From edd59ca44ff2fd41d62f3b62580ad61f87db84cb Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 5 Feb 2018 15:03:45 -0700 Subject: [PATCH] Update changelog, copy CESM Copyright, update README and changelog template, and remove README_cime as no longer applies --- Copyright | 121 ++++++++++++++++++-------------- README | 149 +++++++++++++++++++++------------------- README_cime | 62 ----------------- doc/.ChangeLog_template | 7 +- doc/ChangeLog | 129 ++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 6 files changed, 280 insertions(+), 189 deletions(-) delete mode 100644 README_cime diff --git a/Copyright b/Copyright index 1e8c87a1c6..dc8216347d 100644 --- a/Copyright +++ b/Copyright @@ -1,59 +1,74 @@ --------------------------------------------------------------------------------- - CESM1.0 --------------------------------------------------------------------------------- -The Community Earth System Model (CESM) was developed in cooperation with the -National Science Foundation, the Department of Energy, the National Aeronautics -and Space Administration, and the University Corporation for Atmospheric -Research National Center for Atmospheric Research. +CESM1.5: Copyright Notice and Disclaimer -Except for the segregable components listed below, CESM is public domain software. -There may be other third party tools and libraries that are embedded, and they may -have their own copyright notices and terms. - -The following components are copyrighted and may only be used, modified, or -redistributed under the terms indicated below. - -Code ESMF -Institution University of Illinois/NCSA -Copyright Copyright 2002-2009, University of Illinois/NCSA Open Source License -Terms of Use http://www.gnu.org/copyleft/gpl.html +The Community Earth System Model (CESM was developed in cooperation with +the National Science Foundation, the Department of Energy, +the National Aeronautics and Space Administration, and +the University Corporation for Atmospheric Research National Center for Atmospheric Research. -Code POP, SCRIP, CICE -Institution Los Alamos National Laboratory -Copyright Copyright 2008 Los Alamos National Security, LLC -Terms of Use http://oceans11.lanl.gov/trac/CICE/wiki/CopyRight - -Code Glimmer-CISM -Institution LANL/U. Bristol/U. Edinburgh/U. Montana/U. Swansea) -Copyright Copyright 2004-2010, GNU General Public License -Terms of Use GNU General Public License - -Code AER RRTMG -Institution Atmospheric and Environmental Research, Inc. -Copyright Copyright 2002-2010, Atmospheric and Environmental Research, Inc. -Terms of Use http://rtweb.aer.com/rrtm_frame.html +Except for the segregable components listed below, CESM is public domain software. +There may be other third party tools and libraries that are embedded, and +they may have their own copyright notices and terms. -Code MCT -Institution Argonne National Laboratory -Copyright Copyright 2000, 2010, University of Chicago. -Terms of Use http://www.cesm.ucar.edu/models/cesm1.0/copyright_MCT.html +The following components are copyrighted and may only be used, modified, +or redistributed under the terms indicated below. -Code ICSSP -Institution N/A -Copyright Copyright 2003, 2010, Steve Klein and Mark Webb -Terms of Use http://gcss-dime.giss.nasa.gov/simulator.html +Code Institution Copyright Terms of Use/Disclaimer +---- ----------- --------- ----------------------- +ESMF University of Copyright University of Illinois/NCSA Open Source License + Illinois/NCSA 2002-2009, + University of + Illinois/NCSA + Open Source + License + +POP,SCRIP,CICE Los Alamos National Copyright 2008 Los Alamos National Security, LLC + Laboratory Los Alamos + National + Security, LLC + +Glimmer-CISM LANL/U. Copyright GNU General Public License + Bristol/U. 2004-2010, + Edinburgh/U. GNU General + Montana/U. Public License + Swansea + +AER RRTMG Atmospheric Copyright AER RRTMG Copyright + and 2002-2010, + Environmental Atmospheric + Research, Inc. and + Environmental + Research, Inc. + +MCT Argonne Copyright 2000, MCT Copyright + National 2010, + Laboratory University of + Chicago. + +ICSSP N/A Copyright 2003, ISCCP Simulator Software + 2010, Steve + Klein and Mark + Webb + +XML/Lite Wadsack-Allen Copyright 2001, The documentation for the Perl XML-Lite + Digital Group 2010 module is no longer available on-line. + Wadsack-Allen + Digital Group + +Inf_NaN Lahey Copyright(c) Copies of this source code, or standalone compiled +_Detection Computer 2003, Lahey files derived from this source may not be sold +module Systems, Inc. Computer without permission from Lahey Computers Systems. + Systems, Inc. All or part of this module may be freely incorporated + into executable programs which are offered for sale. + Otherwise, distribution of all or part of this file is + permitted, provided this copyright notice and header + are included. + -Code