[ncl-talk] Segmentation fault
Alexander Schaefer
alexander.schaefer at mines.sdsmt.edu
Mon May 25 13:37:43 MDT 2015
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
>
>
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