GEOS-5 Documentation for Icarus 3.4: Difference between revisions

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__FORCETOC__
__FORCETOC__
This page lists pages with information on setting up and running GEOS-5 Icarus 3.3.  Earlier and later versions of GEOS-5 may differ in details that, while minor, will require different steps for building and running, so ''caveat utilitor''.  
This page lists pages with information on setting up and running GEOS-5 Icarus 3.4.  Earlier and later versions of GEOS-5 may differ in details that, while minor, will require different steps for building and running, so ''caveat utilitor''.  


'''Back to [[GEOS-5 User's and Developer's Guides]]'''
'''Back to [[GEOS-5 User's and Developer's Guides]]'''
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<pre>
<pre>
==========================================================================
13Jul2018, Takacs,    CVS Tag: Icarus-3_4_ESMF7 (zero-diff to Icarus-3_4)
                      Module: GEOSagcm
------------------------------------------------------------------------------
1) Modifications needed for use of ESMF7
2) Mods for RRTMG Longwave to enable zero-diff partitioning
Restart Changes: none
==========================================================================
13Jul2018, Takacs,    CVS Tag: Icarus-3_4 (zero-diff to Icarus-3_3_p3)
                      Module: GEOSagcm
------------------------------------------------------------------------------
1) Updates to StratChem using tag: Icarus-3_2_p9_MEM_MERGE_3
                              and  Icarus-3_2_p9_MEM_MERGE_3-r1
2) Updates using tags: GEOSldas_m4-17_UNSTABLE
                      32_GOSWIM_BUG_FIX
                      b_LANDUPD-change
3) Updates to regrid.pl (and supporting code) to ALLOW split ocean restarts
4) Updates for Icarus-3_3_p3 (i.e., sync with GEOSadas-5_21_2)
Restart Changes: none (for standard model)
==========================================================================
==========================================================================
13Jul2018, Takacs,    CVS Tag: Icarus-3_3_p3 (zero-diff to GEOSadas-5_21_2)
13Jul2018, Takacs,    CVS Tag: Icarus-3_3_p3 (zero-diff to GEOSadas-5_21_2)
Line 149: Line 172:
                 RRTMG requires new solar_internal restart.
                 RRTMG requires new solar_internal restart.
                 Simply delete old restart, and bootstrap new RRTMG restart.
                 Simply delete old restart, and bootstrap new RRTMG restart.
==========================================================================
24Aug2017, Takacs,    CVS Tag: Icarus-2_0_p1 (non-zero diff to Icarus-2_0)
                      Module: GEOSagcm
------------------------------------------------------------------------------
1) Implement bugfix to cloudnew.F90.
  A "typo" error was introduced into Icarus-1_0 when incorporating Tag: mjs100__msuarez to inhibit SNOW during thunderstorms.
  The impact of the error directly affected cloud-liquid water and low-level optical depths.
2) Changed Dry-Mass value in rs_scale.F90 from 983.24 mb (MERRA-2 value) to 983.05 mb due to use of GMTED topography.
  Mean TOPO difference:  1.58436898227561 meters
  Note: 983.05 mb is very similar to value based on ERA-Interim data.
Restart Changes: none
==========================================================================
12Jun2017, Takacs,    CVS Tag: Icarus-2_0 (non-zero diff to Icarus-1_0_p1)
                      Module: GEOSagcm
------------------------------------------------------------------------------
1) Updates from E.Nielsen to remove TR dependence on GMI.
2) GMI Updates to Stratospheric ICE fall speeds.
3) Introduce new terminology for Regular REPLAY (REPLAY_PREDICTOR, REPLAY_CORRECTOR, etc.)
4) Implement Anton's 2-Phase GOCART Tag: asd-Icarus-UNSTABLE-a3
5) Modified PHYSICS dry-mass dwdt calculation to reduce roundoff error
6) Implement Ensemble AMIP (EMIP) strategy within gcm_run.j
7) Modified MKIAU to allow creating Increments on BKG grid.  Default is: GRIDINC = ANA
Restart Changes: YES
        Additional IMPORT Restart: gocart_import_rst (Bootstrappable)
</pre>
</pre>


== Running Icarus 3.3 ==
== Running Icarus 3.4 ==


* [[Icarus 3.3 Quick Start]]: This page describes the minimum steps required to build and run GEOS-5 Icarus 3.3 on NCCS discover and NAS pleiades.  You should successfully complete the steps in these instructions before doing anything more complicated.
* [[Icarus 3.4 Quick Start]]: This page describes the minimum steps required to build and run GEOS-5 Icarus 3.4 on NCCS discover and NAS pleiades.  You should successfully complete the steps in these instructions before doing anything more complicated.


