[Met_help] [rt.rap.ucar.edu #84355] History for MODE: trouble reading observation file

John Halley Gotway via RT met_help at ucar.edu
Tue Jul 9 12:03:42 MDT 2019


----------------------------------------------------------------
  Initial Request
----------------------------------------------------------------

Hi,

A time ago I wrote because I would like to validate the precipitation with
MODE.  I use as the forecast the regional WRF from Argentina (grib files)
and as the observation, the  satellite images from IMERG (HDF5 files).

John told me that MET is unable to read HDF5 so I converted this file in
netcdf file. I tried to convert the HDF5 with ncl_convert2nc but I have a
warning: file contains no dimensions and I think it's because the orginal
file have as dimensions only latitude and longitude, here the time is not a
dimension. So the other opcion is to use NCO. First I convert all the file
and then I trie to extract the precipitationcal variable which I use in the
MODE.

1)ncks
/share/apps/Build_MET_Intel/MET/data/imerg_fr/3B-HHR.MS.MRG.3IMERG.20170707-S003000-E005959.0030.V05B.HDF5
/share/apps/Build_MET_Intel/MET/data/imerg_fr/
3B-HHR.MS.MRG.3IMERG.20170707-S003000-E005959.0030.V05B.nc

2) ncks -v precipitationCal
3B-HHR.MS.MRG.3IMERG.20170707-S0000E002959.0000.V05B.HDF5 cal.nc

 and when I use the Panoply to see the and plot de data, it's ok but
unfortunately, MODE can't read the new file:

[naranda at rayo MET]$ bin/mode data/wrf_pp/prueba1 data/imerg_fr/cal.nc
tutorial/config/MODEConfig_tutorial -outdir tutorial/out/mode_prueba -v 2
DEBUG 1: Default Config File:
/share/apps/Build_MET_Intel/MET/share/met/config/MODEConfig_default
DEBUG 1: Match Config File: tutorial/config/MODEConfig_tutorial
DEBUG 1: Merge Config File: tutorial/config/MODEConfig_tutorial
ERROR  :
ERROR  : Trouble reading observation file "data/imerg_fr/cal.nc"
ERROR  :

I think that the problem is in MODEConfig_tutorial but i can't found the
mistake.
In the configure, I put : level = '(*,*)' because i dont' know this
information to observation files.

In aranda_data I put :
Prueba1 as forecast file
cal.nc and 3B-HHR.MS.MRG.3IMERG.20170707-S003000-E005959.0030.V05B.nc as
observation file
and MODEConfig_tutorial


Sory for the long mail and thanks for your help!

Natalí


----------------------------------------------------------------
  Complete Ticket History
----------------------------------------------------------------

Subject: MODE: trouble reading observation file
From: John Halley Gotway
Time: Wed Mar 07 14:32:01 2018

Natali,

Thanks for sending the sample data file.  The issue is that cal.nc
makes
use of "groups", a feature of NetCDF's enhanced data model.  MET does
not
support these enhanced features of NetCDF.  Here's what I did:

ncdump cal.nc > cal.ncdump
# Edit cal.nc by removing the following lines:
# group: Grid {
#  } // group Grid
ncgen -o cal_NOGROUPS.nc cal.ncdump

# Use MET's plot_data_plane to plot it, using "file_type" option to
tell
MET interpret it as CF-compliant NetCDF
met-6.1/bin/plot_data_plane cal_NOGROUPS.nc cal_NOGROUPS.ps
'name="precipitationCal"; level="(*,*)"; file_type=NETCDF_NCCF;'

I attached a PNG version of the resulting image.  Perhaps there's an
option
to ncks to strip out the use of groups?

John

On Wed, Mar 7, 2018 at 11:38 AM, natali aranda via RT
<met_help at ucar.edu>
wrote:

>
> Wed Mar 07 11:38:01 2018: Request 84355 was acted upon.
> Transaction: Ticket created by natali.g.aranda at gmail.com
>        Queue: met_help
>      Subject: MODE: trouble reading observation file
>        Owner: Nobody
>   Requestors: natali.g.aranda at gmail.com
>       Status: new
>  Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=84355 >
>
>
> Hi,
>
> A time ago I wrote because I would like to validate the
precipitation with
> MODE.  I use as the forecast the regional WRF from Argentina (grib
files)
> and as the observation, the  satellite images from IMERG (HDF5
files).
>
> John told me that MET is unable to read HDF5 so I converted this
file in
> netcdf file. I tried to convert the HDF5 with ncl_convert2nc but I
have a
> warning: file contains no dimensions and I think it's because the
orginal
> file have as dimensions only latitude and longitude, here the time
is not a
> dimension. So the other opcion is to use NCO. First I convert all
the file
> and then I trie to extract the precipitationcal variable which I use
in the
> MODE.
>
> 1)ncks
> /share/apps/Build_MET_Intel/MET/data/imerg_fr/3B-HHR.MS.
> MRG.3IMERG.20170707-S003000-E005959.0030.V05B.HDF5
> /share/apps/Build_MET_Intel/MET/data/imerg_fr/
> 3B-HHR.MS.MRG.3IMERG.20170707-S003000-E005959.0030.V05B.nc
>
> 2) ncks -v precipitationCal
> 3B-HHR.MS.MRG.3IMERG.20170707-S0000E002959.0000.V05B.HDF5 cal.nc
>
>  and when I use the Panoply to see the and plot de data, it's ok but
> unfortunately, MODE can't read the new file:
>
> [naranda at rayo MET]$ bin/mode data/wrf_pp/prueba1
data/imerg_fr/cal.nc
> tutorial/config/MODEConfig_tutorial -outdir tutorial/out/mode_prueba
-v 2
> DEBUG 1: Default Config File:
> /share/apps/Build_MET_Intel/MET/share/met/config/MODEConfig_default
> DEBUG 1: Match Config File: tutorial/config/MODEConfig_tutorial
> DEBUG 1: Merge Config File: tutorial/config/MODEConfig_tutorial
> ERROR  :
> ERROR  : Trouble reading observation file "data/imerg_fr/cal.nc"
> ERROR  :
>
> I think that the problem is in MODEConfig_tutorial but i can't found
the
> mistake.
> In the configure, I put : level = '(*,*)' because i dont' know this
> information to observation files.
>
> In aranda_data I put :
> Prueba1 as forecast file
> cal.nc and 3B-HHR.MS.MRG.3IMERG.20170707-S003000-
E005959.0030.V05B.nc as
> observation file
> and MODEConfig_tutorial
>
>
> Sory for the long mail and thanks for your help!
>
> Natalí
>
>

------------------------------------------------
Subject: MODE: trouble reading observation file
From: natali aranda
Time: Wed Mar 28 09:11:45 2018

Hi John,

It works! I didn't find an option to ncks to strip out the groups but
I
made a script in python where I used ncdump cal.nc | grep -v group >
cal_NOGROUPS.ncdump

Also, I had to change the mode config:

obs =  {
file_type = NETCDF_NCCF;
   field = {
      name  ="precipitationCal";
      level ="(*,*)";
   }

but when I run MODE, I have the problem with the WRF latitude and
longitude: the forecast objects aren 't in the correct place.

I'm going to install the new version, Met 7.0, (I was using Met 6.0),
maybe
it was something wrong when I installed de Met 6.0. I tell you this
because
maybe you have any idea where is my mistake. I attached the ps, Mode
output, to see my problem. I work with WRF  Argentina but the objects
are
on the Pacific Ocean. It 's an example, you will see that the forecast
time
and observation time is different.

Thanks for all!
I really apreciate your help

Natalí


2018-03-07 18:32 GMT-03:00 John Halley Gotway via RT
<met_help at ucar.edu>:

