[RegCNET] error in running CN + nitirification-denitirification in RegCM-4.4.5.7
Samy Rateb
ratebsamy at yahoo.com
Wed Sep 9 14:33:14 CEST 2015
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
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