[RegCNET] error in running chemistry module
Najmeh Kaffahzadeh
kaffashzadeh.najmeh at yahoo.com
Fri Sep 30 19:37:10 CEST 2016
Hello,
I had more or less the same problem with xx_CHEMISS.nc file. Try to create this file at least for one month model run, even if you are going to run the model for three days. It might work for you too.
The CDO version can be another reason as well. I had some problem with CDO 1.7.1, but CDO 1.7.2 works for me.
Najmeh
Sent from my iPad
> On 29 Sep 2016, at 11:13, SUDIPTA GHOSH <sudiptaghosh006 at gmail.com> wrote:
>
> Firstly, thank you Sir for your valuable advice.
>
> I checked the date attribute of both the interpolated and the global emission i.e IIASA file and in both the cases the date attribute is same.
>
> I am using CDO version 1.7.2 compiled with netcdf, jasper and grib. Shall I change the CDO version?
>
> I will be highly obliged if you can give some more suggestions on the same because I am still unable to solve the error.
>
> I am attaching the xx_CHEMISS.nc herewith.
>
>
> CARB_CHEMISS.nc
>
>> On Thu, Sep 29, 2016 at 1:01 PM, <fsolmon at ictp.it> wrote:
>> Hello
>>
>> This error is probably due to a bug of cdo that does reproduce the exact
>> same date attribute than expected by regcm.It depends of which cdo version
>> you are using. With ncdump -h, you should checko the date attribute of
>> your interpolated emission file ( xx_CHEMISS.nc) .. it should be the same
>> as in the global emission file. If not, you can correct the date attribute
>> in the input CHEMISS file with nco for example.
>>
>> Fabien
>>
>>
>> > Hello everyone,
>> >
>> > I am very new to climate modelling, so seeking an apology on the first
>> > hand
>> > if my question is very trivial but seriously I am not able to sort this
>> > error.
>> >
>> > *I'm trying to run the RegCM 4.4.5.11 using the chemistry SUCA and CARB.
>> > I
>> > did all the pre-processing, but when I go to run the model this is the
>> > error which I am getting in the log file:*
>> >
>> > This is RegCM trunk
>> > SVN Revision: tag 4.4.5.10 compiled at: data : Sep 16 2016 time:
>> > 14:07:26
>> >
>> > : this run start at : 2016-09-19 12:11:50+0530
>> > : it is submitted by :
>> > : it is running on : cn086
>> > : it is using : 288 processors
>> > : in directory : /home/cas/phd/asz148358/RCM445_PGI
>> >
>> > CPUS DIM1 = 16
>> > CPUS DIM2 = 18
>> >
>> > Reading model namelist file
>> > SUCA simulation
>> > Initial date of the global simulation: 2004-01-01 00:00:00 UTC
>> > Initial date of this run : 2004-01-01 00:00:00 UTC
>> > Final date of this run : 2004-01-03 00:00:00 UTC
>> > Total simulation lenght : 48 hours
>> > Timestep in seconds = 30.000000
>> > Split explicit dtau = 7.500000 15.000000
>> > Reading Domain file :
>> > /scratch/cas/phd/asz148358/REGCM/input/test_clm45/test_clm_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 CHE files : T
>> > Create OPT 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 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 : 2
>> > 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 : 1
>> > Convective LWP scheme : 1
>> > 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 : 600.000000
>> > time step for radiation model in minutes : 30.000000
>> > time step for emission model in hours : 18.000000
>> > time step for chemistry model in seconds : 900.000000
>> > Domain grid parameters:
>> > Map Projection : ROTMER
>> > Dot Grid Full Extent : 420x 300x 18
>> > Model Top Pressure : 5.000000 cb
>> > Model Grid Spacing : 25.000000 km
>> > Grid Center Latitude : 16.000000 deg
>> > Grid Center longitude : 70.000000 deg
>> > Pole Latitude : 16.000000 deg
>> > Pole longitude : 70.000000 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 : 0.770833
>> > 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. = 0.312500E+05 m^2 s-1
>> > Maximumt hor. diff. coef. = 0.325521E+06 m^2 s-1
>> > READY IC DATA for 2004-01-01 00:00:00 UTC
>> > SEARCH BC data for 2004010106
>> > READY BC from 2004010100 to 2004010106
>> > # Ozone profile at (3,3) #
>> > 0.502E-05 0.219E-05 0.124E-05 0.737E-06 0.407E-06 0.229E-06
>> > 0.159E-06
>> > 0.120E-06 0.957E-07 0.801E-07 0.696E-07 0.630E-07 0.589E-07
>> > 0.563E-07
>> > 0.563E-07 0.546E-07 0.533E-07 0.525E-07 0.523E-07 0.520E-07
>> > tracer cbmz index molw
>> > BC_HL -1 0.000000000000000
>> > BC_HB -1 0.000000000000000
>> > OC_HL -1 0.000000000000000
>> > OC_HB -1 0.000000000000000
>> > SO2 11 64.00000000000000
>> > SO4 -1 0.000000000000000
>> > tracer index coreesponding to bdy species
>> > # ichbdy2trac #
>> > 2 1 4 3 5 6 0
>> > 0 0 0 0 0 0 0
>> > 0 0 0 0 0 0 0
>> > 0 0 0 0 0 0 0
>> > 0 0 0 0 0 0 0
>> > 0 0 0 0 0 0 0
>> > 0 0 0 0 0 0 0
>> > 0 0
>> > READ CHEM EMISSION for 2004010001
>> > Opening ch. emission file
>> > /scratch/cas/phd/asz148358/REGCM/input/test_clm45/test_clm_CHEMISS.nc
>> > -------------------------------------------------------
>> > Primary job terminated normally, but 1 process returned
>> > a non-zero exit code.. Per user-direction, the job has been aborted.
>> > -------------------------------------------------------
>> > --------------------------------------------------------------------------
>> > mpirun detected that one or more processes exited with non-zero status,
>> > thus causing
>> > the job to be terminated. The first process to do so was:
>> >
>> > Process name: [[24040,1],0]
>> > Exit code: 127
>> >
>> > *And the error file gave the following message:*
>> >
>> > PGFIO-F-231/formatted read/internal file/error on data conversion.
>> > In source file mod_date.F90, at line number 1384
>> > *It will be helpful if anybody can help me to sort this issue.*
>> >
>> > --
>> > Regards
>> >
>> > Sudipta Ghosh
>> > PhD Scholar, Center for Atmospheric Sciences
>> > Indian Institute of Technology Delhi,India.
>> > _______________________________________________
>> > RegCNET mailing list
>> > RegCNET at lists.ictp.it
>> > https://lists.ictp.it/mailman/listinfo/regcnet
>>
>>
>
>
>
> --
> Regards
>
> Sudipta Ghosh
> PhD Scholar, Center for Atmospheric Sciences
> Indian Institute of Technology Delhi,India.
> _______________________________________________
> RegCNET mailing list
> RegCNET at lists.ictp.it
> https://lists.ictp.it/mailman/listinfo/regcnet
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