[ncl-talk] Segfault error with Wavelet function in cygwin/x

Dipti Sharma sdipti596 at gmail.com
Sun May 7 20:56:47 MDT 2017 

Mary,

This is an amazing work you have done regarding this issue (for me). Yes,
now it looks it is working. I highly appreciate your responsiveness and
your effort on this. I will let you know if I get any further issues. Thank
you so much again.

regards,

Dipti

On Sun, May 7, 2017 at 1:41 PM, Mary Haley <haley at ucar.edu> wrote:

> Dipti,
>
> I'm responding back to ncl-talk on this one because I think I found the
> source of the problem.
>
> It looks like it's a simple memory issue that fails under 32-bit Cygwin.
>
> I had to reduce the amount of memory that the wavelet Fortran subroutine
> was requesting, and this seemed to make it work.
>
> I compiled a new "ncl" executable for you to try.
>
> To get the new executable, use wget or anonymous ftp:
>
>      wget ftp.ucar.edu:/pub/scd/haley/nclcfix.exe
>
> or
>
>      ftp ftp.ucar.edu
>      <log in as "anonymous">
>      <Use email address as password>
>      cd /pub/scd/haley
>      get nclcfix.exe
>      quit
>
> Once you have the file, move it to $NCARG_ROOT/bin and make sure it is
> executable:
>
>     chmod gou+x nclcfix.exe
>     mv nclcfix.exe $NCARG_ROOT/bin/.
>
> Now you can try this new "nclcfix.exe" executable instead of the one
> already installed on your system:
>
>     nclcfix  your_wavelet_script.ncl
>
> If you are comfortable that this executable works, you can replace your
> old ncl executable with this new one. You should first make a copy of your
> old one:
>
>    mv $NCARG_ROOT/bin/ncl.exe $NCARG_ROOT/bin/nclold.exe
>    mv $NCARG_ROOT/bin/nclcfix.exe $NCARG_ROOT/bin/ncl.exe
>
> Please respond back to ncl-talk and let us know if this fixes the problem.
>
> Thanks,
>
> --Mary
>
>
> On Fri, Apr 21, 2017 at 8:31 AM, Mary Haley <haley at ucar.edu> wrote:
>
>> Dear Dipti,
>>
>> I was able to reproduce this problem on my Cygwin system at home, but I
>> didn't have much time to debug it.
>>
>> Kevin tried your script on a Mac system, and I tried it on both a 32-bit
>> and 64-bit Linux system and it worked fine.  So, it seems to be limited to
>> Cywgin.
>>
>> I will look into this over the weekend.
>>
>> Meanwhile, is your system a 64-bit system running Windows 10?  If so,
>> then you might want to consider using Window's Linux subsystem instead of
>> Cygwin for your UNIX environment.  I'm guessing that your wavelet program
>> might work under this system.
>>
>> Please see this link for more information:
>>
>> http://www.ncl.ucar.edu/Download/windows_linux_subsystem.shtml
>>
>>
>> --Mary
>>
>>
>> On Thu, Apr 20, 2017 at 6:05 PM, Kevin Hallock <hallock at ucar.edu> wrote:
>>
>>> Hi Dipti,
>>>
>>> I tried to run your script on my Mac, but it ran successfully without a
>>> segfault. We will find a Windows system with cygwin to test your script on
>>> and will respond again soon.
>>>
>>> Kevin
>>>
>>> > On Apr 19, 2017, at 12:23 PM, Dipti Sharma <sdipti596 at gmail.com>
>>> wrote:
>>> >
>>> > Dear All,
>>> >
>>> > I am trying to understand how to do the wavelet analysis using NCL. I
>>> am using ncl v6.4.0 in cygwin/x. I started using an example code and the
>>> data that are available online. But I got an error message as "segmentation
>>> fault (core dumped)" when I ran the program. I have given the code that I
>>> used as below for you to review. Also I have attached the data I used in
>>> the email.
>>> >
>>> > So, could you please suggest me how I solve this problem?
>>> >
>>> > Thanks in advance.
>>> >
>>> > Dipti S.
>>> >
>>> > THE CODE is here and the data is attached in the email,
>>> >
>>> >  load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl"
>>> >  load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_csm.ncl"
>>> >  load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/contributed.ncl"
>>> >  load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl"
>>> >  load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl"
>>> >
>>> > ;--------------------------------------------------------------------
>>> > ; CREATE SAME WAVELET FIGURE AS TORRENCE & COMPO using seasonal Nino3
>>> > ; from 1871-1997
>>> > begin
>>> > ninoseas = asciiread("C:\diptic\sst\sst_nino3.dat",-1,"float")
>>> >   ninoseas!0 = "time"
>>> >   ntime = dimsizes(ninoseas)
>>> >   timeo = fspan(1871.25,1996.,ntime)
>>> >   print(ntime)
>>> >   ninoseas&time = timeo
>>> >   ninomam = dim_avg_Wrap(ninoseas(0::4))
>>> >   ninojja = dim_avg_Wrap(ninoseas(1::4))
>>> >   ninoson = dim_avg_Wrap(ninoseas(2::4))
>>> >   ninodjf = dim_avg_Wrap(ninoseas(3::4))
>>> >   ninoseas(0::4) = ninoseas(0::4) - ninomam
>>> >   ninoseas(1::4) = ninoseas(1::4) - ninojja
>>> >   ninoseas(2::4) = ninoseas(2::4) - ninoson
>>> >   ninoseas(3::4) = ninoseas(3::4) - ninodjf
>>> >   time  = timeo
>>> >   N     = dimsizes(time)
>>> > ;_FillValue=1e+36
>>> > ;printMinMax(ninoseas,False)
>>> > ;return
>>> > ;************************************
>>> > ; compute wavelet
>>> > ;************************************
>>> >   mother  = 0
>>> >   param   = 6.0
>>> >   dt      = 0.25    ;timesteps in units of years
>>> >   s0      = dt
>>> >   dj      = 0.25
>>> >   jtot    = 1+floattointeger(((log10(N*dt/s0))/dj)/log10(2.))
>>> >   npad    = N
>>> >   nadof   = 0.0
>>> >   noise   = 1
>>> >   siglvl  = 0.05
>>> >   isigtest= 0
>>> > print(nadof)
>>> > w =wavelet(ninoseas,mother,dt,param,s0,dj,jtot,npad,noise,isig
>>> test,siglvl,nadof)
>>> > printVarSummary(w)
>>> > return
>>> > end
>>> > ;;; This is the output I received,
>>> >
>>> > Variable: ntime
>>> > Type: integer
>>> > Total Size: 4 bytes
>>> >             1 values
>>> > Number of Dimensions: 1
>>> > Dimensions and sizes:   [1]
>>> > Coordinates:
>>> > (0)     504
>>> > (0)     min=-1.8504   max=2.49921
>>> >
>>> > Variable: nadof
>>> > Type: float
>>> > Total Size: 4 bytes
>>> >             1 values
>>> > Number of Dimensions: 1
>>> > Dimensions and sizes:   [1]
>>> > Coordinates:
>>> > (0)      0
>>> > Segmentation fault (core dumped)
>>> >
>>> >
>>> > <sst_nino3.dat>_______________________________________________
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>>
>>
>
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