Re: Segmentation fault (core dumped)

From: Vishali P. <vishali.prat_at_nyahnyahspammersnyahnyah>
Date: Thu Jun 23 2011 - 06:11:43 MDT

Please, can anyone help me with solution of this problem??
I can provide more information if needed

Thank you in advance

Vishali

On Mon, Jun 20, 2011 at 8:54 PM, Vishali P. <vishali.prat@gmail.com> wrote:

> Hi Gus Correa.
>
> It's 32-bit, with 2GB of memory
>
>
>
>
>
> On Mon, Jun 20, 2011 at 8:01 PM, Gus Correa <gus@ldeo.columbia.edu> wrote:
>
>> Hi Vishali
>>
>> If your files have one year of 4x daily data,
>> you have 4*365*17*73*144 = 260,907,840 numbers on each variable
>> stored there.
>> If they're floating point (4 bytes) this is ~ 1GB,
>> if they're double (8 bytes) this is ~ 2GB.
>> You may be on the bleeding edge with variable
>> w = f->WSpeed.
>> You also need memory for the other variables (wMon, etc), for the OS,
>> the NCL executable, and so on.
>>
>> I wonder if the problem is this.
>> How much memory does your computer have?
>> Is it a 32- or 64-bit machine?
>> NCL 5.2 only supports variables up to 2GB large.
>> NCL 6.0 supports up to the physical RAM available,
>> *if* your computer is 64-bit.
>>
>> My two cents,
>> Gus Correa
>>
>> Vishali P. wrote:
>> > Hi
>> >
>> >
>> > [ 1 ] Output of first separated script
>> >
>> > Variable: nfilu
>> > Type: integer
>> > Total Size: 4 bytes
>> > 1 values
>> > Number of Dimensions: 1
>> > Dimensions and sizes: [1]
>> > Coordinates:
>> > (0) 7
>> >
>> >
>> > Variable: filu
>> > Type: string
>> > Total Size: 28 bytes
>> > 7 values
>> > Number of Dimensions: 1
>> > Dimensions and sizes: [7]
>> > Coordinates:
>> > (0) wind.1998.nc <http://wind.1998.nc>
>> > (1) wind.1999.nc <http://wind.1999.nc>
>> > (2) wind.2000.nc <http://wind.2000.nc>
>> > (3) wind.2001.nc <http://wind.2001.nc>
>> > (4) wind.2002.nc <http://wind.2002.nc>
>> > (5) wind.2003.nc <http://wind.2003.nc>
>> > (6) wind.2004.nc <http://wind.2004.nc>
>> >
>> >
>> >
>> > [ 2 ] Output of second separated Script
>> >
>> > (0) success
>> >
>> >
>> >
>> > [ 3 ] Output ncl_filedump of 1st file ( wind speed of 1998), i got :
>> >
>> > Variable: f (file variable)
>> >
>> > filename: wind.1998
>> > path: wind.1998.nc <http://wind.1998.nc>
>> > file global attributes:
>> > CDI : Climate Data Interface version 1.4.1
>> > Conventions : CF-1.0
>> > history : Mon Oct 18 11:24:43 2010: cdo mergetime wind1998a.nc
>> > <http://wind1998a.nc> wind1998b.nc <http://wind1998b.nc> wind.1998.nc
>> > <http://wind.1998.nc>
>> > CDO : Climate Data Operators version 1.4.1
>> > (http://www.mpimet.mpg.de/cdo)
>> > dimensions:
>> > lon = 144
>> > lat = 73
>> > level = 17
>> > time = 1460 // unlimited
>> > variables:
>> > float lon ( lon )
>> > long_name : Longitude
>> > units : degrees_east
>> > standard_name : longitude
>> >
>> > float lat ( lat )
>> > long_name : Latitude
>> > units : degrees_north
>> > standard_name : latitude
>> >
>> > float level ( level )
>> > long_name : Level
>> > units : millibar
>> > axis : z
>> >
>> > double time ( time )
>> > units : hours since 1800-01-01 00:00:00
