[RegCNET] Error in Regcm coupled with crop
Mehran Khodamorad
mkhodamorad at gmail.com
Sat Feb 16 19:16:05 CET 2019
Dear all,
I installed successfully Regcm coupled with crop, but in final step, there
is this following error:
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 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
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
test01
test01
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
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
--WARNING-- skipping CN balance check for first timestep
--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
Dr. Mehraneh Khodamorad Pour,
Assistant Professor,
Bu-Ali Sina University,
Faculty of Agriculture,
Hamedan, IRAN.
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