This is RegCM trunk

SVN Revision: tag-SVN6901 compiled at: data : Jan 29 2019 time: 23:12:18

: this run start at : 2019-02-16 19:12:12+0330

: it is submitted by : root

: it is running on : localhost.localdomain

: it is using : 4 processors

: in directory : /home/mehraneh/REGCM4.7/rgcm_me/REGCM_RUN

CPUS DIM1 = 2

CPUS DIM2 = 2

Reading model namelist file

Forcing scenario from dattyp to RCP4.5

DCCB simulation

Initial date of the global simulation: 2006-02-01 00:00:00 UTC

Initial date of this run : 2006-02-01 00:00:00 UTC

Final date of this run : 2006-12-01 00:00:00 UTC

Total simulation lenght : 7272 hours

Timestep in seconds = 10.000000

Split explicit dtau = 2.500000 5.000000

Reading Domain file : input//Reg_DOMAIN000.nc

Setting IPCC scenario to RCP4.5

Create SAV files : T

Create ATM files : T

Create RAD files : T

Create SRF files : T

Create STS files : T

Create SHF files : T

Create CHE files : T

Create OPT files : F

Monthly new files are created

Monthly SAV files are written

Frequency in hours to create ATM : 6.0

Frequency in hours to create RAD : 6.0

Frequency in hours to create SRF : 3.0

Frequency in hours to create CHE : 6.0

Frequency in hours to create OPT : 6.0

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

Coupling with COP : 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 : 1

Large scale LWP as convect. : 1

Cloud fraction scheme : 0

Marine stratocumulus : 1

Climate O3 dataset : 1

Climate Aerosol dataset : 0

Boundary Pameterizations

Num. of bndy points cross : 12

Num. of bndy points dot : 12

Nudge value high range : 3.000000

Nudge value medium range : 2.000000

Nudge value low range : 1.000000

Nm paramter : -1.000000

Dm paramter : -1.000000

Model Timestep Pameterizations

time step for dynamical model in seconds : 10.000000

time step for surface model in seconds : 30.000000

time step for cumulus model in seconds : 30.000000

time step for radiation model in seconds : 300.000000

time step for emission model in seconds : 36000.000000

time step for chemistry model in seconds : 30.000000

Domain grid parameters:

Map Projection : LAMCON

Dot Grid Full Extent : 25x 25x 14

Model Top Pressure : 5.000000 cb

Model Grid Spacing : 40.000000 km

Proj Center Latitude : 37.380000 deg

Proj Center longitude : 46.860000 deg

True Latitude 1 : 30.000000 deg

True Latitude 2 : 60.000000 deg

Fourth order interior/second order boundary diffusion

PBL limit for Holtstag

Index of highest allowed pbl : 8

Cloud fraction schemes parameters

# of bottom no cloud model levels : 1

Maximum relative humidity : 1.010000

Minimum relative humidity : 0.010000

RH0 temperature threshold : 238.000000

Relative humidity thresholds: Land = 0.800000 Ocean = 0.900000

Maximum total cloud cover for rad : 0.750000

Conv. CF UMF factor deep cumulus : 0.140000

Conv. CF UMF factor k2 : 10.000000

Surface radiation hack : F

Vavrus-Waliser Arctic cloud fix : T

SUBEX large scale precipitation parameters

Auto-conversion rate: Land = 0.000500 Ocean = 0.000500

Gultepe factors: Land = 0.650000 Ocean = 0.300000

Land Raindrop Evaporation Rate : 0.000010

Ocean Raindrop Evaporation Rate : 0.000010

Land Raindrop Accretion Rate : 6.000000

Ocean Raindrop Accretion Rate : 4.000000

Condensation efficiency : 1.000000

Emanuel (1991) Convection Scheme V4.3C used.

Min Convection origin : 0.950000, (13)

Autoconversion Threshold (ocean) : 0.001100

Autoconversion Threshold (land) : 0.001100

Autoconversion Threshold to zero : -55.000000

Entrainment Coefficient : 0.060000

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 : 0.650000

Quasi-equilibrium approach rate 1 : 0.020000

Quasi-equilibrium approach rate 2 : 0.010000

Precipitation efficienct (land) : 0.999000

Precipitation efficienct (ocean) : 0.999000

Convective Cloud Cover parameters after resolution scaling

Maximum Convective Cloud Cover : 0.472222

Convective Cloud Water : 0.000300

The surface energy budget is used to calculate the ground temperature.

The radiation is computed every 5. minutes.

