Re: writing latitude to the file

Hi Alexander,
Dave A. is correct that you are attempting to write a bigger file than the original classic format NetCDF allows. You may be able to use the
"largefile" option and still keep the file as NetCDF3. That would be:

setfileoption("nc","Format","LargeFile") (also aliased as "64BitOffset")

Otherwise you will need to move to NetCDF4 classic model:

setfileoption("nc","Format","NetCDF4Classic")

This call needs to be made prior to opening the output file.
 -dave

On Feb 21, 2012, at 12:30 PM, Dave Allured wrote:

> Alexander,
>
> The first error message mean that you have exceeded one of the size
> limits for a Netcdf-3 format file with fixed dimensions. You can try
> changing the time dimension to unlimited, or try using the
> setfileoption procedure to change the output format to Netcdf-4. The
> latter is the simpler solution.
>
> Also I suggest that you carefully check the dimensions of all
> variables written to the output file, to make sure you are getting
> what you expect. For example, I do not see a printVarSummary for
> "egr", but I infer that this is a very large array.
>
> --Dave
>
> On Tue, Feb 21, 2012 at 11:11 AM, Alexander Semenov <asemenov@alaska.edu> wrote:
>> Hello ncl-talk,
>>
>> I have a problem writing variables to the file. I was hoping you could
>> advise me what to do about it. Here's the script - the line where the error
>> is happening highlighted in yellow. After the script I attached what printed
>> out on the screen as the program was running (the error message is marked in
>> red).
>>
>> THE SCRIPT:
>>
>> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl"
>> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_csm.ncl"
>> load "$NCARG_ROOT/lib/ncarg/nclscripts/wrf/WRFUserARW.ncl"
>> load "$NCARG_ROOT/lib/ncarg/nclscripts/wrf/WRF_contributed.ncl"
>>
>> begin
>>
>> print ("Opening files...")
>> f = addfile
>> ("/import/wrkdir1/asemenov/WRF/WRFV3/10_25.03_res_30_10km/wrfout_d02_2011-03-16_12:00:00"+".nc",
>> "r")
>> a = systemfunc("rm -f eady.nc")
>> fout = addfile ("eady.nc","c")
>>
>> ;wks = gsn_open_wks("x11","eady")
>>
>> ;gsn_define_colormap(wks,"WhiteYellowOrangeRed")
>>
>> res = True
>>
>> ;TICKMARK RESOURCES (ON/OFF - FONT SIZE)
>> res@pmTickMarkDisplayMode = "Always"
>> res@tmXTOn = False
>> res@tmXBOn = True
>> res@tmYLOn = False
>> res@tmYROn = False
>> res@tmXTLabelFontHeightF = 0.025
>> res@tmXBLabelFontHeightF = 0.025
>> res@tmYLLabelFontHeightF = 0.025
>> res@tmYRLabelFontHeightF = 0.025
>> ; MAP RESOURCES.
>> res@mpGridAndLimbOn = True
>> res@mpGridLineDashPattern = 2
>> res@mpGeophysicalLineColor = "Black"
>> res@mpGeophysicalLineThicknessF = 1.5
>> res@mpNationalLineColor = "Black"
>> res@mpNationalLineThicknessF = 1.5
>> res@mpUSStateLineColor = "Black"
>> res@mpUSStateLineThicknessF = 1.5
>> res@mpPerimLineColor = "Black"
>>
>> ;LABEL BAR RESOURCES
>> res@lbLabelAutoStride = True
>> res@lbOrientation = "Vertical"
>> res@lbLabelFontHeightF = 0.025
>> ;CONTOUR RESOURCES
>> res@cnFillOn = True
>> res@cnLinesOn = False
>> res@cnLineColor = "Blue"
>> res@cnLineThicknessF = 2.
>> res@cnInfoLabelOn = False
>> res@cnLineLabelsOn = False
>> res@cnLineLabelPerimOn = True
>> res@cnLineLabelBackgroundColor = 0.
>> ; res@cnLevelSelectionMode = "ManualLevels"
>> ; res@cnMinLevelValF = -20.
>> ; res@cnMaxLevelValF = 30.
>> ; res@cnLevelSpacingF = 2.
