R help - Sep 2011 - Error: in routine alloca() there is a stack overflow: thread 0, max 535822282KB, used 0KB, request 24B

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

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In a previous post I detailed the error indicated in the subject. I am
posting now to indicate the problem was likely an incompatibility between
the versions of netcdf (3.6.2) and ncdf (1.6.5). What I did to resolve the
problem was install netcdf-4.1.3 and then reinstalled ncdf_1.6.5.

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