[ncl-talk] Segmentation fault

Mary Haley haley at ucar.edu
Tue May 26 09:53:02 MDT 2015


This is an FYI that we have an FAQ that includes various NCL error messages
and how to fix them.  You can go to:

http://www.ncl.ucar.edu/FAQ/

and search for the word "spline" and you will see this question and
response that might apply here:

http://www.ncl.ucar.edu/FAQ/#err_msgs_028

You need to look at the values being used for the X axis. If they are "too
irregularly-spaced", then that can cause a spline warning.

--Mary

On Mon, May 25, 2015 at 2:22 PM, Amadou Coulibaly <mpapin24 at gmail.com>
wrote:

> Hi Alexander,
>
> Thank you, this has worked. The problem was like you said the prefix of
> "cool". When I removed that. It has worked. Just some warring messages such
> as:
>
> warning:_NhlCreateSplineCoordApprox: Attempt to create spline
> approximation for X axis failed: consider adjusting trXTensionF value
> warning:IrTransInitialize: error creating spline approximation for
> trXCoordPoints; defaulting to linear
> warning:_NhlCreateSplineCoordApprox: Attempt to create spline
> approximation for X axis failed: consider adjusting trXTensionF value
> warning:IrTransInitialize: error creating spline approximation for
> trXCoordPoints; defaulting to linear
> warning:XyPlotSetValues:xyYStyle is NhlLOG:trYMinF can't be <= 0.0:Setting
> xyComputeYMin to True
>
> Best
>
>
>
> On 25 May 2015 at 19:37, Alexander Schaefer <
> alexander.schaefer at mines.sdsmt.edu> wrote:
>
>> Amadou,
>>
>> NCL might not be finding the .hluresfile since it should be specifically
>> looking for ".hluresfile" so you having the prefix of "cool" might be
>> messing things up.  If you do a "ls -al" in your home directory you will
>> likely see a bunch of files starting with a ".". Try moving the hluresfile
>> to specifically ".hluresfile" and see if that helps.  Otherwise you can
>> also adjust the workspace size in your NCL script.  See below:
>>
>>   wks = gsn_open_wks(type,"my_output_file_title")
>>   setvalues NhlGetWorkspaceObjectId()
>>     "wsMaximumSize" : 200000000
>>   end setvalues
>>
>>
>> Hope that helps,-Alex
>>
>> On Mon, May 25, 2015 at 8:36 AM, Amadou Coulibaly <mpapin24 at gmail.com>
>> wrote:
>>
>>> Hi Karin,
>>>
>>> Of course, I have comment out *wsMaximumSize : 500000000 inside my
>>> ~/.hluresfile, which I called "cool.hluresfile" and it's in my home
>>> directory. But I till have the same error message. Please find attached my
>>> .hluresfile.
>>>
>>> Best
>>>
>>>
>>>
>>> On 25 May 2015 at 07:51, Karin Meier-Fleischer <meier-fleischer at dkrz.de>
>>> wrote:
>>>
>>>> Please take a look at the following .hlures web page:
>>>>
>>>> http://www.ncl.ucar.edu/Document/Graphics/hlures.shtml
>>>>
>>>> Bye,
>>>> Karin
>>>>
>>>>
>>>> Am 25.05.2015 um 07:23 schrieb Amadou Coulibaly <mpapin24 at gmail.com>:
>>>>
>>>> Hi Dennis and Rick,
>>>>
>>>> I have been able to plot one my wavelet spectrum using 5 years of
>>>> hourly data, instead of all the 30 years, which were bringing the following
>>>> error message: Segmentation fault (core dumped).
>>>>
>>>> But I till have some warring and errors messages such as:
>>>>
>>>> warning:_NhlCreateSplineCoordApprox: Attempt to create spline
>>>> approximation for X axis failed: consider adjusting trXTensionF value
>>>> warning:IrTransInitialize: error creating spline approximation for
>>>> trXCoordPoints; defaulting to linear
>>>> warning:_NhlCreateSplineCoordApprox: Attempt to create spline
>>>> approximation for X axis failed: consider adjusting trXTensionF value
>>>> warning:IrTransInitialize: error creating spline approximation for
>>>> trXCoordPoints; defaulting to linear
>>>> warning:XyPlotSetValues:xyYStyle is NhlLOG:trYMinF can't be <=
>>>> 0.0:Setting xyComputeYMin to True