XML/Lite -Institution Wadsack-Allen Digital Group -Copyright Copyright 2001,2010 Wadsack-Allen Digital Group -Terms of Use http://aspn.activestate.com/ASPN/CodeDoc/XML-Lite/Lite.html +THIS SOFTWARE IS PROVIDED BY UCAR AND ANY CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, +INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL UCAR OR ANY CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER +IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF +THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -Code Inf_NaN_Detection module -Institution Lahey Computer Systems, Inc. -Copyright Copyright(c) 2003, Lahey Computer Systems, Inc. -Terms of Use Copies of this source code, or standalone compiled files derived from - this source may not be sold without permission from Lahey Computers Systems. - All or part of this module may be freely incorporated into executable - programs which are offered for sale. Otherwise, distribution of all or - part of this file is permitted, provided this copyright notice and header - are included. diff --git a/README b/README index 029a891482..f646e44e24 100644 --- a/README +++ b/README @@ -1,99 +1,110 @@ -components/clm/README 04/07/2015 +README 02/05/2018 -Community Land Surface Model (CLM) science version 4.5.1 series -- source code, tools, +Community Land Surface Model (CLM) science version 5.0.0 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 +to run CLM with CESM with datm8 to provide CRU NCEP or GSWP3 forcing data in place of a modeled atmosphere. General directory structure: -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. +doc --------------- Documentation of CLM. +bld --------------- Template, configure and build-namelist scripts for clm. +src --------------- CLM Source code. +test -------------- CLM Testing scripts for CLM offline tools. +tools ------------- CLM Offline tools to prepare input datasets and process output. +cime_config ------- Configuration files of cime for compsets and CLM settings +manage_externals -- Script to manage the external source directories 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) +cime/src/drivers/mct/main ----------- CESM top level driver source code. +cime/src/drivers/mct/shr ------------ CESM top level driver shared code. +cime/src/components/data_comps/datm - CESM Data model version 8 source code. +components/cism --------------------- CESM Community land Ice Sheet Model. +components/mosart ------------------- Model for Scale Adaptive River Transport +components/rtm ---------------------- CESM River Transport Model. +cime/src/components/stub_comps/sice - CESM stub sea-ice model source code. +cime/src/components/stub_comps/socn - CESM stub ocean model source code. +cime/src/components/stub_comps/sglc - CESM stub glacier model source code. +cime/src/externals ------------------ CESM external utility codes + (Model Coupling Toolkit (MCT) + (Earth System Model Framework) + (timing -- code timing utility) + (pio -- Parallel Input/Output) Top level documentation: README ------------------- This file -README_EXTERNALS --------- Information on how to work with subversion externals for clm -SVN_EXTERNAL_DIRECTORIES - Subversions externals to use +README_EXTERNALS.rst ----- Information on how to work with subversion externals for clm Copyright ---------------- CESM Copyright file -UpDateChangeLog.pl ------- Script to add documentation on a tag to the +doc/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 components/lnd/clm/doc +doc/ChangeLog ---------------- Documents different CLM versions +doc/ChangeSum ---------------- Summary documentation of different CLM versions Documentation of Namelist Items: (view the following in a web browser) components/clm/bld/namelist_files/namelist_definition.xml --- Definition of all namelist items -components/clm/bld/namelist_files/namelist_defaults_clm.xml - Default values +components/clm/bld/namelist_files/namelist_defaults_clm4_5.xml - Default values for CLM4.5/CLM5.0 ============================================================================================= Important files in main directories: ============================================================================================= -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 +Externals.cfg --------------- File for management of the main high level externals +Externals_CLM.cfg ----------- File for management of the CLM specific externals (i.e. FATES) +parse_cime.cs.status -------- Script to parse test status files cs.status.