===============================================================
Tag name:  clm3_6_00
Originator(s):  erik (Kluzek Erik 1326 CGD)
Date: Thu Mar 20 13:32:07 MDT 2008
One-line Summary: Fully implement sequential-ccsm mode, upgrade configure, 
         build-namelist and testing, upgrade interpolation tool, 
         add mkdatadomain, write to iulog rather than 6 explicitly, SCAM update, 
         Update datasets, add archiving, and build-streams, add in point version 
         of Urban model, change directory structure to mimic CCSM

Software engineering changes:

   Fully implement sequential-ccsm mode.
   Upgrade configure, build-namelist and testing, and build-streams.
   Upgrade interpolation tool, 
   Add mkdatadomain to convert CLM input datasets to CCSM datm7 format.
   Write to iulog rather than 6 explicitly.
   SCAM update.
   Update datasets used.
   Add archiving as a script run after model completes.
   Change directory structure to mimic CCSM.

    QUICKSTART: using the new CPL7 scripts:

         cd scripts
         ./create_newcase            # get help on how to run create_newcase
         ./create_newcase -case testI -mach blueice -res f19_g15 -compset I    # create new "I" case for blueice at 1.9x2.5_gx1v5 res
                                     # "I" case is clm active, datm7, and inactive ice/ocn
         cd testI
         configure -mach blueice     # create scripts
         testI.build                 # build model and create namelists
         bsub < testI.run            # submit script  
                                     # (NOTE: edit env_run to set RESUBMIT to number of times to automatically resubmit)

Science changes:

   Interpinic:

   Get it to work with OMP to run faster and optimized. Validate that different numbers of threads gives the same answers.
   Correct problem to find nearest points for PFT data. Get interpinic to work on a half-degree dataset. Change interpinic 
   so it doesn't work on a given set of variables -- but does all applicable variables based on a set of rules of what the
   variables dimensions are. This allows interpinic to work for CN cases.

   Urban model:

   Urban code was started by Gordon Bonan, and taken up by Mariana Vertenstein and Keith Oleson.
   This represents work that has been ongoing for several years. Revision dates go back to
   before 2003.

   Some papers on the work are available from:

   Oleson et.-al. Journal of Applied Meteorology and Climatology, in-Press as of Jan/2008

   http://www.cgd.ucar.edu/tss/staff/oleson/publications/JAMC1597_rev_jul27_2007.pdf
   http://www.cgd.ucar.edu/tss/staff/oleson/publications/JAMC1598_rev_jul27_2007.pdf

   Newcn06:

   Move newcn06-02_clm3_5_00 branch tag to trunk. Add ability for CN to do pftdyn mode. Add new options to configure
   and namelist.

Known bugs (include bugzilla ID): 251 (TwoStream), 672 (3.5.4-3.5.14 diffs), 680 (t0 precip diff for seq-ccsm), 
                                  698 (cprnc bug gives false difference), 701 (svn keyword), 708, (xlf bug on bluevista)
                                  717 (archiving bug -- only archive 1000 files at a time), 724 (cprnc core dumps)
                                 1079 (rpointer file updated with clm.i files)
                                 1083 (Units of NEE exported should be kg CO2 NOT kg C)
    http://bugs.cgd.ucar.edu/

    Known bugs that will NOT be resolved: 512 (mksurf on PGI), 546(interpinic for DGVM), 
                                          694 (restarts for offline) , 
                                          652 (threads different answers with older PGI versions)
                                          725 (bug in offline mode for lightning with ifort compiler)

Describe any changes made to build system:

   Add new options to configure

     -ad_spinup    Turn on AD_SPINUP mode for bgc setting of CN [on | off]
     -exit_spinup  Turn on EXIT_SPINUP mode for bgc setting of CN [on | off]
     -pergro       Switch enables building CLM for perturbation growth tests.