>>>> fatal:ContourPlotDraw: Workspace reallocation would exceed maximum size
>>>> 100000000
>>>> fatal:ContourPlotDraw: draw error
>>>> fatal:ContourPlotDraw: draw error
>>>> fatal:PlotManagerDraw: error in plot draw
>>>> fatal:_NhlPlotManagerDraw: Draw error
>>>>
>>>> I saw somewhere that to solve the first fatal (fatal:ContourPlotDraw:
>>>> Workspace reallocation would exceed maximum size 100000000), I must
>>>> change that maximum size 100000000 to  *wsMaximumSize : 500000000 in
>>>> the file:.hluresfile and put it in my home directory. I don't understand
>>>> how to put it in my home directory?
>>>>
>>>> How to solve the issues of those errors?
>>>>
>>>> Best
>>>>
>>>> On 23 May 2015 at 19:09, Dennis Shea <shea at ucar.edu> wrote:
>>>>
>>>>> [1] If your data has missing values, you can not use either specx_anal
>>>>> or the wavelet tool.
>>>>>
>>>>> [2] http://www.ncl.ucar.edu/Document/Functions/Built-in/dtrend.shtml
>>>>>
>>>>>      states: "Missing values (_FillValue) are not allowed."
>>>>>
>>>>> [3] If there are **isolated** missing values you could likely do a
>>>>> simple linear interpolation
>>>>>      to fill them. However, **any** interpolation will affect the
>>>>> spectra.
>>>>>
>>>>>      If you have many _FillValue .... I would not even try to fill
>>>>> them in.
>>>>>      The resulting spectra will reflect the effects of the
>>>>> interpolation as much as the 'rea;' data.
>>>>>
>>>>> ---
>>>>> Punch line: I don't think you can get what you want ... given your
>>>>> data.
>>>>>
>>>>> --
>>>>>
>>>>> Your statement:
>>>>>
>>>>> "My script is from this link:
>>>>> http://paos.colorado.edu/research/wavelets/
>>>>>
>>>>> There is no NCL script at that web site.
>>>>>
>>>>> In fact, NCL call the fortran code presented at the website.
>>>>>
>>>>> ---
>>>>> The interactive code there is IDL ... not NCL
>>>>>
>>>>> Regards
>>>>>
>>>>>
>>>>>
>>>>> On Sat, May 23, 2015 at 9:54 AM, Amadou Coulibaly <mpapin24 at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi Dennis,
>>>>>>
>>>>>> My script is from this link:
>>>>>> http://paos.colorado.edu/research/wavelets/
>>>>>>
>>>>>> My Temp look like this:
>>>>>>
>>>>>> Variable: Temp
>>>>>> Type: float
>>>>>> Total Size: 1051968 bytes
>>>>>>             262992 values
>>>>>> Number of Dimensions: 1
>>>>>> Dimensions and sizes:    [time | 262992]
>>>>>> Coordinates:
>>>>>>             time: [410227200..1356994800]
>>>>>> Number Of Attributes: 7
>>>>>>   coordinates :    lon lat
>>>>>>   grid_type :    unstructured
>>>>>>   comment :    Air temperature is the bulk temperature of the air,
>>>>>> not the surf
>>>>>> ace (skin) temperature.
>>>>>>   shortname :    ta
>>>>>>   code :      11
>>>>>>   units :    K
>>>>>>   _FillValue :    9.96921e+36
>>>>>> (0)    299.15
>>>>>> (1)    9.96921e+36
>>>>>> (2)    9.96921e+36
>>>>>> (3)    296.35
>>>>>>
>>>>>> It contains a lot of missing data. That's why I used the following
>>>>>> command:
>>>>>> ; Remove mean and linear trend (recommended, not required)
>>>>>> ; Missing values are not allowed.
>>>>>> ;************************************
>>>>>>  Temp = dtrend(Temp,False)
>>>>>>
>>>>>> After that I printed Temp, but look stange for me with negative
>>>>>> values:
>>>>>>
>>>>>> Variable: Temp
>>>>>> Type: float
>>>>>> Total Size: 1051968 bytes
>>>>>>             262992 values
>>>>>> Number of Dimensions: 1
>>>>>> Dimensions and sizes:    [time | 262992]
>>>>>> Coordinates:
>>>>>>             time: [410227200..1356994800]
>>>>>> Number Of Attributes: 7
>>>>>>   coordinates :    lon lat
>>>>>>   grid_type :    unstructured
>>>>>>   comment :    Air temperature is the bulk temperature of the air,
>>>>>> not the surf
>>>>>> ace (skin) temperature.
>>>>>>   shortname :    ta
>>>>>>   code :      11
>>>>>>   units :    K