* created by create_test +doc/Quickstart.GUIDE -------- Quick guide to using cpl7 scripts. +doc/Quickstart.userdatasets - Quick guide to using your own datasets. +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 +doc/KnownBugs --------------- List of known bugs. +doc/KnownLimitations -------- List of known limitations and workarounds. +doc/ChangeLog --------------- Detailed list of changes for each model version. +doc/ChangeSum --------------- Summary one-line list of changes for each model version. -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 +doc/README ------------------ Documentation similar to this file +doc/UsersGuide -------------- CLM Users Guide +doc/CodeReference ----------- CLM Code Reference Guide + +bld/configure --------------- Script to prepare CLM to be built. + +test/tools/test_driver.sh -- Script for general software testing of + CLM's offline tools. + +tools/clm4_5/mksurfdata_map --- Directory to build program to create surface dataset + at any resolution. +tools/clm4_5/interpinic ------- Directory to build program to interpolate initial + conditions to any resolution. +tools/shared/mkdatadomain ----- Directory to build program to create datm7 or docn7 + domain files from clm files. +tools/shared/mkprocdata_map --- Process history data from unstructed grids to a gridded + format. +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. + +bld/README ------------- Description of how to use the configure and build-namelist scripts. ============================================================================================= Source code directory structure: ============================================================================================= -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) +src/biogeochem -- Biogeochemisty +src/main -------- Main control and high level code +src/cpl --------- Land model high level MCT and ESMF drivers +src/biogeophys -- Biogeophysics (Hydrology) +src/dyn_subgrid - Dynamic land unit change +src/init_interp - Online interpolation +scr/fates ------- FATES model and sub-directories + Functionally Assembled Terrestrial Ecosystem Simulator (FATES) + Experimental Ecosystem Demography model +src/utils ------- Utility codes + +scr_clm40 ------- CLM4.0 source code directory ============================================================================================= QUICKSTART: using the CPL7 scripts: @@ -101,13 +112,13 @@ components/clm/src/biogeophys -- Biogeophysics (Hydrology) 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 - # "I" case is clm active, datm8, and inactive ice/ocn + ./create_newcase --case testI --res f19_g16 --compset I2000Clm50BgcCrop --mach cheyenne + # create new "I" case for cheyenne_intel at 1.9x2.5_gx1v7 res + # "I2000Clm50BgcCrop" case is clm5_0 active, datm8, and inactive ice/ocn cd testI - ./cesm_setup # create the $CASE.run file - ./testI.bluefire.build # build model and create namelists - ./testI.bluefire.submit # submit script + ./case.setup # create the $CASE.run file + ./case.build # build model and create namelists + ./case.submit # submit script # (NOTE: ./xmlchange RESUBMIT=10 to set RESUBMIT to number # # of times to automatically resubmit -- 10 in this example) diff --git a/README_cime b/README_cime deleted file mode 100644 index 98c25c94b7..0000000000 --- a/README_cime +++ /dev/null @@ -1,62 +0,0 @@ -For the trunk: - -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 - - -For branches: - -0.) Make sure ALL your changes are checked into your branch. - -1.) Checkout your branch WITHOUT externals - - svn co --ignore-externals $SVN_MOD_URL/clm2/branches/ - -2.) Move any changes you have under clm on your branch - - svn mkdir components - svn mv models/lnd/clm/ components/clm - -3.) Merge the top level - - svn merge --depth immediates $SVN_MOD_URL/clm2/trunk_tags/clm4_5_1_r104 $SVN_MOD_URL/clm2/trunk_tags/clm4_5_1_r105 - -4.) Merge changes in the clm directory - - svn merge $SVN_MOD_URL/clm2/trunk_tags/clm4_5_1_r104/models/lnd/clm $SVN_MOD_URL/clm2/trunk_tags/clm4_5_1_r105/components/clm - -5.) Bring in updated externals and updates to clm source files - - svn update - -6.) Mark changes to models and components/clm directories as resolved - - svn resolved models - svn resolved components - svn resolved components/clm - diff --git a/doc/.ChangeLog_template b/doc/.ChangeLog_template index 527502df56..2de3362d97 100644 --- a/doc/.ChangeLog_template +++ b/doc/.ChangeLog_template @@ -114,10 +114,7 @@ Detailed list of changes List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): -List all files eliminated: - -List all files added and what they do: - -List all existing files that have been modified, and describe the changes: +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) =============================================================== diff --git a/doc/ChangeLog b/doc/ChangeLog index f5ac5000e2..cdd1dc80d7 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,133 @@ =============================================================== +Tag name: clm4_5_18_r275 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Mon Feb 5 15:02:53 MST 2018 +One-line Summary: Update initial