[ncl-talk] Segmentation fault (core dumped) when mpDataBaseVersion = "HighRes", new NCL build on Ubuntu

[Rick Brownrigg]

Hi Oresti,

Its not the parenthesis, and Ubuntu should be able to handle that fine. To
do an "ls" on those files, you'd need to escape the "(" as the bash shell
otherwise interprets it:

   ls \(0*

Its hard to say what's causing the SEGV. Can you run NCL under gdb and send
me the backtrace?

gdb ncl
...
(gdb) run ...name_of_your_script...
.....
...when the program SEGV's
(gdb) bt
....send me the output generated here..

Thanks
Rick

On Thu, Mar 21, 2019 at 8:19 AM Orestis Speyer <ospeyer at meteo.noa.gr> wrote:

> Kind reminder,
>
> I looked further and I am thinking that perhaps it is the fault in the
> naming of the rangs and gshhs files,
> in particular the parentheses "(" which is a special character and I think
> Ubuntu has trouble with.
>
> I have successfully run the script in:
> Distributor ID: RedHatEnterpriseServer
> Description:    Red Hat Enterprise Linux Server release 6.9 (Santiago)
> Release:        6.9
> Codename:       Santiago
>
> I get the segmentation error when running in Ubuntu:
> Distributor ID: Ubuntu
> Description:    Ubuntu 18.04.2 LTS
> Release:        18.04
> Codename:       bionic
>
> the rangs directory looks like this:
> -rw-r--r-- 1 root root 89496428 Μαΐ  13  1997 'gshhs(0).rim'
> -rw-r--r-- 1 root root 20775224 Μαΐ  13  1997 'gshhs(1).rim'
> -rw-r--r-- 1 root root  5099196 Μαΐ  13  1997 'gshhs(2).rim'
> -rw-r--r-- 1 root root  1109192 Μαΐ  13  1997 'gshhs(3).rim'
> -rw-r--r-- 1 root root   170948 Μαΐ  13  1997 'gshhs(4).rim'
> -rw-r--r-- 1 root root   259200 Μαρ  19 16:48 'rangs(0).cat'
> -rw-r--r-- 1 root root  6518664 Μαρ  19 16:48 'rangs(0).cel'
> -rw-r--r-- 1 root root   259200 Μαρ  19 16:48 'rangs(1).cat'
> -rw-r--r-- 1 root root  5945492 Μαρ  19 16:48 'rangs(1).cel'
> -rw-r--r-- 1 root root   259200 Μαρ  19 16:48 'rangs(2).cat'
> -rw-r--r-- 1 root root  4062215 Μαρ  19 16:48 'rangs(2).cel'
> -rw-r--r-- 1 root root   259200 Μαρ  19 16:48 'rangs(3).cat'
> -rw-r--r-- 1 root root  3398642 Μαρ  19 16:48 'rangs(3).cel'
> -rw-r--r-- 1 root root   259200 Μαρ  19 16:48 'rangs(4).cat'
> -rw-r--r-- 1 root root  3045848 Μαρ  19 16:48 'rangs(4).cel'
>
> The single quotes in the filenames come automatically (for Ubuntu to be
> able
> to handle them) when I download them.
>
> I know that NCL is looking for this file because when I have HighRes and
> when I deliberately export NCARG_RANGS to a different directory, I get
> fatal:MapRGDHDrawMapList: MDRGOL/MDRGOF - ERROR OPENING RANGS/GSHHS CAT.
> When I export NCARG_RANGS= /usr/share/ncarg/database/rangs I get the
> segmentation fault.
>
> Is it an environment thing? Is it Is it a permission thing? I tried running
> with sudo to no avail. I don't know how NCL "reads" these files. Final
> note,
>
> Using ls I get:
> ls gshhs(0).rim
> bash: syntax error near unexpected token `('
> with quotes:
> ls 'gshhs(0).rim'
> 'gshhs(0).rim'
>
> Thanks again for your time,
> Orestis
>
>
>
>
>
>
>
> -----Original Message-----
> From: ospeyer [mailto:ospeyer at noa.gr]
> Sent: Tuesday, March 19, 2019 6:09 PM
> To: ncl-talk at ucar.edu
> Subject: Segmentation fault (core dumped) when mpDataBaseVersion =
> "HighRes", new NCL build on Ubuntu
>
>
>
> Deal all,
>
> I just installed NCL 6.4.0 through the Ubuntu Software in my desktop within
> an Ubuntu virtual machine with 5GB of RAM.
> I am trying to run a script (which runs successfully on a 4gb laptop, with
> a
> virtual machine of 2GB of RAM) but I get a  Segmentation fault (core
> dumped).
> When I use mpDataBaseVersion = "LowRes" it works fine, although no colors
> appear on my contour plot (the label bar has colours just fine).
>
> Is it possible that I run out of memory for some reason? I am suspicious of
> the new build. I followed the rangs procedure for high resolution
> coastlines. I do not know if it's important but the NCARG_ROOT is not set
> as
> in the default that I find in the NCL site. My suspicion increases due to
> the lack of colour in the contour (I'm using
> gsn_define_colormap(wks,"gui_default")).
>
>
> In my script I load:
> load "/usr/share/ncarg/nclscripts/csm/gsn_code.ncl"
> load "/usr/share/ncarg/nclscripts/csm/gsn_csm.ncl"
> load "/usr/share/ncarg/nclscripts/csm/contributed.ncl"
> load "./shapefile_utils.ncl" ; This I need for shapefiles
>
> I found a relative thread in the ncl-archive under "[ncl-talk]
> mpDataBaseVersion ="HighRes" " but there was no solution therein.
>
> Cheers and thanks for your time,
>
> Orestis Speyer, MSc
>
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