[R] ncdf size error

[David W. Pierce]

Remember, you have to *also* set force_v4=TRUE in the nc_create() call.

Regards,

--Dave

On Tue, Sep 16, 2014 at 2:01 PM, Hernan A. Moreno Ramirez
<hmorenor at uwyo.edu> wrote:
> Hi Professor,
>
> Thanks for you valuable help. I did change my code to use ncdf4 package and still I get the same error:
>
> ##### Exporting to NETCDF files #################################################################
> # define the netcdf coordinate variables -- note these have values!
> library(ncdf4)
> cat("--Exporting final NETCDF file to Outputfolder",fill=TRUE)
> dim1 = ncdim_def( "Nodes","", seq(1,19000))
> dim2= ncdim_def( "Time","Hours since 2005-01-01 00:00:00",seq(1:2190)) #final[1,2,]))
> #dim2= dim.def.ncdf( "Time","",as.data.frame(final[1,2,]))
>
>
> # define the EMPTY (elevation) netcdf variable
> varT2 = ncvar_def("T2","celsius", list(dim1,dim2), -99999, longname="T2")
> varQ2 = ncvar_def("Q2","kg kg-1", list(dim1,dim2), -99999, longname="Q2")
> varQVAPOR = ncvar_def("QVAPOR","kg kg-1", list(dim1,dim2), -99999, longname="QVAPOR")
> varQCLOUD = ncvar_def("QCLOUD","kg kg-1", list(dim1,dim2), -99999, longname="QCLOUD")
> varPSFC = ncvar_def("PSFC","Pa", list(dim1,dim2), -99999, longname="PSFC")
> varW10 = ncvar_def("W10","ms-1", list(dim1,dim2), -99999, longname="W10")
> varW = ncvar_def("W","ms-1", list(dim1,dim2), -99999, longname="W")
> varVEGFRA = ncvar_def("VEGFRA","", list(dim1,dim2), -99999, longname="VEGFRA")
> varMAXVEGFRA = ncvar_def("MAXVEGFRA","", list(dim1,dim2), -99999, longname="MAXVEGFRA")
> varTPREC = ncvar_def("TPREC","mm", list(dim1,dim2), -99999, longname="TPREC")
> varFRAC_FROZ_PREC = ncvar_def("FRAC_FROZ_PREC","mm", list(dim1,dim2), -99999, longname="FRAC_FROZ_PREC")
> varSWDOWN = ncvar_def("SWDOWN","W m-2", list(dim1,dim2), -99999, longname="SWDOWN")
> varGLW = ncvar_def("GLW","W m-2", list(dim1,dim2), -99999, longname="GLW")
> varPBLH = ncvar_def("PBLH","m", list(dim1,dim2), -99999, longname="PBLH")
> varTSLB = ncvar_def("TSLB","Celsius", list(dim1,dim2), -99999, longname="TSLB")
>
> nc.ex = nc_create("/media/D/output.nc",list(varT2, varQ2, varQVAPOR, varQCLOUD, varPSFC, varW10, varW, varVEGFRA, varMAXVEGFRA, varTPREC, varFRAC_FROZ_PREC, varSWDOWN, varGLW, varPBLH, varTSLB))
>
> Error in R_nc4_enddef: NetCDF: One or more variable sizes violate format constraints
> Error in R_nc4_sync: NetCDF: Operation not allowed in define mode
>
> Thanks a lot for more help
>
> ---------------------------------------------------------------------------------------
> Hernan A. Moreno, Ph.D.
> Postdoctoral Research Associate
> Department of Civil & Architectural Engineering
> Room 3038, Engineering Building
> University of Wyoming
> Phone: 480-3990571
> http://www.public.asu.edu/~hamoreno/
>
> ________________________________________
> From: davidwilliampierce at gmail.com <davidwilliampierce at gmail.com> on behalf of David W. Pierce <dpierce at ucsd.edu>
> Sent: Tuesday, September 16, 2014 2:21 PM
> To: Hernan A. Moreno Ramirez
> Cc: r-help at r-project.org
> Subject: Re: [R] ncdf size error
>
> On Tue, Sep 16, 2014 at 11:36 AM, Hernan A. Moreno Ramirez
> <hmorenor at uwyo.edu> wrote:
>> Sure, here it is. Thanks for any help with this Dr. Pierce:
>>
>>
>> ##### Exporting to NETCDF files #################################################################
>> # define the netcdf coordinate variables
>> library(ncdf)
>
> ... rest of example omitted ...
>
> Hi Hernan,
>
> The file you are trying to make is violating size constraints imposed
> by the netcdf library/R interface, which is 2 GB in the R ncdf
> package. To get around this switch to the R ncdf4 package, which is
> the replacement for the ncdf package (I stopped supporting the ncdf
> package in 2010) and set force_v4=TRUE in the nc_create() call. This
> requires a modern version of the netcdf library to be installed on
> your machine, which it probably is, since the netcdf version 4 library
> has been out for many years now.
>
> Regards,
>
> --Dave
>
>> http://www.public.asu.edu/~hamoreno/
>>
>> ________________________________________
>> From: davidwilliampierce at gmail.com <davidwilliampierce at gmail.com> on behalf of David W. Pierce <dpierce at ucsd.edu>
>> Sent: Monday, September 15, 2014 7:00 PM
>> To: Hernan A. Moreno Ramirez
>> Cc: r-help at r-project.org
>> Subject: Re: [R] ncdf size error
>>
>> On Mon, Sep 15, 2014 at 4:20 PM, Hernan A. Moreno Ramirez
>> <hmorenor at uwyo.edu> wrote:
>>>
>>> Hi I am using both ncdf and ncdf4 libraries and with both I keep getting the
>>> same error: Error in R_nc_enddef: NetCDF: One or more variable sizes violate
>>> format constraints. Error in R_nc_sync: NetCDF: Operation not allowed in
>>> define mode. This happens when I try to create.ncdf() a file with more than
>>> 13 variables. I think is a problem of memory size. What would you recommend?
>>> Any help will be appreciated
>>
>> Hi Hernan,
>>
>> can you supply an example that shows the problem?
>>
>> Regards,
>>
>> --Dave
>>
>> -------------------
>> David W. Pierce
>> Division of Climate, Atmospheric Science, and Physical Oceanography
>> Scripps Institution of Oceanography, La Jolla, California, USA
>> (858) 534-8276 (voice)  /  (858) 534-8561 (fax)    dpierce at ucsd.edu
>
>
>
> --
> David W. Pierce
> Division of Climate, Atmospheric Science, and Physical Oceanography
> Scripps Institution of Oceanography, La Jolla, California, USA
> (858) 534-8276 (voice)  /  (858) 534-8561 (fax)    dpierce at ucsd.edu



-- 
David W. Pierce
Division of Climate, Atmospheric Science, and Physical Oceanography
Scripps Institution of Oceanography, La Jolla, California, USA
(858) 534-8276 (voice)  /  (858) 534-8561 (fax)    dpierce at ucsd.edu