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

[ChenFeng]

The problem disappeared when I use NCL version 6.3.0.
As you said maybe NCL v6.1.2 has some NetCDF issue.
Thanks for all of your help.
Feng

From: Dennis Shea
Date: 2015-03-25 03:06
To: ChenFeng
CC: alexander.schaefer; ncl-talk
Subject: Re: Re: [ncl-talk] Segmentation fault when reading variables from NC


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
Date: 2015-03-24 13:25
To: ChenFeng
CC: Dennis Shea; ncl-talk
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
Date: 2015-03-24 11:47
To: Dennis Shea; alexander.schaefer
CC: ncl-talk
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
Date: 2015-03-23 22:40
To: ChenFeng
CC: ncl-talk
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
List instructions, subscriber options, unsubscribe:
http://mailman.ucar.edu/mailman/listinfo/ncl-talk
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.ucar.edu/pipermail/ncl-talk/attachments/20150325/741299c8/attachment.html