Re: Segmentation fault (core dumped)

Vishali,

Several people wrote in with suggestions. Dennis suggested trying a different approach. Did you see this? His email was archived at:

http://www.ncl.ucar.edu/Support/talk_archives/2011/1548.html

Gus also pointed out that you likely had a memory problem. This is not necessarily an issue with NCL; you may just not have enough memory to process the variable sizes that you are working with.

You may need to rewrite your script so that it doesn't try to use so much memory at once. Did you give this a try?

--Mary

On Jun 23, 2011, at 6:11 AM, Vishali P. wrote:

> 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)
> > >
> > > _________________________________________________
> > > ncl-talk mailing list
> > > List instructions, subscriber options, unsubscribe:
> > > http://mailman.ucar.edu/__mailman/listinfo/ncl-talk
> > <http://mailman.ucar.edu/mailman/listinfo/ncl-talk>
> >
> >
> >
> >
> > _________________________________________________
> > ncl-talk mailing list
> > List instructions, subscriber options, unsubscribe:
> > http://mailman.ucar.edu/__mailman/listinfo/ncl-talk
> > <http://mailman.ucar.edu/mailman/listinfo/ncl-talk>
> >
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > ncl-talk mailing list
> > List instructions, subscriber options, unsubscribe:
> > http://mailman.ucar.edu/mailman/listinfo/ncl-talk
>
> _______________________________________________
> ncl-talk mailing list
> List instructions, subscriber options, unsubscribe:
> http://mailman.ucar.edu/mailman/listinfo/ncl-talk
>
>
> _______________________________________________
> ncl-talk mailing list
> List instructions, subscriber options, unsubscribe:
> http://mailman.ucar.edu/mailman/listinfo/ncl-talk

_______________________________________________
ncl-talk mailing list
List instructions, subscriber options, unsubscribe:
http://mailman.ucar.edu/mailman/listinfo/ncl-talk
Received on Thu Jun 23 13:28:06 2011