>> ;GSN RESOURCES
>> res@gsnSpreadColors = True
>> res@gsnLeftString = " "
>> res@gsnRightString = " "
>> ;res@gsnDraw = False
>> ;res@gsnFrame = False
>> res@gsnMaximize = True
>> ;TITLE RESOURCES
>> res@tiMainOn = True
>> res@tiMainPosition = "Center"
>> res@tiMainFontHeightF = 0.025
>>
>> ;PROJECTION RESOURCES
>> WRF_map_c(f, res, 0)
>> res@tfDoNDCOverlay = True
>> res@mpCenterLonF = -180.
>> res@mpCenterLatF = 90.
>>
>> times = chartostring(f->Times)
>> ntim = dimsizes(times)
>>
>> print ("Creating array...")
>> temp = f->T
>> egr = temp
>> egr@_FillValue = -999.
>> egr = egr@_FillValue
>> egr@description = "eady growth rate"
>> egr@units = "s-1"
>> delete(temp)
>>
>> do nt=0,ntim-140
>> print (times(nt))
>>
>> res@tiMainString = times(nt)
>>
>>
>> ; get coriolis
>> ;--------------------------------------------------------------------
>> cor = f->F(nt,:,:)
>> ;printVarSummary (cor)
>> ;printMinMax (cor,True)
>>
>>
>>
>>
>> ; get theta, wind and z
>> ;--------------------------------------------------------------------
>> z = wrf_user_getvar(f,"z",nt)
>> ;printVarSummary (z)
>> ;printMinMax (z,True)
>> ;xmax = max(z)
>> ;xmin = min(z)
>> ;x1d = ndtooned(z)
>> ;indmax = ind_resolve(ind(x1d.eq.xmax),dimsizes(z))
>> ;indmin = ind_resolve(ind(x1d.eq.xmin),dimsizes(z))
>> ;print (indmax)
>> ;print (indmin)
>>
>> ;do lv=0,38
>> ;res@gsnLeftString = "level: "+lv
>> ;plot = gsn_csm_contour_map(wks,z(lv,:,:),res)
>> ;end do
>>
>> t = wrf_user_getvar(f,"theta",nt)
>> ;printVarSummary (t)
>> ;printMinMax (t,True)
>> u = wrf_user_getvar(f,"ua",nt)
>> ;printVarSummary (u)
>> ;printMinMax (u,True)
>> v = wrf_user_getvar(f,"va",nt)
>> ;printVarSummary (v)
>> ;printMinMax (v,True)
>> speed = (u*u + v*v)^0.5
>> copy_VarCoords (u,speed)
>>
>>
>> lv=0
>> x=428
>> y=398
>> print("T: "+t(lv,x,y)+" Z: "+z(lv,x,y))
>>
>>
>>
>> ; calculate vertical gradients dtdz and dudz
>> ;--------------------------------------------------------------------
>> dtdz = center_finite_diff_n(t,z,False,0,0)
>> dtdz@_FillValue = -999.
>> dtdz = where ( dtdz .lt. 10e-3, dtdz@_FillValue, dtdz)
>> copy_VarCoords (t,dtdz)
>> ;printVarSummary (dtdz)
>> ;printMinMax (dtdz,True)
>>
>> do lv=0,31
>> print("T: "+t(lv,x,y)+" Z: "+z(lv,x,y)+" dTdZ: "+dtdz(lv,x,y))
>> end do
>>
>>
>> dudz = center_finite_diff_n(speed,z,False,0,0)
>> dudz@_FillValue = -999.
>> copy_VarCoords (u,dudz)
>> ;printVarSummary (dudz)
>> ;printMinMax (dudz,True)
>>
>> do lv=0,31
>> print("U: "+speed(lv,x,y)+" Z: "+z(lv,x,y)+" dUdZ: "+dudz(lv,x,y))
>> end do
>>
>>
>>
>> ; calculate brunt-vaisala
>> ;--------------------------------------------------------------------
>> n2 = (9.81/t)*(dtdz)
>> n2@_FillValue = -999.