   Add BUILDPIO CPP variable

   Implement a build-namelist script to create namelists for you:

build-namelist -help
SYNOPSIS
     build-namelist [options]
OPTIONS
     -cam_config "file"      Read the CAM config cache file (rather than the CLM version) to get
                             build-time configuration information.
                             (Default -- not used.)
     -cam_hist_case "caseid" Use the input CAM simulation caseid to build a streams file with that case id.
                             (Default -- not used).
     -case "name"            Case identifier up to 32 characters
     -clm_cfg "dir"          Directory containing CLM configuration scripts.
     -clm_demand "list"      List of variables to require on clm namelist besides the usuals.
     -config "file"          Read the given config cache file to get the configuration
                             of the CLM executable.  Default: config_cache.xml.
     -csmdata "dir"          Head directory location of CCSM input data.
                             Can also be set by using the CSMDATA environment variable.
     -cycle_beg_year "year"  The begining year to cycle input datasets over.
     -cycle_end_year "year"  The ending year to cycle input datasets over.
     -cycle_init_year "year" The simulation year that will correspond to the data
                             for cycle_beg_year.
     -d "directory"          Output directory name of resulant namelists.
                             Default: ./
     -datm_data_dir "path"   Directory path to the datm data
                             (only used when mode=ccsm_seq)
     -datm_domain "file"     File name of domain file for datm data matching resolution data resolution.
                             (only used when mode=ccsm_seq)
     -datm_dom_dir "path"    Directory path to the datm_domain file.
                             (only used when mode=ccsm_seq)
     -help [or -h]           Print usage to STDOUT.
     -ignore_ic_date         Ignore the date on the initial condition files (ic_ymd and ic_tod)
                             when determining what input initial condition file to use.
     -ignore_ic_year         Ignore just the year part of the date on the initial condition files (ic_ymd and ic_tod)
                             when determining what input initial condition file to use.
     -infile "file"          Specify a namelist file to read values from.
     -lnd_res "Resolution"   Horizontal resolution of fine mesh for land
                             (if different than resolution coupling to atmosphere)
     -mask "land-mask"       Type of land-mask (default, navy, gx3v5, gx1v5 etc.)
     -namelist "namelist"    Specify namelist settings using FORTRAN namelist syntax, e.g.,
                              -namelist "&clm_inparm hist_dov2xy=.true. /"
     -res "Resolution"       Horizontal resolution (default, 64x128, 1.9x2.5, 1x1_brazil etc.)
     -runlength "length"     Length of simulation (e.g. default, 10d, 5s, 2y)
                             (Corresponding to: default, 10 days, 5 steps, or 2 years)
                             classifiers (d=days, s=steps, y=years)
     -s                      Turns on silent mode - only fatal messages issued.
     -sim_year year          Year to simulate for input datasets (i.e. 1890, 2000, etc.)
     -source "source"        Source data to use for datm (for ccsm_seq mode)
     -start_type "type"      Type of simulation (arb_ic, startup, continue, or branch)
     -test                   Enable checking that initial and boundary datasets exist on local filesystem.
     -use_case "case"        Specify a use case which will provide default values.
     -v n                    Set verbosity to level n.  1 (default), 2 or 3.

Note: The precedence for setting the values of namelist variables is (highest to lowest):
      1. interactive prompting,
      2. namelist values set by specific command-line options, e.g., -case -start_type and -ignore_ic_date,
      3. values set on the command-line using the -namelist option,
      4. values read from the file specified by -infile,
      5. values specified by the -use_case option,
      6. values from defaults files in the CLM configuration
         script directory.

      Use the "drv_in" 'virtual namelist' to have build-namelist decide which namelist
      to put driver control information in.
 Use build-streams for sequential-CCSM
  Builds the streams files on the fly. This allows running data over any period.
  Add usecase option to build-namelist to set multiple things (currently only implementing pergro and pergro0)
  Add notes to namelist files generated with build-namelist so can reconstruct.
  See details of new build-namelist options in documentation on build-namelist below.


Describe any changes made to the namelist:

   Remove mss options (mss_irt, mss_wpass and archive_dir)
   Remove ability to change restart pointer filename (rpntpath)
   Actually use pertlim for arbitrary initial conditions if > 0

     o co2_ppmv               = real for CO2 parts per million by volume                         [MUST be set on namelist]
     o model_version          = character for model version running with
     o hostname               = character for model version running with
     o username               = character for model version running with
     o stop_final_ymd         = integer if want to stop early (only offline mode -- use stop_ymd in drv_in for seq_ccsm)
     o furbinp                = character if want to turn urban datasets on                      (default " ")
     o outnc_large_files      = logical true if want to use NetCDF 64-bit large file format      [.FALSE., .TRUE.]
                                for output files (history and restart files)