Relaxation boundary conditions (exponential method)

# k sigma a dsigma twt(1) twt(2) qcon

1 0.0000 0.0200 0.0400 0.0000 0.0000 0.0000

2 0.0400 0.0700 0.0600 0.4000 0.6000 0.6000

3 0.1000 0.1350 0.0700 0.4615 0.5385 0.5385

4 0.1700 0.2100 0.0800 0.4667 0.5333 0.5333

5 0.2500 0.3000 0.1000 0.4444 0.5556 0.5556

6 0.3500 0.4050 0.1100 0.4762 0.5238 0.5238

7 0.4600 0.5100 0.1000 0.5238 0.4762 0.4762

8 0.5600 0.6150 0.1100 0.4762 0.5238 0.5238

9 0.6700 0.7200 0.1000 0.5238 0.4762 0.4762

10 0.7700 0.8150 0.0900 0.5263 0.4737 0.4737

11 0.8600 0.8950 0.0700 0.5625 0.4375 0.4375

12 0.9300 0.9500 0.0400 0.6364 0.3636 0.3636

13 0.9700 0.9800 0.0200 0.6667 0.3333 0.3333

14 0.9900 0.9950 0.0100 0.6667 0.3333 0.3333

15 1.0000

READY IC DATA for 2006-02-01 00:00:00 UTC

SEARCH BC data for 2006020106 , step = 0

READY BC from 2006020100 to 2006020106

Updating orbit parameters at 2006-02-01 00:00:00 UTC

At 2006-02-01 00:00:00 UTC

JDay 31.00000 solar declination angle = -17.41510670 degrees

solar TSI irradiance = 1367.0000 W/m^2

CLM version: 4.5 - RegCM tag-SVN6901

Attempting to initialize the land model .....

Mask given by RegCM model has a total of 409 land points

Attempting to initialize run control settings .....

Read in clm_inparm namelist from: README.namelist1

Read in clm_hydrology1_inparm namelist

Read in clm_soilhydrology_inparm namelist

test01

Successfully initialized run control settings

define run:

source = Community Land Model CLM4.5

model_version = tag-SVN6901

run type = initial

case title = RegCM driven CLM4.5

username = root

hostname = localhost.localdomain

input data files:

PFT physiology = /run/media/mehraneh/Seagate/REGCM_GLOBDAT/CLM45/pftdata/pft-physiology.c130503.nc

surface data = input/Reg_CLM45_surface.nc

land frac data = input/Reg_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.

q10_maintenance, (0 = linear model; 1 = polynomial model): 0

Q10 linear model is activated.

override_bgc_restart_mismatch_dump : F

enable_megan_emission : T

enable_urban_landunit : T

enable_more_crop_pft : F

use_c13 : F

use_c14 : F

use_c14_bombspike : F

atm_c14_filename =

SNICAR optical = /run/media/mehraneh/Seagate/REGCM_GLOBDAT/CLM45/snicardata/snicar_optics_5bnd_c090915.nc

SNICAR aging = /run/media/mehraneh/Seagate/REGCM_GLOBDAT/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 = 25

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/Reg_DOMAIN000.nc

domain_check set = domain_set

domain_check decomped = T

domain_check ns = 484

domain_check ni,nj = 22 22

domain_check clmlevel = gridcell

domain_check nbeg,nend = 1 102

domain_check lonc = 42.169371230155662 51.524633592978034

domain_check latc = 33.418453439094890 34.990133597461622

domain_check mask = 1 1

domain_check frac = 100.00000000000000 100.00000000000000

domain_check topo = 32.158852533494262 2235.5788476048147

domain_check area = 1600.0000000000000 1600.0000000000000

domain_check pftm = 1 1

Reading in urban input data from surface data file ...

UrbanInput : input/Reg_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

surfrd_wtxy_veg_all crop=.T. and irrigate=.F., so merging irrigated pfts with rainfed

Successfully read surface boundary data

Surface Grid Characteristics

total number of gridcells = 409

total number of landunits = 818

total number of columns = 4499

total number of pfts = 10225

---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/Reg_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

Initializing decomposition pools and transitions ...

Attempting to read snow optical properties .....

SnowOptics_init : /run/media/mehraneh/Seagate/REGCM_GLOBDAT/CLM45/snicardata/snicar_optics_5bnd_c090915.nc

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 = 821

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 1.0000000000000000E-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: 2006-02-01 00:00:00 UTC

