[ncl-talk] Segmentation fault
Amadou Coulibaly
mpapin24 at gmail.com
Mon May 25 14:22:48 MDT 2015
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*
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