Re: Segmentation Fault

Hi Cecille,

I see that somebody has already asked for your data offline.

Meanwhile, in the future, it helps if you can provide more information, like if there were *any* kind of errors or warnings when you ran NCL, what your data looks like (i.e. call "printVarSummary" on the data you are plotting).

Sometimes if there's a segmentation fault, it's due to NCL running out of memory. NCL should exit more gracefully, but there are cases where it doesn't. In the latter case, you can try deleting variables that you no longer need, in order to free up memory. I say this because I noticed that you have a lot of "new" statements below, some of which are creating variables that aren't used. If "num_times" is large, then all these new statements might eventually cause you to run out of memory.

--Mary

On Nov 9, 2012, at 4:09 PM, Cecille Villanueva-Birriel wrote:

> Hello,
>
> I am running my ncl script and getting a segmentation fault and don't know why. It will run until it says "print("Test")" and makes the segmentation fault right at the time of the "plot" function. I used to run this script before with no problems until. Can someone help me with this? It would be most appreciated.
>
> Thank you!
> Cecille
>
>
> ;This program will produce vertical profiles of total
> ;hydrometeor species at a given time. This plot can be used
> ;to see relationships such as the melting of graupel / freezing
> ;of rain couplet near the freezing level.
> ;
> ;All previous comments consolidated with general script cleanup.
> ;*****************************************************
>
> ;Standard loading scripts for functions and plotting?
> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl"
> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_csm.ncl"
> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/contributed.ncl"
> ;load "./contributed.ncl"
> load "$NCARG_ROOT/lib/ncarg/nclscripts/wrf/WRFUserARW.ncl"
> external AVERAGE "./average_PURDUE.so"
>
> begin
>
> ;;EDITABLE CODE BEGINS HERE
>
>
>
> type = "Graupel/Hail mixing ratio (g/kg)"
> pdftype = "qg_50-130"
> grid = "2km"
>
> ; timelabl = (/"0000","0005","0010","0015","0020","0025","0030","0035","0040","0045",\
> ; "0050","0055","0100","0105","0110","0115","0120","0125","0130"/)
>
> ; timelabl = (/"0000","0005","0010","0015","0020","0025","0030","0035","0040","0045"/)
> timelabl = (/"0000","0005","0010","0015","0020","0025","0030","0035","0040","0045","0050","0055","0060"/)
>
>
> ;;END EDITABLE CODE
>
> a = addfile("../../Morrison/2km/delt_3/wrfout_d01_0001-01-01_00:00:00_Anderson_SC_2km_delt_3_MOR_past.nc", "r")
> b = addfile("../../Morrison/2km/delt_3/wrfout_d01_0001-01-01_00:00:00_Anderson_SC_2km_delt_3_MOR_fut.nc", "r")
>
> mor = a->QGRAUP(:,0:50,:,:)
>
>
>
> ph = a->PH(:,0:50,:,:)/9.81 ;eliminate geopotential
> phb = a->PHB(:,0:50,:,:)/9.81
> height = (ph + phb)/1000
> ;height = wrf_user_getvar(a,"z",-1)/1000
>
> delete(ph)
> delete(phb)
>
> ; times = a->Times(:,:)
> times = wrf_user_list_times(a)
> ; print(times)
>
> ; delete(a)
> ; delete(b)
>
> q_past = a->QGRAUP(:,0:50,:,:)
> q_fut = b->QGRAUP(:,0:50,:,:)
>
> delete(a)
> delete(b)
>
>
> ;I will need the number of vertical/horiz levels for the height labels later
>
> num_times = dimsizes(times)
> ; num_times = 9
> num_vert = dimsizes(q_past(0,0:50,1,1))
> num_horiza = dimsizes(q_past(0,0,:,0))
> num_horizb = dimsizes(q_past(0,0,0,:))
>
> delete(times)
>
> nt = num_times
> nz = num_vert
> ny = num_horiza
> nx = num_horizb
>
> print (num_times)
> print (num_vert)
> print (num_horiza)
> print (num_horizb)
>
>
> ; timid = ispan(0,18,1)
>
>
> ;*****************************************************
> ;These are all of my array declarations, which will
> ;be the length of the num_vert variable from above
> ;*****************************************************
>
> ; qavg_vapor = new(num_vert, float)
> avg_past = new(num_vert, float)
> avg_fut = new(num_vert, float)
>
> qds_vapor = new((/num_times/), float)
> qds_cloud = new((/num_times/), float)
> qds_rain = new((/num_times/), float)
> qds_ice = new((/num_times/), float)
> qds_snow = new((/num_times/), float)
> qds_graup = new((/num_times/), float)
>
> mavg_past = new((/num_times,num_vert/), float)
> mavg_fut = new((/num_times,num_vert/), float)
>
>
> suma = new((/num_times,num_vert/), float)
> sumb = new((/num_times,num_vert/), float)
>
> suma = 0.
> sumb = 0.
>
> pt = new((/num_times,num_vert/), float)
> ft = new((/num_times,num_vert/), float)
>
> pt = 0.
> ft = 0.
>
>
> ; allq = new((/6, num_vert/), float)
> allq = new((/2, num_vert/), float)
