cube/code-mods/* .
80  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
 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/* .  
81  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_216 SIZE.h
82  \cp packages.conf_hr packages.conf  ../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  
83  make depend  make depend
84  make -j  make -j
85    cd ../run
 cd ..  
 mkdir run  
 cd run  
86  \rm *  \rm *
87  \cp ../input/* .  \cp ../../MITgcm_contrib/high_res_cube/input/* .
88  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  ln -sf ../../run_template/* .
89  ln -sf ../../../../run_template/* .  \rm pickup* *192_94* *.m D*1 E* G*all.bin L* W*10.bin h*[6-7] PHC*
90  \rm pickup*  \mv data.exf_hr data.exf
91  ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216  \mv data_hr data
92  ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216  ln -sf ../../run_template/pickup.0000000216.cube78 pickup.0000000216
93    ln -sf ../../run_template/pickup_seaice.0000000216.cube78 pickup_seaice.0000000216
94    ln -sf ../../run_template/pickup.0000000216.meta.cube78 pickup.0000000216.meta
95    ln -sf ../../run_template/pickup_seaice.0000000216.meta.cube78 pickup_seaice.0000000216.meta
96  \cp ../build/mitgcmuv .  \cp ../build/mitgcmuv .
97  bsub < job_cosmos  \mv job_altix cube81
98    qsub cube81
99    
100    
101  ##########################################################################  ##########################################################################
102  ##########################################################################  # generating initial pickup files for cube78
 # 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  
103    
104  cd ..  data
105  mkdir run  # run for 4 days from time step 216 with 2-min time step
106  cd run   endtime=345600.,
107  \rm *   deltaT=120.,
108  \cp ../input/* .   pChkptFreq=345600.,
109  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .   monitorFreq=1.,
110  qsub job_orion  
111    cd ../../run_template
112    mv pickup.0000000216.cube78 pickup.0000000216.cube78_raw
113  ##########################################################################  mv pickup_seaice.0000000216.cube78 pickup_seaice.0000000216.cube78_raw
114  ##########################################################################  cd ../cube78/MITgcm/run
115  # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc  \mv pickup.0000002880.data ../../run_template/pickup.0000000216.cube78
116  # requires input files in sudirectories run_template and ncep_rgau  \mv pickup_seaice.0000002880.data ../../run_template/pickup_seaice.0000000216.cube78
117  # presently residing under orion:/tmp1/dmenem/cube  \mv pickup.0000002880.meta ../../run_template/pickup.0000000216.meta.cube78
118    \mv pickup_seaice.0000002880.meta ../../run_template/pickup_seaice.0000000216.meta.cube78
119  cd MITgcm/verification/global_ocean.cs32x15/code  \rm *.meta *.data STD* cube78.o*
120  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../MITgcm_contrib/high_res_cube/input/data_hr data
121  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .  ln -sf ../../run_template/pickup.0000000216.cube78 pickup.0000000216
122  \cp SIZE.h_41 SIZE.h  ln -sf ../../run_template/pickup_seaice.0000000216.cube78 pickup_seaice.0000000216
123  \cp packages.conf_hr packages.conf  ln -sf ../../run_template/pickup.0000000216.meta.cube78 pickup.0000000216.meta
124    ln -sf ../../run_template/pickup_seaice.0000000216.meta.cube78 pickup_seaice.0000000216.meta
125  cd ../build  qsub cube78
 \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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