   History experimental options (mostly for PIO which isn't fully implemented yet):

     o hist_pioflag           = logical true if want to turn on hist with pio                    [.FALSE., .TRUE.]
     o ncd_lowmem2d           = logical true if want to turn on low memory 2d writes in clm hist [.TRUE., .FALSE.]
     o ncd_pio_def            = logical true if want default pio use setting                     [.FALSE., .TRUE.]
     o ncd_pio_UseRearranger  = logical true if want to use MCT as Rearranger                    [.TRUE., .FALSE.]
     o ncd_pio_UseBoxRearr    = logical true if want to use box as Rearranger                    [.FALSE., .TRUE.]
     o ncd_pio_SerialCDF      = logical true if want to write with pio serial netcdf mode        [.FALSE., .TRUE.]
     o ncd_pio_IODOF_rootonly = logical true if want to write history in pio from root only      [.FALSE., .TRUE.]
     o ncd_pio_DebugLevel     = integer pio debug level                                          ( default 2)
     o ncd_pio_num_iotasks    = integer number of iotasks to use for PIO                         (default all PEs)

   New output variables added:

        BUILDHEAT     heat flux from urban building interior to walls and roof            W/m^2  active
        LWdown        atmospheric longwave radiation                                      W/m^2
        PSurf         surface pressure                                                    Pa
        Qh            sensible heat                                                       W/m^2
        Qle           total evaporation                                                   W/m^2
        Qstor         storage heat flux (includes snowmelt)                               W/m^2
        RH            atmospheric relative humidity                                       %
        Rainf         atmospheric rain                                                    mm/s
        Rnet          net radiation                                                       W/m^2
        SWdown        atmospheric incident solar radiation                                W/m^2
        TBUILD        internal urban building temperature                                 K      active
        TRAFFICFLUX   sensible heat flux from urban traffic                               W/m^2  active
        Tair          atmospheric air temperature                                         K
        WASTEHEAT     sensible heat flux from heating/cooling sources of urban waste heat W/m^2  active
        HCSOI         soil heat content                                                   MJ     active
        HCSOISNO      soil plus snow heat content                                         MJ     active

   (Fields not mentioned above as active are set to inactive unless asked for. They are "ALMA" variables needed for
    an urban model intercomparision project.)

Describe timing and memory performance:

   On blueice

       128 Tasks, nosmp   = 1.9x2.5_gx1v5 resolution:  115 sim-years/Wall-Day 
                                                        61 sim-years/Wall-Day (CN mode) 3.9 GBytes memory
	64 Tasks, nosmp   = 1.9x2.5_gx1v5 resolution:  143 sim-years/Wall-Day
                                                        73 sim-years/Wall-Day (CN mode) 2.1 GBytes memory
	32 Tasks, nosmp   = 1.9x2.5_gx1v5 resolution:  131 sim-years/Wall-Day 
                                                        60 sim-years/Wall-Day (CN mode) 2.2 GBytes memory
	32 threads, nospmd= 1.9x2.5_gx1v5 resolution:   98 sim-years/Wall-Day 
                                                        49 sim-years/Wall-Day (CN mode) 1.7 GBytes memory
         8 Tasks, nosmp   = 1.9x2.5_gx1v5 resolution:   88 sim-years/Wall-Day 
                                                        38 sim-years/Wall-Day (CN mode) 774 MBytes memory
       Note: With 64 Tasks CLM is spending roughly 40% of it's time on I/O. Hence, increasing the processor
             count doesn't increase the throughput -- since I/O is only on one task.

   Depending on the configuration -- offline mode is about the same to 168% slower (in CN mode)

Versions of any externally defined libraries:

   doc                           doc_060127
   scripts                       scripts4_080311
   models/drv/seq_mct            drvseq2_0_12
   models/atm/datm7              drva07_datm7_071129
   models/ocn//socn              stubs1_0_7
   models/ice//sice              stubs1_0_7
   models/csm_share              loga26_share3_071107
   models/utils/esmf_wrf_timemgr esmf_wrf_timemgr_060616
   models/utils/timing           timing_070525
   models/utils/mct              seqa07_MCT2_4_2_071026
   models/utils/pio              pio11_prod
   models/lnd/clm/tools/cprnc    cprnc_070817
   models/lnd/clm/bld/perl5lib   perl5lib_071204