>>>>>>   _FillValue :    9.96921e+36
>>>>>> (0)    -8.256236e+36
>>>>>> (1)    1.713005e+36
>>>>>> (2)    1.713035e+36
>>>>>> (3)    -8.256145e+36
>>>>>>
>>>>>> I think the problem is from that command trying to remove mean and
>>>>>> linear trend. Because without that I can get the wavelet function (w), but
>>>>>> it contains only zero as values.
>>>>>>
>>>>>> How to handle this issue?
>>>>>>
>>>>>> Best
>>>>>>
>>>>>>
>>>>>> On 23 May 2015 at 14:17, Dennis Shea <shea at ucar.edu> wrote:
>>>>>>
>>>>>>> [1] I have no idea why the script should seg fault. Maybe your
>>>>>>> parameter settings are not appropriate for the input data.
>>>>>>>
>>>>>>> [2] What does "Temp" look like? printVarSummary(Temp)
>>>>>>>
>>>>>>> [3] Are there missing values?
>>>>>>>
>>>>>>> [4] If you want the "power spectrum", why not look at
>>>>>>>
>>>>>>> http://www.ncl.ucar.edu/Document/Functions/Built-in/specx_anal.shtml
>>>>>>> http://www.ncl.ucar.edu/Applications/spec.shtml
>>>>>>>
>>>>>>> Good luck
>>>>>>>
>>>>>>> On Sat, May 23, 2015 at 8:00 AM, Amadou Coulibaly <
>>>>>>> mpapin24 at gmail.com> wrote:
>>>>>>>
>>>>>>>> Dear ncl users,
>>>>>>>>
>>>>>>>> When I tried ti run my script (wavelet1.ncl), I am getting a
>>>>>>>> strange error which is:
>>>>>>>> Segmentation fault (core dumped)
>>>>>>>>
>>>>>>>> I am using ncl.6.2.1 and my system is: Linux amadou-Satellite-C855
>>>>>>>> 3.19.0-16-generic #16-Ubuntu SMP Thu Apr 30 16:09:58 UTC 2015 x86_64 x86_64
>>>>>>>> x86_64 GNU/Linux
>>>>>>>>
>>>>>>>> My dataset contains hourly data (1983-2012) of
>>>>>>>> wind(speed/direction), air_temperature, ... for 46 sites. I just wanted to
>>>>>>>> plot the power spectrum of only one site and for the all 30 years. I think
>>>>>>>> the error comes from line 45 when I tried to compute the wavelet function
>>>>>>>> (w). Please find attached my script.
>>>>>>>>
>>>>>>>> How can I solve this issue?
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> * COULIBALY   AMADOU   *
>>>>>>>> PhD  Student  on  West  African  Climate  System (WACS)
>>>>>>>> FUTA - Federal  University  of  Technology of Akure, Nigeria
>>>>>>>>
>>>>>>>> *Visiting Student - *
>>>>>>>> *University of Cologne, Germany**Institute of Geophysics and
>>>>>>>> Meteorology*
>>>>>>>> Pohligstr. 3 / Office 3.102
>>>>>>>> D-50969 Köln
>>>>>>>>
>>>>>>>> *Project*: WASCAL (West African Science Service Centre on Climate Change
>>>>>>>> and Adapted Land Use)
>>>>>>>> Phone:(+234) 810 795 2836 /(+223) 65 67 27 57 /(+226) 64 57 37 27 /+49
>>>>>>>> 15218352574
>>>>>>>>
>>>>>>>> E-mail: mpapin24 at gmail.com / coulibalya68 at yahoo.com
>>>>>>>>
>>>>>>>> "*The time is always right to do right": Nelson Mandela*
>>>>>>>>
>>>>>>>> *"Character is like a tree and reputation like a shadow.  The
>>>>>>>> shadow is what we think of it; the tree is the real thing" : Abraham
>>>>>>>> Lincoln*
>>>>>>>>
>>>>>>>> *"Do what you can, with what you have, where you are" Theodore
>>>>>>>> Roosevelt*
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> ncl-talk mailing list
>>>>>>>> List instructions, subscriber options, unsubscribe:
>>>>>>>> http://mailman.ucar.edu/mailman/listinfo/ncl-talk
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> * COULIBALY   AMADOU   *
>>>>>> PhD  Student  on  West  African  Climate  System (WACS)
>>>>>> FUTA - Federal  University  of  Technology of Akure, Nigeria
>>>>>>
>>>>>> *Visiting Student - *
>>>>>> *University of Cologne, Germany**Institute of Geophysics and
>>>>>> Meteorology*
>>>>>> Pohligstr. 3 / Office 3.102
>>>>>> D-50969 Köln
>>>>>>
>>>>>> *Project*: WASCAL (West African Science Service Centre on Climate Change
>>>>>> and Adapted Land Use)
>>>>>> Phone:(+234) 810 795 2836 /(+223) 65 67 27 57 /(+226) 64 57 37 27 /+49
>>>>>> 15218352574
>>>>>>