> ;*****************************************************
> ;This code will obtain the maximum values of some
> ;hydrometeor anywhere in the 3D domain for a fixed time.
> ;This may need to be updated to correct for domains
> ;that don't include the cells which develop on the
> ;outflow of my supercell. NOTE: units now in g/kg
> ;*****************************************************
>
>
>
> AVERAGE::average(suma,sumb,q_past,q_fut,pt,ft,mavg_past,mavg_fut,nx,ny,nz,nt)
>
> print (suma*1000)
> print (pt)
>
>
>
>
> mavg_past=mavg_past>0
> mavg_fut=mavg_fut>0
>
> print (mavg_past)
>
> ;The following makes an array with the model height (in km)
> ;to be used for the plot labels, in actuallity, we need to make a
> ;code that plots intergers vs. qmass
>
> tmp1 = floattoint((num_vert/5)+1)
>
> height_array = new(tmp1, float)
>
> height_array(0) = avg(height(:,0,:,:)) ;because (j*5)-1 for 0 gives a negative index
>
> do j=1,tmp1-1
> tmp2 = (j*5)-1
> height_array(j) = floattoint(avg(height(:,tmp2,:,:)))
> end do
>
> ;Now generate the intergers for plotting
>
> ; heightplot = new(num_vert, float)
>
> ; heightplot(0) = 0
> ; do j=1,num_vert-1
> ; heightplot(j) = heightplot(j-1)+1
> ; end do
>
>
> heightplot = ispan(0,num_vert-1,1)
>
> delete(tmp2)
> delete(tmp1)
>
> ;print("Heightplot = "+heightplot)
>
> ;Open the workstation
> wks = gsn_open_wks ("pdf", pdftype+"_scheme_avg_height"+grid)
>
> do i = 0,num_times -1
>
> ;fub = i
>
> ;do k=0,num_vert-1
> ; avg_vapor(k) = (sum(qvapor(fub,k,:,:))) * 1000
>
> avg_past = mavg_past(i,:)* 1000
> avg_fut = mavg_fut(i,:)* 1000
>
> print(avg_past)
> ; delete(mavg_wsm6)
> ; delete(mavg_tho)
> ; delete(mavg_mil)
> ; delete(mavg_mor)
>
> ;print (avg_mor)
> allq(0,:) = avg_past
> allq(1,:) = avg_fut
> ;end do
> ; qds_vapor(i) = sum(avg_vapor)
> ;qds_cloud(i) = sum(avg_cloud)
> ;qds_rain(i) = sum(avg_rain)
> ;qds_ice(i) = sum(avg_ice)
> ;qds_snow(i) = sum(avg_snow)
> ;qds_graup(i) = sum(avg_graup)
>
> ;*****************************************************
> ;Time to make some plots, yo
> ;*****************************************************
>
> ;Open the workstation
> ; wks = gsn_open_wks ("pdf", "Qdiftot_vALT"\
> ; +di2_labl+"")
>
>
> ; allq(0,:) = qavg_vapor(i)
>
> ; leg_label = (/"QVapor","QCloud","QRain","QIce","QSnow","QGraupel"/)
> leg_label = (/"past","fut"/)
>
> res = True
>
> res@tiMainString = timelabl(i)
> res@tiXAxisString = type
> res@tiYAxisString = "Height (km)"
> res@tiXAxisFontHeightF = 0.025 ;resize axis labels
> res@tiYAxisFontHeightF = 0.025
> res@tiXAxisFont = "times-roman" ;change font type for axis labels
> res@tiYAxisFont = "times-roman"
>
>
> res@pmLegendDisplayMode = "Always"
> res@pmLegendZone = 0
> res@pmLegendSide = "Top"
> res@pmLegendWidthF = 0.16
> res@pmLegendHeightF = 0.15
> res@lgLabelFontHeightF = .47
> res@lgLabelFont = "times-roman" ;change font type for legend label
> res@xyExplicitLegendLabels = leg_label
> res@pmLegendParallelPosF = 0.32
> res@pmLegendOrthogonalPosF = 0.32
>
>
> res@tmYLMode = "Explicit"
> res@tmYLMinorOn = True
> res@trYMaxF = num_vert-1
> res@tmYLTickSpacingF = 5
> res@tmYLMinorPerMajor = 4
> res@tmXBLabelFontHeightF = 0.023 ;resize tick labels
> res@tmYLLabelFontHeightF = 0.023
> res@tmXBLabelFont = "times-roman" ;change font type for tick labels
> res@tmYLLabelFont = "times-roman"
> res@tmYLValues = ispan(0,num_vert-1,5)
> res@tmYLMinorValues = ispan(0,num_vert-1,1)
> res@tmYLLabels = height_array
> res@tmYLPrecision = 1
>
>
> ; res@xyMarkLineMode = "MarkLines"
> ; res@xyMarkers = (/9,4/)
> res@xyLineThicknessF = 3.0
> ; res@xyLineThicknesses = (/2.0,3.0,2.0,3.0/)
> ;res@xyLineColors = (/"black","green","blue","brown","orange","purple"/)
> res@xyLineColors = (/"blue","red"/)
> res@xyDashPatterns = (/0,2/)
>
> ;res@TimeLabel = times(i)
>
> print("Test")
> plot = gsn_xy(wks,allq,heightplot,res)
>
>
>
> print("Heightarray = "+height_array)
>
> end do
>
>
> ; grandtotnovap = qds_cloud+qds_rain+qds_ice+qds_snow+qds_graup
>
> ; print (avg_mor)
>
> ; print(qds_vapor)
>
> ; print(qds_cloud)
> ; print(qds_rain)
> ; print(qds_ice)
> ; print(qds_snow)
> ; print(qds_graup)
> ; print(grandtotnovap)
>
> end
>
>> ********************************************************
>> Cecille M. Villanueva Birriel
>> Ph.D. Candidate
>> Cloud Microphysics Research Group
>> Purdue University
>> Department of Earth, Atmospheric, & Planetary Sciences
>> 550 Stadium Mall Drive, West Lafayette, IN 47907-2051
>> email: cvillanu@purdue.edu
>> ********************************************************
>
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Received on Mon Nov 12 12:08:02 2012