[ncl-talk] Unable to read files with addfiles
Dennis Shea
shea at ucar.edu
Wed Jun 21 20:12:49 MDT 2023
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
>>
>> _______________________________________________
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>>
>>
>
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