> Natali,
>
> Thanks for sending the sample data file.  The issue is that cal.nc
makes
> use of "groups", a feature of NetCDF's enhanced data model.  MET
does not
> support these enhanced features of NetCDF.  Here's what I did:
>
> ncdump cal.nc > cal.ncdump
> # Edit cal.nc by removing the following lines:
> # group: Grid {
> #  } // group Grid
> ncgen -o cal_NOGROUPS.nc cal.ncdump
>
> # Use MET's plot_data_plane to plot it, using "file_type" option to
tell
> MET interpret it as CF-compliant NetCDF
> met-6.1/bin/plot_data_plane cal_NOGROUPS.nc cal_NOGROUPS.ps
> 'name="precipitationCal"; level="(*,*)"; file_type=NETCDF_NCCF;'
>
> I attached a PNG version of the resulting image.  Perhaps there's an
option
> to ncks to strip out the use of groups?
>
> John
>
> On Wed, Mar 7, 2018 at 11:38 AM, natali aranda via RT
<met_help at ucar.edu>
> wrote:
>
> >
> > Wed Mar 07 11:38:01 2018: Request 84355 was acted upon.
> > Transaction: Ticket created by natali.g.aranda at gmail.com
> >        Queue: met_help
> >      Subject: MODE: trouble reading observation file
> >        Owner: Nobody
> >   Requestors: natali.g.aranda at gmail.com
> >       Status: new
> >  Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=84355 >
> >
> >
> > Hi,
> >
> > A time ago I wrote because I would like to validate the
precipitation
> with
> > MODE.  I use as the forecast the regional WRF from Argentina (grib
files)
> > and as the observation, the  satellite images from IMERG (HDF5
files).
> >
> > John told me that MET is unable to read HDF5 so I converted this
file in
> > netcdf file. I tried to convert the HDF5 with ncl_convert2nc but I
have a
> > warning: file contains no dimensions and I think it's because the
orginal
> > file have as dimensions only latitude and longitude, here the time
is
> not a
> > dimension. So the other opcion is to use NCO. First I convert all
the
> file
> > and then I trie to extract the precipitationcal variable which I
use in
> the
> > MODE.
> >
> > 1)ncks
> > /share/apps/Build_MET_Intel/MET/data/imerg_fr/3B-HHR.MS.
> > MRG.3IMERG.20170707-S003000-E005959.0030.V05B.HDF5
> > /share/apps/Build_MET_Intel/MET/data/imerg_fr/
> > 3B-HHR.MS.MRG.3IMERG.20170707-S003000-E005959.0030.V05B.nc
> >
> > 2) ncks -v precipitationCal
> > 3B-HHR.MS.MRG.3IMERG.20170707-S0000E002959.0000.V05B.HDF5 cal.nc
> >
> >  and when I use the Panoply to see the and plot de data, it's ok
but
> > unfortunately, MODE can't read the new file:
> >
> > [naranda at rayo MET]$ bin/mode data/wrf_pp/prueba1
data/imerg_fr/cal.nc
> > tutorial/config/MODEConfig_tutorial -outdir
tutorial/out/mode_prueba -v
> 2
> > DEBUG 1: Default Config File:
> >
/share/apps/Build_MET_Intel/MET/share/met/config/MODEConfig_default
> > DEBUG 1: Match Config File: tutorial/config/MODEConfig_tutorial
> > DEBUG 1: Merge Config File: tutorial/config/MODEConfig_tutorial
> > ERROR  :
> > ERROR  : Trouble reading observation file "data/imerg_fr/cal.nc"
> > ERROR  :
> >
> > I think that the problem is in MODEConfig_tutorial but i can't
found the
> > mistake.
> > In the configure, I put : level = '(*,*)' because i dont' know
this
> > information to observation files.
> >
> > In aranda_data I put :
> > Prueba1 as forecast file
> > cal.nc and 3B-HHR.MS.MRG.3IMERG.20170707-S003000-
E005959.0030.V05B.nc as
> > observation file
> > and MODEConfig_tutorial
> >
> >
> > Sory for the long mail and thanks for your help!
> >
> > Natalí
> >
> >
>
>

------------------------------------------------
Subject: MODE: trouble reading observation file
From: John Halley Gotway
Time: Wed Mar 28 10:07:34 2018

Natali,

Glad you've been able to make progress.  If your data is supposed to
be
over Argentina, there's a likely a problem in how the latitudes and
longitudes correspond to the data values.

I would bring up a plot of your WRF output... and then use MET's
plot_data_plane utility to make a plot of the NetCDF data.  And then
adjust
the logic for how you're writing the lat/lon's until the plots match
up.

However, if you're running WRF is there a reason why you're not using
one
of the PostProcessor packages available for WRF?  The Unified Post
Processor (UPP: https://dtcenter.org/upp/users/) writes its output in
GRIB1
or GRIB2, which MET can easily read.  Also, the wrf_interp utility (
http://www2.mmm.ucar.edu/wrf/users/utilities/util.htm) just massages
the
NetCDF output from WRF in a way that MET can read.

Thanks,
John

On Wed, Mar 28, 2018 at 9:11 AM, natali aranda via RT
<met_help at ucar.edu>
wrote:

>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=84355 >
>
> Hi John,
>
> It works! I didn't find an option to ncks to strip out the groups
but I
> made a script in python where I used ncdump cal.nc | grep -v group >
> cal_NOGROUPS.ncdump
>
> Also, I had to change the mode config:
>
> obs =  {
> file_type = NETCDF_NCCF;
>    field = {
>       name  ="precipitationCal";
>       level ="(*,*)";
>    }
>
> but when I run MODE, I have the problem with the WRF latitude and
> longitude: the forecast objects aren 't in the correct place.
>
> I'm going to install the new version, Met 7.0, (I was using Met
6.0), maybe
> it was something wrong when I installed de Met 6.0. I tell you this
because
> maybe you have any idea where is my mistake. I attached the ps, Mode
> output, to see my problem. I work with WRF  Argentina but the
objects are
> on the Pacific Ocean. It 's an example, you will see that the
forecast time
> and observation time is different.
>
> Thanks for all!
> I really apreciate your help
>
> Natalí
>
>
> 2018-03-07 18:32 GMT-03:00 John Halley Gotway via RT
<met_help at ucar.edu>:
>
> > Natali,
> >
> > Thanks for sending the sample data file.  The issue is that cal.nc
makes
> > use of "groups", a feature of NetCDF's enhanced data model.  MET
does not
> > support these enhanced features of NetCDF.  Here's what I did:
> >
> > ncdump cal.nc > cal.ncdump
> > # Edit cal.nc by removing the following lines:
> > # group: Grid {
> > #  } // group Grid
> > ncgen -o cal_NOGROUPS.nc cal.ncdump
> >
> > # Use MET's plot_data_plane to plot it, using "file_type" option
to tell
> > MET interpret it as CF-compliant NetCDF
> > met-6.1/bin/plot_data_plane cal_NOGROUPS.nc cal_NOGROUPS.ps
> > 'name="precipitationCal"; level="(*,*)"; file_type=NETCDF_NCCF;'
> >
> > I attached a PNG version of the resulting image.  Perhaps there's
an
> option
> > to ncks to strip out the use of groups?
> >
> > John
> >
> > On Wed, Mar 7, 2018 at 11:38 AM, natali aranda via RT
<met_help at ucar.edu
> >
> > wrote:
> >
> > >
> > > Wed Mar 07 11:38:01 2018: Request 84355 was acted upon.
> > > Transaction: Ticket created by natali.g.aranda at gmail.com
> > >        Queue: met_help
> > >      Subject: MODE: trouble reading observation file
> > >        Owner: Nobody
> > >   Requestors: natali.g.aranda at gmail.com
> > >       Status: new
> > >  Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=84355
> >
> > >
> > >
> > > Hi,
> > >
> > > A time ago I wrote because I would like to validate the
precipitation
> > with
> > > MODE.  I use as the forecast the regional WRF from Argentina
(grib
> files)
> > > and as the observation, the  satellite images from IMERG (HDF5
files).
> > >
> > > John told me that MET is unable to read HDF5 so I converted this
file
> in
> > > netcdf file. I tried to convert the HDF5 with ncl_convert2nc but
I
> have a
> > > warning: file contains no dimensions and I think it's because
the
> orginal
> > > file have as dimensions only latitude and longitude, here the
time is
> > not a
> > > dimension. So the other opcion is to use NCO. First I convert
all the
> > file
> > > and then I trie to extract the precipitationcal variable which I
use in
> > the
> > > MODE.
> > >
> > > 1)ncks
> > > /share/apps/Build_MET_Intel/MET/data/imerg_fr/3B-HHR.MS.
> > > MRG.3IMERG.20170707-S003000-E005959.0030.V05B.HDF5
> > > /share/apps/Build_MET_Intel/MET/data/imerg_fr/
> > > 3B-HHR.MS.MRG.3IMERG.20170707-S003000-E005959.0030.V05B.nc
> > >
> > > 2) ncks -v precipitationCal
> > > 3B-HHR.MS.MRG.3IMERG.20170707-S0000E002959.0000.V05B.HDF5 cal.nc
> > >
> > >  and when I use the Panoply to see the and plot de data, it's ok
but
> > > unfortunately, MODE can't read the new file:
> > >
> > > [naranda at rayo MET]$ bin/mode data/wrf_pp/prueba1
data/imerg_fr/cal.nc
> > > tutorial/config/MODEConfig_tutorial -outdir
tutorial/out/mode_prueba
> -v
> > 2
> > > DEBUG 1: Default Config File:
> > >
/share/apps/Build_MET_Intel/MET/share/met/config/MODEConfig_default
> > > DEBUG 1: Match Config File: tutorial/config/MODEConfig_tutorial
> > > DEBUG 1: Merge Config File: tutorial/config/MODEConfig_tutorial
> > > ERROR  :
> > > ERROR  : Trouble reading observation file "data/imerg_fr/cal.nc"
> > > ERROR  :
> > >
> > > I think that the problem is in MODEConfig_tutorial but i can't
found
> the
> > > mistake.
> > > In the configure, I put : level = '(*,*)' because i dont' know
this
> > > information to observation files.
> > >
> > > In aranda_data I put :
> > > Prueba1 as forecast file
> > > cal.nc and 3B-HHR.MS.MRG.3IMERG.20170707-S003000-
E005959.0030.V05B.nc
> as
> > > observation file
> > > and MODEConfig_tutorial
> > >
> > >
> > > Sory for the long mail and thanks for your help!
> > >
> > > Natalí
> > >
> > >
> >
> >
>
>

------------------------------------------------
Subject: MODE: trouble reading observation file
From: natali aranda
Time: Wed Apr 04 09:55:01 2018

Hi John,

I use the UPP 3.0, the WRFs files are the output.

