This tag was used to generate results for the mansucript describing t…

…he nutrient dynamic model in Knox et al. 2023

Merge branch 'jgfouca/cime/clean_queues' into master (PR E3SM-Project…

…#2306)

Clean up config_batch.xml entries

Setting nodemin to 0 or 1 is useless since it's not possible to
have less than one node.

It is useless (and sometimes even counterproductive) to put a nodemax
setting on the big-job queue for a machine. nodemax should be used to
keep jobs off of small, debug queues.

[BFB]

* jgfouca/cime/clean_queues:
  Clean up config_batch.xml entries

First public release

Since last tag-
Major fixes/additions: (COUPLED) change CMIP6 water cycle to be hybrid out of box (OCN)
single MPAS source dir, update to v6 public release (LND) update to public versions of
sBeTR, FATES, MPP (CIME) add new wget server

Other fixes/additions: (ATM) remove unsupported compsets, SCM and run with 1 task and full
mpi library, new ne120 comsets, change compilation on PGI/Titan for some files (LND) remove
unsupported compsets, fix C init for ECA, new ECA param file, init a bgc variable to zero
(OCN) rename to mpas-ocean (LND ICE) rename to maps-albany-landice.   Remove CLM40, aquap

CIME: update to cime 5.5.0 (aka 5.4.0-alpha.28), change location of e3sm tests, fix aprun
command, move test_mods dirs, fix gptl warnings, order tests by runtime, update MCT to 2.10rc2,
add shell batch scripts

Config updates:  Change Titan baseline dir, Make Cori layouts so tasks elements, change all
submodules to use https for release.

Used for v1.0 prototype 1950 high-resolution water cycle runs

Major fixes/additions:  (COUPLED) add -DAPPLY_POST_DECK_BUGFIXES for 1950 compsets.
Bugfixes includes: (ATM) cosp1.4 modis fixes, RRTMG limiters (LND) surface water and lakes bug,
Also:  1950 compset fixes, add BGC compsets, remove POP, CISM, WW3.

Other fixes/additions  (ATM) add RRM tests, init cosp arrays correctly, fewer QNEG3,
QNEG4 warnings, perturbation growth tests (SEA ICE) add abort streams (LND) mods for
BGC spinup, update param files for RD, fix dynamic roots for tropics, crop bug fixes,
I cases with GSW, pe layout descriptor, change ocean soil order values (LND ICE) fix
coupler indicies, update calving and stats (RIVER) use MOSART everywhere (MPAS) handle hybrid cases better.

CIME fixes:  Update to 5.4.0-alpha.25, better handling of non-core jobs, allow custom
batch directives, better email support for LSF, add A_WCYCL1850S_CMIP6 test

Config updates:  remove compiler warnings on Theta, adjust Theta optimization settings,
Add Summit, add stampede2, add fp exception checking for KNL, cleanup titan,

Fix Intel17 bug in HOMME on edison. Last version before removing v0 c…

…omponents (POP was removed immediately after this)

Major fixes/additions: (COUPLED) and 1950 compsets (LND) update to BeTRv2, ECA soil P fixes
(SEA ICE) improved graph files (ATM) Fix Intel17 bug with HOMME

Other fixes/additions (ATM) add RELVARC diag, regional output with SE,  update fsnowoptics for high res
(LND) 14C pool bug fix, update MPP, dynamic land units for crops, update EMI, remove autogenerated files,
change ELM dynamic root option, sBetr and gnu, nag, (OCN) salinity restoring under sea ice for G cases,
2 new mid resolution ocean-ice meshes (RIVER) new high res routing file

CIME additions:  update to 5.4.0-alpha.23, rename acme to e3sm, auto-regen batch files,
add multiple sources of input data, fix query_config, performance boost, data model updates, reduce Fortran warnings

Config updates:  Update Titan software, High res layouts for Theta, cori-knl, sandiatoss3 intel to 17.0,
Jenkins test name length, edison layouts for wcycle low res

signed-beta

MPAS split FCT, many land fixes, add BGC compsets, BFB with beta3rc10…

… which was run for 200 years.

Major fixes/addtions:   (OCN) split FCT advection, many updates for BGC (ATM) fix bug in FSUTOAC,
code to read CMIP6 strat aerosols (LND)  P balance error, fix soil decomposition when N,P
are co-limited, fix ne30 land surface datasets, reading of soilorder, many CN updates (ICE) several
bugs fixed, many updates for  BGC

Known problems:  Runs with  Intel17 can possibly have data corruption.
CIME query_config script broken.

Other science fixes: (ATM) new mass gradient option in MG2, SCM with prescribed aerosol,
new limiter option (LND) Fix phosphatase activity parameter dimension, update to FATES 3.0.0
(OCN) correct mpas_forcing, add eddy analysis product (ICE) D-compsets now work
(COUPLER) allow different maps for liquid and ice glc2ocn, add convergence criteria in flux calculation

Other fixes  (ATM) add dyn_npes_stride option, remove norm2 use, error checking in nested threading,
nan check in HOMME (LND) longer htape name, IO of text var, remove unnecessary compilation in MPP,
performance improvement to VSFM (OCN) multiple forcing streams, allow users to point to different
graph files, add wallclock output, reduce halo barriers, reduce default output (ICE) add namelist entries

Compsets:  several BGC compsets, add aqua-planet compsets for FC5AV1C-L, add CMIP6 compsets A_WCYCL20TRS_CMIP6,
F20TRC5-CMIP6, A_WCYCL1850S_CMIP6, F1850C5-CMIP6.  Add MPAS-CICE BGC compset,  GSWP3 and
cpl_bypass compsets for ECA and RD

Tests:  new standalone HOMME tests, add high-res tests for B and G, Add threading test to
developer suite, Get Theta ready for CI, change anvil to run integration

grids:  Remove many unused grids

New datasets:  ne240 land init, map for high res phosphorous data sets, new map for high res runoff to ocean

CIME additions: query_config, case.qstatus, skip-preview-namelist option, script for ESCMI merges/splits,
document time spent before timing lib init, save pre-run provenance, batch email options,
allow different drivers, bless logs, unit tests on skybridge, update to 5.4 (alpha17), hide the run
and archive main scripts, add python3 support, encapsulate XML, many more.

CIME fixes:  cprnc log handling, refactor queue selection, rename PES_PER_NODEpio root 0, refactor
baseline handling, fix bless_test_results, Limit performance archiving to specific projects,
Reduce compiler warnings from Fortran code.  Many more.

run_acme updates:  fix branch runs, cosp, add to model repo, big cleanup, add script for
nightly testing, restart and stop check, submission cleanup, fix branch runs, improve functionality

Config updates:  Theta updates, LLNL updates, work around PGI bugs on Summitdev, updates to
SNL machines (toss3), many updates to NERSC machines some to keep up with environment,
others to speed up simulation.  KNL now default on cori and intel18 default compiler, hyperthreading on Theta   Many more.

added composet and namelist settings for each simulation.

This is an archive tag for manuscript gmd-2017-293 submitted to GMD.

This code version was used for simulations "V1beta Atm" and "V1beta
Coupled" labeled in the manuscript.

cloned from code hash: 7a17edb

This is an archive tag for manuscript gmd-2017-293 submitted to GMD.

This version was used for simulations "V0 Atm" and "V0 Coupled" labeled
in the manuscript.

code hash: 8cd5354