[RegCNET] error in running chemistry module

SUDIPTA GHOSH sudiptaghosh006 at gmail.com
Thu Sep 29 11:13:47 CEST 2016


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
<https://drive.google.com/file/d/0B4jsWDKkVaxXaElKMjJkWjFzVzQ/view?usp=drive_web>
​

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.
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