I put the file wrfprs02_20170707_00.003 in aranda_data, as an example
.

and I use the data_plane_plot to plot the grib:

bin/plot_data_plane data/wrf/wrfprs02_20170707_00.001
tutorial/out/plot_data_plane/ejemplo.ps 'name="APCP"; level="A1";'

I attached the output for data_plane_plot. It seems that the image was
invert but if I use the panoply to see the wrfprs02_20170707_00.003,
it's
ok.


I was searching on the internet and I found this forum:
http://forum.wrfforum.com/viewtopic.php?f=53&t=346.
It's possible that I have a similar problem?

thanks,

Natalí

2018-03-28 13:07 GMT-03:00 John Halley Gotway via RT
<met_help at ucar.edu>:

> Natali,
>
> Glad you've been able to make progress.  If your data is supposed to
be
> over Argentina, there's a likely a problem in how the latitudes and
> longitudes correspond to the data values.
>
> I would bring up a plot of your WRF output... and then use MET's
> plot_data_plane utility to make a plot of the NetCDF data.  And then
adjust
> the logic for how you're writing the lat/lon's until the plots match
up.
>
> However, if you're running WRF is there a reason why you're not
using one
> of the PostProcessor packages available for WRF?  The Unified Post
> Processor (UPP: https://dtcenter.org/upp/users/) writes its output
in
> GRIB1
> or GRIB2, which MET can easily read.  Also, the wrf_interp utility (
> http://www2.mmm.ucar.edu/wrf/users/utilities/util.htm) just massages
the
> NetCDF output from WRF in a way that MET can read.
>
> Thanks,
> John
>
> On Wed, Mar 28, 2018 at 9:11 AM, natali aranda via RT
<met_help at ucar.edu>
> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=84355 >
> >
> > Hi John,
> >
> > It works! I didn't find an option to ncks to strip out the groups
but I
> > made a script in python where I used ncdump cal.nc | grep -v group
>
> > cal_NOGROUPS.ncdump
> >
> > Also, I had to change the mode config:
> >
> > obs =  {
> > file_type = NETCDF_NCCF;
> >    field = {
> >       name  ="precipitationCal";
> >       level ="(*,*)";
> >    }
> >
> > but when I run MODE, I have the problem with the WRF latitude and
> > longitude: the forecast objects aren 't in the correct place.
> >
> > I'm going to install the new version, Met 7.0, (I was using Met
6.0),
> maybe
> > it was something wrong when I installed de Met 6.0. I tell you
this
> because
> > maybe you have any idea where is my mistake. I attached the ps,
Mode
> > output, to see my problem. I work with WRF  Argentina but the
objects are
> > on the Pacific Ocean. It 's an example, you will see that the
forecast
> time
> > and observation time is different.
> >
> > Thanks for all!
> > I really apreciate your help
> >
> > Natalí
> >
> >
> > 2018-03-07 18:32 GMT-03:00 John Halley Gotway via RT
<met_help at ucar.edu
> >:
> >
> > > Natali,
> > >
> > > Thanks for sending the sample data file.  The issue is that
cal.nc
> makes
> > > use of "groups", a feature of NetCDF's enhanced data model.  MET
does
> not
> > > support these enhanced features of NetCDF.  Here's what I did:
> > >
> > > ncdump cal.nc > cal.ncdump
> > > # Edit cal.nc by removing the following lines:
> > > # group: Grid {
> > > #  } // group Grid
> > > ncgen -o cal_NOGROUPS.nc cal.ncdump
> > >
> > > # Use MET's plot_data_plane to plot it, using "file_type" option
to
> tell
> > > MET interpret it as CF-compliant NetCDF
> > > met-6.1/bin/plot_data_plane cal_NOGROUPS.nc cal_NOGROUPS.ps
> > > 'name="precipitationCal"; level="(*,*)"; file_type=NETCDF_NCCF;'
> > >
> > > I attached a PNG version of the resulting image.  Perhaps
there's an
> > option
> > > to ncks to strip out the use of groups?
> > >
> > > John
> > >
> > > On Wed, Mar 7, 2018 at 11:38 AM, natali aranda via RT <
> met_help at ucar.edu
> > >
> > > wrote:
> > >
> > > >
> > > > Wed Mar 07 11:38:01 2018: Request 84355 was acted upon.
> > > > Transaction: Ticket created by natali.g.aranda at gmail.com
> > > >        Queue: met_help
> > > >      Subject: MODE: trouble reading observation file
> > > >        Owner: Nobody
> > > >   Requestors: natali.g.aranda at gmail.com
> > > >       Status: new
> > > >  Ticket <URL: https://rt.rap.ucar.edu/rt/
> Ticket/Display.html?id=84355
> > >
> > > >
> > > >
> > > > Hi,
> > > >
> > > > A time ago I wrote because I would like to validate the
precipitation
> > > with
> > > > MODE.  I use as the forecast the regional WRF from Argentina
(grib
> > files)
> > > > and as the observation, the  satellite images from IMERG (HDF5
> files).
> > > >
> > > > John told me that MET is unable to read HDF5 so I converted
this file
> > in
> > > > netcdf file. I tried to convert the HDF5 with ncl_convert2nc
but I
> > have a
> > > > warning: file contains no dimensions and I think it's because
the
> > orginal
> > > > file have as dimensions only latitude and longitude, here the
time is
> > > not a
> > > > dimension. So the other opcion is to use NCO. First I convert
all the
> > > file
> > > > and then I trie to extract the precipitationcal variable which
I use
> in
> > > the
> > > > MODE.
> > > >
> > > > 1)ncks
> > > > /share/apps/Build_MET_Intel/MET/data/imerg_fr/3B-HHR.MS.
> > > > MRG.3IMERG.20170707-S003000-E005959.0030.V05B.HDF5
> > > > /share/apps/Build_MET_Intel/MET/data/imerg_fr/
> > > > 3B-HHR.MS.MRG.3IMERG.20170707-S003000-E005959.0030.V05B.nc
> > > >
> > > > 2) ncks -v precipitationCal
> > > > 3B-HHR.MS.MRG.3IMERG.20170707-S0000E002959.0000.V05B.HDF5
cal.nc
> > > >
> > > >  and when I use the Panoply to see the and plot de data, it's
ok but
> > > > unfortunately, MODE can't read the new file:
> > > >
> > > > [naranda at rayo MET]$ bin/mode data/wrf_pp/prueba1
data/imerg_fr/
> cal.nc
> > > > tutorial/config/MODEConfig_tutorial -outdir
tutorial/out/mode_prueba
> > -v
> > > 2
> > > > DEBUG 1: Default Config File:
> > > >
/share/apps/Build_MET_Intel/MET/share/met/config/MODEConfig_default
> > > > DEBUG 1: Match Config File:
tutorial/config/MODEConfig_tutorial
> > > > DEBUG 1: Merge Config File:
tutorial/config/MODEConfig_tutorial
> > > > ERROR  :
> > > > ERROR  : Trouble reading observation file
"data/imerg_fr/cal.nc"
> > > > ERROR  :
> > > >
> > > > I think that the problem is in MODEConfig_tutorial but i can't
found
> > the
> > > > mistake.
> > > > In the configure, I put : level = '(*,*)' because i dont' know
this
> > > > information to observation files.
> > > >
> > > > In aranda_data I put :
> > > > Prueba1 as forecast file
> > > > cal.nc and 3B-HHR.MS.MRG.3IMERG.20170707-
> S003000-E005959.0030.V05B.nc
> > as
> > > > observation file
> > > > and MODEConfig_tutorial
> > > >
> > > >
> > > > Sory for the long mail and thanks for your help!
> > > >
> > > > Natalí
> > > >
> > > >
> > >
> > >
> >
> >
>
>

------------------------------------------------
Subject: MODE: trouble reading observation file
From: natali aranda
Time: Wed Apr 04 10:00:23 2018

sorry John, the image is not invert but the precipitation isn't in the
correct region

2018-04-04 12:54 GMT-03:00 natali aranda <natali.g.aranda at gmail.com>:

