[RegCNET] error in RegCM4-CLM4.5-CN due to urban model

‪Samy Rateb‬ ‪ ratebsamy at yahoo.com
Sun Dec 27 09:55:04 CET 2015


Hello RegCNET users,
Good morning. Happy new year. I tried to make RegCM4-CLM4.5-CN reads initial CN file clmi.I1850CRUCLM45BGC.0241-01-01.1.9x2.5_g1v6_simyr1850_c130515.nc by putting the setting finidat in clm4.5 settings in my namelist. The path of this initial file was /home/samy/RCMDATA/CLM45/initial/ . But during running the model an error appeared due to urban model. The error was:
This is RegCM trunk
   SVN Revision: Unversioned directory compiled at: data : Dec 27 2015  time: 10:30:39

 : this run start at  : 2015-12-27 10:49:59+0200
 : it is submitted by : samy
 : it is running on   : localhost.localdomain
 : it is using        :            4   processors
 : in directory       : /home/samy/Videos/run
                       
 CPUS DIM1 =            2
 CPUS DIM2 =            2

 Reading model namelist file
 Initial date of the global simulation: 2005-01-01 00:00:00 UTC         
 Initial date of this run             : 2005-01-01 00:00:00 UTC         
 Final date of this run               : 2005-12-31 00:00:00 UTC         
 Total simulation lenght              :         8736  hours
 Timestep in seconds =  150.000000
 Split explicit dtau =   37.500000  75.000000
 Reading Domain file : ./input/AFR_DOMAIN000.nc
 Setting IPCC scenario to A1B     
 Create SAV files :  T
 Create ATM files :  F
 Create RAD files :  T
 Create SRF files :  T
 Create STS files :  T
 Frequency in hours to create SAV :    0.0
 Frequency in hours to create ATM :    6.0
 Frequency in hours to create RAD :    6.0
 Frequency in hours to create SRF :    3.0
 Physical Parameterizations
  Lateral Boundary conditions :  5
  Semi-Lagrangian Advection   :  0
  Land cumulus conv. scheme   :  4
  Ocean cumulus conv. scheme  :  4
  Moisture schem              :  1
  Ocean Flux scheme           :  2
  Zeng roughness formula      :  1
  Zeng roughness method       :  1
  Coupling with ocean         :  0
  Coupling with wave          :  0
  Pressure gradient force     :  0
  Prescribed LW emissivity    :  0
  Lake model in BATS          :  0
  Simulate diurnal sst cycle  :  0
  Simulate sea ice cover      :  0
  Simulate desert seasons     :  0
  Enable chem/aerosol model   :  0
  Large scale LWP as convect. :  0
  Cloud fraction scheme       :  0
  Marine stratocumulus fraction  0
 Boundary Pameterizations
  Nudge value high range     :  3.000000
  Nudge value medium range   :  2.000000
  Nudge value low range      :  1.000000
 Model Timestep Pameterizations
  time step for dynamical model in seconds :   150.000000
  time step for surface   model in seconds :   450.000000
  time step for cumulus   model in seconds :   150.000000
  time step for radiation model in minutes :    30.000000
  time step for emission  model in hours   :    18.000000
  time step for chemistry model in seconds :   900.000000
 Domain grid parameters:
  Map Projection        : ROTMER
  Dot Grid Full Extent  :  150x 120x 18
  Model Top Pressure    :    5.000000 cb
  Model Grid Spacing    :   60.000000 km
  Grid Center Latitude  :    8.000000 deg
  Grid Center longitude :   20.000000 deg
  Pole Latitude         :    8.000000 deg
  Pole longitude        :   20.000000 deg
 PBL limit for Holtstag
  Index of highest allowed pbl :  10
 SUBEX large scale precipitation parameters
  # of bottom no cloud model levels :  1
  Auto-conversion rate:         Land =    0.000250 Ocean =    0.000250
  Relative humidity thresholds: Land =    0.800000 Ocean =    0.900000
  Gultepe factors:              Land =    0.400000 Ocean =    0.400000
  Maximum relative humidity         :    1.010000
  RH0 temperature threshold         :  238.000000
  Land Raindrop Evaporation Rate    :    0.001000
  Ocean Raindrop Evaporation Rate   :    0.000100