* [[Icarus 3.3 User's Guide]]
* [[Icarus 3.4 User's Guide]]


* [[Regridding Restarts for Icarus 3.3]]
* [[Regridding Restarts for Icarus 3.4]]


* [[Using the ExtData component]]
* [[Using the ExtData component]]
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* [[Icarus Single Column Model]]
* [[Icarus Single Column Model]]


== Icarus 3.3 Documentation ==
== Icarus 3.4 Documentation ==


* [[Media:GEOS5_doc.pdf|GEOS 5 Developer's Guide]] (pdf)
* [[Media:GEOS5_doc.pdf|GEOS 5 Developer's Guide]] (pdf)
* List of Export/Import/Internal states, generated with <code>src/GMAO_Shared/MAPL_Base/mapl_vlist.py</code>
* List of Export/Import/Internal states, generated with <code>src/GMAO_Shared/MAPL_Base/mapl_vlist.py</code>
** [[Icarus 3.3 states sorted by short name | Sorted by short name]]
** [[Icarus 3.4 states sorted by short name | Sorted by short name]]
** [[Icarus 3.3 states sorted by component name | Sorted by component name]]
** [[Icarus 3.4 states sorted by component name | Sorted by component name]]
<!--
<!--
Created by:
Created by:
  $ ./GMAO_Shared/MAPL_Base/mapl_vlist.py --sort comp --format wiki /home/mathomp4/Models/Icarus-3_3_p2/GEOSagcm/src/GEOSgcs_GridComp/ > /home/mathomp4/MindMapFiles/Icarus-3_3_p2/i33_states_sort_by_comp.txt
  $ ./GMAO_Shared/MAPL_Base/mapl_vlist.py --sort comp --format wiki /home/mathomp4/Models/Icarus-3_4/GEOSagcm/src/GEOSgcs_GridComp/ > /home/mathomp4/MindMapFiles/Icarus-3_4/i34_states_sort_by_comp.txt


  $ ./GMAO_Shared/MAPL_Base/mapl_vlist.py --sort short --format wiki /home/mathomp4/Models/Icarus-3_3_p2/GEOSagcm/src/GEOSgcs_GridComp/ > /home/mathomp4/MindMapFiles/Icarus-3_3_p2/i33_states_sort_by_short.txt
  $ ./GMAO_Shared/MAPL_Base/mapl_vlist.py --sort short --format wiki /home/mathomp4/Models/Icarus-3_4/GEOSagcm/src/GEOSgcs_GridComp/ > /home/mathomp4/MindMapFiles/Icarus-3_4/i34_states_sort_by_short.txt
-->
-->


Line 217: Line 209:
* [[GEOS-5 Run-Time Characteristics]]
* [[GEOS-5 Run-Time Characteristics]]


* Hierarchical structure: Below is a (partially folded) view of the Icarus 3.3 hierarchy where each node is a GridComp. Some of the nodes are folded (marked with a circle at the end) for clarity - clicking the composite node reveals the sub-nodes.
* Hierarchical structure: Below is a (partially folded) view of the Icarus 3.4 hierarchy where each node is a GridComp. Some of the nodes are folded (marked with a circle at the end) for clarity - clicking the composite node reveals the sub-nodes.


<!--
<!--
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GEOSgcs (or agcm or ogcm) and ran:
GEOSgcs (or agcm or ogcm) and ran:


   $ tree -d -I CVS -X | sed -f ~/MindMapFiles/mindmap.sedfile > ~/MindMapFiles/Icarus-3_3_p2/i33_tree.mm
   $ tree -d -I CVS -X | sed -f ~/MindMapFiles/mindmap.sedfile > ~/MindMapFiles/Icarus-3_4/i34_tree.mm


You'll then need to manually go into the XML file and change the top
You'll then need to manually go into the XML file and change the top
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-->
-->


<mm>[[i33_tree.mm|flash|500px|parameters startCollapsedToLevel=4]]</mm>
<mm>[[i34_tree.mm|flash|500px|parameters startCollapsedToLevel=4]]</mm>


----  
----  
'''Back to [[GEOS-5 User's and Developer's Guides]]'''
'''Back to [[GEOS-5 User's and Developer's Guides]]'''

Latest revision as of 07:03, 22 August 2018

This page lists pages with information on setting up and running GEOS-5 Icarus 3.4. Earlier and later versions of GEOS-5 may differ in details that, while minor, will require different steps for building and running, so caveat utilitor.