>> ;printVarSummary (n2)
>> ;printMinMax (n2,True)
>>
>> n = where ( n2 .gt. 0, sqrt(n2), n2@_FillValue)
>> copy_VarCoords (t,n)
>> ;printVarSummary (n)
>> ;printMinMax (n,True)
>>
>> do lv=0,31
>> print("T: "+t(lv,x,y)+" dtdz: "+dtdz(lv,x,y)+" N: "+n(lv,x,y))
>> end do
>>
>>
>> ; calculate eady growth rate
>> ;--------------------------------------------------------------------
>>
>>
>> do nl=0,32-1
>> ;print ("level: "+nl)
>> egr(nt,nl,:,:) = 0.31 * cor * (1/n(nl,:,:)) * dudz(nl,:,:)
>> end do
>> ;printVarSummary (egr)
>> printMinMax (egr,True)
>>
>>
>> xmax = max(egr)
>> ;xmin = min(egr)
>> x1d = ndtooned(egr)
>> indmax = ind_resolve(ind(x1d.eq.xmax),dimsizes(egr))
>> ;indmin = ind_resolve(ind(x1d.eq.xmin),dimsizes(egr))
>> print (indmax+" value: "+xmax)
>> ;print (indmin)
>>
>> do lv=0,31
>> print("COR: "+cor(x,y)+" N: "+n(lv,x,y)+" dUdZ: "+dudz(lv,x,y)+" EGR:
>> "+egr(nt,lv,x,y))
>> end do
>>
>>
>> delete(n)
>> delete(n2)
>> delete(dudz)
>> delete(dtdz)
>> delete(cor)
>> delete(z)
>> delete(t)
>> delete(u)
>> delete(v)
>> delete(speed)
>>
>> end do
>>
>>
>>
>> xmax = max(egr)
>> ;xmin = min(egr)
>> x1d = ndtooned(egr)
>> indmax = ind_resolve(ind(x1d.eq.xmax),dimsizes(egr))
>> ;indmin = ind_resolve(ind(x1d.eq.xmin),dimsizes(egr))
>> print (indmax+" value: "+xmax)
>> ;print (indmin)
>>
>>
>>
>>
>> egr = egr*60*60*24
>> egr@units = "day-1"
>>
>> fout@MAP_PROJ=2
>> fout@TRUELAT1=66
>> fout@TRUELAT2=30
>> fout@STAND_LON=-180
>> fout@DX=10000
>> fout@DY=10000
>> fout@CEN_LAT=90
>> fout@CEN_LON= -180
>>
>> lat = f->XLAT
>> lon = f->XLONG
>> printVarSummary(lat)
>> printVarSummary(lon)
>>
>> print("writing EGR...")
>> fout->eady=egr
>> print("writing LAT...")
>> fout->lat=lat
>> print("writing LON...")
>> fout->lon=lon
>>
>> delete(egr)
>> delete(lat)
>> delete(lon)
>>
>> print("Getting P...")
>> p = wrf_user_getvar(f,"pressure",-1)
>> print("writing P...")
>> fout->pres=p
>>
>>
>> end
>>
>>
>> Variable: times (subsection)
>> Type: string
>> Total Size: 8 bytes
>> 1 values
>> Number of Dimensions: 1
>> Dimensions and sizes: [1]
>> Coordinates:
>> (0) 2011-03-16_17:00:00
>> (0) T: 269.386 Z: 26.2992
>> (0) T: 269.386 Z: 26.2992 dTdZ: -999
>> (0) T: 269.166 Z: 90.351 dTdZ: -999
>> (0) T: 269.102 Z: 177.558 dTdZ: -999
>> (0) T: 269.076 Z: 288.493 dTdZ: -999
>> (0) T: 269.067 Z: 427.808 dTdZ: -999
>> (0) T: 269.068 Z: 604.534 dTdZ: -999
>> (0) T: 269.077 Z: 820.468 dTdZ: -999
>> (0) T: 269.093 Z: 1104.6 dTdZ: -999
>> (0) T: 269.118 Z: 1444.25 dTdZ: -999
>> (0) T: 270.502 Z: 1796.01 dTdZ: -999
>> (0) T: 272.674 Z: 2162.31 dTdZ: -999