Summary of testing:

  bluevista:
011 er111 TER.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
016 er112 TER.sh 4p_vodsr_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
021 er113 TER.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
070 smJ11 TSM.sh 4p_casasc_dh clm_std 19981231:NONE:1800 48x96 gx3v5 48 arb_ic ..................FAIL! rc= 4 <<<<< Bug 708
071 erJ11 TER.sh 4p_casasc_dh clm_std 19981231:NONE:1800 48x96 gx3v5 10+38 arb_ic ...............FAIL! rc= 5 <<<<< Bug 708
072 brJ11 TBR.sh 4p_casasc_dh clm_std 19981231:NONE:1800 48x96 gx3v5 24+24 arb_ic ...............FAIL! rc= 5 <<<<< Bug 708
073 blJ11 TBL.sh 4p_casasc_dh clm_std 19981231:NONE:1800 48x96 gx3v5 48 arb_ic ..................FAIL! rc= 4 <<<<< Bug 708
074 smJ15 TSM.sh 4p_casasc_h clm_std 19981231:NONE:1800 48x96 gx3v5 48 arb_ic ...................FAIL! rc= 4 <<<<< Bug 708
  blueice: All PASS except...
011 er111 TER.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
016 er112 TER.sh 4p_vodsr_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
021 er113 TER.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
022 br113 TBR.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ..............FAIL! rc= 11 <<<< Bug 694
032 brE12 TBR.sh 4p_vodsrsc_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ............FAIL! rc= 6 <<<< MPI error...
  jaguarcnl: All PASS except...
009 smB11 TSMruncase.sh .........................................................................FAIL! rc= 4 <<<< bad hostname
013 bl111 TBL.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 5
018 bl112 TBL.sh 4p_vodsr_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 5
023 bl113 TBL.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 7
028 blE11 TBL.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic ...............FAIL! rc= 5
033 blE12 TBL.sh 4p_vodsrsc_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic ...............FAIL! rc= 5
035 smE13 TSM.sh 4p_vodsrsc_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic ...............FAIL! rc= 10
038 blE13 TBL.sh 4p_vodsrsc_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic ...............FAIL! rc= 4
  lightning/pathf90: All PASS except...
011 er111 TER.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
012 br111 TBR.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ..............FAIL! rc= 11 <<<< Bug 694
013 bl111 TBL.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 7 <<<< Bug 694
016 er112 TER.sh 4p_vodsr_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
018 bl112 TBL.sh 4p_vodsr_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 7 <<<< Bug 694
021 er113 TER.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
022 br113 TBR.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ..............FAIL! rc= 11 <<<< Bug 694
023 bl113 TBL.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 7 <<<< Bug 694
028 blE11 TBL.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic ...............FAIL! rc= 7
  lightning/ifort: All PASS except...
004 blA91 TBL.sh _sc_dh clm_std 19990101:NONE:3600 4x5 gx3v5 -10 arb_ic .........................FAIL! rc= 7 <<<< Answers different
008 blA74 TBL.sh _sc_ds clm_std 19990101:NONE:3600 1x1_brazil navy -10 arb_ic ...................FAIL! rc= 7 <<<< Answers different
010 sm111 TSM.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 10 <<<< Bug 725
011 er111 TER.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 5 <<<< Bug 725
012 br111 TBR.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ..............FAIL! rc= 5 <<<< Bug 725
013 bl111 TBL.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 4 <<<< Bug 725
014 sm115 TSM.sh 4p_vodsr_h clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic ..................FAIL! rc= 10 <<<< Bug 725
016 er112 TER.sh 4p_vodsr_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 725
018 bl112 TBL.sh 4p_vodsr_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 7 <<<< Bug 725
021 er113 TER.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 725
022 br113 TBR.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ..............FAIL! rc= 11 <<<< Bug 725
023 bl113 TBL.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 7 <<<< Bug 725
026 erE11 TER.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ............FAIL! rc= 13 <<<< Answers different
027 brE11 TBR.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ............FAIL! rc= 11 <<<< Answers different
ifort tests abort early here...
  bangkok/lf95:  All PASS except...
011 er111 TER.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
016 er112 TER.sh 4p_vodsr_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
021 er113 TER.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
135 sm061 TSMext_ccsmcon.sh ERS f19_g13 .........................................................FAIL! rc= 4 <<<< Bad hostname
      >>>>>>>>>>>>>>>>>>>> Random MPI errors????
029 smE15 TSM.sh 4p_vodsrsc_h clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic ................FAIL! rc= 10
044 smF25 TSM.sh 17p_vodsrsc_h clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic ...............FAIL! rc= 10
045 smE31 TSM.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 64x128^360x720 USGS 48 arb_ic .......FAIL! rc= 10