Back to GEOS-5 User's and Developer's Guides

ChangeLog Entry

In src/Applications/GEOSgcm_App/ChangeLog: 

==========================================================================
13Jul2018, Takacs,    CVS Tag: Icarus-3_4_ESMF7 (zero-diff to Icarus-3_4)
                       Module: GEOSagcm
------------------------------------------------------------------------------
1) Modifications needed for use of ESMF7
2) Mods for RRTMG Longwave to enable zero-diff partitioning

Restart Changes: none

==========================================================================
13Jul2018, Takacs,    CVS Tag: Icarus-3_4 (zero-diff to Icarus-3_3_p3)
                       Module: GEOSagcm
------------------------------------------------------------------------------
1) Updates to StratChem using tag: Icarus-3_2_p9_MEM_MERGE_3
                              and  Icarus-3_2_p9_MEM_MERGE_3-r1 
2) Updates using tags: GEOSldas_m4-17_UNSTABLE
                       32_GOSWIM_BUG_FIX
                       b_LANDUPD-change
3) Updates to regrid.pl (and supporting code) to ALLOW split ocean restarts
4) Updates for Icarus-3_3_p3 (i.e., sync with GEOSadas-5_21_2)

Restart Changes: none (for standard model)

==========================================================================
13Jul2018, Takacs,    CVS Tag: Icarus-3_3_p3 (zero-diff to GEOSadas-5_21_2)
                       Module: GEOSagcm
------------------------------------------------------------------------------
1. This is the model tag used for GEOSadas-5_21_2
2. It is zero-diff to Icarus-3_3_p2, EXCEPT for:
         a) GOCART runs on Heartbeat
         b) DUST emissions have been retuned (updated DU rc files)

Restart Changes: none

==========================================================================
26Apr2018, Takacs,    CVS Tag: Icarus-3_3_p2 (non-zero diff to Icarus-3_3_p1)
                       Module: GEOSagcm
------------------------------------------------------------------------------
1. Changed fvcore_layout_rc to REMAP using Temperature with DZ Filtering
           remap_option =  0
              fv_sg_adj = 450
2. Update to plots.

Restart Changes: none

==========================================================================
05Apr2018, Takacs,    CVS Tag: Icarus-3_3_p1 (non-zero diff to Icarus-3_3)
                       Module: GEOSagcm
------------------------------------------------------------------------------
1. Changed MIN_RI      in MOIST from 20 to 15 microns
2. Changed ANV_ICEFALL in MOIST from 0.5 to 1.0
3. Changed fvcore_layout_rc to REMAP using Total Energy with NO DZ Filtering
           remap_option =  2
              fv_sg_adj = -1
4. Modified MAPL_PI to use MAPL_R8 structure. This fixes AREA calculation withing DYCORE.
5. On DISCOVER, Uses:  Intel-18.0.1.163, MPT-2.17
6. "FAST" compiler options used only for FV3 (Note: zero-diff to SLOW options)

Restart Changes: none

==========================================================================
27Mar2018, Takacs,    CVS Tag: Icarus-3_3 (non-zero diff to Icarus-3_2_p9)
                       Module: GEOSagcm
------------------------------------------------------------------------------
1. Changed MIN_RI for MOIST from 6 to 20 microns
2. Changed to Intel18 with "FAST" compiler options.
3. Changed FV Dynamics to REAL*4.
4. Modified FV and PHYSICS for better conservation of Dry Mass.

Restart Changes: moist_import_rst   (if binary format, simply Bootstrap)

==========================================================================
20Feb2018, Takacs,    CVS Tag: Icarus-3_2_p9 (non-zero diff to Icarus-3_2_p8)
                       Module: GEOSagcm
------------------------------------------------------------------------------
1. Set optics tables Chou-Suarez for SW and and RRTMG for LW.
2. Set HEARTBEAT to a minimum of 450 seconds.
3. Updated Cloud Water and Cloud Ice effective Radii.
4. New Methodology for IAU.  Default:  Traditional P3C6T6_DF
                               4DIAU:  REPLAY_MODE: Exact_4D
                                       CORRECTOR_DURATION: 10800 (3-hours)

Restart Changes: irrad_internal_rst (for RRTMG).  Simply Bootstrap.

==========================================================================
19Jan2018, Takacs,    CVS Tag: Icarus-3_2_p8 (non-zero diff to Icarus-3_2_p7)
                       Module: GEOSagcm
------------------------------------------------------------------------------
1. Enhancement to the diffusion directly in the sponge layer.
2. Set optics tables back to Chou-Suarez for both SW and LW.

Restart Changes: solar_internal_rst (Back to Chou-Suarez).  Simply Bootstrap.