  Land Raindrop Accretion Rate      :    3.000000
  Ocean Raindrop Accretion Rate     :    6.000000
  Maximum total cloud cover for rad :    0.750000
  Condensation threshold            :    1.000000
  Surface radiation hack            :           F
 Emanuel (1991) Convection Scheme V4.3C used.
  Min Convection origin             :    0.950000, (16)
  Autoconversion Threshold (ocean)  :    0.001100
  Autoconversion Threshold (land)   :    0.001100
  Autoconversion Threshold to zero  :  -55.000000
  Entrainment Coefficient           :    1.500000
  Fractional area of uns. downdraft :    0.050000
  Fractional area of uns. downdraft :    0.050000
  Fall speed of rain                :   50.000000
  Fall speed of snow                :    5.500000
  Rain evaporation coefficient      :    1.000000
  Snow evaporation coefficient      :    0.800000
  Convective momentum transport coef:    0.700000
  Downdraft velocity scale          :   10.000000
  Max negative perturbation blw LFC :    0.900000
  Quasi-equilibrium approach rate 1 :    0.200000
  Quasi-equilibrium approach rate 2 :    0.100000
  Precipitation efficienct (land)   :    0.999000
  Precipitation efficienct (ocean)  :    0.999000
 Convective Cloud Cover parameters after resolution scaling
  Maximum Convective Cloud Cover :    0.398148
  Convective Cloud Water         :    0.000300
 The surface energy budget is used to calculate the ground temperature.
 The radiation is computed every   12 time steps.
 Relaxation boundary conditions (exponential method)
# k       sigma           a      dsigma       twt(1)       twt(2)         qcon
  1      0.0000      0.0250      0.0500       0.0000       0.0000       0.0000
  2      0.0500      0.0750      0.0500       0.5000       0.5000       0.5000
  3      0.1000      0.1300      0.0600       0.4545       0.5455       0.5455
  4      0.1600      0.1950      0.0700       0.4615       0.5385       0.5385
  5      0.2300      0.2700      0.0800       0.4667       0.5333       0.5333
  6      0.3100      0.3500      0.0800       0.5000       0.5000       0.5000
  7      0.3900      0.4300      0.0800       0.5000       0.5000       0.5000
  8      0.4700      0.5100      0.0800       0.5000       0.5000       0.5000
  9      0.5500      0.5900      0.0800       0.5000       0.5000       0.5000
 10      0.6300      0.6700      0.0800       0.5000       0.5000       0.5000
 11      0.7100      0.7450      0.0700       0.5333       0.4667       0.4667
 12      0.7800      0.8100      0.0600       0.5385       0.4615       0.4615
 13      0.8400      0.8650      0.0500       0.5455       0.4545       0.4545
 14      0.8900      0.9100      0.0400       0.5556       0.4444       0.4444
 15      0.9300      0.9450      0.0300       0.5714       0.4286       0.4286
 16      0.9600      0.9700      0.0200       0.6000       0.4000       0.4000
 17      0.9800      0.9850      0.0100       0.6667       0.3333       0.3333
 18      0.9900      0.9950      0.0100       0.5000       0.5000       0.5000
 19      1.0000
  Constant hor. diff. coef. =  0.360000E+05 m^2 s-1
  Maximumt hor. diff. coef. =  0.375000E+06 m^2 s-1
 READY IC DATA for 2005-01-01 00:00:00 UTC         
 SEARCH BC data for 2005010106, ktau =        0
 READY  BC from       2005010100  to   2005010106
 JDay      0.00000 solar declination angle = -23.16019960 degrees
                   solar TSI irradiance    =    1361.1704 W/m^2
 CLM version: 4.5 - RegCM Unversioned directory
 Attempting to initialize the land model .....
 Mask given by RegCM model has a total of         9914  land points
 Attempting to initialize run control settings .....
 Read in clm_inparm namelist from: regcm.in
 Read in clm_hydrology1_inparm namelist
 Read in clm_soilhydrology_inparm namelist
 Successfully initialized run control settings

