[ncl-talk] segmentation default when reading variables

Tue Dec 12 00:19:23 MST 2017

Hi,

Ok, thanks for looking at this. I'll handle it with another version.

Cheers,

2017-12-11 17:00 GMT+01:00 Dennis Shea <shea at ucar.edu>:

> This is a netCDF-4 file:
>
> %>  *ncdump -k* EDIII_BIC_1990.nc
>
>
> *netCDF-4*
> NCL's netCDF-4 capabilities have evolved  substantially over last few
> years.
>
> NCL 6.3.0 was released in March 2015 (2.5+ years ago). It seg faults ...
> on my box also.
>
> The following NCL versions handle the "w" mode correctly:
>
> NCL 6.4.0 released  February 28, 2017
>
> NCL 6.5.0*-beta* not yet released
>
> *Solution:* Download the current release 6.4.0 or, perhaps, the 6.5.0
> beta realse
>
>
> =====================
> My 6.3.0 version of NCL handles this correctly when using  "r"
>
> %>  ncl
>  Copyright (C) 1995-2015 - All Rights Reserved
>  University Corporation for Atmospheric Research
>  NCAR Command Language Version *6.3.0*
>  The use of this software is governed by a License Agreement.
>  See http://www.ncl.ucar.edu/ for more details.
>
> ncl 0> wrfout = addfile("EDIII_BIC_1990.nc",*"**r"*)
> ncl 1> lat2d = (/wrfout->lat/)
> ncl 2> print(lat2d)
>
> Variable: lat2d
> Type: float
> Total Size: 55216 bytes
>             13804 values
> Number of Dimensions: 2
> Dimensions and sizes:   [116] x [119]
> Coordinates:
> (0,0)   18.24825
> (0,1)   18.41432
> (0,2)   18.57843
> [SNIP]
>
> ==================
> When using the *"w"* mode 6.3.0 seg faults::
>
> ncl 1> wrfout = addfile("EDIII_BIC_1990.nc",*"**w"*)
> ncl 2> lat2d = (/wrfout->lat/)
> Segmentation fault
>
> ====================
> %> ncl
>
>  Copyright (C) 1995-2017 - All Rights Reserved
>  University Corporation for Atmospheric Research
>  NCAR Command Language Version *6.4.0*
>  The use of this software is governed by a License Agreement.
>  See http://www.ncl.ucar.edu/ for more details.
>
> ncl 0> wrfout = addfile("EDIII_BIC_1990.nc","w")
> ncl 1> lat2d = (/wrfout->lat/)
> ncl 2> print(lat2d)
> [SNIP]
>
> =========
> %> ncl
>  Copyright (C) 1995-2017 - All Rights Reserved
>  University Corporation for Atmospheric Research
>  NCAR Command Language Version *6.5.0 -11Dec2017_0148*
>  The use of this software is governed by a License Agreement.
>  See http://www.ncl.ucar.edu/ for more details.
>
> ncl 0>  wrfout = addfile("EDIII_BIC_1990.nc","w")
> ncl 1> lat2d = (/wrfout->lat/)
> ncl 2> print(lat2d)
> [SNIP]
>
>
>
>
>
>
>
>
> On Mon, Dec 11, 2017 at 12:49 AM, Noelia otero <noeli1680 at gmail.com>
> wrote:
>
>> Hi Dennis,
>>
>> I just uploaded the file:
>> name: EDIII_BIC_1990.nc
>>
>> uname -a:
>> Darwin Noelias-MBP.fritz.box 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr
>> 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
>>
>> gcc --version
>> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
>> --with-gxx-include-dir=/usr/include/c++/4.2.1
>> Apple LLVM version 7.3.0 (clang-703.0.31)
>> Target: x86_64-apple-darwin15.5.0
>> Thread model: posix
>> InstalledDir: /Applications/Xcode.app/Conten
>> ts/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>>
>> Please let me know if the file was totally uploaded (I think it was 100%
>> uploaded before the connection was closed).
>>
>> Thanks again,
>>
>> Noelia
>>
>> 2017-12-10 16:48 GMT+01:00 Dennis Shea <shea at ucar.edu>:
>>
>>> I just tried ... there is a problem with the ftp area. Systems will have
>>> to address that issue. Likely ... tomorrow.
>>>
>>> On Sun, Dec 10, 2017 at 8:41 AM, Noelia otero <noeli1680 at gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>> I can't login actually..it seems that it's down ? (at least I can't
>>>> now, sorry)
>>>>
>>>> Thanks!
>>>>
>>>> 2017-12-10 16:39 GMT+01:00 Dennis Shea <shea at ucar.edu>:
>>>>
>>>>> The ftp site does not care if a file is gzipped or not.
>>>>>
>>>>> Did you
>>>>>
>>>>> cd incoming
>>>>>
>>>>> before attempting to upload the file?
>>>>>
>>>>> On Sun, Dec 10, 2017 at 8:20 AM, Barry Lynn <barry.h.lynn at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi Noelia:
>>>>>>
>>>>>> I noticed that the ftp system prefers the files gzipped.  If you are
>>>>>> able to log on, but not upload, it maybe because the file is too large.
>>>>>>
>>>>>> Barry
>>>>>>
>>>>>> On Sun, Dec 10, 2017 at 4:15 PM, Noelia otero <noeli1680 at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi again,
>>>>>>>
>>>>>>> I am trying to upload the file but the ftp is not working now (maybe
>>>>>>> is temporary) .
>>>>>>> In any case, I also wanted that I tried again with an older version
>>>>>>> of NCL (6.2.1) and it works..yesterday I was using 6.3.0 and I got the