> Hi John,
>
> I use the UPP 3.0, the WRFs files are the output.
>
> I put the file wrfprs02_20170707_00.003 in aranda_data, as an
example .
>
> and I use the data_plane_plot to plot the grib:
>
> bin/plot_data_plane data/wrf/wrfprs02_20170707_00.001
> tutorial/out/plot_data_plane/ejemplo.ps 'name="APCP"; level="A1";'
>
> I attached the output for data_plane_plot. It seems that the image
was
> invert but if I use the panoply to see the wrfprs02_20170707_00.003,
it's
> ok.
>
>
> I was searching on the internet and I found this forum:
> http://forum.wrfforum.com/viewtopic.php?f=53&t=346.
> It's possible that I have a similar problem?
>
> thanks,
>
> Natalí
>
> 2018-03-28 13:07 GMT-03:00 John Halley Gotway via RT
<met_help at ucar.edu>:
>
>> Natali,
>>
>> Glad you've been able to make progress.  If your data is supposed
to be
>> over Argentina, there's a likely a problem in how the latitudes and
>> longitudes correspond to the data values.
>>
>> I would bring up a plot of your WRF output... and then use MET's
>> plot_data_plane utility to make a plot of the NetCDF data.  And
then
>> adjust
>> the logic for how you're writing the lat/lon's until the plots
match up.
>>
>> However, if you're running WRF is there a reason why you're not
using one
>> of the PostProcessor packages available for WRF?  The Unified Post
>> Processor (UPP: https://dtcenter.org/upp/users/) writes its output
in
>> GRIB1
>> or GRIB2, which MET can easily read.  Also, the wrf_interp utility
(
>> http://www2.mmm.ucar.edu/wrf/users/utilities/util.htm) just
massages the
>> NetCDF output from WRF in a way that MET can read.
>>
>> Thanks,
>> John
>>
>> On Wed, Mar 28, 2018 at 9:11 AM, natali aranda via RT
<met_help at ucar.edu>
>> wrote:
>>
>> >
>> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=84355 >
>> >
>> > Hi John,
>> >
>> > It works! I didn't find an option to ncks to strip out the groups
but I
>> > made a script in python where I used ncdump cal.nc | grep -v
group >
>> > cal_NOGROUPS.ncdump
>> >
>> > Also, I had to change the mode config:
>> >
>> > obs =  {
>> > file_type = NETCDF_NCCF;
>> >    field = {
>> >       name  ="precipitationCal";
>> >       level ="(*,*)";
>> >    }
>> >
>> > but when I run MODE, I have the problem with the WRF latitude and
>> > longitude: the forecast objects aren 't in the correct place.
>> >
>> > I'm going to install the new version, Met 7.0, (I was using Met
6.0),
>> maybe
>> > it was something wrong when I installed de Met 6.0. I tell you
this
>> because
>> > maybe you have any idea where is my mistake. I attached the ps,
Mode
>> > output, to see my problem. I work with WRF  Argentina but the
objects
>> are
>> > on the Pacific Ocean. It 's an example, you will see that the
forecast
>> time
>> > and observation time is different.
>> >
>> > Thanks for all!
>> > I really apreciate your help
>> >
>> > Natalí
>> >
>> >
>> > 2018-03-07 18:32 GMT-03:00 John Halley Gotway via RT
<met_help at ucar.edu
>> >:
>> >
>> > > Natali,
>> > >
>> > > Thanks for sending the sample data file.  The issue is that
cal.nc
>> makes
>> > > use of "groups", a feature of NetCDF's enhanced data model.
MET does
>> not
>> > > support these enhanced features of NetCDF.  Here's what I did:
>> > >
>> > > ncdump cal.nc > cal.ncdump
>> > > # Edit cal.nc by removing the following lines:
>> > > # group: Grid {
>> > > #  } // group Grid
>> > > ncgen -o cal_NOGROUPS.nc cal.ncdump
>> > >
>> > > # Use MET's plot_data_plane to plot it, using "file_type"
option to
>> tell
>> > > MET interpret it as CF-compliant NetCDF
>> > > met-6.1/bin/plot_data_plane cal_NOGROUPS.nc cal_NOGROUPS.ps
>> > > 'name="precipitationCal"; level="(*,*)";
file_type=NETCDF_NCCF;'
>> > >
>> > > I attached a PNG version of the resulting image.  Perhaps
there's an
>> > option
>> > > to ncks to strip out the use of groups?
>> > >
>> > > John
>> > >
>> > > On Wed, Mar 7, 2018 at 11:38 AM, natali aranda via RT <
>> met_help at ucar.edu
>> > >
>> > > wrote:
>> > >
>> > > >
>> > > > Wed Mar 07 11:38:01 2018: Request 84355 was acted upon.
>> > > > Transaction: Ticket created by natali.g.aranda at gmail.com
>> > > >        Queue: met_help
>> > > >      Subject: MODE: trouble reading observation file
>> > > >        Owner: Nobody
>> > > >   Requestors: natali.g.aranda at gmail.com
>> > > >       Status: new
>> > > >  Ticket <URL: https://rt.rap.ucar.edu/rt/Tic
>> ket/Display.html?id=84355
>> > >
>> > > >
>> > > >
>> > > > Hi,
>> > > >
>> > > > A time ago I wrote because I would like to validate the
>> precipitation
>> > > with
>> > > > MODE.  I use as the forecast the regional WRF from Argentina
(grib
>> > files)
>> > > > and as the observation, the  satellite images from IMERG
(HDF5
>> files).
>> > > >
>> > > > John told me that MET is unable to read HDF5 so I converted
this
>> file
>> > in
>> > > > netcdf file. I tried to convert the HDF5 with ncl_convert2nc
but I
>> > have a
>> > > > warning: file contains no dimensions and I think it's because
the
>> > orginal
>> > > > file have as dimensions only latitude and longitude, here the
time
>> is
>> > > not a
>> > > > dimension. So the other opcion is to use NCO. First I convert
all
>> the
>> > > file
>> > > > and then I trie to extract the precipitationcal variable
which I
>> use in
>> > > the
>> > > > MODE.
>> > > >
>> > > > 1)ncks
>> > > > /share/apps/Build_MET_Intel/MET/data/imerg_fr/3B-HHR.MS.
>> > > > MRG.3IMERG.20170707-S003000-E005959.0030.V05B.HDF5
>> > > > /share/apps/Build_MET_Intel/MET/data/imerg_fr/
>> > > > 3B-HHR.MS.MRG.3IMERG.20170707-S003000-E005959.0030.V05B.nc
>> > > >
>> > > > 2) ncks -v precipitationCal
>> > > > 3B-HHR.MS.MRG.3IMERG.20170707-S0000E002959.0000.V05B.HDF5
cal.nc
>> > > >
>> > > >  and when I use the Panoply to see the and plot de data, it's
ok but
>> > > > unfortunately, MODE can't read the new file:
>> > > >
>> > > > [naranda at rayo MET]$ bin/mode data/wrf_pp/prueba1
data/imerg_fr/
>> cal.nc
>> > > > tutorial/config/MODEConfig_tutorial -outdir
>> tutorial/out/mode_prueba
>> > -v
>> > > 2
>> > > > DEBUG 1: Default Config File:
>> > > >
/share/apps/Build_MET_Intel/MET/share/met/config/MODEConfig_default
>> > > > DEBUG 1: Match Config File:
tutorial/config/MODEConfig_tutorial
>> > > > DEBUG 1: Merge Config File:
tutorial/config/MODEConfig_tutorial
>> > > > ERROR  :
>> > > > ERROR  : Trouble reading observation file
"data/imerg_fr/cal.nc"
>> > > > ERROR  :
>> > > >
>> > > > I think that the problem is in MODEConfig_tutorial but i
can't found
>> > the
>> > > > mistake.
>> > > > In the configure, I put : level = '(*,*)' because i dont'
know this
>> > > > information to observation files.
>> > > >
>> > > > In aranda_data I put :
>> > > > Prueba1 as forecast file
>> > > > cal.nc and 3B-HHR.MS.MRG.3IMERG.20170707-
>> S003000-E005959.0030.V05B.nc
>> > as
>> > > > observation file
>> > > > and MODEConfig_tutorial
>> > > >
>> > > >
>> > > > Sory for the long mail and thanks for your help!
>> > > >
>> > > > Natalí
>> > > >
>> > > >
>> > >
>> > >
>> >
>> >
>>
>>
>

------------------------------------------------
Subject: MODE: trouble reading observation file
From: John Halley Gotway
Time: Wed Apr 04 10:29:41 2018

Natali,


Thanks for sending the sample data file.  I grabbed it and ran a
couple of
plot_data_plane commands where the output looks pretty good.  I
plotted 2-m
temperature and see that the values track well with topography.  I
also
plotted 1-hour precip since that what you sent:


   met-6.1/bin/plot_data_plane wrfprs02_20170707_00.003 APCP_A1.ps
'name="APCP"; level="A1";'

   met-6.1/bin/plot_data_plane wrfprs02_20170707_00.003 TMP_Z2.ps
'name="TMP"; level="Z2";'


Do you agree that the attached plots look good over your domain?
Perhaps
the image you sent is off by 180 degrees of longitude?  The landmass
in
your plot might be Australia?


My best guess here is that we have an issue with the patch level of
the MET
software.  What version of MET are you running?  And do you know what
patches have been applied?  The plot_data_plane commands I ran were
version
6.1 of MET using the latest set of patches.


