[ncl-talk] Segmentation fault with addfiles and addfile

[Jenney,Andrea]

Thanks Dennis and Gus for your help,

addfile(s) ended up not being the issue. I found a bug further down in my code from trying convert my f variable (the output of addfile) to character data type (i.e., tochar(f)). I fixed this and everything works as it should now. Interestingly, I am no longer getting the "file format not supported or file is corrupted" message.

---
Andrea Jenney
PhD Candidate | Randall & Barnes Groups
Colorado State University | Dept. of Atmospheric Science

On Aug 27, 2019, at 1:55 PM, Gus Correa via ncl-talk <ncl-talk at ucar.edu<mailto:ncl-talk at ucar.edu>> wrote:

Hi Jenney

1) Maybe a missing trailing "/" in the "dir" variable?
This would make the file names wrong, and could explain the error message
Error: "warning:_NclOpenFile: Can not open file <filename> file format not supported or file is corrupted"

2) Have you tried to add
print(files)
after
files=systemfunc(...)
to check what is in the "files" variable, just to see if it is really what you want?
Once you know the "files" variable is correct, you can comment out that "print".

I hope this helps,
Gus Correa

On Tue, Aug 27, 2019 at 2:43 PM Jenney,Andrea via ncl-talk <ncl-talk at ucar.edu<mailto:ncl-talk at ucar.edu>> wrote:
All,

I’m getting a segmentation fault error when using addfile and addfiles to read in netcdf files. Each single file is a monthly mean (only one time step) of many variables that are resolved in space. I’ve uploaded an example file to the link, (file is called "spcesm_cam5_control.cam.h0.1910-05.nc<http://spcesm_cam5_control.cam.h0.1910-05.nc/>"): http://saddleback.atmos.colostate.edu/rr/docexch.php. Running ncl_filedump and ncl_convert2nc on the files works fine and everything looks great. The non-ncl ncview and ncdump also show that things look normal to me. My files are smaller than 400 MB each, all variables are 3D or smaller, and the largest dimension is length 144.

Relevant code:
(when using addfiles)

fnameIn = dir + "spcesm_cam5_*.h0.*.nc"
files = systemfunc("ls "+fnameIn)
f     = addfiles(files, "r") ; <- Error: "warning:_NclOpenFile: Can not open file <filename> file format not supported or file is corrupted"


(when using addfile)
fnameIn = dir + "spcesm_cam5_*.h0.*.nc"
files = systemfunc("ls "+fnameIn)
nf    = dimsizes(files)
do ifile = 0,nf-1
f = addfile(files(ifile), "r") ; <- Error: "Segmentation fault"
…
end do

Thanks in advance for your help
---
Andrea Jenney
PhD Candidate | Randall & Barnes Groups
Colorado State University | Dept. of Atmospheric Science

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