 define run:
    source                = Community Land Model CLM4.5
    model_version         = Unversioned directory
    run type              = initial
    case title            = RegCM driven CLM4.5
    username              = samy
    hostname              = localhost.localdomain
 input data files:
    PFT physiology = /home/samy/RCMDATA/CLM45/pftdata/pft-physiology.c130503.nc
    surface data   = ./input/AFR_CLM45_surface.nc
    land frac data = ./input/AFR_DOMAIN000.nc
    nfix_timeconst == zero, use standard N fixation scheme. 
    spinup_state, (0 = normal mode; 1 = AD spinup)         :            0
    model is currently NOT in AD spinup mode.
    override_bgc_restart_mismatch_dump                    :  F
    enable_megan_emission                                 :  F
    enable_urban_landunit                                 :  T
    enable_more_crop_pft                                  :  F
    use_c13                                               :  F
    use_c14                                               :  F
    use_c14_bombspike                                     :  F
    atm_c14_filename = 
    SNICAR optical = /home/samy/RCMDATA/CLM45/snicardata/snicar_optics_5bnd_c090915.nc
    SNICAR aging = /home/samy/RCMDATA/CLM45/snicardata/snicar_drdt_bst_fit_60_c070416.nc
    initial data is from RegCM atm model
    atmospheric forcing data is from RegCM atm model
 Large file support for output files is ON
 model physics parameters:
    flag for random perturbation test is not set
    CO2 volume mixing ratio   (umol/mol)   =    355.00000000000000     
    land albedos  (unitless 0-1)   =   0.80000000000000004     
    ice albedos   (unitless 0-1)   =   0.55000000000000004     
    urban air conditioning/heating and wasteheat   = OFF             
    urban traffic flux   =  F
    more vertical layers =  F
    maxpatch_pft         =           17
    allocate_all_vegpfts =  T
    perchroot (PWS based on unfrozen layers only) =  F
    perchroot (PWS based on time-integrated active layer only) =  F

 Lake Model Namelists:
 Hostetler eddy increase low    :    25.000000000000000     
 Hostetler eddy increase factor :    10.000000000000000     
 Albedo melting lakes (visible) :  0.10000000000000001     
 Albedo melting lakes (NIR)     :  0.10000000000000001     
 Attempting to read ldomain from ./input/AFR_DOMAIN000.nc
   domain_check set       = domain_set
   domain_check decomped  =  T
   domain_check ns        =        17199
   domain_check ni,nj     =          147         117
   domain_check clmlevel  = gridcell
   domain_check nbeg,nend =            1        2478
   domain_check lonc      =    9.3304138183593750        50.474418640136719     
   domain_check latc      =   -22.826822280883789        1.0030002593994141     
   domain_check mask      =            1           1
   domain_check frac      =    100.00000000000000        100.00000000000000     
   domain_check topo      =    0.0000000000000000        2159.9472656250000     
   domain_check area      =    3600.0000000000000        3600.0000000000000     
   domain_check pftm      =            1           1
  
  Reading in urban input data from surface data file ...
  UrbanInput : ./input/AFR_CLM45_surface.nc
  Sucessfully read urban input data

 Attempting to read PFT physiological data .....
 Successfully read PFT physiological data
 Attempting to read surface boundary data .....
 Checked LAT/LON compliance
 Successfully read surface boundary data

  Surface Grid Characteristics
    total number of gridcells =         9914
    total number of landunits =        20538
    total number of columns   =        33188
    total number of pfts      =       171256
  
 ---clm_ptrs_check:
    clm_ptrs_check: g index ranges - OK
    clm_ptrs_check: l index ranges - OK
    clm_ptrs_check: c index ranges - OK
    clm_ptrs_check: p index ranges - OK
    clm_ptrs_check: g mono increasing - OK
    clm_ptrs_check: l mono increasing - OK
    clm_ptrs_check: c mono increasing - OK
    clm_ptrs_check: p mono increasing - OK
    clm_ptrs_check: tree consistent - OK
  
 Attempting to initialize time invariant variables
 Attempting to read soil color, sand and clay boundary data .....
 WARNING:: ETALAKE not found on surface data set.
 All lake columns will have eta set equal to default value
 WARNING:: LAKEFETCH not found on surface data set.
 All lake columns will have fetch set equal to default value
 Successfully read fmax, soil color, sand and clay boundary data

 Attempting to read organic matter data .....
  organicrd : ./input/AFR_CLM45_surface.nc
 Successfully read organic matter data

