/[MITgcm]/MITgcm_contrib/ecco_darwin/v2_cs510_Brix/readme.txt
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revision 1.2 by dimitri, Tue Aug 28 15:09:54 2018 UTC revision 1.4 by dimitri, Thu Aug 1 02:10:28 2019 UTC
# Line 1  Line 1 
1  # Build executable for ECCO-Darwin version 3  # Build executable for ECCO-Darwin version 2 (ag4)
2  # with circa-2011 MITgcm code, equivalent to  # corresponding to optimized solution in Brix et al. (2015)
3  # /nobackup/hbrix/MITgcm_110502/build_darwin_p6/mitgcmuv  # This reproduces executable with circa-2011 MITgcm code from
4    # /nobackup/hbrix/MITgcm_110502/build_darwin_ag4/mitgcmuv
5    
6  cvs -d :pserver:cvsanon:cvsanon@mitgcm.org:/u/gcmpack co -D "2011-05-12 10:30:47" MITgcm_code  cvs -d :pserver:cvsanon:cvsanon@mitgcm.org:/u/gcmpack co -D "2011-05-12 10:30:47" MITgcm_code
7  cvs -d :pserver:cvsanon:cvsanon@mitgcm.org:/u/gcmpack co -D "2011-05-12 10:30:47" MITgcm_contrib/darwin/pkg/darwin  cvs -d :pserver:cvsanon:cvsanon@mitgcm.org:/u/gcmpack co -D "2011-05-12 10:30:47" MITgcm_contrib/darwin/pkg/darwin
8  cvs -d :pserver:cvsanon:cvsanon@mitgcm.org:/u/gcmpack co MITgcm_contrib/ecco_darwin/v3_cs510_Brix  cvs -d :pserver:cvsanon:cvsanon@mitgcm.org:/u/gcmpack co MITgcm_contrib/ecco_darwin/v2_cs510_Brix
9  cd MITgcm/pkg  cd MITgcm/pkg
10  ln -sf ../../MITgcm_contrib/darwin/pkg/darwin .  ln -sf ../../MITgcm_contrib/darwin/pkg/darwin .
11  cd ..  cd ..
# Line 13  cd build Line 14  cd build
14  module purge  module purge
15  module load comp-intel/2016.2.181 mpi-sgi/mpt.2.14r19 hdf4/4.2.12 hdf5/1.8.18_mpt netcdf/4.4.1.1_mpt  module load comp-intel/2016.2.181 mpi-sgi/mpt.2.14r19 hdf4/4.2.12 hdf5/1.8.18_mpt netcdf/4.4.1.1_mpt
16  ../tools/genmake2 -of \  ../tools/genmake2 -of \
17      ../../MITgcm_contrib/ecco_darwin/v3_cs510_Brix/code/linux_amd64_ifort+mpi_ice_nas \      ../../MITgcm_contrib/ecco_darwin/v2_cs510_Brix/code/linux_amd64_ifort+mpi_ice_nas \
18      -mo ../../MITgcm_contrib/ecco_darwin/v3_cs510_Brix/code      -mo ../../MITgcm_contrib/ecco_darwin/v2_cs510_Brix/code
19  make depend  make depend
20  make -j 16  make -j 16
21    
22  ==============  ==============
23  # Instructions for running Version 3 (cg1) to 2009-2013.  # Instructions for running Version 2 (ag4) to 2009-2010.
24    # lou:~hbrix/ECCO2/darwin_ag4
25    #
26    # darwin_ag4:
27    # Starting beginning of 2009 from a weighted combination of the ptracers
28    # and dic pickup files from darwin runs 'a4v' 'a5v' 'a6v' 'a7v' 'a9v'
29    # with fact1 = 0.16033; fact2 = 0.56404; fact3 = -0.077899; fact4 = 0.10418;
30    # fact5 = 0.24935; Base run is a5v. Factors are from Green's
31    # function analysis of these four runs for 2009/10 using LDEO surface
32    # pCO2, Takahashi pCO2 climatology (variability, not absolute values and
33    # the global mean CO2 flux for 2010. pickup and pickup_seaice file are
34    # from 2009 adjoint integration.
35    #
36    # runs={'a4v' 'a5v' 'a6v' 'a7v' 'a9v'}; gfrun='ag4';
37    # fact1 = 0.16033;
38    # fact2 = 0.56404;
39    # fact3 = -0.077899;
40    # fact4 = 0.10418;
41    # fact5 = 0.24935;
42    # piston velocity factor in dic_surfforcing.F from 0.337 to 0.34822
43    # R_PICPOC in darwin_generate_phyto.F from 0.04 to 0.133.
44    # optimization based on:
45    #     'a4v'    'a6v'    'a7v'    'a9v'    'a10v'    'a13v'
46    # Globflux_err = 0.01
47    # a5v -0.57061
48    # a4v 0.16033 +/- 0.010098
49    # a6v -0.077899 +/- 0.035022
50    # a7v 0.10418 +/- 0.0089553
51    # a9v 0.24935 +/- 0.0076539
52    # a10v -0.41537 +/- 0.047835
53    #  -> piston factor = 0.34822
54    # a13v 1.55 +/- 0.064771
55    #  -> R_PICPOC = 0.133
56    # global-mean flux: -2.5471
57    
58  cd ..  cd ..
