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Move test lists to beneath active components, change build scripts from cshell
to perl, move to new cime directory structure
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@ekluzek @bjandre
ekluzek authored and bjandre committed Dec 19, 2017
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137 changes: 64 additions & 73 deletions README
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clm/README 05/15/2013
components/clm/README 04/07/2015

Community Land Surface Model (CLM) version 4.5.06 -- source code, tools,
Community Land Surface Model (CLM) science version 4.5.1 series -- source code, tools,
offline-build and test scripts. This gives you everything you need
to run CLM with CESM with datm8 to provide Qian or CRU NCEP forcing data in
place of a modeled atmosphere.

What is new in this version of CLM (compared to previous CESM and CCSM releases)?

See the ChangeLog file for a summary description of the most recent major
version changes leading up to clm4_0_00, from CLM4.0.00 to CLM4.0.14,
from CLM4.0.14 to CLM4.0.32, and then from CLM4.0.32 to CLM4.0.53.
The User's Guide also has a section on this as well.

General directory structure:

models/lnd/clm/doc ---- Documentation of CLM.
models/lnd/clm/bld ---- Template, configure and build-namelist scripts for clm.
models/lnd/clm/src ---- CLM Source code.
models/lnd/clm/test --- CLM Testing scripts for CLM offline tools.
models/lnd/clm/tools -- CLM Offline tools to prepare input datasets and process output.

scripts --------------- CPL7 scripts

models/drv/driver ----- CESM top level driver source code.
models/drv/shr -------- CESM top level driver shared code.
models/drv/shr_esmf --- CESM top level driver shared code for ESMF.
models/atm/datm ------- CESM Data model version 8 source code.
models/glc/cism ------- CESM Community land Ice Sheet Model.
models/rof/rtm -------- CESM River Transport Model.
models/ice/sice ------- CESM stub sea-ice model source code.
models/ocn/socn ------- CESM stub ocean model source code.
models/glc/sglc ------- CESM stub glacier model source code.
models/utils ---------- CESM utility codes
(Model Coupling Toolkit (MCT)
(Earth System Model Framework)
(timing -- code timing utility)
(pio -- Parallel Input/Output)
components/clm/doc ---- Documentation of CLM.
components/clm/bld ---- Template, configure and build-namelist scripts for clm.
components/clm/src ---- CLM Source code.
components/clm/test --- CLM Testing scripts for CLM offline tools.
components/clm/tools -- CLM Offline tools to prepare input datasets and process output.

cime/scripts --------------- CPL7 scripts

cime/driver_cpl/driver ---------- CESM top level driver source code.
cime/driver_cpl/shr ------------- CESM top level driver shared code.
cime/driver_cpl/shr_esmf -------- CESM top level driver shared code for ESMF.
cime/components/data_comps/datm - CESM Data model version 8 source code.
components/cism ----------------- CESM Community land Ice Sheet Model.
components/rtm ------------------ CESM River Transport Model.
cime/components/stub_comps/sice - CESM stub sea-ice model source code.
cime/components/stub_comps/socn - CESM stub ocean model source code.
cime/components/stub_comps/sglc - CESM stub glacier model source code.
cime/external ------------------- CESM external utility codes
(Model Coupling Toolkit (MCT)
(Earth System Model Framework)
(timing -- code timing utility)
(pio -- Parallel Input/Output)

Top level documentation:

Expand All @@ -47,68 +40,66 @@ UpDateChangeLog.pl ------- Script to add documentation on a tag to the
ChangeLog/ChangeSum files
ChangeLog ---------------- Documents different CLM versions
ChangeSum ---------------- Summary documentation of different CLM versions
ChangeLog/ChangeSum ------ Also copied to models/lnd/clm/doc
ChangeLog/ChangeSum ------ Also copied to components/lnd/clm/doc

