GEOS-5

GEOS-5 Checkout and Build Instructions (Fortuna): Difference between revisions

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'''AGCM.rc'''
'''AGCM.rc'''


This file controls the model run characteristics.  For example, my '''AGCM.rc''' file has the following lines characteristic (to run '''GOCART''' with climatological aerosol forcing):
This file controls the model run characteristics.  For example, for our tag (and answering the setup questions as above) the '''AGCM.rc''' file has the following lines characteristic (to run '''GOCART''' with interactive aerosol forcing):
  GOCART_INTERNAL_RESTART_FILE:          gocart_internal_rst  
  GOCART_INTERNAL_RESTART_FILE:          gocart_internal_rst  
  GOCART_INTERNAL_RESTART_TYPE:          binary
  GOCART_INTERNAL_RESTART_TYPE:          binary
  GOCART_INTERNAL_CHECKPOINT_FILE:        gocart_internal_checkpoint
  GOCART_INTERNAL_CHECKPOINT_FILE:        gocart_internal_checkpoint
  GOCART_INTERNAL_CHECKPOINT_TYPE:        binary
  GOCART_INTERNAL_CHECKPOINT_TYPE:        binary
#AEROCLIM:    ExtData/CMIP/L72/aero_clm/gfedv2.aero.eta.%y4%m2clm.nc
#AEROCLIMDEL: ExtData/CMIP/L72/aero_clm/gfedv2.del_aero.eta.%y4%m2clm.nc
#AEROCLIMYEAR: 2002
DU_OPTICS: ExtData/CMIP/x/opticsBands_DU.v4.nc
SS_OPTICS: ExtData/CMIP/x/opticsBands_SS.v3.nc
SU_OPTICS: ExtData/CMIP/x/opticsBands_SU.v3.nc
OC_OPTICS: ExtData/CMIP/x/opticsBands_OC.nc
BC_OPTICS: ExtData/CMIP/x/opticsBands_BC.nc
NUM_BANDS: 18
DIURNAL_BIOMASS_BURNING: yes
      RATS_PROVIDER: PCHEM  # options: PCHEM, GMICHEM, STRATCHEM (Radiatively active tracers)
      AERO_PROVIDER: GOCART  # options: PCHEM, GOCART            (Radiatively active aerosols)
ANALYSIS_OX_PROVIDER: PCHEM  # options: PCHEM, GMICHEM, STRATCHEM, GOCART
To run with climatological aerosol forcing, modify the appropriate lines above to look like:
  AEROCLIM:    ExtData/AeroCom/L72/aero_clm/gfedv2.aero.eta.%y4%m2clm.nc
  AEROCLIM:    ExtData/AeroCom/L72/aero_clm/gfedv2.aero.eta.%y4%m2clm.nc
  AEROCLIMDEL: ExtData/AeroCom/L72/aero_clm/gfedv2.del_aero.eta.%y4%m2clm.nc
  AEROCLIMDEL: ExtData/AeroCom/L72/aero_clm/gfedv2.del_aero.eta.%y4%m2clm.nc
  AEROCLIMYEAR: 2002
  AEROCLIMYEAR: 2002
DIURNAL_BIOMASS_BURNING: no
RATS_PROVIDER: PCHEM  # options: PCHEM, GMICHEM, STRATCHEM (Radiatively active tracers)
  AERO_PROVIDER: PCHEM  # options: PCHEM, GOCART            (Radiatively active aerosols)
  AERO_PROVIDER: PCHEM  # options: PCHEM, GOCART            (Radiatively active aerosols)
To run with interactive aerosol forcing, modify the appropriate lines above to look like:
#AEROCLIM:    ExtData/AeroCom/L72/aero_clm/gfedv2.aero.eta.%y4%m2clm.nc
#AEROCLIMDEL: ExtData/AeroCom/L72/aero_clm/gfedv2.del_aero.eta.%y4%m2clm.nc
#AEROCLIMYEAR: 2002
AERO_PROVIDER: GOCART  # options: PCHEM, GOCART            (Radiatively active aerosols)


'''HISTORY.rc'''
'''HISTORY.rc'''
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               'tavg2d_aer_x'
               'tavg2d_aer_x'
               'inst3d_aer_v'
               'inst3d_aer_v'
               ::
               'tavg3d_aer_p'
              'tavg2d_chm_x'
              'tavg3d_chm_p'
              'inst2d_hwl_x'
              'inst2d_force_x'
              'inst3d_force_p'
            ::