>> (0) T: 274.685 Z: 2702.22 dTdZ: -999
>> (0) T: 277.1 Z: 3407.48 dTdZ: -999
>> (0) T: 279.437 Z: 4111.92 dTdZ: -999
>> (0) T: 281.421 Z: 4815.02 dTdZ: -999
>> (0) T: 283.422 Z: 5516.41 dTdZ: -999
>> (0) T: 286.003 Z: 6216.98 dTdZ: -999
>> (0) T: 289.875 Z: 6919.17 dTdZ: -999
>> (0) T: 296.174 Z: 7627.6 dTdZ: 0.0111892
>> (0) T: 305.878 Z: 8349.35 dTdZ: 0.015808
>> (0) T: 319.338 Z: 9092.96 dTdZ: 0.0184768
>> (0) T: 333.865 Z: 9864.11 dTdZ: 0.0179032
>> (0) T: 347.445 Z: 10662.9 dTdZ: 0.0162813
>> (0) T: 360.298 Z: 11487.6 dTdZ: 0.0156873
>> (0) T: 373.725 Z: 12338.1 dTdZ: 0.0160434
>> (0) T: 388.039 Z: 13216.7 dTdZ: 0.0161163
>> (0) T: 402.528 Z: 14125.3 dTdZ: 0.0154951
>> (0) T: 416.673 Z: 15064.6 dTdZ: 0.0152086
>> (0) T: 431.595 Z: 16036.5 dTdZ: 0.0157116
>> (0) T: 447.791 Z: 17045.2 dTdZ: 0.0169141
>> (0) T: 466.457 Z: 18097.7 dTdZ: 0.0181188
>> (0) T: 486.877 Z: 19202.4 dTdZ: 0.0184836
>> (0) U: 7.24182 Z: 26.2992 dUdZ: 0.00452681
>> (0) U: 7.53177 Z: 90.351 dUdZ: 0.00287064
>> (0) U: 7.67603 Z: 177.558 dUdZ: 0.00124111
>> (0) U: 7.77768 Z: 288.493 dUdZ: 0.000767294
>> (0) U: 7.86804 Z: 427.808 dUdZ: 0.000591649
>> (0) U: 7.96467 Z: 604.534 dUdZ: 0.000558145
>> (0) U: 8.0872 Z: 820.468 dUdZ: 0.000574196
>> (0) U: 8.2518 Z: 1104.6 dUdZ: 0.000430489
>> (0) U: 8.35573 Z: 1444.25 dUdZ: 0.00324907
>> (0) U: 10.4982 Z: 1796.01 dUdZ: 0.00458332
>> (0) U: 11.6468 Z: 2162.31 dUdZ: 0.00286422
>> (0) U: 13.0938 Z: 2702.22 dUdZ: 0.00288011
>> (0) U: 15.233 Z: 3407.48 dUdZ: 0.00231421
>> (0) U: 16.3562 Z: 4111.92 dUdZ: 0.000649345
>> (0) U: 16.147 Z: 4815.02 dUdZ: -0.000906107
>> (0) U: 15.0836 Z: 5516.41 dUdZ: -0.00116657
>> (0) U: 14.5115 Z: 6216.98 dUdZ: -0.000121356
>> (0) U: 14.9133 Z: 6919.17 dUdZ: 0.00109491
>> (0) U: 16.056 Z: 7627.6 dUdZ: 0.00175679
>> (0) U: 17.4259 Z: 8349.35 dUdZ: 0.00272068
>> (0) U: 20.0428 Z: 9092.96 dUdZ: 0.00369331
>> (0) U: 23.0203 Z: 9864.11 dUdZ: 0.00321505
>> (0) U: 25.0903 Z: 10662.9 dUdZ: 0.00225974
>> (0) U: 26.6889 Z: 11487.6 dUdZ: 0.00272598
>> (0) U: 29.6569 Z: 12338.1 dUdZ: 0.00388331
>> (0) U: 33.4039 Z: 13216.7 dUdZ: 0.00381624
>> (0) U: 36.4773 Z: 14125.3 dUdZ: 0.00254732
>> (0) U: 38.111 Z: 15064.6 dUdZ: 0.0015964
>> (0) U: 39.5283 Z: 16036.5 dUdZ: 0.00165963
>> (0) U: 41.3981 Z: 17045.2 dUdZ: 0.00252997
>> (0) U: 44.743 Z: 18097.7 dUdZ: 0.00346344
>> (0) U: 48.8695 Z: 19202.4 dUdZ: 0.00373518
>> (0) T: 269.386 dtdz: -999 N: -999
>> (0) T: 269.166 dtdz: -999 N: -999
>> (0) T: 269.102 dtdz: -999 N: -999
>> (0) T: 269.076 dtdz: -999 N: -999
>> (0) T: 269.067 dtdz: -999 N: -999
>> (0) T: 269.068 dtdz: -999 N: -999