046 erE31 TER.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 64x128^360x720 USGS 10+38 arb_ic ....FAIL! rc= 5
047 brE31 TBR.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 64x128^360x720 USGS 24+24 arb_ic ....FAIL! rc= 5
049 smE35 TSM.sh 4p_vodsrsc_h clm_std 19981231:YEARLY:1800 64x128^360x720 USGS 48 arb_ic ........FAIL! rc= 10
054 smG45 TSM.sh 17p_sc_h clm_pftdyn 10001230:MONTHLY:1800 10x15 USGS 48 arb_ic .................FAIL! rc= 10
063 smH06 TSM.sh 17p_cnnsc_m clm_std^nl_lfiles 19800101:NONE:1800 0.47x0.63 gx1v5@2000 48 startup FAIL! rc= 10
074 smJ15 TSM.sh 4p_casasc_h clm_std 19981231:NONE:1800 48x96 gx3v5 48 arb_ic ...................FAIL! rc= 10
079 smK15 TSM.sh 10p_dgvmsc_h clm_std 19981231:NONE:1800 48x96 gx3v5 48 arb_ic ..................FAIL! rc= 10
080 smK18 TSM.sh 10p_dgvmsc_h clm_std 19981231:NONE:1800 48x96 gx3v5 -213 arb_ic ................FAIL! rc= 10
081 erK18 TER.sh 10p_dgvmsc_h clm_std 19981231:NONE:1800 48x96 gx3v5 -90+-121 arb_ic ............FAIL! rc= 5
093 smL61 TSM.sh _sc_h clm_std 19980101:MONTHLY:1800 1.9x2.5 gx1v5 -10 startup ..................FAIL! rc= 10
094 erL61 TER.sh _sc_h clm_std 19980101:MONTHLY:1800 1.9x2.5 gx1v5 -5+-5 startup ................FAIL! rc= 5
095 brL61 TBR.sh _sc_h clm_std 19980101:MONTHLY:1800 1.9x2.5 gx1v5 -10+-10 startup ..............FAIL! rc= 5
  bangkok/pgi: All PASS except...
011 er111 TER.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
012 br111 TBR.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ..............FAIL! rc= 11 <<<< Bug 694
016 er112 TER.sh 4p_vodsr_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
021 er113 TER.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
022 br113 TBR.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ..............FAIL! rc= 11 <<<< Bug 694
135 sm061 TSMext_ccsmcon.sh ERS f19_g13 .........................................................FAIL! rc= 4 <<<< Bad hostname
045 smE31 TSM.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 64x128^360x720 USGS 48 arb_ic .......FAIL! rc= 10 <<<< Bug 464
046 erE31 TER.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 64x128^360x720 USGS 10+38 arb_ic ....FAIL! rc= 5 <<<< Bug 464
047 brE31 TBR.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 64x128^360x720 USGS 24+24 arb_ic ....FAIL! rc= 5 <<<< Bug 464
049 smE35 TSM.sh 4p_vodsrsc_h clm_std 19981231:YEARLY:1800 64x128^360x720 USGS 48 arb_ic ........FAIL! rc= 10 <<<< Bug 464
      >>>>>>>>>>>>>>>>>>>> Random MPI errors???? (seems to randoming have trouble finding files -- but they are there later...)
040 smF21 TSM.sh 17p_vodsrsc_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic ..............FAIL! rc= 10
041 erF21 TER.sh 17p_vodsrsc_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ...........FAIL! rc= 5
042 brF21 TBR.sh 17p_vodsrsc_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ...........FAIL! rc= 5
055 smG74 TSM.sh 17p_sc_ds clm_pftdyn 10001230:NONE:3600 1x1_tropicAtl test -1100 arb_ic ........FAIL! rc= 10
063 smH06 TSM.sh 17p_cnnsc_m clm_std^nl_lfiles 19800101:NONE:1800 0.47x0.63 gx1v5@2000 48 startup FAIL! rc= 10
069 smI58 TSMcnspinup.sh 17p_cnadspinupsc_dh 17p_cnexitspinupsc_dh 17p_cnsc_dh clm_std 19980115:NONEFAIL! rc= 5
080 smK18 TSM.sh 10p_dgvmsc_h clm_std 19981231:NONE:1800 48x96 gx3v5 -213 arb_ic ................FAIL! rc= 10
081 erK18 TER.sh 10p_dgvmsc_h clm_std 19981231:NONE:1800 48x96 gx3v5 -90+-121 arb_ic ............FAIL! rc= 5
083 erK74 TER.sh 10p_dgvmsc_s clm_std 19971231:NONE:1800 1x1_brazil navy -334+-336 arb_ic .......FAIL! rc= 6
  tempest: All PASS except..
009 smB11 TSMruncase.sh .........................................................................FAIL! rc= 4 <<<< No tempest run script
011 er111 TER.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<< Bug 694
012 br111 TBR.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ..............FAIL! rc= 11 <<< Bug 694
013 bl111 TBL.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 7 <<< Bug 694
016 er112 TER.sh 4p_vodsr_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<< Bug 694
021 er113 TER.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<< Bug 694
022 br113 TBR.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ..............FAIL! rc= 11 <<< Bug 694
023 bl113 TBL.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 7 <<< Bug 694
046 erE31 TER.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 64x128^360x720 USGS 10+38 arb_ic ....FAIL! rc= 7 <<<< Stack memory problem
047 brE31 TBR.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 64x128^360x720 USGS 24+24 arb_ic ....FAIL! rc= 6 <<<< Stack memory problem
063 smH06 TSM.sh 17p_cnnsc_m clm_std^nl_lfiles 19800101:NONE:1800 0.47x0.63 gx1v5@2000 48 startup FAIL! rc= 10 <<<< Memory limit
123 sm921 TSMext_ccsmseq_cam.sh ext_ccsm_seq_4x5_dh ext_ccsm_seq_cam 48 .........................FAIL! rc= 8 <<<<< MPI_GROUP_MAX limit
124 bl921 TSMext_ccsmseq_cam.sh ext_ccsm_seq_4x5_dh ext_ccsm_seq_cam 48 .........................FAIL! rc= 2 <<<<< MPI_GROUP_MAX limit
135 sm061 TSMext_ccsmcon.sh ERS f19_g13 .........................................................FAIL! rc= 4 <<<<< Bad hostname