>> > calendar : standard
>> >
>> > float WSpeed ( time, level, lat, lon )
>> > long_name : Wind Speed
>> > standard_name : eastward_wind
>> > units : m/s
>> > _FillValue : -32767
>> > valid_range : ( -140, 174.989990234375 )
>> > parent_stat : Other
>> > statistic : Individual Obs
>> > level_desc : Pressure Levels
>> > dataset : NCEP/DOE AMIP-II Reanalysis (Reanalysis-2)
>> > var_desc : u-wind
>> > GRIB_name : UGRD
>> > GRIB_id : 33
>> > least_significant_digit : 1
>> > precision : 2
>> > actual_range : ( -87.30000305175781, 129.5 )
>> > unpacked_valid_range : ( -140, 175 )
>> >
>> >
>> >
>> >
>> > Thank you
>> >
>> > Vishali
>> >
>> >
>> >
>> >
>> >
>> > On Mon, Jun 20, 2011 at 4:06 PM, Dennis Shea <shea@ucar.edu
>> > <mailto:shea@ucar.edu>> wrote:
>> >
>> > You must help with more information:
>> >
>> > ==============================__====
>> > Try some different approaches. Isolate the following,
>> > as a separate script. run it
>> >
>> >
>> >
>> > diru = "/home/Vishali/Documents/__dadosVentos/Speed/"
>> > filu = systemfunc("cd "+diru+" ; ls wind*nc")
>> > nfilu = dimsizes(filu)
>> >
>> > print(nfilu)
>> > print(filu)
>> >
>> > ==============================__==
>> > Another separate script:
>> >
>> >
>> > yrStrt = 1998
>> > yrLast = 2004
>> > nyrs = yrLast-yrStrt+1
>> > klev = 17
>> > nlat = 73
>> > mlon = 144
>> > ntim = 12*nyrs ; number of months
>> >
>> >
>> > wMon = new ( (/ntim,klev,nlat,mlon/), "float", 1e20)
>> > tMon = new ( ntim, "double", "No_FillValue")
>> >
>> > print("success")
>> > ==============================
>> >
>> > Also, pick out (say) the 1st file and use ncl_filedump
>> >
>> > %> ncl_filedump wind...nc
>> >
>> >
>> > On 6/20/11 9:45 AM, Vishali P. wrote:
>> >
>> > Hi.
>> >
>> > When I tried to run normally, it only appeared : ' Segmentation
>> > fault
>> > (core dumped)'
>> >
>> > When I've tried to run with Mary's command ncl -x
>> > CalculateSeasonalMeans.ncl :
>> >
>> > Loading file
>> > "$NCARG_ROOT/lib/ncarg/__nclscripts/csm/contributed.__ncl"
>> > +
>> > +
>> > + yrStrt = 1998
>> > + yrLast = 2004
>> > + nyrs = yrLast-yrStrt+1
>> > + klev = 17
>> > + nlat = 73
>> > + mlon = 144
>> > + ntim = 12*nyrs ; number of months
>> > +
>> > + wMon = new ( (/ntim,klev,nlat,mlon/), "float", 1e20)
>> > + tMon = new ( ntim, "double", "No_FillValue")
>> > +
>> > +
>> > + diru = "/home/Vishali/Documents/__dadosVentos/SpeedTest/"
>> > + filu = systemfunc("cd "+diru+" ; ls wind*nc")
>> > + nfilu = dimsizes(filu)
>> > +
>> > + ; calculate monthly means from 6hrly
>> > + nmoStrt = 0
>> > + nmoLast = 11
>> > + do nf=0,nfilu-1
>> > +
>> > + f = addfile(diru+filu(nf), "r")
>> > + w = f->WSpeed
>> > + wMon(nmoStrt:nmoLast,:,:,:) =
>> calculate_monthly_values(w,
>> > "avg",0, False)
>> > + nmoStrt = nmoStrt+12
>> > + nmoLast = nmoLast+12
>> > + delete(w) ; may change size next iteration (leap yr)
>> > + end do
>> > Segmentation fault (core dumped)
>> >
>> >
>> >
>> >
>> > On Mon, Jun 20, 2011 at 3:16 PM, Mary Haley <haley@ucar.edu
>> > <mailto:haley@ucar.edu>