Documentation of Namelist Items: (view the following in a web browser)

models/lnd/clm/bld/namelist_files/namelist_definition.xml --- Definition of all namelist items
models/lnd/clm/bld/namelist_files/namelist_defaults_clm.xml - Default values
components/clm/bld/namelist_files/namelist_definition.xml --- Definition of all namelist items
components/clm/bld/namelist_files/namelist_defaults_clm.xml - Default values

=============================================================================================
Important files in main directories:
=============================================================================================

models/lnd/clm/doc/Quickstart.GUIDE -------- Quick guide to using cpl7 scripts.
models/lnd/clm/doc/Quickstart.userdatasets - Quick guide to using your own datasets.
models/lnd/clm/doc/IMPORTANT_NOTES --------- Some important notes about this version of
clm, configuration modes and namelist items
that are not validated or functional.
models/lnd/clm/doc/KnownBugs --------------- List of known bugs.
models/lnd/clm/doc/KnownLimitations -------- List of known limitations and workarounds.
models/lnd/clm/doc/ChangeLog --------------- Detailed list of changes for each model version.
models/lnd/clm/doc/ChangeSum --------------- Summary one-line list of changes for each
components/lnd/clm/doc/Quickstart.GUIDE -------- Quick guide to using cpl7 scripts.
components/lnd/clm/doc/Quickstart.userdatasets - Quick guide to using your own datasets.
components/lnd/clm/doc/IMPORTANT_NOTES --------- Some important notes about this version of
clm, configuration modes and namelist items
that are not validated or functional.
components/clm/doc/KnownBugs --------------- List of known bugs.
components/clm/doc/KnownLimitations -------- List of known limitations and workarounds.
components/clm/doc/ChangeLog --------------- Detailed list of changes for each model version.
components/clm/doc/ChangeSum --------------- Summary one-line list of changes for each
model version.
models/lnd/clm/doc/README ------------------ Documentation similar to this file
models/lnd/clm/doc/UsersGuide -------------- CLM Users Guide
models/lnd/clm/doc/CodeReference ----------- CLM Code Reference Guide

models/lnd/clm/bld/configure --------------- Script to prepare CLM to be built.

models/lnd/clm/test/tools/test_driver.sh -- Script for general software testing of
CLM's offline tools.

models/lnd/clm/tools/clm4_5/mksurfdata_map --- Directory to build program to create surface dataset
at any resolution.
models/lnd/clm/tools/clm4_5/interpinic ------- Directory to build program to interpolate initial
conditions to any resolution.
models/lnd/clm/tools/shared/mkdatadomain ----- Directory to build program to create datm7 or docn7
domain files from clm files.
models/lnd/clm/tools/shared/mkprocdata_map --- Process history data from unstructed grids to a gridded
format.
models/lnd/clm/tools/shared/ncl_scripts ----- Directory of NCL and perl scripts to do various
tasks. Most notably to plot perturbation error growth
testing and to extract regional information from
global datasets for single-point/regional simulations.

models/lnd/clm/bld/README ------------- Description of how to use the configure and
components/clm/doc/README ------------------ Documentation similar to this file
components/clm/doc/UsersGuide -------------- CLM Users Guide
components/clm/doc/CodeReference ----------- CLM Code Reference Guide

components/clm/bld/configure --------------- Script to prepare CLM to be built.

components/clm/test/tools/test_driver.sh -- Script for general software testing of
CLM's offline tools.

components/clm/tools/clm4_5/mksurfdata_map --- Directory to build program to create surface dataset
at any resolution.
components/clm/tools/clm4_5/interpinic ------- Directory to build program to interpolate initial
conditions to any resolution.
components/clm/tools/shared/mkdatadomain ----- Directory to build program to create datm7 or docn7
domain files from clm files.
components/clm/tools/shared/mkprocdata_map --- Process history data from unstructed grids to a gridded
format.
components/clm/tools/shared/ncl_scripts ----- Directory of NCL and perl scripts to do various
tasks. Most notably to plot perturbation error growth
testing and to extract regional information from
global datasets for single-point/regional simulations.

components/clm/bld/README ------------- Description of how to use the configure and
build-namelist scripts.