==========================================================================
08Jan2018, Takacs,    CVS Tag: Icarus-3_2_p7 (non-zero diff to Icarus-3_2_p6)
                       Module: GEOSagcm
------------------------------------------------------------------------------
1. Modified GEOS_MoistGridComp.F90 to have RAS settings behave like x0027_ctl DAS experiments.
   No resolution dependency for AGCM.rc file.

Restart Changes: none

==========================================================================
15Dec2017, Takacs,    CVS Tag: Icarus-3_2_p6 (non-zero diff to Icarus-3_2_p5)
                       Module: GEOSagcm
------------------------------------------------------------------------------
1. A bug fix in RRTMG shortwave found by Max that will fix the SW Albedo issues Gary has seen in x0029 (Land & Radiation Consistency)
2. An update in FV3 that allows us to use the non-monotonic advection schemes for momentum and thermodynamic 
   variables without any degradation in edge effects, plus the truly linear PPM schemes in the sponge layers.

Restart Changes: none

==========================================================================
06Dec2017, Takacs,    CVS Tag: Icarus-3_2_p5 (non-zero diff to Icarus-3_2)
                       Module: GEOSagcm
------------------------------------------------------------------------------
1) Updates to FV3 dynamics.  Resolution dependency is automatic.
2) CBL_TPERT = 0 by default.  Brings back PBL heights.
3) Revert REPLAY parameters back to version from GEOSadas-5_18_0 (x0029 configuration)

Restart Changes: none

==========================================================================
__Nov2017, Takacs,    CVS Tag: Icarus-3_2 (zero-diff to Icarus-3_1 when NOT running Brown Carbon)
                       Module: GEOSagcm
------------------------------------------------------------------------------
1) Merge with tag:  asd+Icarus-3_0_UNSTABLE-a2  to allow option for Brown Carbon
2) Enable IAU_DIGITAL_FILTER as default for DAS and REPLAY modes. (non-zero diff)
3) Changed BKGAVE default to 0 (from 2/3 * CORRECTOR_DURATION).   (non-zero diff)
   A better approach is to use:  IAU_DIGITAL_FILTER: YES

Restart Changes: none

==========================================================================
__Nov2017, Takacs,    CVS Tag: Icarus-3_1 (zero-diff to Icarus-3_0 when NOT running NewLand)
                       Module: GEOSagcm
------------------------------------------------------------------------------
1) Implement Code to enable option for running NewLand


==========================================================================
04Oct2017, Takacs,    CVS Tag: Icarus-3_0 (non-zero diff to Icarus-2_0_p1)
                       Module: GEOSagcm
------------------------------------------------------------------------------
1) Implement R8 version of FV3 VLAB p3 dynamics. Note, current R4 version loses Dry-Mass. R8 version conserves.
2) Updated Single-Moment Physics (MOIST Processes)
3) AGCM now runs RRTMG Shortwave Radiation and Chou-Suarez Longwave Radiation by default (NOTE: cannot use old solar_internal restarts)
4) Implement cubic time-interpolation option for MKIAU in REPLAY (Default: Linear)
5) Updates to MAPL_Base and MAPL_cfio
6) Updates to QuickPlots
7) Implement bugfix to cloudnew.F90 as in Icarus-1_0_p2
8) Changed Dry-Mass value in rs_scale.F90 from 983.24 mb (MERRA-2 value) to 983.05 mb due to use of GMTED topography.
   Mean TOPO difference:  1.58436898227561 meters
   Note: 983.05 mb is very similar to value based on ERA-Interim data.
9) Modified GEOS_TurbulenceGridComp.F90 with more REAL*8 code to improve Dry-Mass Conservation
10) Due to updated FVCORE, GWD BGSTRESSMAX Default changed from 1.2 to 0.9 for 72-levels (Note: 132-levels probably requires re-tuning).

NOTE:  Regular REPLAY to itself FAILS under certain Predictor/Corrector configurations.
      (Reason UNKNOWN)  P3_C6 and P0_C1 seem to work properly.

Restart Changes: YES
                 RRTMG requires new solar_internal restart.
                 Simply delete old restart, and bootstrap new RRTMG restart.

Running Icarus 3.4

  • Icarus 3.4 Quick Start: This page describes the minimum steps required to build and run GEOS-5 Icarus 3.4 on NCCS discover and NAS pleiades. You should successfully complete the steps in these instructions before doing anything more complicated.

Icarus 3.4 Documentation

  • Hierarchical structure: Below is a (partially folded) view of the Icarus 3.4 hierarchy where each node is a GridComp. Some of the nodes are folded (marked with a circle at the end) for clarity - clicking the composite node reveals the sub-nodes.


<mm>flash|500px|parameters startCollapsedToLevel=4</mm>

Back to GEOS-5 User's and Developer's Guides

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