59  mkdir run  mkdir run
60  cd run  cd run
61  ln -sf ../build/mitgcmuv .  ln -sf ../build/mitgcmuv .
62  cp ../../MITgcm_contrib/ecco_darwin/v3_cs510_Brix/input/* .  cp ../../MITgcm_contrib/ecco_darwin/v2_cs510_Brix/input/* .
63  ln -sf ~dmenemen/CMS/run_template_cg1/darwin* .  ln -sf ~dmenemen/CMS/run_template_cg1/darwin* .
64  ln -sf ~dmenemen/CMS/run_template_cg1/DIFFKR_2_20_1_lat6070_cube81 .  ln -sf ~dmenemen/CMS/run_template_cg1/DIFFKR_2_20_1_lat6070_cube81 .
65  ln -sf /nobackup/hzhang1/cs510/run_template/GEBCO_510x6x510_ver06_dig.bin .  ln -sf /nobackup/hzhang1/cs510/run_template/GEBCO_510x6x510_ver06_dig.bin .
# Line 34  ln -sf /nobackup/hzhang1/cs510/ICBC_2009 Line 68  ln -sf /nobackup/hzhang1/cs510/ICBC_2009
68  ln -sf /nobackup/hbrix/ICBC/pco2a_blended_* .  ln -sf /nobackup/hbrix/ICBC/pco2a_blended_* .
69  ln -sf pco2a_blended_2012 pco2a_blended_2013  ln -sf pco2a_blended_2012 pco2a_blended_2013
70  ln -sf pco2a_blended_2012 pco2a_blended_2014  ln -sf pco2a_blended_2012 pco2a_blended_2014
71  ln -sf /nobackup/hzhang1/cs510/ICBC_2009_iter26/pickup.0000000001.data_xx pickup.0000000001.data  ln -sf /nobackupp8/dmenemen/CMS/lou_brix_ECCO2/darwin_ag4/pick* .
 ln -sf /nobackup/hzhang1/cs510/ICBC_2009/pickup*.0000000001.??ta .  
72  ln -sf /nobackup/dmenemen/forcing/runoff/runoff-360x180x12.bin .  ln -sf /nobackup/dmenemen/forcing/runoff/runoff-360x180x12.bin .
73  ln -sf /nobackup/hzhang1/cs510/run_template/tile00* .  ln -sf /nobackup/hzhang1/cs510/run_template/tile00* .
74    
# Line 43  ln -sf /nobackup/hzhang1/cs510/run_templ Line 76  ln -sf /nobackup/hzhang1/cs510/run_templ
76  qsub run_darwin_450  qsub run_darwin_450
77    
78  ##############################################################  ##############################################################
79    # From ftp://ecco.jpl.nasa.gov/ECCO2/Darwin/CarbFlux_v2
80  From ftp://ecco.jpl.nasa.gov/ECCO2/Darwin/CarbFlux_v2  # Global Attributes:
81  Global Attributes:  # description             = 'ECCO2-Darwin CS510 run ag4 monthly average'
82   description              = 'ECCO2-Darwin CS510 run ag4 monthly average'  # MITgcmUV_version        = 'checkpoint62w'
83   MITgcmUV_version         = 'checkpoint62w'  # IntegrationPeriod       = '2009-01-01 -- 2010-12-31'
84   IntegrationPeriod        = '2009-01-01 -- 2010-12-31'  # InitialConditionsPhysics= 'ECCO2-CS510 ver. 2 (adjoint), Jan09-Apr10,
85   InitialConditionsPhysics = 'ECCO2-CS510 ver. 2 (adjoint), Jan09-Apr10,  #                            iter. 22.'
86                               iter. 22.'  # InitialConditionsBGC    = 'Linear combination of the initial conditions of
87   InitialConditionsBGC     = 'Linear combination of the initial conditions of  #                            five sensitivity experiments for all
88                               five sensitivity experiments for all  #                            biogeochemical tracers (Greens functions run ag4)'
89                               biogeochemical tracers (Greens functions run  # SurfaceForcingPhysics   = 'ECCO2-CS510 ver. 2 (adjoint), Jan09-Apr10,
90                               ag4)'  #                            iter. 22. JRA-25 after Apr10.'
91   SurfaceForcingPhysics    = 'ECCO2-CS510 ver. 2 (adjoint), Jan09-Apr10,  # SurfaceForcingBGC       = 'Time and space variable atmospheric pCO2 blended
92                               iter. 22. JRA-25 after Apr10.'  #                            from daily 2009 GEOS-Chem results provided by K.
93   SurfaceForcingBGC        = 'Time and space variable atmospheric pCO2 blended  #                            Bowman (JPL) on 3/3/2011 and global atmospheric
94                               from daily 2009 GEOS-Chem results provided by  #                            monthly means from NOAA ESRL. Iron/dust
95                               Kevin Bowman (JPL) on 3/3/2011 and global  #                            climatological values from Mahowald (2006).'