condition files, update fates, new CMIP6 pop-dens, more lnd_tuning_mod options, updated ndep for fully coupled + +Purpose of changes +------------------ + +Update the initial condition files for clm4_0, clm4_5, clm5_0 at f09_g16 for both CRUNCEpv7 +forcing and GSWP3v1 forcing. Update FATES with science change to science-1.4.1_api-3.0.0. +New CMIP6 population density file that has years beyond 1850 (the old one just had 1850, so +was incorrect for historical or present-day). clm4_0 compsets now use CRUNCEPv7 forcing rather than +the CRUNCEPv4 forcing. LND_TUNING_MODE is now used for initial conditions +for different forcing. For fully coupled 1850 cases the ndep file is updated to a preliminary CMIP6 +version. Fix the tools testing and build-namelist testing to work in the git checkout. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #: + #247 -- Clm40 1850 and HIST compsets are incorrect + #246 -- New CMIP6 population density file is incorrect as it's constant in time + #171 -- CLM is getting the mask from the clm namelist_defaults rather than from top level scripts + +Known bugs introduced in this tag (include github issue ID): + #253 -- Bad new IC file for clm4_0 + #254 -- Failing test ERS_D_Ld3.f10_f10_musgs.I1850Clm50BgcCrop.cheyenne_gnu.clm-default (sporadic glitch?) + #255 -- PTCLMmkdata doesn't work in the CLM git checkout + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): + LND_TUNING_MODE is set by default according to the compset the case is created with. + If you change the CLM physics or DATM forcing, you'll want to update the LND_TUNING_MODE. + +Changes to CLM's user interface (e.g., new/renamed XML or namelist variables): + LND_TUNING_MODE options changed to: + clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_cam6.0,clm5_0_cam6.0,clm5_0_CRUv7,clm5_0_GSWP3v1 + + Several new compset aliases added: + + CLM50: I1850Clm50Sp, I1850Clm50SpCru, I1850Clm50BgcCropCru + CLM45: I1850Clm45BgcCruGs, I1850Clm45BgcGs + CLM40 I1850Clm40CnGswGs (fixed I2000Clm40SpCruGs, I1850Clm40SpCruGs, and IHistClm40SpCruGs) + +Changes made to namelist defaults (e.g., changed parameter values): + +Changes to the datasets (e.g., parameter, surface or initial files): New IC files for f09_g16 + CMIP6 ndep file for fully coupled, pop-density beyond 1850 + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + Setting of ndep_taxmode/ndep_varlist should be simplified in CLMBuildNamelist.pm + Change name of setup_logic_lnd_tuning to setup_cmdl_lnd_tuning in CLMBuildNamelist.pm + +Changes to tests or testing: Change a few tests and add a few + Add I1850Clm50SpCru, I1850Clm50BgcCropCru, I1850Clm40CnGswGs and I1850Clm50Sp tests at f09_g16 + Change I1850Clm40SpCruGs f09_f09_mg16 to f09_g16 + Change I2000Clm50BgcCruGs f09_g17 test to I1850Clm50BgcCruGs f09_g16 + +Code reviewed by: self + +Did you follow the steps in .CLMTrunkChecklist: yes + +CLM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (134 comparison tests are different than clm4_5_18_r275) + + unit-tests (components/clm/src): + + cheyenne - PASS + + tools-tests (components/clm/test/tools): + + cheyenne - OK + + PTCLM testing (components/clm/tools/shared/PTCLM/test): + + cheyenne - FAIL + + regular tests (aux_clm): + + cheyenne_intel ---- OK + cheyenne_gnu ------ OK + hobart_nag -------- OK + hobart_pgi -------- OK + hobart_intel ------ OK + +CLM tag used for the baseline comparisons: clm4_5_18_r275 + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes! + + Summarize any changes to answers: + - what code configurations: clm4_0 for f09_g16 + clm4_0 updated to CRUv7 Forcing + all clm4_5 and clm5_0 configurations, FATES-update + - what platforms/compilers: All + - nature of change: initialization, BGC for HIST/2000 compsets + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): FATES + fates to fates_s1.4.1_a3.0.0_rev3 + +Pull Requests that document changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) + + #252 -- New IC files + #251 -- README update + #248 -- Documentation of SMB in namelist_definition + #228 -- Get tools and testing working + + +=============================================================== +=============================================================== Tag name: clm4_5_18_r274 Originator(s): sacks (Bill Sacks) Date: Tue Jan 30 05:55:53 MST 2018 diff --git a/doc/ChangeSum b/doc/ChangeSum index cfcddc8cc0..50ad73cca4 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + clm4_5_18_r275 erik 02/05/2018 Update initial condition files, update fates, new CMIP6 pop-dens, more lnd_tuning_mod options, updated ndep for fully coupled clm4_5_18_r274 sacks 01/30/2018 Fix auto-detection of CIME_MODEL in a standalone checkout clm4_5_18_r273 sacks 01/26/2018 Support a standalone checkout from git clm4_5_18_r272 erik 01/25/2018 Bring in latest FATES release version to CLM trunk: fates_s1.4.1_a3.0.0_rev2