This website lists all known issues and fixes for each MET release:

   https://dtcenter.org/met/users/support/known_issues/index.php


Thanks,
John


On Wed, Apr 4, 2018 at 10:00 AM, natali aranda via RT
<met_help at ucar.edu>
wrote:

>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=84355 >
>
> sorry John, the image is not invert but the precipitation isn't in
the
> correct region
>
> 2018-04-04 12:54 GMT-03:00 natali aranda
<natali.g.aranda at gmail.com>:
>
> > Hi John,
> >
> > I use the UPP 3.0, the WRFs files are the output.
> >
> > I put the file wrfprs02_20170707_00.003 in aranda_data, as an
example .
> >
> > and I use the data_plane_plot to plot the grib:
> >
> > bin/plot_data_plane data/wrf/wrfprs02_20170707_00.001
> > tutorial/out/plot_data_plane/ejemplo.ps 'name="APCP"; level="A1";'
> >
> > I attached the output for data_plane_plot. It seems that the image
was
> > invert but if I use the panoply to see the
wrfprs02_20170707_00.003, it's
> > ok.
> >
> >
> > I was searching on the internet and I found this forum:
> > http://forum.wrfforum.com/viewtopic.php?f=53&t=346.
> > It's possible that I have a similar problem?
> >
> > thanks,
> >
> > Natalí
> >
> > 2018-03-28 13:07 GMT-03:00 John Halley Gotway via RT
<met_help at ucar.edu
> >:
> >
> >> Natali,
> >>
> >> Glad you've been able to make progress.  If your data is supposed
to be
> >> over Argentina, there's a likely a problem in how the latitudes
and
> >> longitudes correspond to the data values.
> >>
> >> I would bring up a plot of your WRF output... and then use MET's
> >> plot_data_plane utility to make a plot of the NetCDF data.  And
then
> >> adjust
> >> the logic for how you're writing the lat/lon's until the plots
match up.
> >>
> >> However, if you're running WRF is there a reason why you're not
using
> one
> >> of the PostProcessor packages available for WRF?  The Unified
Post
> >> Processor (UPP: https://dtcenter.org/upp/users/) writes its
output in
> >> GRIB1
> >> or GRIB2, which MET can easily read.  Also, the wrf_interp
utility (
> >> http://www2.mmm.ucar.edu/wrf/users/utilities/util.htm) just
massages
> the
> >> NetCDF output from WRF in a way that MET can read.
> >>
> >> Thanks,
> >> John
> >>
> >> On Wed, Mar 28, 2018 at 9:11 AM, natali aranda via RT <
> met_help at ucar.edu>
> >> wrote:
> >>
> >> >
> >> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=84355 >
> >> >
> >> > Hi John,
> >> >
> >> > It works! I didn't find an option to ncks to strip out the
groups but
> I
> >> > made a script in python where I used ncdump cal.nc | grep -v
group >
> >> > cal_NOGROUPS.ncdump
> >> >
> >> > Also, I had to change the mode config:
> >> >
> >> > obs =  {
> >> > file_type = NETCDF_NCCF;
> >> >    field = {
> >> >       name  ="precipitationCal";
> >> >       level ="(*,*)";
> >> >    }
> >> >
> >> > but when I run MODE, I have the problem with the WRF latitude
and
> >> > longitude: the forecast objects aren 't in the correct place.
> >> >
> >> > I'm going to install the new version, Met 7.0, (I was using Met
6.0),
> >> maybe
> >> > it was something wrong when I installed de Met 6.0. I tell you
this
> >> because
> >> > maybe you have any idea where is my mistake. I attached the ps,
Mode
> >> > output, to see my problem. I work with WRF  Argentina but the
objects
> >> are
> >> > on the Pacific Ocean. It 's an example, you will see that the
forecast
> >> time
> >> > and observation time is different.
> >> >
> >> > Thanks for all!
> >> > I really apreciate your help
> >> >
> >> > Natalí
> >> >
> >> >
> >> > 2018-03-07 18:32 GMT-03:00 John Halley Gotway via RT <
> met_help at ucar.edu
> >> >:
> >> >
> >> > > Natali,
> >> > >
> >> > > Thanks for sending the sample data file.  The issue is that
cal.nc
> >> makes
> >> > > use of "groups", a feature of NetCDF's enhanced data model.
MET
> does
> >> not
> >> > > support these enhanced features of NetCDF.  Here's what I
did:
> >> > >
> >> > > ncdump cal.nc > cal.ncdump
> >> > > # Edit cal.nc by removing the following lines:
> >> > > # group: Grid {
> >> > > #  } // group Grid
> >> > > ncgen -o cal_NOGROUPS.nc cal.ncdump
> >> > >
> >> > > # Use MET's plot_data_plane to plot it, using "file_type"
option to
> >> tell
> >> > > MET interpret it as CF-compliant NetCDF
> >> > > met-6.1/bin/plot_data_plane cal_NOGROUPS.nc cal_NOGROUPS.ps
> >> > > 'name="precipitationCal"; level="(*,*)";
file_type=NETCDF_NCCF;'
> >> > >
> >> > > I attached a PNG version of the resulting image.  Perhaps
there's an
> >> > option
> >> > > to ncks to strip out the use of groups?
> >> > >
> >> > > John
> >> > >
> >> > > On Wed, Mar 7, 2018 at 11:38 AM, natali aranda via RT <
> >> met_help at ucar.edu
> >> > >
> >> > > wrote:
> >> > >
> >> > > >
> >> > > > Wed Mar 07 11:38:01 2018: Request 84355 was acted upon.
> >> > > > Transaction: Ticket created by natali.g.aranda at gmail.com
> >> > > >        Queue: met_help
> >> > > >      Subject: MODE: trouble reading observation file
> >> > > >        Owner: Nobody
> >> > > >   Requestors: natali.g.aranda at gmail.com
> >> > > >       Status: new
> >> > > >  Ticket <URL: https://rt.rap.ucar.edu/rt/Tic
> >> ket/Display.html?id=84355
> >> > >
> >> > > >
> >> > > >
> >> > > > Hi,
> >> > > >
> >> > > > A time ago I wrote because I would like to validate the
> >> precipitation
> >> > > with
> >> > > > MODE.  I use as the forecast the regional WRF from
Argentina (grib
> >> > files)
> >> > > > and as the observation, the  satellite images from IMERG
(HDF5
> >> files).
> >> > > >
> >> > > > John told me that MET is unable to read HDF5 so I converted
this
> >> file
> >> > in
> >> > > > netcdf file. I tried to convert the HDF5 with
ncl_convert2nc but I
> >> > have a
> >> > > > warning: file contains no dimensions and I think it's
because the
> >> > orginal
> >> > > > file have as dimensions only latitude and longitude, here
the time
> >> is
> >> > > not a
> >> > > > dimension. So the other opcion is to use NCO. First I
convert all
> >> the
> >> > > file
> >> > > > and then I trie to extract the precipitationcal variable
which I
> >> use in
> >> > > the
> >> > > > MODE.
> >> > > >
> >> > > > 1)ncks
> >> > > > /share/apps/Build_MET_Intel/MET/data/imerg_fr/3B-HHR.MS.
> >> > > > MRG.3IMERG.20170707-S003000-E005959.0030.V05B.HDF5
> >> > > > /share/apps/Build_MET_Intel/MET/data/imerg_fr/
> >> > > > 3B-HHR.MS.MRG.3IMERG.20170707-S003000-E005959.0030.V05B.nc
> >> > > >
> >> > > > 2) ncks -v precipitationCal
> >> > > > 3B-HHR.MS.MRG.3IMERG.20170707-S0000E002959.0000.V05B.HDF5
cal.nc
> >> > > >
> >> > > >  and when I use the Panoply to see the and plot de data,
it's ok
> but
> >> > > > unfortunately, MODE can't read the new file:
> >> > > >
> >> > > > [naranda at rayo MET]$ bin/mode data/wrf_pp/prueba1
data/imerg_fr/
> >> cal.nc
> >> > > > tutorial/config/MODEConfig_tutorial -outdir
> >> tutorial/out/mode_prueba
> >> > -v
> >> > > 2
> >> > > > DEBUG 1: Default Config File:
> >> > > > /share/apps/Build_MET_Intel/MET/share/met/config/
> MODEConfig_default
> >> > > > DEBUG 1: Match Config File:
tutorial/config/MODEConfig_tutorial
> >> > > > DEBUG 1: Merge Config File:
tutorial/config/MODEConfig_tutorial
> >> > > > ERROR  :
> >> > > > ERROR  : Trouble reading observation file
"data/imerg_fr/cal.nc"
> >> > > > ERROR  :
> >> > > >
> >> > > > I think that the problem is in MODEConfig_tutorial but i
can't
> found
> >> > the
> >> > > > mistake.
> >> > > > In the configure, I put : level = '(*,*)' because i dont'
know
> this
> >> > > > information to observation files.
> >> > > >
> >> > > > In aranda_data I put :
> >> > > > Prueba1 as forecast file
> >> > > > cal.nc and 3B-HHR.MS.MRG.3IMERG.20170707-
> >> S003000-E005959.0030.V05B.nc
> >> > as
> >> > > > observation file
> >> > > > and MODEConfig_tutorial
> >> > > >
> >> > > >
> >> > > > Sory for the long mail and thanks for your help!
> >> > > >
> >> > > > Natalí
> >> > > >
> >> > > >
> >> > >
> >> > >
> >> >
> >> >
> >>
> >>
> >
>
>

------------------------------------------------
Subject: MODE: trouble reading observation file
From: natali aranda
Time: Wed Apr 04 11:38:54 2018

John! Thanks!

I use the version 6.0 of MET and I realize that maybe I do something
wrong
with the patches. I'm going to install the new version,

Thanks again for your help!