Constant hor. diff. coef. = 0.240000E+06 m^2 s-1

Maximum hor. diff. coef. = 0.250000E+07 m^2 s-1

Computed background diff. coeff. = 0.490339E+03 - 0.240000E+06 m^2 s-1

tracer cbmz index molw

NO 55 30.000000000000000

NO2 56 46.000000000000000

N2O5 24 108.00000000000000

HNO2 21 47.000000000000000

HNO3 29 63.000000000000000

HNO4 17 79.000000000000000

O3 53 48.000000000000000

H2O2 10 34.000000000000000

CO 28 28.000000000000000

SO2 11 64.000000000000000

DMS 16 62.000000000000000

H2SO4 2 98.000000000000000

CH4 13 16.000000000000000

C2H6 14 30.070000000000000

PAR 30 44.000000000000000

CH3OH 20 32.000000000000000

HCHO 39 30.000000000000000

ALD2 45 44.000000000000000

AONE 36 72.000000000000000

ETH 25 28.000000000000000

OLET 40 42.000000000000000

OLEI 37 56.000000000000000

TOL 8 92.000000000000000

XYL 12 106.00000000000000

ISOP 38 68.000000000000000

ONIT 51 119.00000000000000

PAN 7 121.00000000000000

HCOOH 3 46.000000000000000

RCOOH 4 59.100000000000001

CH3OOH 22 48.000000000000000

ETHOOH 23 74.000000000000000

ROOH 49 48.000000000000000

MGLY 42 72.000000000000000

ISOPRD 47 68.000000000000000

ISOPN 32 68.000000000000000

OPEN 31 1.0000000000000000

CRES 26 108.00000000000000

NH3 -1 0.0000000000000000

DUST01 -1 0.0000000000000000

DUST02 -1 0.0000000000000000

DUST03 -1 0.0000000000000000

DUST04 -1 0.0000000000000000

BC_HL -1 0.0000000000000000

BC_HB -1 0.0000000000000000

OC_HL -1 0.0000000000000000

OC_HB -1 0.0000000000000000

SSLT01 -1 0.0000000000000000

SSLT02 -1 0.0000000000000000

ANO3 -1 0.0000000000000000

ANH4 -1 0.0000000000000000

tracer index coreesponding to bdy species

# ichbdy2trac #

7 1 2 5 6 3 8

13 9 10 12 11 15 14

20 21 22 23 24 25 37

36 35 34 26 33 19 27

30 31 18 17 16 44 43

46 45 10 47 48 39 40

41 42 0 0 0 0 0

0 0

Calling inidust TOTFRAC = 1.4530364794793116

TOTFRAC = 1.4530364794793116

. Success.

HVREAD: TUVGRID

READ CHEM EMISSION for 2006020001

Opening ch. emission file input/Reg_CHEMISS.nc

CHE_EMISS: Reading record 1

Emission read in success.

READY ICCH DATA for 2006-02-01 00:00:00 UTC

SEARCH CHBC data for 2006020106

READY CHBC from 2006020100 to 2006020106

Calculating Vertical Modes

Linearization about standard atmosphere

# sigma #

0.00 0.400E-01 0.100 0.170 0.250 0.350 0.460

0.560 0.670 0.770 0.860 0.930 0.970 0.990

0.990 1.00

# t mean #

218. 218. 218. 221. 234. 246. 256.

264. 272. 278. 282. 285. 287. 288.

288.

# ps mean #

101.

