[RegCNET] Time out of RegCM run
Samy Rateb
ratebsamy at yahoo.com
Tue Sep 16 11:11:46 CEST 2014
Hello Dr.Graziano Giuliani
I ran RegCM-4.4-SVN4648 successfully with nsg=1 with resolution 45 km, and made nest down to 10 km with nsg=5, all steps ( terrain, sst , icbc and mksurfdataNETCDF4_HDF5_CLM45_CN_CROP) ran successfully but during step regcmMPINETCDF4_HDF5_CLM45_CN_CROP, an error appeared
mpirun -np 4 ./bin/regcmMPINETCDF4_HDF5_CLM45_CN_CROP regcm45.in
This is RegCM trunk
SVN Revision: 4648 compiled at: data : Sep 15 2014 time: 14:19:01
: this run start at : 2014-09-16 11:33:29+0200
: it is submitted by : samy
: it is running on : localhost.localdomain
: it is using : 4 processors
: in directory : /home/samy/rcm33run
CPUS DIM1 = 2
CPUS DIM2 = 2
Reading model namelist file
Initial date of the global simulation: 2008-01-01 06:00:00 UTC
Initial date of this run : 2008-01-01 06:00:00 UTC
Final date of this run : 2008-01-31 06:00:00 UTC
Total simulation lenght : 720 hours
Timestep in seconds = 30.000000
Split explicit dtau = 7.500000 15.000000
Reading Domain file : ./input/MENA50_DOMAIN000.nc
Setting IPCC scenario to A1B
Create SAV files : T
Create ATM files : T
Create RAD files : T
Create SRF files : T
Create STS files : T
Create SUB files : T
Frequency in hours to create SAV : 7200.0
Frequency in hours to create ATM : 6.0
Frequency in hours to create RAD : 6.0
Frequency in hours to create SRF : 3.0
Frequency in hours to create SUB : 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
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 : 30.000000
time step for surface model in seconds : 90.000000
time step for radiation model in minutes : 30.000000
time step for emission model in hours : 18.000000
Reading Sub-Domain file : ./input/MENA50_DOMAIN005.nc
Domain grid parameters:
Map Projection : ROTMER
Dot Grid Full Extent : 60x 40x 18
Model Top Pressure : 5.000000 cb
Model Grid Spacing : 10.000000 km
Grid Center Latitude : 30.000000 deg
Grid Center longitude : 30.000000 deg
Pole Latitude : 30.000000 deg
Pole longitude : 30.000000 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 : 1.000000
Convective Cloud Water : 0.000300
The surface energy budget is used to calculate the ground temperature.
The radiation is computed every 60 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. = 0.500000E+04 m^2 s-1
Maximumt hor. diff. coef. = 0.520833E+05 m^2 s-1
READY IC DATA for 2008-01-01 06:00:00 UTC
SEARCH BC data for 2008010112
READY BC from 2008010106 to 2008010112
# Ozone profile at (3,3) #
0.496E-07 0.496E-07 0.496E-07 0.496E-07 0.503E-07 0.527E-07 0.538E-07
0.577E-07 0.638E-07 0.729E-07 0.868E-07 0.111E-06 0.152E-06 0.235E-06
0.235E-06 0.428E-06 0.815E-06 0.143E-05 0.321E-05 0.00
CLM version: 4.5 - RegCM 4648
Attempting to initialize the land model .....
Mask given by RegCM model has a total of 45400 land points
Attempting to initialize run control settings .....
Read in clm_inparm namelist from: regcm45.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 = 4648
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/MENA50_CLM45_surface.nc
land frac data = ./input/MENA50_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 = 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/MENA50_DOMAIN000.nc
domain_check set = domain_set
domain_check decomped = T
domain_check ns = 2109
domain_check ni,nj = 57 37
domain_check clmlevel = gridcell
domain_check nbeg,nend = 1 11350
domain_check lonc = 27.036890029907227 32.868476867675781
domain_check latc = 28.276361465454102 29.071319580078125
domain_check mask = 1 1
domain_check frac = 100.00000000000000 100.00000000000000
domain_check topo = -73.148262023925781 1316.3111572265625
domain_check area = 100.00000000000000 100.00000000000000
domain_check pftm = 1 1
Reading in urban input data from surface data file ...
UrbanInput : ./input/MENA50_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 = 45400
total number of landunits = 104273
total number of columns = 566262
total number of pfts = 1200420
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 17909 on node localhost.localdomain exited on signal 9 (Killed).
--------------------------------------------------------------------------
Any advice plz
--- On Mon, 9/15/14, Graziano Giuliani <ggiulian at ictp.it> wrote:
> From: Graziano Giuliani <ggiulian at ictp.it>
> Subject: Re: [RegCNET] Fw: error mksurfdataCLM45_CN_CROP run
> To: "Samy Rateb" <ratebsamy at yahoo.com>
> Cc: "regcnet at lists.ictp.it" <regcnet at lists.ictp.it>
> Date: Monday, September 15, 2014, 12:37 PM
> On 09/15/2014 11:21 AM,
> Graziano Giuliani wrote:
> > On 09/15/2014
> 11:04 AM, Graziano Giuliani wrote:
> >>
> On 09/14/2014 12:36 PM, Samy Rateb wrote:
> >>> Hello Dr.Graziano Giuliani,
> >>>
> >>> In
> this run, i tried to make nsg=5, so core dumped in the step
> ./bin/mksurfdataCLM45_CN_CROP regcm45.in, but when i made
> nsg=1, it ran successfully and the step mpirun -np 4
> ./bin/regcmMPI CLM45_CN_CROP regcm45.in runs successfully.
> So i can do nest down to 10 km with CLM4.5. So I think that
> the problem i cannot do nsg=5 with CLM4.5
> >>>
> >> [...]
> [...]
> > On my workstation
> with the SVN4648 I am able to got past the mksurfdata
> > step, but, with just 4GB of RAM, I am not
> able to run the model using
> > your
> configuration with nsg=5.
> [...]
>
> And the previous only with:
>
> ./configure --enable-clm45
> --enable-nc4
>
> The output
> file size for the CN+CROP is in ths case with the 500x500
> grid:
>
> 7.4G
> MENA50_CLM45_surface.nc
>
> --
> Graziano Giuliani - Earth System Physics
> Section
> The Abdus Salam International Centre
> for Theoretical Physics
> Strada Costiera 11 -
> I - 34151 Trieste Italy
>
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