96                               atmospheric monthly means from NOAA  # ModelParametersPhysics  = 'ECCO2-CS510 ver. 2 (adjoint), Jan09-Apr10,
97                               ESRL. Iron/dust climatological values from  #                            iter. 22.'
98                               Mahowald (2006).'  # ModelParametersBGC      = '5 phytoplankton species, set-up from Stephanie
99   ModelParametersPhysics   = 'ECCO2-CS510 ver. 2 (adjoint), Jan09-Apr10,  #                            Dutkiewicz (MIT);  PIC phytoplankton production
100                               iter. 22.'  #                            relative to organic carbon (R_PICPOC) = 0.133.'
101   ModelParametersBGC       = '5 phytoplankton species, set-up from Stephanie  # author                  = 'Holger Brix -- UCLA/JPL'
102                               Dutkiewicz (MIT);  PIC phytoplankton production  # date                    = '10-Feb-2012'
103                               relative to organic carbon (R_PICPOC) = 0.133.'  # contact                 = 'hbrix@ucla.edu'
104   author                   = 'Holger Brix -- UCLA/JPL'  
105   date                     = '10-Feb-2012'  # From pfe:/home5/hbrix/README_runs
106   contact                  = 'hbrix@ucla.edu'  # darwin_ag4:
107    # Starting beginning of 2009 from a weighted comination of the ptracers
108  From pfe:/home5/hbrix/README_gf  # and dic pickup files from darwin runs 'a4v' 'a5v' 'a6v' 'a7v' 'a9v'
109  runs={'a4v' 'a5v' 'a6v' 'a7v' 'a9v'}; gfrun='ag4';  # with fact1 = 0.16033; fact2 = 0.56404; fact3 = -0.077899; fact4 = 0.10418;
110  fact1 = 0.16033;  # fact5 = 0.24935; Base run is a5v. Factors are from Green's
111  fact2 = 0.56404;  # function analysis of these four runs for 2009/10 using LDEO surface
112  fact3 = -0.077899;  # pCO2, Takahashi pCO2 climatology (variability, not absolute values and
113  fact4 = 0.10418;  # the global mean CO2 flux for 2010. pickup and pickup_seaice file are
114  fact5 = 0.24935;  # from 2009 adjoint integration.
115  piston velocity factor in dic_surfforcing.F from 0.337 to 0.34822  
116  R_PICPOC in darwin_generate_phyto.F from 0.04 to 0.133.  # From pfe:/home5/hbrix/README_gf
117  optimization based on:  # runs={'a4v' 'a5v' 'a6v' 'a7v' 'a9v'}; gfrun='ag4';
118      'a4v'    'a6v'    'a7v'    'a9v'    'a10v'    'a13v'  # fact1 = 0.16033;
119  Globflux_err = 0.01  # fact2 = 0.56404;
120  a5v -0.57061  # fact3 = -0.077899;
121  a4v 0.16033 +/- 0.010098  # fact4 = 0.10418;
122  a6v -0.077899 +/- 0.035022  # fact5 = 0.24935;
123  a7v 0.10418 +/- 0.0089553  # piston velocity factor in dic_surfforcing.F from 0.337 to 0.34822
124  a9v 0.24935 +/- 0.0076539  # R_PICPOC in darwin_generate_phyto.F from 0.04 to 0.133.
125  a10v -0.41537 +/- 0.047835  # optimization based on:
126   -> piston factor = 0.34822  #    'a4v'    'a6v'    'a7v'    'a9v'    'a10v'    'a13v'
127  a13v 1.55 +/- 0.064771  # Globflux_err = 0.01
128   -> R_PICPOC = 0.133  # a5v -0.57061
129  global-mean flux: -2.5471  # a4v 0.16033 +/- 0.010098
130    # a6v -0.077899 +/- 0.035022
131  From pfe:/home5/hbrix/README_runs  # a7v 0.10418 +/- 0.0089553
132  darwin_ag4:  # a9v 0.24935 +/- 0.0076539
133  Starting beginning of 2009 from a weighted comination of the ptracers and dic  # a10v -0.41537 +/- 0.047835
134  pickup files from darwin runs 'a4v' 'a5v' 'a6v' 'a7v' 'a9v' with fact1 =  # -> piston factor = 0.34822
135  0.16033; fact2 = 0.56404; fact3 = -0.077899; fact4 = 0.10418; fact5 = 0.24935;  # a13v 1.55 +/- 0.064771
136  Base run is a5v. Factors are from Green's function analysis of these four runs  # -> R_PICPOC = 0.133
137  for 2009/10 using LDEO surface pCO2, Takahashi pCO2 climatology (variability,  # global-mean flux: -2.5471
 not absolute values and the global mean CO2 flux for 2010. pickup and  
 pickup_seaice file are from 2009 adjoint integration. More info about  
 parameters in README_gf.  01FEB12  
   
 There is instructions how to set-up the run in  
 /home5/hbrix/README_preprun_darwin  
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