>> > <mailto:haley@ucar.edu <mailto:haley@ucar.edu>>> wrote:
>> >
>> >
>> > On Jun 20, 2011, at 2:40 AM, Vishali P. wrote:
>> >
>> > > Dear NCL users
>> > >
>> > > I'm using 4x Daily NCEP/DOE AMIP-II Reanalysis wind data
>> > 1998 to
>> > 2004. I've calculated wind speed for each year...and created
>> > outputs.
>> > > I was suggested a script to calculate unweighted seasonal
>> > means.
>> > And then, average of each season from 1998 to 2004, ie,
>> > average if
>> > season 1 from 1998 to 2004,average of season 2 from 1998 to
>> 2004,
>> > then 3rd and 4th.
>> > >
>> > > But when I try to run,appears error "Segmentation fault
>> (core
>> > dumped)".
>> > > Can anyone help me ?
>> > > Current version of my NCL is 5.2.1.
>> > >
>> > >
>> > > Thank you in advance
>> > >
>> > > Vishali
>> >
>> > Hi Vishali,
>> >
>> > It could be a memory issue, but I don't have enough
>> > information to
>> > determine this.
>> >
>> > Do you know where the code is seg faulting? To get this
>> > information,
>> > run ncl with the -x option, which causes every line to be
>> > executed
>> > as it is run:
>> >
>> > ncl -x your_script.ncl
>> >
>> > It would help if you could include all the output from
>> > running this
>> > command, plus all the output from your various
>> printVarSummary
>> > statements.
>> >
>> > Thanks,
>> >
>> > --Mary
>> >
>> > >
>> > >
>> >
>> >
>> ==============================__==============================__=============================
>> > > load
>> > "$NCARG_ROOT/lib/ncarg/__nclscripts/csm/contributed.__ncl"
>> > >
>> > > yrStrt = 1998
>> > > yrLast = 2004
>> > > nyrs = yrLast-yrStrt+1
>> > > klev = 17
>> > > nlat = 73
>> > > mlon = 144
>> > > ntim = 12*nyrs ; number of months
>> > >
>> > > wMon = new ( (/ntim,klev,nlat,mlon/), "float", 1e20)
>> > > tMon = new ( ntim, "double", "No_FillValue")
>> > >
>> > >
>> > > diru = "/home/Vishali/Documents/__dadosVentos/Speed/"
>> > > filu = systemfunc("cd "+diru+" ; ls wind*nc")
>> > > nfilu = dimsizes(filu)
>> > >
>> > > ; calculate monthly means from 6hrly
>> > > nmoStrt = 0
>> > > nmoLast = 11
>> > > do nf=0,nfilu-1
>> > > f = addfile(diru+filu(nf), "r")
>> > > w = f->WSpeed
>> > > wMon(nmoStrt:nmoLast,:,:,:) =
>> > calculate_monthly_values(w,
>> > "avg",0, False)
>> > > nmoStrt = nmoStrt+12
>> > > nmoLast = nmoLast+12
>> > > delete(w) ; may change size next iteration (leap
>> yr)
>> > > end do
>> > > delete(wMon&time)
>> > >
>> > > printVarSummary(wMon) ; wMon(84,17,73,144)
>> > >
>> > > time = yyyymm_time(yrStrt, yrLast, "integer")
>> > > wMon&time = time
>> > >
>> > > wMon!1 = "level" ; minor bug in
>> > "calculate_monthly_values"
>> > > wMon&level = f->level
>> > >
>> > > printVarSummary(wMon)
>> > >
>> > > ; unweighted seasonal means
>> > >
>> > > wAllSea = wgt_runave_n_Wrap(wMon, 3, 0, 0)
>> > > printVarSummary(wAllSea)
>> > >
>> > > wSea = wAllSea(::3,:,:,:) ; (28,14,73,144)
>> > > printVarSummary(wSea)
>> > >
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Received on Thu Jun 23 06:12:02 2011

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