ACME v1.0_beta2

v1.0.0-beta.2

Major fixes:   (OCN) The critical path fixes:  correct del2 scaling, new BL smoothing for KP, rayleigh damping in bottom layer, horizontal flux limiting, (ATM) add IEFLX fixer, correct MG2 rain number convection limiter, correct MG2 ice number sub tend,  avoid ice sublimation divzero in MG2, limiter for MG2 precip frac,  static frozen energy bug. (LND) Add and update FATES, add BETR_v2, N imbalance and fixation, organic pools and radiocarbon, fire and p mass budget bug, urban albedo bug

Other science fixes: (ATM) add i_ieflx_fix namelist, Switch RTM to SROF in F-cases, surface fluxes in SCM,  CAM4 albedo, momentum flux in gustiness, fix HOMME areas, SCM idealizations for relaxation and precipitation, fix floating invalid in MG2, provide aerosol init for SCM, fix CALYPSO simulator and MG2 precip fluxes, gamma terms in mo_strata (LND) add interface with NGEE-Actic CLM-PFLOTRAN, init unset vars in CNAllocationMOD, forest N fert. exp, soil P pools, varsoil in ZD, make sure ci is positive after photoshythesismod (OCN)  ocean/tracer heat budget, bottom drag option, CPL_ALBAV fix, budget terms post-cime5, double the EC60to30v3 timesetep (CICE) fix snicar path bug, history write bug (COUPLER) update coszrs calc with jday, fix coupling intervals and add salinity restoring for C,G cases, BFBFLAG is true

Other fixes  (ATM) reduce h0 size, shr_repo_sum NAN check, HOMME I/O init, zoltan in HOMME, HOMME build, add dyn_npes, add aerosol and cloud history, update nosmp config, allow physics load balancing by default and fix twin init, fix dyn_npes < npes bug, HOMME performance optimizations  (LND) ALM v2 pieces, build script and BGC, memleak in landunit, threading and clm-bgcint, fix threads and CN, unalloc pointer in ALM, add EMI to VSFM, change units of water flux btw root, soil (OCN) Threading optimizations, Don't always write ts restarts,  new high freq stats, PIO_TYPENAME control, Fix analysis, new log system, fix block partitioning, update  regionalStatistics analysis defaults

Compsets:   many high-res added. I-Compsets for ECA with CRUNCEP and 20th transient, spun up with v0atm, E and I for BGC, ne120 F and WCYCL compsets for F1850 and 20TR.

Tests:  COSP and cosplite in developer, hi-res and extended suites, land 20th trans, FATES, low-res in atm, SCM test for ARM97, add  PEM_Ld3.ne30_oECv3_ICG.A_WCYCL1850S and other tests for that compset, shorten crop model run length, ECA tests

New grids:  TWP RRM, EC60to30v3wLI, ENA RRM, ne120_oRRS18v3_ICG, 

New datasets: Many land ic updates, P dataset and 1850,2000 ic for land ne240np4, include phosphorous in land surface datasets, update IC files for  oRRS18to6v3_ICG and oEC60to30v3_ICG, update ic for land ne120_oRRS18v3

CIME additions: update to 5.3 (alpha06 then alpha10), charge to subaccount, allow jenkins to run mutlple compilers, check tput, build with MOAB, allow running short-term archiving during a run.

CIME fixes:  handle corrupted TestStatus, don't move to many files in short term archiving dashboard resubmit, Fix SEQ on skybridge/chama, archive Macros, Fix TIMER_DETAIL, TIMER_LEVEL,  build_env.txt file, highwater memory stats, st_archive template, $ENV resolutions, remove SAVE_TIMING from non-prod machines, make SVN check less strict, remove submodule hacks, add Pat's performance fixes in MCT, use MPI_Isends in PIO to avoid buggy mpi_irsends, don't build hdf5 if using mpi-serial, always save interim restarts, archive mpas files, refactor perf provenance saving, man fixes to jenkins_generic_job,  PIO2 bug in restart physics, interaction with HOMME

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

Config updates:  too many to list.  Every machine was updated since beta1.  Many pe layouts added.

Critical path fixes to MPAS-o, MG2 fixes in atm, CIME5.3.0