Vertical mode problem for kz = 14

Number of errors (should be 0) = 0

Split : 1 => aam : 4.0000, fac : 2.2222

Split : 2 => aam : 2.0000, fac : 4.0000

Opening new output file ./output//Reg_ATM.2006020100.nc

Opening new output file ./output//Reg_SHF.2006020100.nc

Opening new output file ./output//Reg_SRF.2006020100.nc

Opening new output file ./output//Reg_STS.2006020100.nc

Opening new output file ./output//Reg_RAD.2006020100.nc

Opening new output file ./output//Reg_NO.2006020100.nc

Opening new output file ./output//Reg_NO2.2006020100.nc

Opening new output file ./output//Reg_N2O5.2006020100.nc

Opening new output file ./output//Reg_HNO2.2006020100.nc

Opening new output file ./output//Reg_HNO3.2006020100.nc

Opening new output file ./output//Reg_HNO4.2006020100.nc

Opening new output file ./output//Reg_O3.2006020100.nc

Opening new output file ./output//Reg_H2O2.2006020100.nc

Opening new output file ./output//Reg_CO.2006020100.nc

Opening new output file ./output//Reg_SO2.2006020100.nc

Opening new output file ./output//Reg_DMS.2006020100.nc

Opening new output file ./output//Reg_H2SO4.2006020100.nc

Opening new output file ./output//Reg_CH4.2006020100.nc

Opening new output file ./output//Reg_C2H6.2006020100.nc

Opening new output file ./output//Reg_PAR.2006020100.nc

Opening new output file ./output//Reg_CH3OH.2006020100.nc

Opening new output file ./output//Reg_HCHO.2006020100.nc

Opening new output file ./output//Reg_ALD2.2006020100.nc

Opening new output file ./output//Reg_AONE.2006020100.nc

Opening new output file ./output//Reg_ETH.2006020100.nc

Opening new output file ./output//Reg_OLET.2006020100.nc

Opening new output file ./output//Reg_OLEI.2006020100.nc

Opening new output file ./output//Reg_TOL.2006020100.nc

Opening new output file ./output//Reg_XYL.2006020100.nc

Opening new output file ./output//Reg_ISOP.2006020100.nc

Opening new output file ./output//Reg_ONIT.2006020100.nc

Opening new output file ./output//Reg_PAN.2006020100.nc

Opening new output file ./output//Reg_HCOOH.2006020100.nc

Opening new output file ./output//Reg_RCOOH.2006020100.nc

Opening new output file ./output//Reg_CH3OOH.2006020100.nc

Opening new output file ./output//Reg_ETHOOH.2006020100.nc

Opening new output file ./output//Reg_ROOH.2006020100.nc

Opening new output file ./output//Reg_MGLY.2006020100.nc

Opening new output file ./output//Reg_ISOPRD.2006020100.nc

Opening new output file ./output//Reg_ISOPN.2006020100.nc

Opening new output file ./output//Reg_OPEN.2006020100.nc

Opening new output file ./output//Reg_CRES.2006020100.nc

Opening new output file ./output//Reg_NH3.2006020100.nc

Opening new output file ./output//Reg_DUST01.2006020100.nc

Opening new output file ./output//Reg_DUST02.2006020100.nc

Opening new output file ./output//Reg_DUST03.2006020100.nc

Opening new output file ./output//Reg_DUST04.2006020100.nc

Opening new output file ./output//Reg_BC_HL.2006020100.nc

Opening new output file ./output//Reg_BC_HB.2006020100.nc

Opening new output file ./output//Reg_OC_HL.2006020100.nc

Opening new output file ./output//Reg_OC_HB.2006020100.nc

Opening new output file ./output//Reg_SSLT01.2006020100.nc

Opening new output file ./output//Reg_SSLT02.2006020100.nc

Opening new output file ./output//Reg_ANO3.2006020100.nc

Opening new output file ./output//Reg_ANH4.2006020100.nc

ATM variables written at 2006-02-01 00:00:00 UTC

CHE variables written at 2006-02-01 00:00:00 UTC

Computing weights.. Done.

Reading Ozone Data...

# Updated ozone profile at (3,3) #

0.190E-05 0.181E-05 0.166E-05 0.149E-05 0.130E-05 0.106E-05 0.826E-06

0.733E-06 0.632E-06 0.555E-06 0.485E-06 0.431E-06 0.400E-06 0.384E-06

0.384E-06 0.377E-06

--WARNING-- skipping CN balance check for first timestep

SHF variables written at 2006-02-01 01:00:00 UTC

SHF variables written at 2006-02-01 02:00:00 UTC

$$$ 2006-02-01 03:00:00 UTC

$$$ 1st, 2nd time deriv of ps = 0.48794E-05 0.84924E-07

$$$ no. of points with active convection = 0

SRF variables written at 2006-02-01 03:00:00 UTC

SHF variables written at 2006-02-01 03:00:00 UTC

Error in CN Summary: tempsum_npp = NaN at pft 501

npp(p) = NaN

gpp(p) = 0.0000000000000000

ar(p) = NaN

mr(p) = NaN

gr(p) = 0.0000000000000000

leaf_mr(p) = 0.0000000000000000

froot_mr(p) = NaN

livestem_mr(p) = 0.0000000000000000

livecroot_mr(p) = 0.0000000000000000

tempsum_npp(p) = NaN

-------------- FATAL CALLED ---------------

Fatal in file: mod_clm_cnsummary.F90 at line: 810

clm now stopping

-------------------------------------------

mod_clm_cnsummary.F90 : 810: 1

Abort called by computing node 0 at 2019-02-16 19:14:27.362 +0330

Execution terminated because of runtime error

--------------------------------------------------------------------------

MPI_ABORT was invoked on rank 0 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.

--------------------------------------------------------------------------

Error in CN Summary: tempsum_npp = NaN at pft 2726

npp(p) = NaN

gpp(p) = 0.0000000000000000

ar(p) = NaN

mr(p) = NaN

gr(p) = 0.0000000000000000

leaf_mr(p) = 0.0000000000000000

froot_mr(p) = NaN

livestem_mr(p) = 0.0000000000000000

livecroot_mr(p) = 0.0000000000000000

tempsum_npp(p) = NaN

-------------- FATAL CALLED ---------------

Fatal in file: mod_clm_cnsummary.F90 at line: 810

clm now stopping

-------------------------------------------

Abort called by computing node 1 at 2019-02-16 19:14:27.362 +0330

Execution terminated because of runtime error

[localhost.localdomain:08938] 1 more process has sent help message help-mpi-api.txt / mpi-abort

[localhost.localdomain:08938] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

Could anyone help me fix this error? By the way, The attachment is the file of my namelist to run Regcm.

Many thanks in advance.

best,

Mehraneh