[ncl-talk] Crashing with bad OpenDAP Link

Rick Brownrigg brownrig at ucar.edu
Tue Mar 6 09:04:52 MST 2018 

Hi Carl,

Looking at output from "strace" while the addfiles statement runs indicates
there are two variables of the same name in that file, but of different
dimensions, -- V-component_of_wind(179,1,181,360) and
V-component_of_wind(1,1,190,384).  I'd surmise that's the likely source of
the "double free or corruption" error message. In any case, I unfortunately
don't know how to work around that, offhand. The error seems to be
happening within the NetCDF library. I'll look into it further, but the
question is whether NCL ever gets a chance to field that error from the
library.

Wish I had a better answer...
Rick

On Mon, Mar 5, 2018 at 12:57 PM, Carl Schreck <cjschrec at ncsu.edu> wrote:

> I'm having an issue trying to read some CFS-Reforecast data through
> OpenDAP in NCL. Most files work, but there are occasional ones that make
> NCL crash pretty hard (see output below). One such file is this one
> <https://nomads.ncdc.noaa.gov/thredds/dodsC/cfsr-hpr-ts45/wnd200_f/2006/200601/catalog.html?dataset=cfsr-hpr-ts45/wnd200_f/2006/200601/wnd200_f.01.2006012406.2006031006.2006012406.grb2>
> .
>
> Any suggestions on how I can detect a bad file like this before it crashes
> NCL? Just passing it to addfile causes the crash.
>
> Thanks!
> Carl
>
>  Copyright (C) 1995-2017 - All Rights Reserved
>  University Corporation for Atmospheric Research
>  NCAR Command Language Version 6.4.1-04May2017_1732
>  The use of this software is governed by a License Agreement.
>  See http://www.ncl.ucar.edu/ for more details.
> *ncl 0>
> f=addfile("https://nomads.ncdc.noaa.gov/thredds/dodsC/cfsr-hpr-ts45/wnd200_f/2006/200601/wnd200_f.01.2006012406.2006031006.2006012406.grb2
> <https://nomads.ncdc.noaa.gov/thredds/dodsC/cfsr-hpr-ts45/wnd200_f/2006/200601/wnd200_f.01.2006012406.2006031006.2006012406.grb2>","r")*
> Duplicate dataset field names: cfsr-hpr-ts45%2fwnd200_f%
> 2f2006%2f200601%2fwnd200_f%2e01%2e2006012406%2e2006031006%2e2006012406%
> 2egrb2
> context: Dataset { Float32 U-component_of_wind[time1 = 177][pressure =
> 1][lat = 181][lon = 360]; Float32 V-component_of_wind[time = 179][pressure
> = 1][lat = 181][lon = 360]; Int32 time[time = 179]; Int32 time1[time1 =
> 177]; Float64 lat[lat = 181]; Float64 lon[lon = 360]; String
> latLonCoordSys; Float64 pressure[pressure = 1]; Float32
> V-component_of_wind[time2 = 1][height_above_ground = 1][lat = 190][lon =
> 384]; Int32 time[time = 179]; Int32 time1[time1 = 177]; Int32 time2[time2 =