===============================================================
===============================================================
Tag name:  clm3_5_00
Originator(s):  erik (Erik Kluzek)
Date: Thu May  3 12:03:53 MDT 2007
Date:One-line Summary: New surface datasets, improved canopy integration, and various improvements to Hydrology

Purpose of changes (Since CLM3.0):

  CLM3.5 is considerably different to CLM3.0, particularly with respect to its 
  simulation of the hydrologic cycle.   The modifications consist of new surface 
  datasets based on Moderate Resolution Imaging Spectroradiometer (MODIS) products 
  (Lawrence and Chase 2007), an improved canopy integration scheme 
  (Thornton and Zimmermann 2007), scaling of canopy interception (Lawrence et al. 2007), 
  a simple TOPMODEL-based model for surface and sub-surface runoff (Niu et al. 2005), a 
  simple groundwater model for determining water table depth (Niu et al. 2007), and a 
  new frozen soil scheme (Niu and Yang 2006).  

  There are four additional modifications.  Three of these, an improved description of 
  soil water availability, a resistance term to reduce excessive soil evaporation, and the
  introduction of a factor to simulate nitrogen limitation on plant productivity, can be 
  categorized as new or improved parameterizations from the perspective of CLM3.  The 
  other may be categorized as fixing an algorithmically defective existing parameterization
  (correction to snowage calculation so that snowage increases monotonically) 
  (Dickinson et al. 2006).

  See:

  http://www.cgd.ucar.edu/tss/clm/distribution/clm3.5/

  for more information, and for technical and scientific papers that describe CLM3.5.

  Lastly, we are distributing a new forcing dataset with the new code.  This
  dataset was derived by combining observation-based analyses of monthly precipitation and
  surface air temperature with intramonthly variations from the NCEP/NCAR reanalysis 
  (Qian et al., 2006)

  If you would like to run CLM-CN, please contact Peter Thornton (thornton@ucar.edu).
  If you would like to run CLM-DGVM, please contact Sam Levis (slevis@ucar.edu).
  If you would like to run CLM-CASA', please contact Forrest Hoffman (hof@ornl.gov).