=============================================================================================
Source code directory structure:
=============================================================================================

models/lnd/clm/src/clm4_5/biogeochem -- Biogeochemisty
models/lnd/clm/src/clm4_5/main -------- Main control and high level code
models/lnd/clm/src/cpl_mct ------------ Land model high level MCT driver
models/lnd/clm/src/cpl_esmf ----------- Land model high level ESMF driver
models/lnd/clm/src/cpl_share ---------- Land model high level driver code shared between MCT/ESMF
models/lnd/clm/src/clm4_5/biogeophys -- Biogeophysics (Hydrology)
components/clm/src/biogeochem -- Biogeochemisty
components/clm/src/main -------- Main control and high level code
components/clm/src/cpl --------- Land model high level MCT and ESMF drivers
components/clm/src/biogeophys -- Biogeophysics (Hydrology)

=============================================================================================
QUICKSTART: using the CPL7 scripts:
=============================================================================================

cd scripts
cd cime/scripts
./create_newcase # get help on how to run create_newcase
./create_newcase -case testI -mach bluefire -res f19_g16 -compset I
# create new "I" case for bluefire at 1.9x2.5_gx1v6 res
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Expand Up @@ -18,7 +18,7 @@ view the property set for clm's external definitions
> svn propget svn:externals clm_trunk_head_wc

view revision, URL and other useful information specific to external files
> cd clm_trunk_head_wc/models/lnd/clm/src
> cd clm_trunk_head_wc/components/clm/src
> svn info main

create new clm branch for mods required of clm
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30 changes: 30 additions & 0 deletions README_cime
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1.) Start at the top level directory of your sandbox

cd $clm_root

2.) Update JUST the top level directory with the externals.

svn update --depth immediates

3.) Move any local changes you have under clm
(This preserves any local changes you have in your sandbox, as well as changes on your branch)

svn mv models/lnd/clm/ components/clm

4.) Move any local changes you have under scripts to save your cases
(if you don't have cases to save under scripts, you don't have
to do this step)

svn mkdir --parents cime/scripts
mv scripts cime/scripts/

5.) Bring in updated externals and updates to clm source files

svn update

6.) Mark changes to models directory as resolved

svn resolved models

7.) Commit these changes to your branch

40 changes: 4 additions & 36 deletions SVN_EXTERNAL_DIRECTORIES.standalone
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# CESM scripts, machines and driver
scripts https://svn-ccsm-models.cgd.ucar.edu/scripts/trunk_tags/scripts4_150108
scripts/doc https://svn-ccsm-models.cgd.ucar.edu/doc/trunk_tags/doc_140519
scripts/ccsm_utils/Machines https://svn-ccsm-models.cgd.ucar.edu/Machines/trunk_tags/Machines_150113b
scripts/ccsm_utils/CMake https://github.com/quantheory/CMake_Fortran_utils/tags/CMake_Fortran_utils_141122
models/drv https://svn-ccsm-models.cgd.ucar.edu/drv/seq_mct/trunk_tags/drvseq5_1_07
cime https://svn-ccsm-models.cgd.ucar.edu/cime/trunk_tags/cime0_3_20
components/clm/tools/shared/gen_domain https://svn-ccsm-models.cgd.ucar.edu/cime/trunk_tags/cime0_3_20/tools/mapping/gen_domain_files
components/cism https://svn-ccsm-models.cgd.ucar.edu/glc/branch_tags/newdirs_tags/newdirs_n03_cism2_0_08
components/rtm https://svn-ccsm-models.cgd.ucar.edu/rivrtm/trunk_tags/rtm1_0_47