> 1]; Float64 lat[lat = 190]; Float64 gaussw[lat = 190]; Float64 lon[lon =
> 384]; String latLonCoordSys; Float64 height_above_ground[height_above_ground
> = 1]; Float64 pressure[pressure = 1];} cfsr-hpr-ts45%2fwnd200_f%
> 2f2006%2f200601%2fwnd200_f%2e01%2e2006012406%2e2006031006%2e2006012406%
> 2egrb2;^
> *** Error in `ncl': double free or corruption (!prev): 0x000000000d932fb0
> ***
> ======= Backtrace: =========
> /usr/lib64/libc.so.6(+0x7c619)[0x7f7eb746b619]
> ncl(ocfree+0x1f)[0xe8034e]
> ncl(ocnodes_free+0x1e0)[0xe86800]
> ncl[0xec6099]
> ncl(DAPparse+0x1f5)[0xec632a]
> ncl(ocfetch+0x2dd)[0xe83db8]
> ncl(oc_fetch+0x79)[0xe7a600]
> ncl(dap_fetch+0x17f)[0xebd349]
> ncl[0xe782b0]
> ncl(NCD2_open+0x4a5)[0xe73fc1]
> ncl(NC_open+0x2a0)[0xe3f06c]
> ncl(nc__open+0x46)[0xe3e521]
> ncl[0x822ca9]
> ncl(_NclFileCreate+0x3c7)[0x805302]
> ncl(_NclOpenFile+0x483)[0x7d0b69]
> ncl(_NclIAddFile+0x1b7)[0x8cd741]
> ncl(CallINTRINSIC_FUNC_CALL+0x43)[0x8a2b48]
> ncl(_NclExecute+0x3eb)[0x8ae005]
> ncl(yyparse+0x6bd)[0x777de9]
> ncl(NclDriver+0xc16)[0x774025]
> ncl(main+0x9)[0x7707b6]
> /usr/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f7eb7410c05]
> ncl[0x7706e1]
> ======= Memory map: ========
> 00400000-02846000 r-xp 00000000 00:4a 771250262
> /snfs2/home/carl/ncl_ncarg/bin/ncl
> 02a45000-02b12000 r--p 02445000 00:4a 771250262
> /snfs2/home/carl/ncl_ncarg/bin/ncl
> 02b12000-02c61000 rw-p 02512000 00:4a 771250262
> /snfs2/home/carl/ncl_ncarg/bin/ncl
> 02c61000-06512000 rw-p 00000000 00:00 0
> 08214000-0d956000 rw-p 00000000 00:00 0
> [heap]
> 7f7eac000000-7f7eac021000 rw-p 00000000 00:00 0
> 7f7eac021000-7f7eb0000000 ---p 00000000 00:00 0
> 7f7eb37d7000-7f7eb380c000 r--s 00000000 fd:01 1611467726
>  /var/db/nscd/hosts
> 7f7eb380c000-7f7eb3a0d000 rw-p 00000000 00:00 0
> 7f7eb3a0d000-7f7eb3a6d000 r-xp 00000000 fd:01 1077832509
>  /usr/lib64/libpcre.so.1.2.0
> 7f7eb3a6d000-7f7eb3c6d000 ---p 00060000 fd:01 1077832509
>  /usr/lib64/libpcre.so.1.2.0
> 7f7eb3c6d000-7f7eb3c6e000 r--p 00060000 fd:01 1077832509
>  /usr/lib64/libpcre.so.1.2.0
> 7f7eb3c6e000-7f7eb3c6f000 rw-p 00061000 fd:01 1077832509
>  /usr/lib64/libpcre.so.1.2.0
> 7f7eb3c6f000-7f7eb3c71000 r-xp 00000000 fd:01 1076477375
>  /usr/lib64/libfreebl3.so
> 7f7eb3c71000-7f7eb3e70000 ---p 00002000 fd:01 1076477375
>  /usr/lib64/libfreebl3.so
> 7f7eb3e70000-7f7eb3e71000 r--p 00001000 fd:01 1076477375
>  /usr/lib64/libfreebl3.so
> 7f7eb3e71000-7f7eb3e72000 rw-p 00002000 fd:01 1076477375
>  /usr/lib64/libfreebl3.so