Natalí


2018-04-04 13:29 GMT-03:00 John Halley Gotway via RT
<met_help at ucar.edu>:

> Natali,
>
>
> Thanks for sending the sample data file.  I grabbed it and ran a
couple of
> plot_data_plane commands where the output looks pretty good.  I
plotted 2-m
> temperature and see that the values track well with topography.  I
also
> plotted 1-hour precip since that what you sent:
>
>
>    met-6.1/bin/plot_data_plane wrfprs02_20170707_00.003 APCP_A1.ps
> 'name="APCP"; level="A1";'
>
>    met-6.1/bin/plot_data_plane wrfprs02_20170707_00.003 TMP_Z2.ps
> 'name="TMP"; level="Z2";'
>
>
> Do you agree that the attached plots look good over your domain?
Perhaps
> the image you sent is off by 180 degrees of longitude?  The landmass
in
> your plot might be Australia?
>
>
> My best guess here is that we have an issue with the patch level of
the MET
> software.  What version of MET are you running?  And do you know
what
> patches have been applied?  The plot_data_plane commands I ran were
version
> 6.1 of MET using the latest set of patches.
>
>
> This website lists all known issues and fixes for each MET release:
>
>    https://dtcenter.org/met/users/support/known_issues/index.php
>
>
> Thanks,
> John
>
>
> On Wed, Apr 4, 2018 at 10:00 AM, natali aranda via RT
<met_help at ucar.edu>
> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=84355 >
> >
> > sorry John, the image is not invert but the precipitation isn't in
the
> > correct region
> >
> > 2018-04-04 12:54 GMT-03:00 natali aranda
<natali.g.aranda at gmail.com>:
> >
> > > Hi John,
> > >
> > > I use the UPP 3.0, the WRFs files are the output.
> > >
> > > I put the file wrfprs02_20170707_00.003 in aranda_data, as an
example .
> > >
> > > and I use the data_plane_plot to plot the grib:
> > >
> > > bin/plot_data_plane data/wrf/wrfprs02_20170707_00.001
> > > tutorial/out/plot_data_plane/ejemplo.ps 'name="APCP";
level="A1";'
> > >
> > > I attached the output for data_plane_plot. It seems that the
image was
> > > invert but if I use the panoply to see the
wrfprs02_20170707_00.003,
> it's
> > > ok.
> > >
> > >
> > > I was searching on the internet and I found this forum:
> > > http://forum.wrfforum.com/viewtopic.php?f=53&t=346.
> > > It's possible that I have a similar problem?
> > >
> > > thanks,
> > >
> > > Natalí
> > >
> > > 2018-03-28 13:07 GMT-03:00 John Halley Gotway via RT <
> met_help at ucar.edu
> > >:
> > >
> > >> Natali,
> > >>
> > >> Glad you've been able to make progress.  If your data is
supposed to
> be
> > >> over Argentina, there's a likely a problem in how the latitudes
and
> > >> longitudes correspond to the data values.
> > >>
> > >> I would bring up a plot of your WRF output... and then use
MET's
> > >> plot_data_plane utility to make a plot of the NetCDF data.  And
then
> > >> adjust
> > >> the logic for how you're writing the lat/lon's until the plots
match
> up.
> > >>
> > >> However, if you're running WRF is there a reason why you're not
using
> > one
> > >> of the PostProcessor packages available for WRF?  The Unified
Post
> > >> Processor (UPP: https://dtcenter.org/upp/users/) writes its
output in
> > >> GRIB1
> > >> or GRIB2, which MET can easily read.  Also, the wrf_interp
utility (
> > >> http://www2.mmm.ucar.edu/wrf/users/utilities/util.htm) just
massages
> > the
> > >> NetCDF output from WRF in a way that MET can read.
> > >>
> > >> Thanks,
> > >> John
> > >>
> > >> On Wed, Mar 28, 2018 at 9:11 AM, natali aranda via RT <
> > met_help at ucar.edu>
> > >> wrote:
> > >>
> > >> >
> > >> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=84355
>
> > >> >
> > >> > Hi John,
> > >> >
> > >> > It works! I didn't find an option to ncks to strip out the
groups
> but
> > I
> > >> > made a script in python where I used ncdump cal.nc | grep -v
group
> >
> > >> > cal_NOGROUPS.ncdump
> > >> >
> > >> > Also, I had to change the mode config:
> > >> >
> > >> > obs =  {
> > >> > file_type = NETCDF_NCCF;
> > >> >    field = {
> > >> >       name  ="precipitationCal";
> > >> >       level ="(*,*)";
> > >> >    }
> > >> >
> > >> > but when I run MODE, I have the problem with the WRF latitude
and
> > >> > longitude: the forecast objects aren 't in the correct place.
> > >> >
> > >> > I'm going to install the new version, Met 7.0, (I was using
Met
> 6.0),
> > >> maybe
> > >> > it was something wrong when I installed de Met 6.0. I tell
you this
> > >> because
> > >> > maybe you have any idea where is my mistake. I attached the
ps, Mode
> > >> > output, to see my problem. I work with WRF  Argentina but the
> objects
> > >> are
> > >> > on the Pacific Ocean. It 's an example, you will see that the
> forecast
> > >> time
> > >> > and observation time is different.
> > >> >
> > >> > Thanks for all!
> > >> > I really apreciate your help
> > >> >
> > >> > Natalí
> > >> >
> > >> >
> > >> > 2018-03-07 18:32 GMT-03:00 John Halley Gotway via RT <
> > met_help at ucar.edu
> > >> >:
> > >> >
> > >> > > Natali,
> > >> > >
> > >> > > Thanks for sending the sample data file.  The issue is that
> cal.nc
> > >> makes
> > >> > > use of "groups", a feature of NetCDF's enhanced data model.
MET
> > does
> > >> not
> > >> > > support these enhanced features of NetCDF.  Here's what I
did:
> > >> > >
> > >> > > ncdump cal.nc > cal.ncdump
> > >> > > # Edit cal.nc by removing the following lines:
> > >> > > # group: Grid {
> > >> > > #  } // group Grid
> > >> > > ncgen -o cal_NOGROUPS.nc cal.ncdump
> > >> > >
> > >> > > # Use MET's plot_data_plane to plot it, using "file_type"
option
> to
> > >> tell
> > >> > > MET interpret it as CF-compliant NetCDF
> > >> > > met-6.1/bin/plot_data_plane cal_NOGROUPS.nc cal_NOGROUPS.ps
> > >> > > 'name="precipitationCal"; level="(*,*)";
file_type=NETCDF_NCCF;'
> > >> > >
> > >> > > I attached a PNG version of the resulting image.  Perhaps
there's
> an
> > >> > option
> > >> > > to ncks to strip out the use of groups?
> > >> > >
> > >> > > John
> > >> > >
> > >> > > On Wed, Mar 7, 2018 at 11:38 AM, natali aranda via RT <
> > >> met_help at ucar.edu
> > >> > >
> > >> > > wrote:
> > >> > >
> > >> > > >
> > >> > > > Wed Mar 07 11:38:01 2018: Request 84355 was acted upon.
> > >> > > > Transaction: Ticket created by natali.g.aranda at gmail.com
> > >> > > >        Queue: met_help
> > >> > > >      Subject: MODE: trouble reading observation file
> > >> > > >        Owner: Nobody
> > >> > > >   Requestors: natali.g.aranda at gmail.com
> > >> > > >       Status: new
> > >> > > >  Ticket <URL: https://rt.rap.ucar.edu/rt/Tic
> > >> ket/Display.html?id=84355
> > >> > >
> > >> > > >
> > >> > > >
> > >> > > > Hi,
> > >> > > >
> > >> > > > A time ago I wrote because I would like to validate the
> > >> precipitation
> > >> > > with
> > >> > > > MODE.  I use as the forecast the regional WRF from
Argentina
> (grib
> > >> > files)
> > >> > > > and as the observation, the  satellite images from IMERG
(HDF5
> > >> files).
> > >> > > >
> > >> > > > John told me that MET is unable to read HDF5 so I
converted this
> > >> file
> > >> > in
> > >> > > > netcdf file. I tried to convert the HDF5 with
ncl_convert2nc
> but I
> > >> > have a
> > >> > > > warning: file contains no dimensions and I think it's
because
> the
> > >> > orginal
> > >> > > > file have as dimensions only latitude and longitude, here
the
> time
> > >> is
> > >> > > not a
> > >> > > > dimension. So the other opcion is to use NCO. First I
convert
> all
> > >> the
> > >> > > file
> > >> > > > and then I trie to extract the precipitationcal variable
which I
> > >> use in
> > >> > > the
> > >> > > > MODE.
> > >> > > >
> > >> > > > 1)ncks
> > >> > > > /share/apps/Build_MET_Intel/MET/data/imerg_fr/3B-HHR.MS.
> > >> > > > MRG.3IMERG.20170707-S003000-E005959.0030.V05B.HDF5
> > >> > > > /share/apps/Build_MET_Intel/MET/data/imerg_fr/
> > >> > > > 3B-HHR.MS.MRG.3IMERG.20170707-S003000-
E005959.0030.V05B.nc
> > >> > > >
> > >> > > > 2) ncks -v precipitationCal
> > >> > > > 3B-HHR.MS.MRG.3IMERG.20170707-S0000E002959.0000.V05B.HDF5
> cal.nc
> > >> > > >
> > >> > > >  and when I use the Panoply to see the and plot de data,
it's ok
> > but
> > >> > > > unfortunately, MODE can't read the new file:
> > >> > > >
> > >> > > > [naranda at rayo MET]$ bin/mode data/wrf_pp/prueba1
data/imerg_fr/
> > >> cal.nc
> > >> > > > tutorial/config/MODEConfig_tutorial -outdir
> > >> tutorial/out/mode_prueba
> > >> > -v
> > >> > > 2
> > >> > > > DEBUG 1: Default Config File:
> > >> > > > /share/apps/Build_MET_Intel/MET/share/met/config/
> > MODEConfig_default
> > >> > > > DEBUG 1: Match Config File:
tutorial/config/MODEConfig_tutorial
> > >> > > > DEBUG 1: Merge Config File:
tutorial/config/MODEConfig_tutorial
> > >> > > > ERROR  :
> > >> > > > ERROR  : Trouble reading observation file
"data/imerg_fr/cal.nc
> "
> > >> > > > ERROR  :
> > >> > > >
> > >> > > > I think that the problem is in MODEConfig_tutorial but i
can't
> > found
> > >> > the
> > >> > > > mistake.
> > >> > > > In the configure, I put : level = '(*,*)' because i dont'
know
> > this
> > >> > > > information to observation files.
> > >> > > >
> > >> > > > In aranda_data I put :
> > >> > > > Prueba1 as forecast file
> > >> > > > cal.nc and 3B-HHR.MS.MRG.3IMERG.20170707-
> > >> S003000-E005959.0030.V05B.nc
> > >> > as
> > >> > > > observation file
> > >> > > > and MODEConfig_tutorial
> > >> > > >
> > >> > > >
> > >> > > > Sory for the long mail and thanks for your help!
> > >> > > >
> > >> > > > Natalí
> > >> > > >
> > >> > > >
> > >> > >
> > >> > >
> > >> >
> > >> >
> > >>
> > >>
> > >
> >
> >
>
>