'''CAP.rc'''
'''CAP.rc'''
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'''gcm_run.j'''
'''gcm_run.j'''


This is the model run script.  You might not need to edit anything, but check in here to see if we are pointing to the right emission files.  Mine has the following line:
This is the model run script.  You might not need to edit anything, but check in here to see if we are pointing to the right emission files.  This is system dependent.  For our tag, on discover, there is a line:
  setenv CHMDIR  /share/dasilva/fvInput
  setenv CHMDIR  /discover/nobackup/projects/gmao/share/dao_ops/fvInput_nc3
which points to the PIESA chemistry emission files presumed in this run.  You might have to modify this line on a different system or to use different emission inventories.
which points to the emission files presumed in this run.  You might have to modify this line on a different system or to use different emission inventories.
 
'''cap_restart'''
 
This file doesn't exist here by default, so create it with your favorite editor.  It will have the model start date (ignore BEG_DATE in CAP.rc; if this file exists it supersedes that).  It should just specify YYYYMMDD HHMMSS start time of model run.  For example:
19991231 210000


'''An Optional Modification'''
'''An Optional Modification'''
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substituting the appropriate YYYYMM in END_DATE for the overall time you want your experiment to end.
substituting the appropriate YYYYMM in END_DATE for the overall time you want your experiment to end.


Edit '''gcm_run.j''' so the following environment variables are set like this
By default the '''gcm_run.j''' on this tag has the following environment variables set like this:
  set STOP_MID_MONTH = 1
  set STOP_MID_MONTH = 1
  set DFLT_JOB_SGMT = 16
  set DFLT_JOB_SGMT = 16
(By default, STOP_MID_MONTH = 0, which bypasses the logic here). 


Here's what is happening: overall model control is handled by '''CAP.rc'''.  We specify the model finish time with END_DATE in '''CAP.rc'''.  As set up, JOB_SGMT is the number of days to run the model in a single segment, and NUM_SGMT is the number of segments to run in a single queue submission.  With STOP_MID_MONTH set to '''1''' what happens is that the JOB_SGMT environment variable is tweaked for each half-month of the model run.  That is, the first segment runs the initial number of days (in this case, 17) and the next segment runs for however many days are needed to reach the 1st of the next month.  (In this example, I'm presuming we're starting from an initial date of 19991231, which requires us to run for 17 days to cause the model to stop on 20000117, which is the desired monthly mid-point.)  What's really happening is that CAP.rc is being edited after each segment to specify the (hopefully) correct number of days to run the next segment.  Here, NUM_SGMT is set to '''12''', which will run the model for 6 months in a single queue submission (1/2 month per segment).  This seems to fit conservatively for our resolution in a single 8-hour wallclock time request.
Here's what is happening: overall model control is handled by '''CAP.rc'''.  We specify the model finish time with END_DATE in '''CAP.rc'''.  As set up, JOB_SGMT is the number of days to run the model in a single segment, and NUM_SGMT is the number of segments to run in a single queue submission.  With STOP_MID_MONTH set to '''1''' what happens is that the JOB_SGMT environment variable is tweaked for each half-month of the model run.  That is, the first segment runs the initial number of days (in this case, 17) and the next segment runs for however many days are needed to reach the 1st of the next month.  (In this example, I'm presuming we're starting from an initial date of 19991231, which requires us to run for 17 days to cause the model to stop on 20000117, which is the desired monthly mid-point.)  What's really happening is that CAP.rc is being edited after each segment to specify the (hopefully) correct number of days to run the next segment.  Here, NUM_SGMT is set to '''12''', which will run the model for 6 months in a single queue submission (1/2 month per segment).  This seems to fit conservatively for our resolution in a single 8-hour wallclock time request.
If you don't care about any of this, you can set STOP_MID_MONTH = 0, which bypasses this logic and all segments are exactly as long as JOB_SGMT specifies.


'''Running on Pleiades'''
'''Running on Pleiades'''


This tag has successfully checked out, built, run, and archived results on NAS machine Pleiades.  There seem to be only two modifications to what is described to make, both to the '''gcm_run.j''' script. First, the PIESA style emissions are located differently on Pleiades, so:
This tag has successfully checked out, built, run, and archived results on NAS machine Pleiades.  No modifications to scripts are needed, as the appropriate choices for that machine are handled in gcm_setup.
setenv CHMDIR  /nobackup/pcolarco/fvInput


=== Setup the Experiment EXPDIR ===
=== Setup the Experiment EXPDIR ===
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