Describe any bug fixes:

  o A revision of RTM-subcycling and corrections to a few land-locked grid cells.
  o A more efficient soil evaporation calculation based on PFT demand.
  o A fix to aggregation of LAI from high-resolution source data to CLM surface data.
  o Changing Temperature of freezing of water from 273.16 (triple point of water) to 273.15.

Summarize any software engineering improvements:

  o Add option to run CLM at a finer resolution than the atmospheric model coupled to
     (Tony Craig and others)
  o MCT (Model Coupling Toolkit) used to describe decompositions and do redistributions.
  o Remove dependences on CAM modules and data structures.
  o Use csm_share clocks and CCSMInit objects for simulation time information and
    initialization information needed by all CCSM models.
  o Update time-management to ESMF_2_2_2r interfaces and use the WRF implementation of
    ESMF time-management modules.
  o Made restart datasets double precision NetCDF rather than binary 
    (except history restarts).
  o Add interface layers to link to Sequential CCSM (formally standalone CAM) using MCT.
  o Parallelize RTM, by Tony Craig and Pat Worley.
  o Add a new testing suite to do automated testing for any code changes.
  o Improve memory scaling with a new decomposition from Tony Craig.
  o Move make surface dataset capability to an offline tool (mksurfdata).
  o Add an offline tool to create grid datasets needed for initialization (mkgriddata).
  o Add ability to run concurrent CCSM in single-executable mode.
  o Running with SCAM (Single Column Atmospheric Model) mode modularized better.

Versions of any externally defined libraries: (under src/utils)

  o csm_share:        share3_070321 (add flds, eshr and dshr directories, 
                                     add shr_inputinfo_mod, eshr_timemgr_mod, 
                                     other modules for shared data work)
  o esmf_wrf_timemgr: esmf_wrf_timemgr_060616 (or can link to full ESMF_2_2_2r)
  o timing:           timing_070328 (extensive updates and utilize PAPI and new namelist)
  o mct:              MCT2_3_0_070206 (allow to build with code, Cray mods, misc.)

Describe any changes made to build system: 

  o A configure script was created to create files needed to build the model. 
  o There are also cshell run scripts for different platforms to: 
       configure, build and run the model.
  o Remove SPMD CPP token -- use src/utils/mct/mpi-serial library for serial mode.
  o Remove HIDE_MPI token.
  o Remove CAM and COUP_CAM CPP tokens -- replace with SEQ_MCT and SEQ_ESMF.
  o Remove NOCOMPETE CPP token.
  o Most SCAM #ifdef's removed.
  o Remove TIMING_BARRIERS CPP token -- add option to prof_inparm namelist.
  o See src/utils/timing for new tokens added for timing library 
     (HAVE_PAPI, THREADED_OMP, DIAG, HASH).
  o MCT included with offline CLM.

  Build features added -- but unsupported for public release:

  o Port to jaguar.ccs.ornl.gov (Cray XT3/XT4)
  o Port to Bluegene/L (frost.ucar.edu) (add BGL CPP token)
  o Port to lightning.ucar.edu (frost.ucar.edu with Pathscale)
  o Add SINGLE_EXEC CPP token for running concurrent CCSM in single-executable mode.
  o Add CN CPP token and CN BGC code.
  o Add NO_FIRE CPP token for use by CN mode.
  o Add AD_SPINUP and EXIT_SPINUP CPP token for initial spinup of CN.
  o Add DUST and PROGSST CPP tokens.
  o Add COUP_WRF CPP token.

Describe any changes made to the namelist:

  Main namelist name changed from clmexp to clm_inparm

  Option to run clm at a finer mesh than the atmosphere added several namelist items.

  flndtopo        = 256 character land topography file name
  fatmgrid        = 256 character atmosphere grid data file name
  fatmlndfrc      = 256 character landfrac (on atm grid) file name
  fatmtopo        = 256 character atmosphere topography file name

  Decomposition/performance control:

  nsegspc         = Number of segments per clump for new decomp. 
                    1 will produce poor loadbalance, infinity yields too many
                    segments per pe but good load balance. (default 20)

  All mksrf_* options moved to the mksurfdata offline tool. So instead of
  creating surface datasets by running clm -- you run the mksurfdata tool
  to create them.

  mksrf_* = Removed from namelist.