# Model components: Data atmosphere, and stub components as well as land-ice model
# Note that dlnd, satm and srof are not needed for CLM runs, but are included to allow
# running TG compsets (CISM-only, forced by data land) from a CLM tag.
models/atm/datm https://svn-ccsm-models.cgd.ucar.edu/datm7/trunk_tags/datm8_141113
models/lnd/dlnd https://svn-ccsm-models.cgd.ucar.edu/dlnd7/trunk_tags/dlnd8_131201
models/atm/satm https://svn-ccsm-models.cgd.ucar.edu/stubs/trunk_tags/stubs1_4_04/satm
models/ocn/socn https://svn-ccsm-models.cgd.ucar.edu/stubs/trunk_tags/stubs1_4_04/socn
models/ice/sice https://svn-ccsm-models.cgd.ucar.edu/stubs/trunk_tags/stubs1_4_04/sice
models/glc/sglc https://svn-ccsm-models.cgd.ucar.edu/stubs/trunk_tags/stubs1_4_04/sglc
models/rof/srof https://svn-ccsm-models.cgd.ucar.edu/stubs/trunk_tags/stubs1_4_04/srof
models/wav/swav https://svn-ccsm-models.cgd.ucar.edu/stubs/trunk_tags/stubs1_4_04/swav
models/rof/rtm https://svn-ccsm-models.cgd.ucar.edu/rivrtm/trunk_tags/rtm1_0_41
models/glc/cism https://svn-ccsm-models.cgd.ucar.edu/glc/trunk_tags/cism2_0_05

# Utilities: csm_share, esmf, timing, MCT, PIO
models/csm_share https://svn-ccsm-models.cgd.ucar.edu/csm_share/trunk_tags/share3_141219
models/utils/esmf_wrf_timemgr https://svn-ccsm-models.cgd.ucar.edu/esmf_wrf_timemgr/trunk_tags/esmf_wrf_timemgr_141217
models/utils/timing https://svn-ccsm-models.cgd.ucar.edu/timing/trunk_tags/timing_141202
models/utils/mct https://github.com/quantheory/MCT/tags/compiler_fixes_n04_MCT_2.8.3
models/utils/pio http://parallelio.googlecode.com/svn/trunk_tags/pio1_9_9/pio

# Mapping tools:
tools/cprnc https://svn-ccsm-models.cgd.ucar.edu/tools/cprnc/trunk_tags/cprnc_141222
tools/mapping https://svn-ccsm-models.cgd.ucar.edu/tools/mapping/trunk_tags/mapping_141106
models/lnd/clm/tools/shared/gen_domain https://svn-ccsm-models.cgd.ucar.edu/tools/mapping/trunk_tags/mapping_141106/gen_domain_files

# Other tools:
tools/load_balancing_tool https://svn-ccsm-models.cgd.ucar.edu/tools/load_balancing_tool/trunk_tags/load_balancing_tool_141008
tools/pyReshaper https://proxy.subversion.ucar.edu/pubasap/pyReshaper/tags/v0.9.1
tools/unit_testing https://svn-ccsm-models.cgd.ucar.edu/unit_testing/trunk_tags/unit_testing_0_12
8 changes: 4 additions & 4 deletions UpDateChangeLog.pl
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Expand Up @@ -228,10 +228,10 @@ sub usage {
system( "$EDITOR $changelog" );
system( "$EDITOR $changesum" );
}
system( "/bin/cp -fp $changelog models/lnd/clm/doc/." );
system( "/bin/cp -fp $changesum models/lnd/clm/doc/." );
system( "/bin/chmod 0444 models/lnd/clm/doc/$changelog" );
system( "/bin/chmod 0444 models/lnd/clm/doc/$changesum" );
system( "/bin/cp -fp $changelog components/clm/doc/." );
system( "/bin/cp -fp $changesum components/clm/doc/." );
system( "/bin/chmod 0444 components/clm/doc/$changelog" );
system( "/bin/chmod 0444 components/clm/doc/$changesum" );

sub AddExpectedFailDiff {
#
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