Error with ems_run. Wrong grid options in domain?

Forum dedicated to older versions of EMS package (WRFEMS v3.2, v3.1 or older). Support is user-to-user based, so please help others if you can.
Yonas
Posts: 11
Joined: Mon Dec 10, 2012 7:27 pm

Error with ems_run. Wrong grid options in domain?

Post by Yonas » Mon Dec 10, 2012 7:48 pm

Hello! I have installed on Ubuntu 12.04 LTS 64bit. (Can share little how2; there is some problems with java and shell). Benchmark works fine. But when i compute on my own domain (generated by dwiz) i've got an error in ems_run routine:

Code: Select all

   II.  Creating the initial and boundary condition files for the user domain(s)


         *  The WRF REAL program shall be run on the following systems and processors:

            >  4  processors on yonas-server    

         *  Creating the WRF initial and boundary condition files

         EMS ERROR  : UGH! Creation of model initial and boundary conditions failed!                      
                      
                      I hate when this #%^!#!!% happens.
                      
                      Hopefully the log files will provide some help.

         EMS ERROR  : Here are the last few lines of the the log file:

                         ips,ipe,jps,jpe 1 355 1 341
                         *************************************
                         DYNAMICS OPTION: Eulerian Mass Coordinate
                         alloc_space_field: domain 1 , -893667640 bytes allocated
                         d01 2012-12-10_12:00:00 Timing for input 101 s.
                         d01 2012-12-10_12:00:00 flag_soil_layers read from met_em file is 1
                         d01 2012-12-10_12:00:00 Old data, no inland lake information
                         Assume Noah LSM input
                         d01 2012-12-10_12:00:00 forcing artificial silty clay loam at 182 points, out of
                        121055
                         d01 2012-12-10_12:00:00 Timing for processing 340 s.
                         d01 2012-12-10_12:00:00 Timing for output 105 s.
                         d01 2012-12-10_12:00:00 Timing for loop # 1 = 546 s.
                         d01 2012-12-10_15:00:00 Timing for input 20 s.
                         d01 2012-12-10_15:00:00 flag_soil_layers read from met_em file is 1
                         d01 2012-12-10_15:00:00 Old data, no inland lake information
                         Assume Noah LSM input
                         d01 2012-12-10_15:00:00 forcing artificial silty clay loam at 182 points, out of
                        121055
                         d01 2012-12-10_15:00:00 Timing for processing 6 s.



         !  A little help from your friend            
            
            The log files from your failed run have been written to:
            
                /usr1/wrfems/runs/yana/log/2012121018.real_crash_logs.tgz
            
            Feel free to send them to a person that cares if you need some assistance
            troubleshooting this problem.


  WRF EMS Program ems_run failure (3) at Mon Dec 10 18:56:31 2012 UTC


There is 2012121018.real_crash_logs.tgz
Maybe i generate domain with wrong grid point distance/dimensions?
Thank you.

meteoadriatic
Posts: 1512
Joined: Wed Aug 19, 2009 10:05 am

Re: Error with ems_run. Wrong grid options in domain?

Post by meteoadriatic » Tue Dec 11, 2012 8:32 am

Hello,

I don't see any error in log files. However, you created strange domain. Few points I would look to:

1) You created 2km resolution single domain without nesting, and starting it on input data from 50km GFS model. This is technically possible but very unlikely that you will get satisfying results. However, should not be a direct reason for real to fail creating IBC.

2) Your domain is pretty large. You have 710x628 points (445,880 points). Do you have enough system memory to work this out? I would guess that something like 64GB of RAM is needed to work with 450,000 of points! Maybe this is a reason why your run fails silently (process gets killed by kernel because of lacking system memory)?

Yonas
Posts: 11
Joined: Mon Dec 10, 2012 7:27 pm

Re: Error with ems_run. Wrong grid options in domain?

Post by Yonas » Tue Dec 11, 2012 10:30 am

Oh, I see. I will change domain resolution and its dimensions, and try.

Where can i read about right choosing domain resolution and model? Model resolution must be less than domain resolution for satisfying results?

About installing on Ubuntu 12.04 LTS 64bit:
1) prepare for installation:
sudo apt-get update && sudo apt-get upgrade
sudo apt-get install curl csh tcsh
add user wrf (in group administator for sudoers)
login as wrf in ubuntu after restart
change shell by typing in shell "chsh" for /bin/tcsh
relogin (or just reopen terminal)
check current shell "echo $SHELL". Must be "/bin/tcsh"

sudo rm /bin/sh
sudo ln -s /bin/bash /bin/sh

sudo mkdir /usr1
sudo chown wrf:wrf /usr1


2) installing java for dwiz:
download jre-6u31-linux-i586.bin from http://www.oracle.com/technetwork/java/ ... 01637.html in local directory
chmod 777 jre-6u31-linux-i586.bin
./jre-6u31-linux-i586.bin
sudo mv jre1.6.0_31/ /usr/lib/jvm
sudo update-alternatives --install "/usr/bin/java" "java" "/usr/lib/jvm/bin/java" 1
sudo update-alternatives --set java /usr/lib/jvm/bin/java


3) install ems:
gunzip ems_install.pl
chmod +x ems_install.pl
ems_install.pl --install


4) read User Guide on http://strc.comet.ucar.edu/software/newrems/ for further instructions.