> 7f7eb3e72000-7f7eb3e96000 r-xp 00000000 fd:01 1074687352
>  /usr/lib64/libselinux.so.1
> 7f7eb3e96000-7f7eb4095000 ---p 00024000 fd:01 1074687352
>  /usr/lib64/libselinux.so.1
> 7f7eb4095000-7f7eb4096000 r--p 00023000 fd:01 1074687352
>  /usr/lib64/libselinux.so.1
> 7f7eb4096000-7f7eb4097000 rw-p 00024000 fd:01 1074687352
>  /usr/lib64/libselinux.so.1
> 7f7eb4097000-7f7eb4099000 rw-p 00000000 00:00 0
> 7f7eb4099000-7f7eb409b000 r-xp 00000000 fd:01 1078494182
>  /usr/lib64/libXau.so.6.0.0
> 7f7eb409b000-7f7eb429b000 ---p 00002000 fd:01 1078494182
>  /usr/lib64/libXau.so.6.0.0
> 7f7eb429b000-7f7eb429c000 r--p 00002000 fd:01 1078494182
>  /usr/lib64/libXau.so.6.0.0
> 7f7eb429c000-7f7eb429d000 rw-p 00003000 fd:01 1078494182
>  /usr/lib64/libXau.so.6.0.0
> 7f7eb429d000-7f7eb42a4000 r-xp 00000000 fd:01 1078457975
>  /usr/lib64/librt-2.17.so
> 7f7eb42a4000-7f7eb44a3000 ---p 00007000 fd:01 1078457975
>  /usr/lib64/librt-2.17.so
> 7f7eb44a3000-7f7eb44a4000 r--p 00006000 fd:01 1078457975
>  /usr/lib64/librt-2.17.so
> 7f7eb44a4000-7f7eb44a5000 rw-p 00007000 fd:01 1078457975
>  /usr/lib64/librt-2.17.so
> 7f7eb44a5000-7f7eb44ad000 r-xp 00000000 fd:01 1075307386
>  /usr/lib64/libcrypt-2.17.so
> 7f7eb44ad000-7f7eb46ac000 ---p 00008000 fd:01 1075307386
>  /usr/lib64/libcrypt-2.17.so
> 7f7eb46ac000-7f7eb46ad000 r--p 00007000 fd:01 1075307386
>  /usr/lib64/libcrypt-2.17.so
> 7f7eb46ad000-7f7eb46ae000 rw-p 00008000 fd:01 1075307386
>  /usr/lib64/libcrypt-2.17.so
> 7f7eb46ae000-7f7eb46dc000 rw-p 00000000 00:00 0
> 7f7eb46dc000-7f7eb46df000 r-xp 00000000 fd:01 1074820322
>  /usr/lib64/libkeyutils.so.1.5
> 7f7eb46df000-7f7eb48de000 ---p 00003000 fd:01 1074820322
>  /usr/lib64/libkeyutils.so.1.5
> 7f7eb48de000-7f7eb48df000 r--p 00002000 fd:01 1074820322
>  /usr/lib64/libkeyutils.so.1.5
> 7f7eb48df000-7f7eb48e0000 rw-p 00003000 fd:01 1074820322
>  /usr/lib64/libkeyutils.so.1.5
> 7f7eb48e0000-7f7eb48ed000 r-xp 00000000 fd:01 1074821491
>  /usr/lib64/libkrb5support.so.0.1
> 7f7eb48ed000-7f7eb4aec000 ---p 0000d000 fd:01 1074821491
>  /usr/lib64/libkrb5support.so.0.1
> 7f7eb4aec000-7f7eb4aed000 r--p 0000c000 fd:01 1074821491
>  /usr/lib64/libkrb5support.so.0.1
> 7f7eb4aed000-7f7eb4aee000 rw-p 0000d000 fd:01 1074821491
>  /usr/lib64/libkrb5support.so.0.1
> 7f7eb4aee000-7f7eb4b29000 r-xp 00000000 fd:01 1075015850
>  /usr/lib64/libquadmath.so.0.0.0
> 7f7eb4b29000-7f7eb4d28000 ---p 0003b000 fd:01 1075015850
>  /usr/lib64/libquadmath.so.0.0.0
> 7f7eb4d28000-7f7eb4d29000 r--p 0003a000 fd:01 1075015850
>  /usr/lib64/libquadmath.so.0.0.0
