[ncl-talk] Unable to read files with addfiles
Dennis Shea
shea at ucar.edu
Thu Jun 22 10:19:19 MDT 2023
Glad you found the issue.
Buona Fortuna
On Thu, Jun 22, 2023 at 4:10 AM Giorgio Graffino <g.graffino at tim.it> wrote:
> Sorry Dennis,
>
>
>
> I forgot your golden rule: always look at your data! I was trying to open
> a 156 annual-mean time steps file believing it was a 1752 monthly-mean time
> steps file. That's why the subscript was out of range. The command slp =
> SLP(:,:,{-10:10},{135:270}) works perfectly.
>
>
>
> Thanks for your help,
>
> Giorgio
>
>
>
> ------ Messaggio Originale ------
> Da: shea at ucar.edu
> A: g.graffino at tim.it Cc: ncl-talk at ucar.edu
> Inviato: giovedì 22 giugno 2023 03:12
> Oggetto: Re: [ncl-talk] Unable to read files with addfiles
>
>
> mslp = mslp_file[:]->slp(:,20*12:155*12+12-1,{-10:10},{135:270})
>
>
> fatal:["NclFile.c":2100]:Subscript out of range, error in subscript #0
> fatal:Memory allocation failure:[errno=12]
> fatal:["Execute.c":8635]:Execute: Error occurred at or near line 36
>
> ------------------------------
>
> Ummmm .... subscript #0 is the leftmost subscript
>
> The ":" means all of the leftmost indices. It should not be "out of range"
>
> Sorry but more information is needed.
>
> SLP = mslp_file[:]->slp
>
> printVarSummary(SLP) ; I assume 4 subscripts; SLP(ncl_join , time,
> lat , lon )
>
> slp = SLP(:,:,{-10:10},{135:270})
>
> printVarSummary(slp)
>
>
> ====
>
>
>
>
>
>
>
> MSLP= mslp_file[:]->slp(:, :,{-10:10},{135:270})
>
>
>
>
> mslp = mslp_file[:]->slp(:,20*12:155*12+12-1,{-10:10},{135:270})
>
>
>
>
>
>
>
>
>
> On Wed, Jun 21, 2023 at 11:42 AM Giorgio Graffino <g.graffino at tim.it>
> wrote:
>
>
>> Hi Dennis,
>>
>>
>>
>> Thanks for your reply. I just realized that I skipped one line in the
>> list of commands, which is the one actually triggering the error. Please
>> see the list of commands below, plus the one you asked me to run.
>>
>>
>>
>> dir = "/home/users/ggraffin/CMIP5/"
>>
>>
>> mslp_list = systemfunc("ls
>> "+dir+"historical/MPI-ESM1.1/MPI-ESM1.1_historical_lkm011*
>> mslp_commongrid.nc")
>>
>>
>> print(mslp_list)
>>
>>
>>
>> Variable: mslp_list
>> Type: string
>> Total Size: 80 bytes
>> 10 values
>> Number of Dimensions: 1
>> Dimensions and sizes: [10]
>> Coordinates:
>> (0) /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>> MPI-ESM1.1_historical_lkm0110_mslp_commongrid.nc
>> (1) /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>> MPI-ESM1.1_historical_lkm0111_mslp_commongrid.nc
>> (2) /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>> MPI-ESM1.1_historical_lkm0112_mslp_commongrid.nc
>> (3) /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>> MPI-ESM1.1_historical_lkm0113_mslp_commongrid.nc
>> (4) /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>> MPI-ESM1.1_historical_lkm0114_mslp_commongrid.nc
>> (5) /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>> MPI-ESM1.1_historical_lkm0115_mslp_commongrid.nc
>> (6) /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>> MPI-ESM1.1_historical_lkm0116_mslp_commongrid.nc
>> (7) /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>> MPI-ESM1.1_historical_lkm0117_mslp_commongrid.nc
>> (8) /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>> MPI-ESM1.1_historical_lkm0118_mslp_commongrid.nc
>> (9) /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>> MPI-ESM1.1_historical_lkm0119_mslp_commongrid.nc
>>
>>
>> mslp_file = addfiles(mslp_list,"r")
>>
>>
>> print(mslp_file)
>>
>>
>>
>> Variable: mslp_file
>> Type: list
>> Total Size: 4 bytes
>> 1 values
>> Number of Dimensions: 1
>> Dimensions and sizes: [1]
>> Coordinates:
>> Type: list <concat | fifo>
>> Total items: 10
>>
>> List Item 0: NclFileVarClass
>> Variable: unnamed
>> Type: file
>> File path: /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>> MPI-ESM1.1_historical_lkm0110_mslp_commongrid.nc
>> Number of global attributes: 7
>> Number of dimensions: 4
>> Number of variables: 5
>>
>> List Item 1: NclFileVarClass
>> Variable: unnamed
>> Type: file
>> File path: /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>> MPI-ESM1.1_historical_lkm0111_mslp_commongrid.nc
>> Number of global attributes: 7
>> Number of dimensions: 4
>> Number of variables: 5
>>
>> List Item 2: NclFileVarClass