>>>>>>> segmentation default. Then, it seems that it could be related to version of
>>>>>>> ncl?
>>>>>>>
>>>>>>> I'll try to upload the file later, if you still suggest me to do it.
>>>>>>>
>>>>>>> Thanks a lot,
>>>>>>>
>>>>>>> Best
>>>>>>>
>>>>>>> Noelia
>>>>>>>
>>>>>>>
>>>>>>> 2017-12-10 6:36 GMT+01:00 Rick Brownrigg <brownrig at ucar.edu>:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> Are you able you able to ftp the file in question to us?  Using
>>>>>>>> "addfile()" with "w" to both read and write should work, and in any case,
>>>>>>>> it should not segv!
>>>>>>>>
>>>>>>>> ftp ftp.cgd.ucar.edu
>>>>>>>> anonymous*<enter your email address for the password>*
>>>>>>>> cd incoming
>>>>>>>> put *file1*
>>>>>>>> put *file2*
>>>>>>>> . . .*continue with 'put' commands until all desired files are uploaded*. . .
>>>>>>>> quit
>>>>>>>>
>>>>>>>> When the upload is complete, send email to ncl-talk
>>>>>>>> <ncl-talk at ucar.edu> or the NCL team member that you've already
>>>>>>>> been working with and include the exact names of the files, and the
>>>>>>>> approximate size of each file.
>>>>>>>>
>>>>>>>> For security reasons, you cannot list the contents of the
>>>>>>>> 'incoming' directory. This is why we need to know the exact names of the
>>>>>>>> files.
>>>>>>>>
>>>>>>>> On Sat, Dec 9, 2017 at 3:18 PM, Noelia otero <noeli1680 at gmail.com>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Hi Dennis,
>>>>>>>>>
>>>>>>>>> This is not a wrfout_nc file, sorry, it was just the name used in
>>>>>>>>> the script to call "file_in". What confuses me it's that when I open the
>>>>>>>>> file with addfile with the option "r" I can get the variables (lat, lon or
>>>>>>>>> whatever). The problem is when I want to overwrite some the values in
>>>>>>>>> there, because I open it as addfile with the option "w". Then when I try to
>>>>>>>>> read any variable the segmentation defaul happens. Any idea ?
>>>>>>>>>
>>>>>>>>> Many thanks again,
>>>>>>>>> Noelia
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 2017-12-09 22:42 GMT+01:00 Dennis Shea <shea at ucar.edu>:
>>>>>>>>>
>>>>>>>>>> Typically, wrfout_nc files do not have variable named 'lat'
>>>>>>>>>>
>>>>>>>>>> XLAT(Time, south_north, west_east)
>>>>>>>>>> also
>>>>>>>>>> XLONG(Time, south_north, west_east)
>>>>>>>>>>
>>>>>>>>>> So, maybe it should be
>>>>>>>>>>
>>>>>>>>>> lat2d = (/wrfout->XLAT(0,:,:)/)     ; 0 refers to the 1st time
>>>>>>>>>> step
>>>>>>>>>> printVarSummary(lat2d)
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Sat, Dec 9, 2017 at 12:56 PM, Noelia otero <
>>>>>>>>>> noeli1680 at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi
>>>>>>>>>>>
>>>>>>>>>>> I am getting a Segmentation fault (core dumped) when trying to
>>>>>>>>>>> read a variable from one file opened as:
>>>>>>>>>>>
>>>>>>>>>>> wrfout = addfile(file_in,"w")
>>>>>>>>>>> lat2d = (/wrfout->lat/)
>>>>>>>>>>> Segmentation fault (core dumped)
>>>>>>>>>>>
>>>>>>>>>>> I thought that it could due to a problem in the file, but I
>>>>>>>>>>> looked at the file and it seems fine. If I use:
>>>>>>>>>>> wrfout = addfile(file_in,"r")
>>>>>>>>>>> lat2d = (/wrfout->lat/)
>>>>>>>>>>> it works.
>>>>>>>>>>> The file I'm using is 52M..no too large...so I'm quite lost
>>>>>>>>>>> about what the problem can be... and the version of ncl Version 6.3.0.
>>>>>>>>>>>
>>>>>>>>>>> Any idea?
>>>>>>>>>>>
>>>>>>>>>>> Thanks!
>>>>>>>>>>>
>>>>>>>>>>> Best
>>>>>>>>>>> Noelia
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> ncl-talk mailing list
>>>>>>>>>>> ncl-talk at ucar.edu
>>>>>>>>>>> List instructions, subscriber options, unsubscribe:
>>>>>>>>>>> http://mailman.ucar.edu/mailman/listinfo/ncl-talk
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> ncl-talk mailing list
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>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Barry H. Lynn, Ph.D
>>>>>> Senior Lecturer,
>>>>>> The Institute of the Earth Science,
>>>>>> The Hebrew University of Jerusalem,
>>>>>> Givat Ram, Jerusalem 91904, Israel
>>>>>> Tel: 972 547 231 170
>>>>>> Fax: (972)-25662581
>>>>>>
>>>>>> C.E.O, Weather It Is, LTD
>>>>>> Weather and Climate Focus
>>>>>> http://weather-it-is.com
>>>>>> Jerusalem, Israel
>>>>>> Local: 02 930 9525
>>>>>> Cell: 054 7 231 170
>>>>>> Int-IS: x972 2 930 9525
>>>>>> US 914 432 3108 <(914)%20432-3108>
>>>>>>
>>>>>> _______________________________________________
>>>>>> ncl-talk mailing list
>>>>>> ncl-talk at ucar.edu
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>>>>>> http://mailman.ucar.edu/mailman/listinfo/ncl-talk
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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