  Miscellaneous:

  rest_flag            = logical, turns restart file writing on (default .true.)
  wrtdia               = true if want output written  (default .false.)
  create_crop_landunit = true => separate crop landunit is not created by default
                         (currently broken see KnownBugs) (default .false.)

  New prof_inparm namelist added for timing library.

   profile_single_file  = Write timing output to single file or file per task 
                          (default single)
   profile_disable      = Turn timing off. (default .false.)
   profile_barrier      = Turn MPI barriers on in t_barrierf calls. (default .false.)
   profile_depth_limit  = Integer indicating maximum number of levels of timer nesting 
                          (default 99999)
   profile_detail_limit = integer indicating maximum detail level to profile (default 0)
   profile_timer        = integer indicating which timer to use
      GPTLwall           = 1
      GPTLcpu            = 2
      GPTLabort_on_error = 3
      GPTLoverhead       = 4
      GPTLdepthlimit     = 5
      GPTLgettimeofday   = 6
      GPTLnanotime       = 7
      GPTLrtc            = 8
      GPTLmpiwtime       = 9
      GPTLclockgettime   = 10
      GPTLpapitime       = 11
      (default is 9, except on UNICOSMP where it is 8)

  Namelist items added -- but unsupported in public release:

  co2_type             = values of 'prognostic','diagnostic','constant' 
                         (only constant mode for OFFLINE)

  CASA':

  spunup   =  0=no, 1=yes (used with nsrest/=1 only)   (default 0)
  lalloc   =  0=fixed allocation, 1=dynamic allocation (default 1)
  lnpp     =  1=gpp*gppfact,2=fn(lgrow)*gppfact        (default 2)
  q10      =  temperature dependence                   (default 2.0)
  fcpool   =  Carbon Pool initial state filename

List any changes to the defaults for the boundary datasets:

 Use following files for T42 resolution:

 finidat        = '$CSMDATA/inidata_3.1/offline/clmi_0000-01-01_064x128_c070403.nc'
 fsurdat        = '$CSMDATA/surfdata/surfdata_64x128_c070501.nc'
 fatmgrid       = '$CSMDATA/griddata/griddata_64x128_060829.nc'
 fatmlndfrc     = '$CSMDATA/griddata/fracdata_64x128_USGS_070110.nc'
 fpftcon        = '$CSMDATA/pftdata/pft-physiology.c070207'
 offline_atmdir = '$CSMDATA/NCEPDATA.Qian.T62.c051024'
 frivinp_rtm    = '$CSMDATA/rtmdata/rdirc.05.061026'

 Only needed for CN mode:

 fndepdat       = '$CSMDATA/ndepdata/ndep_clm_2000_64x128_c060414.nc'

Code reviewed by: 
   bonan, dlawren, erik, mvertens, nanr, oleson, pworley, slevis, tcraig, thornton

Summary of testing: Other than bugs documented in KnownBugs works on following machines:

   bluevista.ucar.edu ---- IBM/SP running AIX
   blueice.ucar.edu ------ IBM/SP running AIX
   bangkok.cgd.ucar.edu -- Linux cluster (both PGI and Lahey compilers)
   tempest.ucar.edu ------ SGI running IRIX
   lightning.ucar.edu ---- Linux cluster (using Pathscale compiler)
   jaguar.ccs.ornl.edu --- Cray XT3/XT4 (using Cray-specific PGI compiler) (builds)
   phoenix.ccs.ornl.edu -- Cray X1 (using Cray-specific PGI compiler) (builds)

  MSS location of control simulations used to validate new climate:

	OFFLINE: /OLESON/csm/hydp2_off_communn_hk44
        CAM/CLM: /OLESON/csm/hydp2_communn_hk44a
        CCSM:    /CCSM/csm/b31.020ws
   
  URL for LMWG diagnostics output used to validate new climate:

OFFLINE:
http://www.cgd.ucar.edu/tss/clm/diagnostics/lmwg_hydro/hydp2_off_communn_hk44a-hyd_off_con3d/setsIndex.html

CAM/CLM:
http://www.cgd.ucar.edu/tss/clm/diagnostics/lmwg_hydro/hydp2_communn_hk44aa-hyd_sstb/setsIndex.html

CCSM:
http://www.cgd.ucar.edu/tss/clm/diagnostics/ccsm2_prod/b31.020wsb-b31.002b/setsIndex.html

===============================================================
