Dear Colleagues:

Through your help an R related installation issue was resolved, but I now
have the following usage issue.

On any "get.var.ncdf" usage I am seeing:

         Error: in routine alloca() there is a stack overflow: thread 0, max
535822282KB, used 0KB, request 24B

The same error is posted on a file as small as 50MB and as large as 500GB,
with ulimit set to unlimited. I have seen the 'double netcdf import'
references and do not feel that is an issue as netcdf is not being imported
(i.e. fails with and without the import). The system is: Red Hat Enterprise
Linux AS release 4 (Nahant Update 5), using R-2.13.1 with the latest ncdf
package, and netcdf-3.6.2. If someone suggests the latest netcdf, please
point me to an associated symptom/fix reference if one is available, but
that is likely my next step.

Your assistance is greatly appreciated.

### Here is the relevant portion of the R script:

# load R libraries
  library(ncdf)
  library(maps)
  library(fields)

# file path
  gcfilename <-
"/users/me/MEGANv2.04/Output/latlong_spec2_WOCONV_150s_2004187.ncf"
  gcfilename.ori <-
"/users/me/MEGANv2.04/Output/latlong_spec2_WOCONV_2001187.ncf"

  # ----------------
  # Open file
  # ----------------
  nc      <- open.ncdf(gcfilename)
  nc.ori      <- open.ncdf(gcfilename.ori)

  print ("fininshed open file")
  print(nc)

  print("Reading TFLAG")

 # error occurs on any of the following "get.var.ncdf" calls:

  tflag<-  get.var.ncdf(nc,varid="TFLAG")   # So this would produce the
failure
  isop <-  get.var.ncdf(nc,varid="ISOPRENE")
  isop.ori <-  get.var.ncdf(nc.ori,varid="ISOPRENE")
  meoh <-  get.var.ncdf(nc,varid="MEOH")
  meoh.ori <-  get.var.ncdf(nc.ori,varid="MEOH")


### Here is the output associated with the print ("fininshed open file") and
print(nc) portion of the script:

[1] "fininshed open file"
[1] "file /users/me/latlong_spec2_WOCONV_150s_2004187.ncf has 6 dimensions:"
[1] "TSTEP   Size: 2"
[1] "DATE-TIME   Size: 2"
[1] "LAY   Size: 1"
[1] "VAR   Size: 30"
[1] "ROW   Size: 1200"
[1] "COL   Size: 2496"
[1] "------------------------"
[1] "file
/users/huxxx249/MEGANv2.04/Output/latlong_spec2_WOCONV_150s_2004187.ncf has
31 variables:"
[1] "int TFLAG[DATE-TIME,VAR,TSTEP]  Longname:TFLAG            Missval:NA"
[1] "float ISOPRENE[COL,ROW,LAY,TSTEP]  Longname:ISOPRENE
Missval:1e+30"
[1] "float TRP1[COL,ROW,LAY,TSTEP]  Longname:TRP1             Missval:1e+30"
[1] "float MEOH[COL,ROW,LAY,TSTEP]  Longname:MEOH             Missval:1e+30"
[1] "float ACET[COL,ROW,LAY,TSTEP]  Longname:ACET             Missval:1e+30"
[1] "float CH4[COL,ROW,LAY,TSTEP]  Longname:CH4              Missval:1e+30"
[1] "float NO[COL,ROW,LAY,TSTEP]  Longname:NO               Missval:1e+30"
[1] "float NO2[COL,ROW,LAY,TSTEP]  Longname:NO2              Missval:1e+30"
[1] "float NH3[COL,ROW,LAY,TSTEP]  Longname:NH3              Missval:1e+30"
[1] "float CCHO[COL,ROW,LAY,TSTEP]  Longname:CCHO             Missval:1e+30"
[1] "float HCOOH[COL,ROW,LAY,TSTEP]  Longname:HCOOH
Missval:1e+30"
[1] "float HCHO[COL,ROW,LAY,TSTEP]  Longname:HCHO             Missval:1e+30"
[1] "float CCO_OH[COL,ROW,LAY,TSTEP]  Longname:CCO_OH
Missval:1e+30"
[1] "float BALD[COL,ROW,LAY,TSTEP]  Longname:BALD             Missval:1e+30"
[1] "float MEK[COL,ROW,LAY,TSTEP]  Longname:MEK              Missval:1e+30"
[1] "float RCO_OH[COL,ROW,LAY,TSTEP]  Longname:RCO_OH
Missval:1e+30"
[1] "float CO[COL,ROW,LAY,TSTEP]  Longname:CO               Missval:1e+30"
[1] "float ETHENE[COL,ROW,LAY,TSTEP]  Longname:ETHENE
Missval:1e+30"
[1] "float ALK1[COL,ROW,LAY,TSTEP]  Longname:ALK1             Missval:1e+30"
[1] "float ALK2[COL,ROW,LAY,TSTEP]  Longname:ALK2             Missval:1e+30"
[1] "float ALK3[COL,ROW,LAY,TSTEP]  Longname:ALK3             Missval:1e+30"
[1] "float ALK4[COL,ROW,LAY,TSTEP]  Longname:ALK4             Missval:1e+30"
[1] "float ALK5[COL,ROW,LAY,TSTEP]  Longname:ALK5             Missval:1e+30"
[1] "float ARO1[COL,ROW,LAY,TSTEP]  Longname:ARO1             Missval:1e+30"
[1] "float ARO2[COL,ROW,LAY,TSTEP]  Longname:ARO2             Missval:1e+30"
[1] "float OLE1[COL,ROW,LAY,TSTEP]  Longname:OLE1             Missval:1e+30"
[1] "float OLE2[COL,ROW,LAY,TSTEP]  Longname:OLE2             Missval:1e+30"
[1] "float RCHO[COL,ROW,LAY,TSTEP]  Longname:RCHO             Missval:1e+30"
[1] "float NONR[COL,ROW,LAY,TSTEP]  Longname:NONR             Missval:1e+30"
[1] "float LAT[COL,ROW,LAY,TSTEP]  Longname:LAT              Missval:1e+30"
[1] "float LONG[COL,ROW,LAY,TSTEP]  Longname:LONG             Missval:1e+30"
[1] "Reading TFLAG"
Error: in routine alloca() there is a
stack overflow: thread 0, max 535822282KB, used 0KB, request 24B

	[[alternative HTML version deleted]]

