Hello RegCNET users,



I tried to run CN + nitirification-denitirification in RegCM-4.4.5.7,  successfully installed them together without any problem. But  during running the last step:

mpirun -np 4 ./bin/regcmMPICLM45_CN_NITRIF_DENITRIF regcm.in

The following error occured:

  This is RegCM trunk
   SVN Revision: tag 4.4.5.7 compiled at: data : Sep  6 2015  time: 12:08:42

 : this run start at  : 2015-09-06 13:13:22+0200
 : it is submitted by : samy
 : it is running on   : localhost.localdomain
 : it is using        :            4   processors
 : in directory       : /home/samy/run_4.4.5.7
                      
 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               : 2005-04-30 00:00:00 UTC        
 Total simulation lenght              :         2856  hours
 Timestep in seconds =  200.000000
 Split explicit dtau =   50.000000 100.000000
 Reading Domain file : ./input/AFR_DOMAIN000.nc
 Setting IPCC scenario to A1B    
 Create SAV files :  T
 Create ATM files :  F
 Create RAD files :  F
 Create SRF files :  T
 Create STS files :  T
 Frequency in hours to create SAV : 7200.0
 Frequency in hours to create ATM :    6.0
 Frequency in hours to create RAD :    3.0
 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
  Coupling with ROMS ocean    :  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
  Convective LWP scheme       :  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 :   200.000000
  time step for surface   model in seconds :   600.000000
  time step for radiation model in minutes :    30.000000
  time step for emission  model in hours   :    18.000000
 Domain grid parameters:
  Map Projection        : ROTMER
  Dot Grid Full Extent  :  140x 120x 18
  Model Top Pressure    :    5.000000 cb
  Model Grid Spacing    :   60.000000 km
  Grid Center Latitude  :   10.000000 deg
  Grid Center longitude :   21.000000 deg
  Pole Latitude         :   10.000000 deg
  Pole longitude        :   21.000000 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   :    0.001000
  Land Raindrop Accretion Rate      :    3.000000
  Ocean Raindrop Accretion Rate     :    3.000000
  Maximum total cloud cover for rad :    0.750000
  Condensation threshold            :    1.000000
 Emanuel (1991) Convection Scheme V4.3C used.
  Min Convection origin             :    0.950000
  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    9 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. =  0.270000E+05 m^2 s-1
  Maximumt hor. diff. coef. =  0.281250E+06 m^2 s-1
 READY IC DATA for 2005-01-01 00:00:00 UTC        
 SEARCH BC data for   2005010106
 READY  BC from       2005010100  to   2005010106
  # Ozone profile at (3,3) #
    0.502E-05  0.194E-05  0.106E-05  0.571E-06  0.299E-06  0.174E-06  0.124E-06
    0.946E-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
 CLM version: 4.5 - RegCM tag 4.4.5.7
 Attempting to initialize the land model .....
 Mask given by RegCM model has a total of         9860  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         = tag 4.4.5.7
    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, timescale for smoothing npp in N fixation term:    10.000000000000000    
    spinup_state, (0 = normal mode; 1 = AD spinup)         :            0
    model is currently NOT in AD spinup mode.
    override_bgc_restart_mismatch_dump                    :  F
    no_frozen_nitrif_denitrif                             :  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        =        16029
   domain_check ni,nj     =          137         117
   domain_check clmlevel  = gridcell
   domain_check nbeg,nend =            1        2465
   domain_check lonc      =    9.3382234573364258        50.473365783691406    
   domain_check latc      =   -21.054103851318359        2.4677600860595703    
   domain_check mask      =            1           1
   domain_check frac      =    100.00000000000000        100.00000000000000    
   domain_check topo      =    11.780488014221191        2172.8012695312500    
   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 =         9860
    total number of landunits =        10671
    total number of columns   =        13668
    total number of pfts      =       170804
 
 ---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     1 100% special land-units points to zero slope
 Set    25 100% 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    19 100% special land-units points to zero slope
 Set     4 100% 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 =          827
 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    2.3094010767585028E-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

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x31B2C19037
#1  0x31B2C19604
#2  0x3A39C35CCF
#3  0x90501F in __mod_clm_cnallocation_MOD_cnallocation
#4  0x92EFC6 in __mod_clm_cndecomp_MOD_cndecompalloc
#5  0x878EFD in __mod_clm_cnecosystemdyn_MOD_cnecosystemdyn
#6  0xA97EF7 in __mod_clm_initsurfalb_MOD_initsurfalb
#7  0x87825B in __mod_clm_initialize_MOD_initialize2
#8  0x86F072 in __mod_clm_regcm_MOD_initclm45
#9  0x48D56C in __mod_lm_interface_MOD_initialize_surface_model
#10  0x4D8631 in __mod_init_MOD_init
#11  0x47C914 in __mod_regcm_interface_MOD_rcm_initialize

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x31B2C19037
#1  0x31B2C19604
#2  0x3A39C35CCF
#3  0x90501F in __mod_clm_cnallocation_MOD_cnallocation
#4  0x92EFC6 in __mod_clm_cndecomp_MOD_cndecompalloc
#5  0x878EFD in __mod_clm_cnecosystemdyn_MOD_cnecosystemdyn
#6  0xA97EF7 in __mod_clm_initsurfalb_MOD_initsurfalb
#7  0x87825B in __mod_clm_initialize_MOD_initialize2
#8  0x86F072 in __mod_clm_regcm_MOD_initclm45
#9  0x48D56C in __mod_lm_interface_MOD_initialize_surface_model
#10  0x4D8631 in __mod_init_MOD_init
#11  0x47C914 in __mod_regcm_interface_MOD_rcm_initialize

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x31B2C19037
#1  0x31B2C19604
#2  0x3A39C35CCF
#0  0x31B2C19037
#1  0x#3  0x90501F in __mod_clm_cnallocation_MOD_cnallocation
31B2C19604
#2  0x3A39C35CCF#4  0x92EFC6 in __mod_clm_cndecomp_MOD_cndecompalloc

#5  0x878EFD in __mod_clm_cnecosystemdyn_MOD_cnecosystemdyn
#3  0x90501F in #6  0xA97EF7 in __mod_clm_initsurfalb_MOD_initsurfalb
__mod_clm_cnallocation_MOD_cnallocation
#7  0x87825B in __mod_clm_initialize_MOD_initialize2
#4  0x92EFC6 in __mod_clm_cndecomp_MOD_cndecompalloc
#8  0x86F072 in __mod_clm_regcm_MOD_initclm45
#5  0x878EFD in __mod_clm_cnecosystemdyn_MOD_cnecosystemdyn
#9  0x48D56C in __mod_lm_interface_MOD_initialize_surface_model
#6  0xA97EF7 in __mod_clm_initsurfalb_MOD_initsurfalb
#10  0x4D8631 in __mod_init_MOD_init
#7  0x87825B in __mod_clm_initialize_MOD_initialize2
#11  0x47C914 in __mod_regcm_interface_MOD_rcm_initialize
#8  0x86F072 in __mod_clm_regcm_MOD_initclm45
#9  0x48D56C in __mod_lm_interface_MOD_initialize_surface_model
#10  0x4D8631 in __mod_init_MOD_init
#11  0x47C914 in __mod_regcm_interface_MOD_rcm_initialize

Any advice plz

I attached my namelist.

Regards

Samy