------------------------------------------------
Subject: MODE: trouble reading observation file
From: natali aranda
Time: Fri Apr 13 13:54:03 2018

Hi John,

I installed METv7.0 and now I don't have problem with the WRF
Argentina,
the plots are ok!

But I have a new question. Do you remember that I would like to use as
observation the IMERG data ? So I converted these HDF5 files in NETCDF
files. I see that MET has a problem to read de valid time in this file

For example when I use MODE, I have this warning: *NcCfFile::open() ->
could not determine the valid time, using 0.*

However, MODE produces outscript and in the PostScript file, the
initial
and valid time in the observation is wrong:




Also, I can't use Pcp_combine to Imerg file. It's a possible that the
problem is because the data is every 30 minutes?
I put in aranda_data 2 files as example to this files

Thanks,


Natalí

2018-04-06 12:38 GMT-03:00 John Halley Gotway via RT
<met_help at ucar.edu>:

> According to our records, your request has been resolved. If you
have any
> further questions or concerns, please respond to this message.
>

------------------------------------------------
Subject: MODE: trouble reading observation file
From: John Halley Gotway
Time: Fri Apr 13 14:39:13 2018

Natali,

I grabbed your sample data files.  We are telling MET to interpret
these as
CF-compliant NetCDF files.  But the timing info is not included in the
file
in a CF-compliant way... and that's why the times are listed as 0.

You can still run pcp_combine on them though.  Here's an example:

/usr/local/met-7.0/bin/pcp_combine -add \
3B-HHR.MS.MRG.3IMERG.20170707-S003000-E005959.0030.V05B.nc
'name="precipitationCal"; level="(*,*)"; file_type=NETCDF_NCCF;' \
3B-HHR.MS.MRG.3IMERG.20170707-S010000-E012959.0060.V05B.nc
'name="precipitationCal"; level="(*,*)"; file_type=NETCDF_NCCF;' \
3B-HHR.MS.MRG.3IMERG.20170707-1hour.nc

You'll see that the timestamp of the output has unixtime = 0 (i.e.
19700101):

ncdump -h 3B-HHR.MS.MRG.3IMERG.20170707-1hour.nc | grep time
                precipitationCal:init_time = "19700101_000000" ;
                precipitationCal:init_time_ut = "0" ;
                precipitationCal:valid_time = "19700101_000000" ;
                precipitationCal:valid_time_ut = "0" ;

But this NetCDF file uses MET's internal file format.  So updating the
timestamp is a little easier:

# Use date command to convert between date string and unixtime
setenv INIT_TIME_UT     `date -ud ''20170707' UTC '00:30:00'' +%s`
setenv VALID_TIME_UT `date -ud ''20170707' UTC '01:30:00'' +%s`

# Use ncatted to update the NetCDF timing attributes
ncatted \
-a init_time,precipitationCal,o,c,20170707_003000 \
-a init_time_ut,precipitationCal,o,c,${INIT_TIME_UT} \
-a valid_time,precipitationCal,o,c,20170707_013000 \
-a valid_time_ut,precipitationCal,o,c,${VALID_TIME_UT} \
3B-HHR.MS.MRG.3IMERG.20170707-1hour.nc

# Run plot_data_plane to plot the result
/usr/local/met-7.0/bin/plot_data_plane \
3B-HHR.MS.MRG.3IMERG.20170707-1hour.nc \
3B-HHR.MS.MRG.3IMERG.20170707-1hour.ps \
'name="precipitationCal"; level="(*,*)";'

And the resulting image is attached.

BUT WAIT... THERE'S A HUGE CAVEAT HERE.

Your input data is a *precipitation rate* and the units are mm/hr.
You
really should add together two rates.  Instead, you should probably
take
their average.  pcp_combine doesn't do that.  I adds and subtracts but
doesn't compute an average value.

Hope this helps clarify.

Thanks,
John





On Fri, Apr 13, 2018 at 1:54 PM, natali aranda via RT
<met_help at ucar.edu>
wrote:

>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=84355 >
>
> Hi John,
>
> I installed METv7.0 and now I don't have problem with the WRF
Argentina,
> the plots are ok!
>
> But I have a new question. Do you remember that I would like to use
as
> observation the IMERG data ? So I converted these HDF5 files in
NETCDF
> files. I see that MET has a problem to read de valid time in this
file
>
> For example when I use MODE, I have this warning: *NcCfFile::open()
->
> could not determine the valid time, using 0.*
>
> However, MODE produces outscript and in the PostScript file, the
initial
> and valid time in the observation is wrong:
>
>
>
>
> Also, I can't use Pcp_combine to Imerg file. It's a possible that
the
> problem is because the data is every 30 minutes?
> I put in aranda_data 2 files as example to this files
>
> Thanks,
>
>
> Natalí
>
> 2018-04-06 12:38 GMT-03:00 John Halley Gotway via RT
<met_help at ucar.edu>:
>
> > According to our records, your request has been resolved. If you
have any
> > further questions or concerns, please respond to this message.
> >
>
>

------------------------------------------------
Subject: MODE: trouble reading observation file
From: natali aranda
Time: Fri May 11 15:25:04 2018

John,

I followed your advice. I changed de Netcdf file (Imerg file) with
ncatted,
previously I used pcp_combine -add.
I could see the same that you but when I run mode, I have the same
problem
with the time:

[naranda at rayo MET-7.0BF_I18]$ bin/mode pcp_combine/wrf_00_02.nc
pcp_combine/
3B-HHR.MS.MRG.3IMERG.20170707_02.nc share/met/config/MODEConfig_1
-outdir
figuras -v 2
DEBUG 1: Default Config File:
/share/apps/contrib/MET-7.0BF_I18/share/met/config/MODEConfig_default
DEBUG 1: Match Config File: share/met/config/MODEConfig_1
DEBUG 1: Merge Config File: share/met/config/MODEConfig_1
WARNING:
WARNING: NcCfFile::open() -> could not determine the valid time, using
0.
....

I put wrf_00_02.nc, 3B-HHR.MS.MRG.3IMERG.20170707_02.nc, and the
config
file in aranda_data



Thanks,
Natalí

2018-04-13 17:39 GMT-03:00 John Halley Gotway via RT
<met_help at ucar.edu>:

> Natali,
>
> I grabbed your sample data files.  We are telling MET to interpret
these as
> CF-compliant NetCDF files.  But the timing info is not included in
the file
> in a CF-compliant way... and that's why the times are listed as 0.
>
> You can still run pcp_combine on them though.  Here's an example:
>
> /usr/local/met-7.0/bin/pcp_combine -add \
> 3B-HHR.MS.MRG.3IMERG.20170707-S003000-E005959.0030.V05B.nc
> 'name="precipitationCal"; level="(*,*)"; file_type=NETCDF_NCCF;' \
> 3B-HHR.MS.MRG.3IMERG.20170707-S010000-E012959.0060.V05B.nc
> 'name="precipitationCal"; level="(*,*)"; file_type=NETCDF_NCCF;' \
> 3B-HHR.MS.MRG.3IMERG.20170707-1hour.nc
>
> You'll see that the timestamp of the output has unixtime = 0 (i.e.
> 19700101):
>
> ncdump -h 3B-HHR.MS.MRG.3IMERG.20170707-1hour.nc | grep time
>                 precipitationCal:init_time = "19700101_000000" ;
>                 precipitationCal:init_time_ut = "0" ;
>                 precipitationCal:valid_time = "19700101_000000" ;
>                 precipitationCal:valid_time_ut = "0" ;
>
> But this NetCDF file uses MET's internal file format.  So updating
the
> timestamp is a little easier:
>
> # Use date command to convert between date string and unixtime
> setenv INIT_TIME_UT     `date -ud ''20170707' UTC '00:30:00'' +%s`
> setenv VALID_TIME_UT `date -ud ''20170707' UTC '01:30:00'' +%s`
>
> # Use ncatted to update the NetCDF timing attributes
> ncatted \
> -a init_time,precipitationCal,o,c,20170707_003000 \
> -a init_time_ut,precipitationCal,o,c,${INIT_TIME_UT} \
> -a valid_time,precipitationCal,o,c,20170707_013000 \
> -a valid_time_ut,precipitationCal,o,c,${VALID_TIME_UT} \
> 3B-HHR.MS.MRG.3IMERG.20170707-1hour.nc
>
> # Run plot_data_plane to plot the result
> /usr/local/met-7.0/bin/plot_data_plane \
> 3B-HHR.MS.MRG.3IMERG.20170707-1hour.nc \
> 3B-HHR.MS.MRG.3IMERG.20170707-1hour.ps \
> 'name="precipitationCal"; level="(*,*)";'
>
> And the resulting image is attached.
>
> BUT WAIT... THERE'S A HUGE CAVEAT HERE.
>
> Your input data is a *precipitation rate* and the units are mm/hr.
You
> really should add together two rates.  Instead, you should probably
take
> their average.  pcp_combine doesn't do that.  I adds and subtracts
but
> doesn't compute an average value.
>
> Hope this helps clarify.
>
> Thanks,
> John
>
>
>
>
>
> On Fri, Apr 13, 2018 at 1:54 PM, natali aranda via RT
<met_help at ucar.edu>
> wrote:
>
> >
> > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=84355 >
> >
> > Hi John,
> >
> > I installed METv7.0 and now I don't have problem with the WRF
Argentina,
> > the plots are ok!
> >
> > But I have a new question. Do you remember that I would like to
use as
> > observation the IMERG data ? So I converted these HDF5 files in
NETCDF
> > files. I see that MET has a problem to read de valid time in this
file
> >
> > For example when I use MODE, I have this warning:
*NcCfFile::open() ->
> > could not determine the valid time, using 0.*
> >
> > However, MODE produces outscript and in the PostScript file, the
initial
> > and valid time in the observation is wrong:
> >
> >
> >
> >
> > Also, I can't use Pcp_combine to Imerg file. It's a possible that
the
> > problem is because the data is every 30 minutes?
> > I put in aranda_data 2 files as example to this files
> >
> > Thanks,
> >
> >
> > Natalí
> >
> > 2018-04-06 12:38 GMT-03:00 John Halley Gotway via RT
<met_help at ucar.edu
> >:
> >
> > > According to our records, your request has been resolved. If you
have
> any
> > > further questions or concerns, please respond to this message.
> > >
> >
> >
>
>

------------------------------------------------
Subject: MODE: trouble reading observation file
From: John Halley Gotway
Time: Mon May 14 15:46:23 2018

Natali,

I see that you're still getting a warning message about the timing
info.
This is easy to fix.  Just remove the "file_type = NETCDF_NCCF" line
from
the MODE config file.

To demonstrate, I ran plot_data_plane with/without it:

(1) With NETCDF_NCCF produces the warning:

/usr/local/met-7.0/bin/plot_data_plane 3B-
HHR.MS.MRG.3IMERG.20170707_02.nc
3B-HHR.MS.MRG.3IMERG.20170707_02.ps 'name="precipitationCal";
level="(*,*)"; file_type=NETCDF_NCCF;'
...
WARNING: NcCfFile::open() -> could not determine the valid time, using
0.

(2) Without it, the warning disappears:

/usr/local/met-7.0/bin/plot_data_plane 3B-
HHR.MS.MRG.3IMERG.20170707_02.nc
3B-HHR.MS.MRG.3IMERG.20170707_02.ps 'name="precipitationCal";
level="(*,*)";'

We're using the internal MET NetCDF format.  Setting
file_type=NETCDF_NCCF
routes the logic through a different MET library.

Hope this helps.

Thanks,
John



On Fri, May 11, 2018 at 3:25 PM, natali aranda via RT
<met_help at ucar.edu>
wrote:

>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=84355 >
>
> John,
>
> I followed your advice. I changed de Netcdf file (Imerg file) with
ncatted,
> previously I used pcp_combine -add.
> I could see the same that you but when I run mode, I have the same
problem
> with the time:
>
> [naranda at rayo MET-7.0BF_I18]$ bin/mode pcp_combine/wrf_00_02.nc
> pcp_combine/
> 3B-HHR.MS.MRG.3IMERG.20170707_02.nc share/met/config/MODEConfig_1
-outdir
> figuras -v 2
> DEBUG 1: Default Config File:
> /share/apps/contrib/MET-
7.0BF_I18/share/met/config/MODEConfig_default
> DEBUG 1: Match Config File: share/met/config/MODEConfig_1
> DEBUG 1: Merge Config File: share/met/config/MODEConfig_1
> WARNING:
> WARNING: NcCfFile::open() -> could not determine the valid time,
using 0.
> ....
>
> I put wrf_00_02.nc, 3B-HHR.MS.MRG.3IMERG.20170707_02.nc, and the
config
> file in aranda_data
>
>
>
> Thanks,
> Natalí
>
> 2018-04-13 17:39 GMT-03:00 John Halley Gotway via RT
<met_help at ucar.edu>:
>
> > Natali,
> >
> > I grabbed your sample data files.  We are telling MET to interpret
these
> as
> > CF-compliant NetCDF files.  But the timing info is not included in
the
> file
> > in a CF-compliant way... and that's why the times are listed as 0.
> >
> > You can still run pcp_combine on them though.  Here's an example:
> >
> > /usr/local/met-7.0/bin/pcp_combine -add \
> > 3B-HHR.MS.MRG.3IMERG.20170707-S003000-E005959.0030.V05B.nc
> > 'name="precipitationCal"; level="(*,*)"; file_type=NETCDF_NCCF;' \
> > 3B-HHR.MS.MRG.3IMERG.20170707-S010000-E012959.0060.V05B.nc
> > 'name="precipitationCal"; level="(*,*)"; file_type=NETCDF_NCCF;' \
> > 3B-HHR.MS.MRG.3IMERG.20170707-1hour.nc
> >
> > You'll see that the timestamp of the output has unixtime = 0 (i.e.
> > 19700101):
> >
> > ncdump -h 3B-HHR.MS.MRG.3IMERG.20170707-1hour.nc | grep time
> >                 precipitationCal:init_time = "19700101_000000" ;
> >                 precipitationCal:init_time_ut = "0" ;
> >                 precipitationCal:valid_time = "19700101_000000" ;
> >                 precipitationCal:valid_time_ut = "0" ;
> >
> > But this NetCDF file uses MET's internal file format.  So updating
the
> > timestamp is a little easier:
> >
> > # Use date command to convert between date string and unixtime
> > setenv INIT_TIME_UT     `date -ud ''20170707' UTC '00:30:00'' +%s`
> > setenv VALID_TIME_UT `date -ud ''20170707' UTC '01:30:00'' +%s`
> >
> > # Use ncatted to update the NetCDF timing attributes
> > ncatted \
> > -a init_time,precipitationCal,o,c,20170707_003000 \
> > -a init_time_ut,precipitationCal,o,c,${INIT_TIME_UT} \
> > -a valid_time,precipitationCal,o,c,20170707_013000 \
> > -a valid_time_ut,precipitationCal,o,c,${VALID_TIME_UT} \
> > 3B-HHR.MS.MRG.3IMERG.20170707-1hour.nc
> >
> > # Run plot_data_plane to plot the result
> > /usr/local/met-7.0/bin/plot_data_plane \
> > 3B-HHR.MS.MRG.3IMERG.20170707-1hour.nc \
> > 3B-HHR.MS.MRG.3IMERG.20170707-1hour.ps \
> > 'name="precipitationCal"; level="(*,*)";'
> >
> > And the resulting image is attached.
> >
> > BUT WAIT... THERE'S A HUGE CAVEAT HERE.
> >
> > Your input data is a *precipitation rate* and the units are mm/hr.
You
> > really should add together two rates.  Instead, you should
probably take
> > their average.  pcp_combine doesn't do that.  I adds and subtracts
but
> > doesn't compute an average value.
> >
> > Hope this helps clarify.
> >
> > Thanks,
> > John
> >
> >
> >
> >
> >
> > On Fri, Apr 13, 2018 at 1:54 PM, natali aranda via RT
<met_help at ucar.edu
> >
> > wrote:
> >
> > >
> > > <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=84355 >
> > >
> > > Hi John,
> > >
> > > I installed METv7.0 and now I don't have problem with the WRF
> Argentina,
> > > the plots are ok!
> > >
> > > But I have a new question. Do you remember that I would like to
use as
> > > observation the IMERG data ? So I converted these HDF5 files in
NETCDF
> > > files. I see that MET has a problem to read de valid time in
this file
> > >
> > > For example when I use MODE, I have this warning:
*NcCfFile::open() ->
> > > could not determine the valid time, using 0.*
> > >
> > > However, MODE produces outscript and in the PostScript file, the
> initial
> > > and valid time in the observation is wrong:
> > >
> > >
> > >
> > >
> > > Also, I can't use Pcp_combine to Imerg file. It's a possible
that the
> > > problem is because the data is every 30 minutes?
> > > I put in aranda_data 2 files as example to this files
> > >
> > > Thanks,
> > >
> > >
> > > Natalí
> > >
> > > 2018-04-06 12:38 GMT-03:00 John Halley Gotway via RT <
> met_help at ucar.edu
> > >:
> > >
> > > > According to our records, your request has been resolved. If
you have
> > any
> > > > further questions or concerns, please respond to this message.
> > > >
> > >
> > >
> >
> >
>
>

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