>>>>>> E-mail: mpapin24 at gmail.com / coulibalya68 at yahoo.com
>>>>>>
>>>>>> "*The time is always right to do right": Nelson Mandela*
>>>>>>
>>>>>> *"Character is like a tree and reputation like a shadow.  The shadow
>>>>>> is what we think of it; the tree is the real thing" : Abraham Lincoln*
>>>>>>
>>>>>> *"Do what you can, with what you have, where you are" Theodore
>>>>>> Roosevelt*
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> * COULIBALY   AMADOU   *
>>>> PhD  Student  on  West  African  Climate  System (WACS)
>>>> FUTA - Federal  University  of  Technology of Akure, Nigeria
>>>>
>>>> *Visiting Student - *
>>>> *University of Cologne, Germany**Institute of Geophysics and
>>>> Meteorology*
>>>> Pohligstr. 3 / Office 3.102
>>>> D-50969 Köln
>>>>
>>>> *Project*: WASCAL (West African Science Service Centre on Climate Change
>>>> and Adapted Land Use)
>>>> Phone:(+234) 810 795 2836 /(+223) 65 67 27 57 /(+226) 64 57 37 27 /+49
>>>> 15218352574
>>>>
>>>> E-mail: mpapin24 at gmail.com / coulibalya68 at yahoo.com
>>>>
>>>> "*The time is always right to do right": Nelson Mandela*
>>>>
>>>> *"Character is like a tree and reputation like a shadow.  The shadow is
>>>> what we think of it; the tree is the real thing" : Abraham Lincoln*
>>>>
>>>> *"Do what you can, with what you have, where you are" Theodore
>>>> Roosevelt*
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> <wavelet2.ncl>
>>>>
>>>> _______________________________________________
>>>> ncl-talk mailing list
>>>> List instructions, subscriber options, unsubscribe:
>>>> http://mailman.ucar.edu/mailman/listinfo/ncl-talk
>>>>
>>>>
>>>
>>>
>>> --
>>> * COULIBALY   AMADOU   *
>>> PhD  Student  on  West  African  Climate  System (WACS)
>>> FUTA - Federal  University  of  Technology of Akure, Nigeria
>>>
>>> *Visiting Student - *
>>> *University of Cologne, Germany**Institute of Geophysics and
>>> Meteorology*
>>> Pohligstr. 3 / Office 3.102
>>> D-50969 Köln
>>>
>>> *Project*: WASCAL (West African Science Service Centre on Climate Change
>>> and Adapted Land Use)
>>> Phone:(+234) 810 795 2836 /(+223) 65 67 27 57 /(+226) 64 57 37 27 /+49
>>> 15218352574
>>>
>>> E-mail: mpapin24 at gmail.com / coulibalya68 at yahoo.com
>>>
>>> "*The time is always right to do right": Nelson Mandela*
>>>
>>> *"Character is like a tree and reputation like a shadow.  The shadow is
>>> what we think of it; the tree is the real thing" : Abraham Lincoln*
>>>
>>> *"Do what you can, with what you have, where you are" Theodore Roosevelt*
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> ncl-talk mailing list
>>> List instructions, subscriber options, unsubscribe:
>>> http://mailman.ucar.edu/mailman/listinfo/ncl-talk
>>>
>>>
>>
>
>
> --
> * COULIBALY   AMADOU   *
> PhD  Student  on  West  African  Climate  System (WACS)
> FUTA - Federal  University  of  Technology of Akure, Nigeria
>
> *Visiting Student - *
> *University of Cologne, Germany**Institute of Geophysics and Meteorology*
> Pohligstr. 3 / Office 3.102
> D-50969 Köln
>
> *Project*: WASCAL (West African Science Service Centre on Climate Change
> and Adapted Land Use)
> Phone:(+234) 810 795 2836 /(+223) 65 67 27 57 /(+226) 64 57 37 27 /+49
> 15218352574
>
> E-mail: mpapin24 at gmail.com / coulibalya68 at yahoo.com
>
> "*The time is always right to do right": Nelson Mandela*
>
> *"Character is like a tree and reputation like a shadow.  The shadow is
> what we think of it; the tree is the real thing" : Abraham Lincoln*
>
> *"Do what you can, with what you have, where you are" Theodore Roosevelt*
>
>
>
>
>
>
> _______________________________________________
> ncl-talk mailing list
> List instructions, subscriber options, unsubscribe:
> http://mailman.ucar.edu/mailman/listinfo/ncl-talk
>
>
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