denominator of seconds cannot be negative

With soon inclusion of the NEMS NMM-B model into the EMS package, WRF EMS changes its name and becomes UEMS.
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skosecki
Posts: 20
Joined: Wed Aug 31, 2016 7:37 am

denominator of seconds cannot be negative

Post by skosecki » Thu Apr 13, 2017 8:49 am

Hello,
During my analysis computation after 11 simulated days I stuck on this error message:

askid: 0 hostname: gv0147
-------------- FATAL CALLED ---------------
normalize_basetime: denominator of seconds cannot be negative
-------------------------------------------
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0


My intuition says that it is a matter of adaptive time step. But my calendar says that I want to use the adaptive time step. Did You have similar problem?

Here are my settings:

Code: Select all

EMS MODEL RUN SUMMARY FOR THE "14_west-spitsbergen" DOMAIN


                                     WRF ARW core             WRF REAL program
    ******************************************************************************

     System Name                                Scheduled Processors

       tryton-ap                 :          22                     22

     Total Processors            :          22                     22
     Domain Decomposition        :        2 x 11                   2 x 11


     Active Domains                  Domain 01                    Domain 02                    Domain 03                    Domain 04
    ********************************************************************************************************************************************

     Domain & Run Information

       Domain Type               :  Limited Area                 Limited Area                 Limited Area                 Limited Area
       Primary Time Step         :  Adaptive                     Adaptive                     Adaptive                     Adaptive
       Step to Output Time       :  Yes                          Yes                          Yes                          Yes
       Grid dimensions (NX x NY) :  120 x 120                    118 x 118                    116 x 116                    116 x 116
       Vertical Layers (NZ)      :  45                           45                           45                           45
       Grid Spacing              :  12.00km                      4.00 km                      0.80 km                      0.80 km
       Top of Model Atmosphere   :  50mb                         50mb                         50mb                         50mb
       Parent Domain             :  NA                           Domain 01                    Domain 02                    Domain 02
       Nesting Feedback          :  Feedback On                  Feedback On                  Feedback On                  Feedback On
       Smoothing Technique       :  No Smoothing                 No Smoothing                 No Smoothing                 No Smoothing


     Timing Information

       Start Date                :  2010 Jan 01 18:00 UTC        2010 Jan 01 18:00 UTC        2010 Jan 01 18:00 UTC        2010 Jan 01 18:00 UTC
       End Date                  :  2010 Feb 12 18:00 UTC        2010 Feb 12 18:00 UTC        2010 Feb 12 18:00 UTC        2010 Feb 12 18:00 UTC
       Simulation Length         :  1008 Hours                   1008 Hours                   1008 Hours                   1008 Hours
       Boundry Update Freq       :  06 Hours


     Data Output Information

       File Output Freq          :  01 Hour                      01 Hour                      01 Hour
       Output File Format        :  netCDF                       netCDF                       netCDF
       Aux 1 File Output Freq    :  01 Hour                      01 Hour                      01 Hour
       Aux 1 File Format         :  netCDF                       netCDF                       netCDF
       Adjust Output Times       :  Yes                          Yes                          Yes


     Model Physics

       Cumulus Scheme            :  None                         None                         None
       Shallow Cumulus Scheme    :  Off                          Off                          Off
       Microphysics Scheme       :  Thompson Aerosol-Aware       Thompson Aerosol-Aware       Thompson Aerosol-Aware
       PBL Scheme                :  Yonsei University            Yonsei University            Yonsei University
       YSU Wind Correction       :  Jimenez and Dudhia Method    Jimenez and Dudhia Method    Jimenez and Dudhia Meth
       Gravitational Settling    :  No Gravitational Settling    No Gravitational Settling    No Gravitational Settli
       Land Surface Scheme       :  Noah 4-Layer LSM             Noah 4-Layer LSM             Noah 4-Layer LSM
       Snow Cover Physics        :  New School                   New School                   New School
       Number Land Categories    :  20 (MODIS)                   20 (MODIS)                   20 (MODIS)
       Number Soil Categories    :  16                           16                           16
       Number Soil Layers        :  4                            4                            4
       Surface Layer Physics     :  Monin-Obukhov                Monin-Obukhov                Monin-Obukhov
       Sfc Heat & Moisture Flux  :  Model Computed u* and Sfc Fluxes Model Computed u* and Sfc Fluxes Model Computed
       Long Wave Radiation       :  RRTM                         RRTM                         RRTM
       Short Wave Radiation      :  Goddard (GFDL) Short Wave    Goddard (GFDL) Short Wave    Goddard (GFDL) Short Wa
       SW Update Between Calls   :  Update SW Radiation          Update SW Radiation          Update SW Radiation
       Slope Radiation Effects   :  No Slope Effects             Slope Effects On             Slope Effects On
       Topography Shading        :  No Shading Effects           Shading Effects On           Shading Effects On