>> Variable: unnamed
>> Type: file
>> File path: /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>> MPI-ESM1.1_historical_lkm0112_mslp_commongrid.nc
>> Number of global attributes: 7
>> Number of dimensions: 4
>> Number of variables: 5
>>
>> List Item 3: NclFileVarClass
>> Variable: unnamed
>> Type: file
>> File path: /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>> MPI-ESM1.1_historical_lkm0113_mslp_commongrid.nc
>> Number of global attributes: 7
>> Number of dimensions: 4
>> Number of variables: 5
>>
>> List Item 4: NclFileVarClass
>> Variable: unnamed
>> Type: file
>> File path: /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>> MPI-ESM1.1_historical_lkm0114_mslp_commongrid.nc
>> Number of global attributes: 7
>> Number of dimensions: 4
>> Number of variables: 5
>>
>> List Item 5: NclFileVarClass
>> Variable: unnamed
>> Type: file
>> File path: /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>> MPI-ESM1.1_historical_lkm0115_mslp_commongrid.nc
>> Number of global attributes: 7
>> Number of dimensions: 4
>> Number of variables: 5
>>
>> List Item 6: NclFileVarClass
>> Variable: unnamed
>> Type: file
>> File path: /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>> MPI-ESM1.1_historical_lkm0116_mslp_commongrid.nc
>> Number of global attributes: 7
>> Number of dimensions: 4
>> Number of variables: 5
>>
>> List Item 7: NclFileVarClass
>> Variable: unnamed
>> Type: file
>> File path: /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>> MPI-ESM1.1_historical_lkm0117_mslp_commongrid.nc
>> Number of global attributes: 7
>> Number of dimensions: 4
>> Number of variables: 5
>>
>> List Item 8: NclFileVarClass
>> Variable: unnamed
>> Type: file
>> File path: /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>> MPI-ESM1.1_historical_lkm0118_mslp_commongrid.nc
>> Number of global attributes: 7
>> Number of dimensions: 4
>> Number of variables: 5
>>
>> List Item 9: NclFileVarClass
>> Variable: unnamed
>> Type: file
>> File path: /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>> MPI-ESM1.1_historical_lkm0119_mslp_commongrid.nc
>> Number of global attributes: 7
>> Number of dimensions: 4
>> Number of variables: 5
>>
>>
>> ListSetType(mslp_file,"join")
>>
>>
>> mslp = mslp_file[:]->slp(:,20*12:155*12+12-1,{-10:10},{135:270})
>>
>>
>> fatal:["NclFile.c":2100]:Subscript out of range, error in subscript #0
>> fatal:Memory allocation failure:[errno=12]
>> fatal:["Execute.c":8635]:Execute: Error occurred at or near line 36
>>
>>
>>
>> Cheers,
>>
>> Giorgio
>>
>>
>> ------ Messaggio Originale ------
>> Da: shea at ucar.edu
>> A: g.graffino at tim.it Cc: ncl-talk at ucar.edu
>> Inviato: martedì 20 giugno 2023 19:40
>> Oggetto: Re: [ncl-talk] Unable to read files with addfiles
>>
>> I can not see an obvious issue.
>>
>> Given and the "join" option
>>
>>
>> time = 156 // unlimited
>> bnds = 2
>> lon = 180
>> lat = 120
>>
>>
>> and, say, 10 ensembles, the slp variable should be
>>
>>
>> slp(ncl_join , time, lat , lon ) => slp(10,156,120,180)
>>
>> ================================================
>>
>> What do the following 'print' statements show?
>>
>>
>> mslp_list = systemfunc("ls
>> /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/MPI-ESM1.1_historical_lkm011*
>> mslp_commongrid.nc")
>>
>> print(mslp_list) ; <========
>>
>>
>> mslp_file = addfiles(mslp_list,"r")
>>
>> print(mslp_file) ; <========
>>
>> ListSetType(mslp_file,"join")
>>
>>
>>
>>
>> On Tue, Jun 20, 2023 at 11:37 AM Giorgio Graffino via ncl-talk <
>> ncl-talk at mailman.ucar.edu> wrote:
>>
>>
>>> Hello NCL people,
>>>
>>>
>>>
>>> I'm trying to read files from the MPI-ESM1.1 large ensemble with
>>> addfiles. I'm always getting the same error, regardless of the sample size,
>>> so it shouldn't be an actual memory issue.
>>>
>>>
>>>
>>> mslp_list = systemfunc("ls
>>> /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/MPI-ESM1.1_historical_lkm011*
>>> mslp_commongrid.nc")
>>>
>>> mslp_file = addfiles(mslp_list,"r")
>>>
>>> ListSetType(mslp_file,"join")
>>>
>>> fatal:["NclFile.c":2100]:Subscript out of range, error in subscript #0
>>> fatal:Memory allocation failure:[errno=12]
>>>
>>>
>>>
>>> I can't even use functions like getfiledimsizes or getfileatts, because
>>> I get the following error.