  # zsoi #
    0.710E-02  0.279E-01  0.623E-01  0.119      0.212      0.366      0.620    
     1.04       1.73       2.86       4.74       7.83       12.9       21.3    
     21.3       35.2    
  # zisoi #
     0.00      0.175E-01  0.451E-01  0.906E-01  0.166      0.289      0.493    
    0.829       1.38       2.30       3.80       6.28       10.4       17.1    
     17.1       28.3       42.1    
  # dzsoi #
    0.175E-01  0.276E-01  0.455E-01  0.750E-01  0.124      0.204      0.336    
    0.554      0.913       1.51       2.48       4.09       6.75       11.1    
     11.1       13.9    
 dzsoi_decomp   1.0000000000000000     
 Set    27 100% special land-units points to zero slope
 Initializing decomposition pools and transitions ...
 Attempting to read snow optical properties .....
 SnowOptics_init : /home/samy/RCMDATA/CLM45/snicardata/snicar_optics_5bnd_c090915.nc
 Set     3 100% special land-units points to zero slope
 Set    34 100% special land-units points to zero slope
 Successfully read snow optical properties
 Attempting to read snow aging parameters .....
 Successfully read snow aging properties
 Successfully initialized time invariant variables
 CLM_hist_printflds : number of master fields =          801
 Setting initial data to non-spun up values
 Attempting to initialize time invariant variables for lakes
 CLM timestep appears to differ from 1800s. 
 Adjusting minimum snow layer thickness over lakes to maintain stability.
 New minimum thickness is    2.0000000000000000E-002 .
 Successfully initialized time invariant variables for lakes
 Setting initial data to non-spun up values for lake points
 Initializing clm2 history files
 There will be a total of            1  history tapes
 History tape            1  write frequency is MONTHLY
 All fields on history tape            1  are grid averaged
 Output precision on history tape            1 =           2
 hist tape =            1  written with dov2xy=  T
 Successfully initialized clm2 history files
 Successfully initialized the land model
 begin initial run at: 
    ktau    =                     0
    year    =         2005
    month   =            1
    day     =            1
    seconds =            0
 Calculating Vertical Modes
 Linearization about standard atmosphere
  # sigma    #
     0.00      0.500E-01  0.100      0.160      0.230      0.310      0.390    
    0.470      0.550      0.630      0.710      0.780      0.840      0.890    
    0.890      0.930      0.960      0.980      0.990       1.00    
  # t mean   #
     218.       218.       218.       218.       230.       239.       248.    
     255.       262.       268.       273.       277.       280.       283.    
     283.       285.       286.       287.       287.    
  # ps mean  #
     100.    
 Vertical mode problem for kz   =  18
 Number of errors (should be 0) =   0
 Split :    1 => aam :     4.0000, fac :    33.3333
 Split :    2 => aam :     2.0000, fac :    60.0000
 Opening new output file ./output//AFR_SRF.2005010100.nc
 Opening new output file ./output//AFR_STS.2005010100.nc
 Opening new output file ./output//AFR_RAD.2005010100.nc
 JDay      0.00000 solar declination angle = -23.16019960 degrees
                   solar TSI irradiance    =    1361.1704 W/m^2
  # Ozone profile at (3,3) #
    0.502E-05  0.194E-05  0.106E-05  0.572E-06  0.299E-06  0.174E-06  0.124E-06
    0.947E-07  0.770E-07  0.660E-07  0.591E-07  0.550E-07  0.523E-07  0.509E-07
    0.509E-07  0.498E-07  0.496E-07  0.496E-07  0.496E-07  0.496E-07
 urban net longwave radiation error: no convergence
 Critical =                        NaN  > 0.001 !
 -------------- FATAL CALLED ---------------
  Fatal in file: mod_clm_urban.F90 at line:     2614
 clm now stopping
 -------------------------------------------
 Abort called by computing node            2 at 2015-12-27 10:50:11.821 +0200
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 2 in communicator MPI COMMUNICATOR 3 DUP FROM 0 
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
 urban net longwave radiation error: no convergence
 Critical =                        NaN  > 0.001 !
 -------------- FATAL CALLED ---------------
  Fatal in file: mod_clm_urban.F90 at line:     2614
 clm now stopping
 -------------------------------------------
 Abort called by computing node            3 at 2015-12-27 10:50:11.821 +0200
 urban net longwave radiation error: no convergence
 Critical =                        NaN  > 0.001 !
 -------------- FATAL CALLED ---------------
  Fatal in file: mod_clm_urban.F90 at line:     2614
 clm now stopping
 -------------------------------------------
 Abort called by computing node            1 at 2015-12-27 10:50:11.822 +0200
 urban net longwave radiation error: no convergence
 Critical =                        NaN  > 0.001 !
 -------------- FATAL CALLED ---------------
  Fatal in file: mod_clm_urban.F90 at line:     2614
 clm now stopping
 -------------------------------------------
 mod_clm_urban.F90 :     2614:            1
 Abort called by computing node            0 at 2015-12-27 10:50:11.824 +0200
--------------------------------------------------------------------------
mpirun has exited due to process rank 2 with PID 23167 on
node localhost.localdomain exiting improperly. There are two reasons this could occur:

1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.

2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"

This may have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
[localhost.localdomain:23164] 3 more processes have sent help message help-mpi-api.txt / mpi-abort
[localhost.localdomain:23164] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

I don't know why. So can any one help me? I would be grateful.
P.S. I attached my namelist. Also I used RegCM-4.5-rc12 version.

Regards
Samy
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