     ARW Core Model Dynamics

       Dynamics                  :  Non-Hydrostatic              Non-Hydrostatic              Non-Hydrostatic
       Gravity Wave Drag         :  On                           On                           On
       Time-Integration Scheme   :  Runge-Kutta 3rd Order        Runge-Kutta 3rd Order        Runge-Kutta 3rd Order
       Diffusion Sheme           :  Simple Diffusion             Simple Diffusion             Simple Diffusion
       6th-order Diffusion       :  No 6th-Order Diffusion       No 6th-Order Diffusion       No 6th-Order Diffusion
       Eddy Coefficient Scheme   :  2D 1st Order Closure         2D 1st Order Closure         2D 1st Order Closure
       Damping Option            :  No Damping                   No Damping                   No Damping
       W Damping                 :  W Damping On                 W Damping On                 W Damping On
       Horiz Momentum Advection  :  5th Order                    5th Order                    5th Order
       Horiz Scalar Advection    :  5th Order                    5th Order                    5th Order
       Vert Momentum Advection   :  3rd Order                    3rd Order                    3rd Order
       Vert Scalar Advection     :  3rd Order                    3rd Order                    3rd Order
       Sound Time Step Ratio     :  Automatic                    Automatic                    Automatic
       Moisture Advection Option :  Positive-Definite            Positive-Definite            Positive-Definite
       Scalar Advection Option   :  Positive-Definite            Positive-Definite            Positive-Definite
       Momentum Advection Option :  Positive-Definite            Positive-Definite            Positive-Definite
       TKE Advection Option      :  Positive-Definite            Positive-Definite            Positive-Definite
The things I've changed lastly are:
- modified the model decomposition to use more processors
- activated the Gravity Wave Drag for first and second domain (why --runinfo show that I enable it for all domains??)

Code: Select all

 GWD_OPT = 1, 1, 0, 0
- I put the self-calculated VAR_SSO field in the geofor all domains.

smartie
Posts: 94
Joined: Sat May 21, 2011 7:34 am

Re: denominator of seconds cannot be negative

Post by smartie » Wed Apr 19, 2017 7:39 am

it's the adaptive timestep. One fix can be to set a mininum time step other than the default eg 3 sec. Failing that using a 1km fine domain should work and i doubt if you'll find much significant difference to 800m.
I see your domains are quite small ~100X100 pt this could be the root of the problem as small domains are more likely to generate noise and force small time steps esp if a boundary crosses steep terrain.
I think there may be a fix for fractional timesteps in 3.9.

skosecki
Posts: 20
Joined: Wed Aug 31, 2016 7:37 am

Re: denominator of seconds cannot be negative

Post by skosecki » Wed Apr 19, 2017 10:25 am

smartie wrote:
Wed Apr 19, 2017 7:39 am
it's the adaptive timestep. One fix can be to set a mininum time step other than the default eg 3 sec. Failing that using a 1km fine domain should work and i doubt if you'll find much significant difference to 800m.
I see your domains are quite small ~100X100 pt this could be the root of the problem as small domains are more likely to generate noise and force small time steps esp if a boundary crosses steep terrain.
I think there may be a fix for fractional timesteps in 3.9.
Thank you Smartie,
Is it possible in EMS to set a minimum time step and still use adaptive time step?
You suggest to use 1km resolution for finer domain? Due to high orography impact in the fjord it is also important to get a proper resolution..
I could try to recreate my domain with 120x120-15km/118x118-5km/116x116-1km nested domains .. or maybe 200x200-5km/106x106-1km would be enough?
Greetings!

smartie
Posts: 94
Joined: Sat May 21, 2011 7:34 am

Re: denominator of seconds cannot be negative

Post by smartie » Wed Apr 19, 2017 1:09 pm

you can set a min time step in this entry in ...conf/ems_run/run_timestep.conf
# MIN_TIME_STEP: The minimum time step (seconds; positive integer) that can be achieved.
# A value of -1 (default) tells ARW to use a value of 0.5*starting_time_step.
#
MIN_TIME_STEP = -1,-1,-1
Personally I would be unhappy using fine domains less than 200x200 pt, but I see you want to do long simulations. Another thing to try is doing extra smoothing of the terrain with the setting in geogrid.tbl- you'll have to find some compromise (as ever).
Can you provide a plot of your domain set up?
David

skosecki
Posts: 20
Joined: Wed Aug 31, 2016 7:37 am

Re: denominator of seconds cannot be negative

Post by skosecki » Thu Apr 20, 2017 7:59 am

Yes, the simulation will be very long :) I'm planning to make 2010-2015 hindcast. Here you have briefly about my previous run approach (which ended successfully, surprisingly) With very small domain, but with lower finest resolution (1,2km).
viewtopic.php?f=9&t=1062

I've decided to extend the range of model and added a large parent domain (12km) and use the 2-way nesting. Concerning about future reviews, cause I have to publish this work since it is the first part of my PHD.

Here is what the situation looks like for now:
Image

I'll change the MIN_TIME_STEP, add some extra smoothing (SMOOTH_OPTION = 2 or 1 ?) and rerun all of my test simulations.
Szymon

smartie
Posts: 94
Joined: Sat May 21, 2011 7:34 am

Re: denominator of seconds cannot be negative

Post by smartie » Thu Apr 20, 2017 10:04 am

Thanks for the plots. I wonder if intersection of the 800m domain boundary with the terrain is causing problems, you could test this by outputting MAX_CFL from the model and seeing where area where the timestep is likely being forced down.
If you need really long data runs have you considered doing overlapping shorter runs and discarding the the first hours as spin up- say ~8 day runs and discard first day?

skosecki
Posts: 20
Joined: Wed Aug 31, 2016 7:37 am

Re: denominator of seconds cannot be negative

Post by skosecki » Thu Apr 20, 2017 10:38 am

smartie wrote:
Thu Apr 20, 2017 10:04 am
If you need really long data runs have you considered doing overlapping shorter runs and discarding the the first hours as spin up- say ~8 day runs and discard first day?
No way :) I need to have consistent time scale and I don't have time to write post-processing programs. I like to make it simple :) The data will be used as a atmospheric forcing for my fjord-ocean hydrodynamic model.
I don't have the CFL field in my results. Don't know how to configure it in EMS

For the purpouse of my article (applying of different wind speed parameterizations for west Spitsbergen fjords) I'll need ~6 week hindcast..

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