Yonas
Posts: 11
Joined: Mon Dec 10, 2012 7:27 pm

Re: Error with ems_run. Wrong grid options in domain?

Post by Yonas » Tue Dec 11, 2012 10:40 am

An error with 10x10 points and 24 km resolution domain with ems_prep --dset tile12:

Code: Select all

    IV.  Horizontal interpolation of the intermediate files to the computational domain


             EMS ERROR  : In metgrid - This is not looking good!

             *  Missing values encountered in interpolated fields.                
                
                Check to make sure the areal coverage of your domain lies entirely
                within the initialization data set.

             See:
             
               /usr1/wrfems/runs/third/log/prep_metgrid.log
             
             For more information.

         !  A little help from your friend            
            
            The log files from your failed run have been written to:
            
                /usr1/wrfems/runs/third/log/2012121110.metgrid_crash_logs.tgz
            
            Feel free to send them to a person that cares if you need some assistance
            troubleshooting this problem.
2012121110.metgrid_crash_logs.tgz

meteoadriatic
Posts: 1512
Joined: Wed Aug 19, 2009 10:05 am

Re: Error with ems_run. Wrong grid options in domain?

Post by meteoadriatic » Tue Dec 11, 2012 12:57 pm

If you can run included benchmark case installation is probably OK.

Now, you created way too small domain. 10x10 points in my opinion can NOT be run at all.

Go on and create sane domain size. Let's say, 100x100 points, with resolution of ~20km. Try that first.

If you need 2km resolution, and use GFS as initial/boundary conditions, you will need to create nesting with three telescopic domains; something like 18-6-2 km. Try to keep domain size with at least 100x100 points each, but don't create more than your harware is capable of running. To determine if your RAM is large enough to support your run, look at output of htop command during model run and keep an eye on "Mem" field. You can use top insted of htop but htop is much simpler to watch.

Yonas
Posts: 11
Joined: Mon Dec 10, 2012 7:27 pm

Re: Error with ems_run. Wrong grid options in domain?

Post by Yonas » Tue Dec 11, 2012 3:44 pm

with 102x102 and 20km resolution:
ems_prep --dset tile12

Code: Select all

  IV.  Horizontal interpolation of the intermediate files to the computational domain


             EMS ERROR  : In metgrid - This is not looking good!

             *  Missing values encountered in interpolated fields.                
                
                Check to make sure the areal coverage of your domain lies entirely
                within the initialization data set.

             See:
             
               /usr1/wrfems/runs/4th/log/prep_metgrid.log
             
             For more information.

         !  A little help from your friend            
            
            The log files from your failed run have been written to:
            
                /usr1/wrfems/runs/4th/log/2012121115.metgrid_crash_logs.tgz
            
            Feel free to send them to a person that cares if you need some assistance
            troubleshooting this problem.

meteoadriatic
Posts: 1512
Joined: Wed Aug 19, 2009 10:05 am

Re: Error with ems_run. Wrong grid options in domain?

Post by meteoadriatic » Tue Dec 11, 2012 6:49 pm

Try
ems_prep --dset gfsptile

Yonas
Posts: 11
Joined: Mon Dec 10, 2012 7:27 pm

Re: Error with ems_run. Wrong grid options in domain?

Post by Yonas » Tue Dec 11, 2012 9:11 pm

meteoadriatic wrote:Try
ems_prep --dset gfsptile

Code: Select all

WRF EMS Program ems_prep (V3.1.1.5.1) started on yonas-server at Tue Dec 11 21:08:57 2012 UTC


                       The WRF EMS Says: "Who's Awesome? You're Awesome!"