>> (0) T: 269.077 dtdz: -999 N: -999
>> (0) T: 269.093 dtdz: -999 N: -999
>> (0) T: 269.118 dtdz: -999 N: -999
>> (0) T: 270.502 dtdz: -999 N: -999
>> (0) T: 272.674 dtdz: -999 N: -999
>> (0) T: 274.685 dtdz: -999 N: -999
>> (0) T: 277.1 dtdz: -999 N: -999
>> (0) T: 279.437 dtdz: -999 N: -999
>> (0) T: 281.421 dtdz: -999 N: -999
>> (0) T: 283.422 dtdz: -999 N: -999
>> (0) T: 286.003 dtdz: -999 N: -999
>> (0) T: 289.875 dtdz: -999 N: -999
>> (0) T: 296.174 dtdz: 0.0111892 N: 0.0192514
>> (0) T: 305.878 dtdz: 0.015808 N: 0.0225164
>> (0) T: 319.338 dtdz: 0.0184768 N: 0.0238244
>> (0) T: 333.865 dtdz: 0.0179032 N: 0.0229358
>> (0) T: 347.445 dtdz: 0.0162813 N: 0.0214406
>> (0) T: 360.298 dtdz: 0.0156873 N: 0.0206671
>> (0) T: 373.725 dtdz: 0.0160434 N: 0.0205214
>> (0) T: 388.039 dtdz: 0.0161163 N: 0.0201851
>> (0) T: 402.528 dtdz: 0.0154951 N: 0.0194327
>> (0) T: 416.673 dtdz: 0.0152086 N: 0.0189226
>> (0) T: 431.595 dtdz: 0.0157116 N: 0.0188976
>> (0) T: 447.791 dtdz: 0.0169141 N: 0.0192496
>> (0) T: 466.457 dtdz: 0.0181188 N: 0.0195206
>> (0) T: 486.877 dtdz: 0.0184836 N: 0.0192983
>> (0)
>> (0) eady growth rate: min=-0.000226797 max=0.000179462
>> (0,0) 4 value: 0.000179462
>> (0,1) 0 value: 0.000179462
>> (0,2) 245 value: 0.000179462
>> (0,3) 239 value: 0.000179462
>> (0) COR: 0.000127135 N: -999 dUdZ: 0.00452681 EGR: -999
>> (0) COR: 0.000127135 N: -999 dUdZ: 0.00287064 EGR: -999
>> (0) COR: 0.000127135 N: -999 dUdZ: 0.00124111 EGR: -999
>> (0) COR: 0.000127135 N: -999 dUdZ: 0.000767294 EGR: -999
>> (0) COR: 0.000127135 N: -999 dUdZ: 0.000591649 EGR: -999
>> (0) COR: 0.000127135 N: -999 dUdZ: 0.000558145 EGR: -999
>> (0) COR: 0.000127135 N: -999 dUdZ: 0.000574196 EGR: -999
>> (0) COR: 0.000127135 N: -999 dUdZ: 0.000430489 EGR: -999
>> (0) COR: 0.000127135 N: -999 dUdZ: 0.00324907 EGR: -999
>> (0) COR: 0.000127135 N: -999 dUdZ: 0.00458332 EGR: -999
>> (0) COR: 0.000127135 N: -999 dUdZ: 0.00286422 EGR: -999
>> (0) COR: 0.000127135 N: -999 dUdZ: 0.00288011 EGR: -999
>> (0) COR: 0.000127135 N: -999 dUdZ: 0.00231421 EGR: -999
>> (0) COR: 0.000127135 N: -999 dUdZ: 0.000649345 EGR: -999
>> (0) COR: 0.000127135 N: -999 dUdZ: -0.000906107 EGR: -999
>> (0) COR: 0.000127135 N: -999 dUdZ: -0.00116657 EGR: -999
>> (0) COR: 0.000127135 N: -999 dUdZ: -0.000121356 EGR: -999
>> (0) COR: 0.000127135 N: -999 dUdZ: 0.00109491 EGR: -999
>> (0) COR: 0.000127135 N: 0.0192514 dUdZ: 0.00175679 EGR: 3.59653e-06
>> (0) COR: 0.000127135 N: 0.0225164 dUdZ: 0.00272068 EGR: 4.76215e-06
>> (0) COR: 0.000127135 N: 0.0238244 dUdZ: 0.00369331 EGR: 6.10969e-06