>>>
>>> dsizes = getfileatts(mslp_file(0))
>>> fatal:Argument type mismatch on argument (0) of (getfileatts) can not
>>> coerce
>>>
>>>
>>>
>>> Both mslp_file and mslp_list have 10 elements as they should.
>>>
>>>
>>>
>>> printVarSummary(mslp_file)
>>>
>>> Variable: mslp_file
>>> Type: list <join | fifo>
>>> Total items: 10
>>>
>>> printVarSummary(mslp_list)
>>>
>>> Variable: mslp_list
>>> Type: string
>>> Total Size: 80 bytes
>>> 10 values
>>> Number of Dimensions: 1
>>> Dimensions and sizes: [10]
>>> Coordinates:
>>>
>>>
>>> I'm sure it's a file-dependent issue, because addfiles works fine on
>>> subset of files from other sources. I'm asking for suggestions about things
>>> I can try so I can understand what's going on. Here is the file dump of one
>>> of the files.
>>>
>>>
>>>
>>> Copyright (C) 1995-2019 - All Rights Reserved
>>> University Corporation for Atmospheric Research
>>> NCAR Command Language Version 6.6.2
>>> The use of this software is governed by a License Agreement.
>>> See http://www.ncl.ucar.edu/ for more details.
>>>
>>> Variable: f
>>> Type: file
>>> filename: MPI-ESM1.1_historical_lkm0110_mslp_commongrid
>>> path: /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>>> MPI-ESM1.1_historical_lkm0110_mslp_commongrid.nc
>>> file global attributes:
>>> CDI : Climate Data Interface version 1.9.5 (
>>> http://mpimet.mpg.de/cdi)
>>> Conventions : CF-1.4
>>> history : Tue Jun 20 17:34:23 2023: ncap2 -O -s time=float(time)
>>> /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>>> MPI-ESM1.1_historical_lkm0110_mslp_commongrid.nc
>>> /home/users/ggraffin/CMIP5/historical/MPI-ESM1.1/
>>> MPI-ESM1.1_historical_lkm0110_mslp_commongrid.nc
>>> Tue Apr 18 17:40:36 2023: cdo remapbil,CMIP5/CMIP5_grid.txt
>>> /home/users/qx920595/baobab/CMIP5/historical/MPI-ESM1.1/
>>> MPI-ESM1.1_historical_lkm0110_mslp_year.nc
>>> /home/users/qx920595/baobab/CMIP5/historical/MPI-ESM1.1/
>>> MPI-ESM1.1_historical_lkm0110_mslp_commongrid.nc
>>> Tue Apr 18 17:40:30 2023: ncks -v slp
>>> /storage/basic/baobab/jonathan/thorsten/
>>> MPI-ESM1.1_historical_lkm0110_yearmean.nc
>>> /home/users/qx920595/baobab/CMIP5/historical/MPI-ESM1.1/
>>> MPI-ESM1.1_historical_lkm0110_mslp_year.nc
>>> Sat Sep 24 17:07:31 2016: cdo -f nc -t echam6 yearmean
>>> /scratch/m/m300057/historical_ensemble/lkm0110_BOT
>>> /scratch/m/m300057/historical_ensemble/
>>> MPI-ESM1.1_historical_lkm0110_yearmean.nc
>>> source : ECHAM6
>>> institution : Max-Planck-Institute for Meteorology
>>> NCO : netCDF Operators version 5.0.7 (Homepage = http://nco.sf.net,
>>> Code = http://github.com/nco/nco)
>>> CDO : Climate Data Operators version 1.9.5 (
>>> http://mpimet.mpg.de/cdo)
>>> dimensions:
>>> time = 156 // unlimited
>>> bnds = 2
>>> lon = 180
>>> lat = 120
>>> variables:
>>> float time ( time )
>>> axis : T
>>> bounds : time_bnds
>>> calendar : proleptic_gregorian
>>> standard_name : time
>>> units : day as %Y%m%d.%f
>>>
>>> double time_bnds ( time, bnds )
>>>
>>> double lon ( lon )
>>> standard_name : longitude
>>> long_name : longitude
>>> units : degrees_east
>>> axis : X
>>>
>>> double lat ( lat )
>>> standard_name : latitude
>>> long_name : latitude
>>> units : degrees_north
>>> axis : Y
>>>
>>> float slp ( time, lat, lon )
>>> long_name : mean sea level pressure
>>> units : Pa
>>> code : 151
>>> table : 128
>>>
>>>
>>>
>>> Thanks a lot.
>>>
>>>
>>>
>>> Giorgio
>>>
>>> _______________________________________________
>>> ncl-talk mailing list
>>> ncl-talk at mailman.ucar.edu
>>> List instructions, subscriber options, unsubscribe:
>>> https://mailman.ucar.edu/mailman/listinfo/ncl-talk
>>>
>>>
>>
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