[ncl-talk] Segmentation fault when reading variables from NC

[Dennis Shea]

Sorry ... I meant 6.1.2 had issues not 6.2.1

Please upgrade.

THX

On Tue, Mar 24, 2015 at 1:17 PM, Dennis Shea <shea at ucar.edu> wrote:

> Forgot to mention:
>
> NCL 6.2.1 did have some netCDF4 issues.
>
> Please download the 6.3.0 version of NCL
>
> On Tue, Mar 24, 2015 at 1:06 PM, Dennis Shea <shea at ucar.edu> wrote:
>
>>
>> I 'found' 6.2.0 and 6.2.1. I have run the attached test script with:
>> 6.2.0, 6.2.1, 6.3.0
>>
>> It runs correctly under all versions. The file is netCDF4 which,
>> 'under-the-hood', is HDF5.
>>
>> %> ncdump -k geo_em.d01.nc
>> netCDF-4
>>
>> %> ncl_filedump geo_em.d01.nc >&! dump.geo_em
>>
>> %> ncl tst_geo.ncl
>>
>> ===
>> Summary: I do not know what is wrong. I can not replicate the problem.
>>
>> D
>>
>> On Tue, Mar 24, 2015 at 12:13 AM, ChenFeng <fengfengabc003 at 163.com>
>> wrote:
>>
>>>
>>> What I do not understand is the file is generated from the standard WRF-WPS program, which I used several times with no problem.
>>>
>>> I can read the variable without the dimention name, and then reorder or subcite the data. This approach can solve the problem temporarily.
>>> Thanks for your help.
>>>
>>> Feng
>>>
>>>  *From:* Alex Schaefer <alexander.schaefer at mines.sdsmt.edu>
>>> *Date:* 2015-03-24 13:25
>>> *To:* ChenFeng <fengfengabc003 at 163.com>
>>> *CC:* Dennis Shea <shea at ucar.edu>; ncl-talk <ncl-talk at ucar.edu>
>>> *Subject:* Re: [ncl-talk] Segmentation fault when reading variables
>>> from NC
>>>  Feng,
>>>
>>> I got the same seg fault that you got with your file.  My guess is
>>> something is just not quite right with that file.  The size of that  domain
>>> should not be an issue.  My ncl 6.1.2 is compiled from source so the
>>> precompiled binary theory affecting it is not the case.  I am not sure what
>>> other things will spit out seg faults so Dennis will have to take lead.
>>>
>>> Sorry I couldn’t be of more help,
>>> -Alex
>>>
>>>
>>>  On Mar 23, 2015, at 9:51 PM, ChenFeng <fengfengabc003 at 163.com> wrote:
>>>
>>>  And I use the  pre-compiled binary version which is downloaded from
>>> the NCAR website.
>>>
>>>  *From:* ChenFeng <fengfengabc003 at 163.com>
>>> *Date:* 2015-03-24 11:47
>>> *To:* Dennis Shea <shea at ucar.edu>; alexander.schaefer
>>> <alexander.schaefer at mines.sdsmt.edu>
>>> *CC:* ncl-talk <ncl-talk at ucar.edu>
>>> *Subject:* Re: Re: [ncl-talk] Segmentation fault when reading variables
>>> from NC
>>>   Thanks Dennis and Alexander
>>>
>>> The reason I use the printVarSummary(lon2d) is only want to make sure whether the code above this line is correct.
>>> There is no problem when I use this code to read another geo_em.d01.nc
>>>  file. So I think there is something wrong with the NC file. But I can use ncdump to see the structure and find nothing special.
>>>
>>> Is the variable dimention too large (474*524)?  But I have also use this ncl version to read variables more large than this.
>>>
>>> I attached the file. Could you please help me check it with another ncl version and platform.
>>> Thanks.
>>>
>>> Feng
>>>
>>>  *From:* Dennis Shea <shea at ucar.edu>
>>> *Date:* 2015-03-23 22:40
>>> *To:* ChenFeng <fengfengabc003 at 163.com>
>>> *CC:* ncl-talk <ncl-talk at ucar.edu>
>>> *Subject:* Re: [ncl-talk] Segmentation fault when reading variables
>>> from NC
>>>  Also, forgot to mention ...
>>>
>>> Using named dimensions should only be done when reordering an array.
>>> Nothing wrong with doing so but is is  less efficient than ..
>>>
>>> lon2d = inp0->XLONG_M (0, :, :)
>>>
>>> On Mon, Mar 23, 2015 at 8:11 AM, Dennis Shea <shea at ucar.edu> wrote:
>>>
>>>>  I don't understand why either.  6.1.2 is no longer available here so
>>>> I can not test with 6.1.2
>>>>
>>>> When it does work ... what does printVarSummary(lon2d) indicate?
>>>>
>>>>  On Mon, Mar 23, 2015 at 2:47 AM, ChenFeng <fengfengabc003 at 163.com>
>>>> wrote:
>>>>
>>>>>   Hi ncl-users,
>>>>>
>>>>> I have encounted an error when reading a variable from an NC file.
>>>>> the code is listed below:
>>>>> ;************************************************
>>>>> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl"
>>>>> ;************************************************
>>>>> begin
>>>>>   inp0 = addfile("/public/home/chenf/AHWRF/TEST/WPSwks.T02/
>>>>> geo_em.d01.nc","r")
>>>>>   lon2d = inp0->XLONG_M (Time|0, south_north|:, west_east|:)
>>>>>   printVarSummary(lon2d)
>>>>> ;************************************************
>>>>> end
>>>>>
>>>>> the error message is:
>>>>>  Copyright (C) 1995-2013 - All Rights Reserved
>>>>>  University Corporation for Atmospheric Research
>>>>>  NCAR Command Language Version 6.1.2
>>>>>  The use of this software is governed by a License Agreement.
>>>>>  See http://www.ncl.ucar.edu/ for more details.
>>>>> Segmentation fault (core dumped)
>>>>>
>>>>>
>>>>> The strange thing is when i'm reading the variable without any dimention name cited, the error disappeared.
>>>>> The code changes into :
>>>>> ;************************************************
>>>>> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl"
>>>>> ;************************************************
>>>>> begin
>>>>>   inp0 = addfile("/public/home/chenf/AHWRF/TEST/WPSwks.T02/
>>>>> geo_em.d01.nc","r")
>>>>>   lon2d = inp0->XLONG_M
>>>>>   printVarSummary(lon2d)
>>>>> ;************************************************
>>>>> end
>>>>>
>>>>> I don't understand why. It is very appreciate if anybody can tell me
>>>>> the reason.
>>>>> Thanks.
>>>>>
>>>>> Feng
>>>>>
>>>>> _______________________________________________
>>>>> ncl-talk mailing list
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>>>>
>>>>
>>>
>>
>
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