>> (0) COR: 0.000127135 N: 0.0229358 dUdZ: 0.00321505 EGR: 5.52458e-06
>> (0) COR: 0.000127135 N: 0.0214406 dUdZ: 0.00225974 EGR: 4.15382e-06
>> (0) COR: 0.000127135 N: 0.0206671 dUdZ: 0.00272598 EGR: 5.1984e-06
>> (0) COR: 0.000127135 N: 0.0205214 dUdZ: 0.00388331 EGR: 7.45798e-06
>> (0) COR: 0.000127135 N: 0.0201851 dUdZ: 0.00381624 EGR: 7.45128e-06
>> (0) COR: 0.000127135 N: 0.0194327 dUdZ: 0.00254732 EGR: 5.16625e-06
>> (0) COR: 0.000127135 N: 0.0189226 dUdZ: 0.0015964 EGR: 3.32495e-06
>> (0) COR: 0.000127135 N: 0.0188976 dUdZ: 0.00165963 EGR: 3.46123e-06
>> (0) COR: 0.000127135 N: 0.0192496 dUdZ: 0.00252997 EGR: 5.17988e-06
>> (0) COR: 0.000127135 N: 0.0195206 dUdZ: 0.00346344 EGR: 6.99261e-06
>> (0) COR: 0.000127135 N: 0.0192983 dUdZ: 0.00373518 EGR: 7.62815e-06
>> (0,0) 4 value: 0.000179462
>> (0,1) 0 value: 0.000179462
>> (0,2) 245 value: 0.000179462
>> (0,3) 239 value: 0.000179462
>>
>> Variable: lat
>> Type: float
>> Total Size: 99279180 bytes
>> 24819795 values
>> Number of Dimensions: 3
>> Coordinates:
>> Number Of Attributes: 5
>> FieldType : 104
>> MemoryOrder : XY
>> description : LATITUDE, SOUTH IS NEGATIVE
>> units : degree_north
>> stagger :
>>
>> Variable: lon
>> Type: float
>> Total Size: 99279180 bytes
>> 24819795 values
>> Number of Dimensions: 3
>> Dimensions and sizes: [Time | 145] x [south_north | 429] x [west_east | 399]
>> Coordinates:
>> Number Of Attributes: 5
>> FieldType : 104
>> MemoryOrder : XY
>> description : LONGITUDE, WEST IS NEGATIVE
>> units : degree_east
>> stagger :
>> (0) writing EGR...
>> (0) writing LAT...
>> ncendef: ncid 131072: NetCDF: One or more variable sizes violate format
>> constraints
>> ncvarput: ncid 131072: NetCDF: Operation not allowed in define mode
>> fatal:NetCdf: An error occurred while attempting to write variable (lat) to
>> file (eady.nc)
>> fatal:Execute: Error occurred at or near line 260 in file EADY.ncl
>>
>> ncclose: ncid 131072: NetCDF: One or more variable sizes violate format
>> constraints
>> pacman3 2236%
>>
>>
>> --
>> regards
>>
>> *******************************************************
>> Alexander Semenov
>>
>> PhD Student - Research Assistant
>> International Arctic Research Center
>> Department of atmospheric sciences
>> University of Alaska Fairbanks
>>
>> 930 Koyukuk dr, 408c3
>> Fairbanks, AK, USA, 99775
>> work phone +19074742672
>>
>>
>> _______________________________________________
>> ncl-talk mailing list
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>>
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Received on Tue Feb 21 12:59:24 2012