     I.  WRF EMS ems_prep Model Initialization Summary

           Initialization Start Time    : Tue Dec 11 18:00:00 2012 UTC
           Initialization End   Time    : Wed Dec 12 18:00:00 2012 UTC
           Boundary Condition Frequency : 180 Minutes
           Initialization Data Set      : gfsptile
           Boundary Condition Data Set  : gfsptile
           Static Surface Data Sets     : None
           Land Surface Data Sets       : None

    II.  Search out requested files for WRF model initialization


         *  Locating gfsptile files for model initial and boundary conditions


            Areal coverage of the GFS Latitude-Longitude personal tiles
              
                Corner Lat-Lon points of the domain:
              
                   59.000, 14.500             59.000, 26.500
                  *                            *
              
                                 * 54.715, 20.513
              
                  *                            *
                   50.500, 14.500             50.500, 26.500




            Initiating HTTP process to emsdata1.comet.ucar.edu

              Making request #1 of 3 for personal tile data

              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f00  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f03  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f06  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f09  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f12  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f15  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f18  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f21  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f24  - File Not Available


            Areal coverage of the GFS Latitude-Longitude personal tiles
              
                Corner Lat-Lon points of the domain:
              
                   59.000, 14.500             59.000, 26.500
                  *                            *
              
                                 * 54.715, 20.513
              
                  *                            *
                   50.500, 14.500             50.500, 26.500




            Initiating HTTP process to emsdata2.comet.ucar.edu

              Making request #1 of 3 for personal tile data

              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f00  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f03  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f06  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f09  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f12  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f15  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f18  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f21  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f24  - File Not Available


            Areal coverage of the GFS Latitude-Longitude personal tiles
              
                Corner Lat-Lon points of the domain:
              
                   59.000, 14.500             59.000, 26.500
                  *                            *
              
                                 * 54.715, 20.513
              
                  *                            *
                   50.500, 14.500             50.500, 26.500




            Initiating HTTP process to soostrc.comet.ucar.edu

              Making request #1 of 3 for personal tile data

              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f00  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f03  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f06  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f09  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f12  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f15  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f18  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f21  - File Not Available
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f24  - File Not Available


         !  Problems acquiring gfsptile files for model initialization


         EMS ERROR  : Some of the initialization or boundary condition files were unavailable


  WRF EMS Program ems_prep failure (3) at Tue Dec 11 21:09:06 2012 UTC
What is valid source for data?

meteoadriatic
Posts: 1512
Joined: Wed Aug 19, 2009 10:05 am

Re: Error with ems_run. Wrong grid options in domain?

Post by meteoadriatic » Tue Dec 11, 2012 9:41 pm

18z was not ready yet. Go on and try again or specify previous cycle if that happens (--cycle 12 for this particular time).

Yonas
Posts: 11
Joined: Mon Dec 10, 2012 7:27 pm

Re: Error with ems_run. Wrong grid options in domain?

Post by Yonas » Wed Dec 12, 2012 12:05 am

It's ok with gfsptile.

Code: Select all

wrf@yonas-server-> ems_prep --dset gfsptile

  WRF EMS Program ems_prep (V3.1.1.5.1) started on yonas-server at Tue Dec 11 23:55:55 2012 UTC


                       The WRF EMS Says: "Who's Awesome? You're Awesome!"

     I.  WRF EMS ems_prep Model Initialization Summary

           Initialization Start Time    : Tue Dec 11 18:00:00 2012 UTC
           Initialization End   Time    : Wed Dec 12 18:00:00 2012 UTC
           Boundary Condition Frequency : 180 Minutes
           Initialization Data Set      : gfsptile
           Boundary Condition Data Set  : gfsptile
           Static Surface Data Sets     : None
           Land Surface Data Sets       : None

    II.  Search out requested files for WRF model initialization


         *  Locating gfsptile files for model initial and boundary conditions


            Areal coverage of the GFS Latitude-Longitude personal tiles
              
                Corner Lat-Lon points of the domain:
              
                   61.500, 8.000             61.500, 33.000
                  *                            *
              
                                 * 54.677, 20.602
              
                  *                            *
                   47.500, 8.000             47.500, 33.000




            Initiating HTTP process to emsdata1.comet.ucar.edu

              Making request #1 of 3 for personal tile data

              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f00  - Success (0.22 mb)
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f03  - Success (0.22 mb)
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f06  - Success (0.22 mb)
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f09  - Success (0.22 mb)
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f12  - Success (0.22 mb)
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f15  - Success (0.22 mb)
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f18  - Success (0.22 mb)
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f21  - Success (0.22 mb)
              -> Attempting to acquire 12121118.gfs.t18z.pgrb2f24  - Success (0.22 mb)

         *  All requested gfsptile files are available for model initialization


         Excellent! - Your master plan is working!


   III.  Create the WPS NMM intermediate format files

         *  Processing gfsptile files for use as model initial and boundary conditions - Dyn-o-mite!!

         NMM core intermediate file processing completed in 1 second


    IV.  Horizontal interpolation of the intermediate files to the computational domain

         *  Files are located in
            
            /usr1/wrfems/runs/3rd/wpsprd

         Horizontal interpolation to computational domain completed in 4 seconds

  WRF EMS Program ems_prep completed at Tue Dec 11 23:57:52 2012 UTC

But doesn't work with nam212 or nam218

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