[ncl-talk] issue when writing netCDF4

[Laura Fowler]

Hi Mary:

Thanks for replying to this e-mail. The arrays are actually filled
with _FillValues when I try to read the individual arrays. An ncdump
would show "_/". I think that it is because the netcdf array I am not
properly closing the netcdf array before the do loop goes to the next
array, and so on. Of course, this does not happen all the time either.

Over the week-end, it looks like adding the line "delete(ncdf)" at the
bottom of the loop works. I am not sure if it is the actual proper way
to close the file though as Rick Browing suggested to use filesystem?

As for the getenv, you can use the following:

setenv dir "./../"
setenv diri "./../run.20151129_to_20151205/"

setenv diro "./run.20151129_to_20151205/20151129/"
setenv file_i  centeredPacific.history_3d.r4.2015-11-29_00.00.00.nc
unbuffer ncl test.ncl >& logfile.20151129.out

from the directory
/glade2/scratch2/laura/MPAS.PacificOcean/run.centeredPacificOceanMesh.15-3km.20151129-20151231/3Dfields

I also use "unbuffer" which was the best way Davide (at cisl) found to
force cheyenne to dump the logfile as test.ncl runs? Is this right?


Many thanks for your help,
Laura




On Sat, Oct 28, 2017 at 9:49 AM, Mary Haley <haley at ucar.edu> wrote:
> Hi Laura,
>
> By "empty" do you mean that the NetCDF file itself doesn't have much written
> to it, or that it does have values written to it, but the values are equal
> to _FillValue?
>
> And when you say it sometimes happens and sometimes it doesn't, is this from
> running the exact same script without any changes?
>
> In order to run this script, it looks like I need to know the values of some
> environment variables:
>
> dir = getenv("dir")
> diri = getenv("diri")
> diro = getenv("diro")
> file_i = getenv("file_i")
>
> Thanks,
>
> --Mary
>
>
> On Fri, Oct 27, 2017 at 2:02 PM, Laura Fowler <laura at ucar.edu> wrote:
>>
>> Hello:
>>
>> I am not understanding why the content of a netCDF4 file remains
>> empty, but one in a while. I wrote an ncl script that reads an array
>> from a history file  (in a cdf5 format), interpolates the data on
>> fixed pressure levels, and writes the interpolated data to a separate
>> netCDF4 file. It happens that my output netCDF4 file is empty (the
>> output data is all missing), but not all the times. I do print the max
>> value of the interpolated data before writing the data to the output
>> file, so that I know that the output data is not garbage. I am really
>> puzzled because sometimes it works and sometimes it does. It does not
>> matter if I run the script in a batch job or interactively.
>>
>> The only error I got once is:
>>
>> (0) itime = 22 max diag = 1 max diag_pFixed = 1
>> (0) itime = 23 max diag = 1 max diag_pFixed = 1
>> (0) max diag_pFixed = 1
>> (0) fname = qc_cu
>>
>>
>> fatal:NclMalloc Failed:[errno=12]
>> ncl: putget.c:6833: getNCvx_float_float: Assertion `value != ((void*)0)'
>> failed.
>>
>>
>> Has anybody got this error message before? If interested, my script is in
>>
>> /glade2/scratch2/laura/MPAS.PacificOcean/run.centeredPacificOceanMesh.15-3km.20151129-20151231/3Dfields/test/ncl
>>
>>
>> Thanks,
>> Laura
>>
>>
>>
>>
>> --
>>
>> !-------------------------------------------------------------------------------------------------------------
>> Laura D. Fowler
>> Mesoscale and Microscale Meteorology Division (MMM)
>> National Center for Atmospheric Research
>> P.O. Box 3000, Boulder CO 80307-3000
>>
>> e-mail: laura at ucar.edu
>> phone: 303-497-1628
>>
>>
>> !-------------------------------------------------------------------------------------------------------------
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>
>



-- 
!-------------------------------------------------------------------------------------------------------------
Laura D. Fowler
Mesoscale and Microscale Meteorology Division (MMM)
National Center for Atmospheric Research
P.O. Box 3000, Boulder CO 80307-3000

e-mail: laura at ucar.edu
phone: 303-497-1628

!-------------------------------------------------------------------------------------------------------------