> 7f7eb4d29000-7f7eb4d2a000 rw-p 0003b000 fd:01 1075015850
>  /usr/lib64/libquadmath.so.0.0.0
> 7f7eb4d2a000-7f7eb4d51000 r-xp 00000000 fd:01 1143288053
>  /usr/lib64/libxcb.so.1.1.0
> 7f7eb4d51000-7f7eb4f50000 ---p 00027000 fd:01 1143288053
>  /usr/lib64/libxcb.so.1.1.0
> 7f7eb4f50000-7f7eb4f51000 r--p 00026000 fd:01 1143288053
>  /usr/lib64/libxcb.so.1.1.0
> 7f7eb4f51000-7f7eb4f52000 rw-p 00027000 fd:01 1143288053
>  /usr/lib64/libxcb.so.1.1.0
> 7f7eb4f52000-7f7eb4f79000 r-xp 00000000 fd:01 1074687455
>  /usr/lib64/libexpat.so.1.6.0
> 7f7eb4f79000-7f7eb5179000 ---p 00027000 fd:01 1074687455
>  /usr/lib64/libexpat.so.1.6.0
> 7f7eb5179000-7f7eb517b000 r--p 00027000 fd:01 1074687455
>  /usr/lib64/libexpat.so.1.6.0
> 7f7eb517b000-7f7eb517c000 rw-p 00029000 fd:01 1074687455
>  /usr/lib64/libexpat.so.1.6.0
> 7f7eb517c000-7f7eb521c000 r-xp 00000000 fd:01 1142930368
>  /usr/lib64/libfreetype.so.6.10.0
> 7f7eb521c000-7f7eb541b000 ---p 000a0000 fd:01 1142930368
>  /usr/lib64/libfreetype.so.6.10.0
> 7f7eb541b000-7f7eb5421000 r--p 0009f000 fd:01 1142930368
>  /usr/lib64/libfreetype.so.6.10.0
> 7f7eb5421000-7f7eb5422000 rw-p 000a5000 fd:01 1142930368
>  /usr/lib64/libfreetype.so.6.10.0
> 7f7eb5422000-7f7eb545c000 r-xp 00000000 fd:01 1097103702
>  /usr/lib64/libnspr4.so
> 7f7eb545c000-7f7eb565b000 ---p 0003a000 fd:01 1097103702
>  /usr/lib64/libnspr4.so
> 7f7eb565b000-7f7eb565c000 r--p 00039000 fd:01 1097103702
>  /usr/lib64/libnspr4.so
> 7f7eb565c000-7f7eb565e000 rw-p 0003a000 fd:01 1097103702
>  /usr/lib64/libnspr4.so
> 7f7eb565e000-7f7eb5660000 rw-p 00000000 00:00 0
> 7f7eb5660000-7f7eb5664000 r-xp 00000000 fd:01 1097205616
>  /usr/lib64/libplc4.so
> 7f7eb5664000-7f7eb5863000 ---p 00004000 fd:01 1097205616
>  /usr/lib64/libplc4.so
> 7f7eb5863000-7f7eb5864000 r--p 00003000 fd:01 1097205616
>  /usr/lib64/libplc4.so
> 7f7eb5864000-7f7eb5865000 rw-p 00004000 fd:01 1097205616
>  /usr/lib64/libplc4.soAborted
>
>
> --
>
> <https://ncics.org/> *Carl J. Schreck III, PhD*
> *Research Scholar*
> North Carolina State University <http://ncsu.edu/>
> North Carolina Institute for Climate Studies (NCICS) <https://ncics.org/>
> 151 Patton Ave, Asheville, NC 28801
> e: cjschrec at ncsu.edu
> o: +1 828 257 3140 <(828)%20257-3140>
> c: +1 828 484 1702 <(828)%20484-1702>
> Publications
> <http://scholar.google.com/citations?hl=en&user=th8ONEcAAAAJ&view_op=list_works&sortby=pubdate>
> ncics.org/mjo
> CycloneCenter.org <https://www.cyclonecenter.org/>
>
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