xenial gdalinfo segfault on concrete netcdf file

[Marcos Sánchez Provencio]

When trying to get information on a .nc file, gdalinfo (and many other uses of gdal on this concrete file) segfaults.

meteogrid@xenial:~$ gdalinfo salida.nc
Segmentation fault

gdb on a similar file shows this:

#0 strlen () at ../sysdeps/x86_64/strlen.S:106
#1 0x00007ffff7356ec3 in NCDFSafeStrcat (ppszDest=ppszDest@entry=0x7fffffff1378, pszSrc=pszSrc@entry=0x7ffff787d21d "}", nDestSize=nDestSize@entry=0x7fffffff1370) at netcdfdataset.cpp:6268
#2 0x00007ffff7357125 in NCDFGetAttr1 (nCdfId=nCdfId@entry=65536, nVarId=nVarId@entry=7, pszAttrName=pszAttrName@entry=0x7fffffff33f0 "valid_range", pdfValue=pdfValue@entry=0x0, pszValue=pszValue@entry=0x7fffffff33e8,
    bSetPszValue=bSetPszValue@entry=1) at netcdfdataset.cpp:6426
#3 0x00007ffff7357dc4 in NCDFGetAttr (pszValue=0x7fffffff33e8, pszAttrName=0x7fffffff33f0 "valid_range", nVarId=7, nCdfId=65536) at netcdfdataset.cpp:6449
#4 netCDFDataset::ReadAttributes (this=this@entry=0x65d0d0, cdfid=65536, var=7) at netcdfdataset.cpp:4085
#5 0x00007ffff735fcf2 in netCDFDataset::Open (poOpenInfo=<optimized out>) at netcdfdataset.cpp:4809
#6 0x00007ffff74ae10d in GDALOpenInternal (oOpenInfo=..., papszAllowedDrivers=papszAllowedDrivers@entry=0x0) at gdaldataset.cpp:2314
#7 0x00007ffff74ae366 in GDALOpenInternal (pszFilename=pszFilename@entry=0x65c5c0 "NETCDF:mermaid/CTTH/S_NWC_CTTH_MSG3_Europe-VISIR_20161009T000000Z.nc:ctth_quality", eAccess=eAccess@entry=GA_ReadOnly,
    papszAllowedDrivers=papszAllowedDrivers@entry=0x0) at gdaldataset.cpp:2263
#8 0x00007ffff74ae3b7 in GDALOpen (pszFilename=pszFilename@entry=0x65c5c0 "NETCDF:mermaid/CTTH/S_NWC_CTTH_MSG3_Europe-VISIR_20161009T000000Z.nc:ctth_quality", eAccess=eAccess@entry=GA_ReadOnly) at gdaldataset.cpp:2254
#9 0x0000000000402bb5 in main (argc=2, argv=0x65c580) at gdalinfo.c:183

Thank you very much.

[Bas Couwenberg (sebastic)]

Is this gdal from the Ubuntu xenial repositories or from the UbuntuGIS PPA?

Please also provide the salida.nc file to help reproduce this issue.

[Marcos Sánchez Provencio (rapto)]

I was quite sure I had attached the file, sorry for that.

This is the standard gdal package. I am trying ubuntugis now, although only unstable is available for xenial.

[Marcos Sánchez Provencio (rapto)]

ubuntugis unstable does work

[Bas Couwenberg (sebastic)]

Ubuntu xenial has GDAL 1.11.3 and the ubuntugis-unstable PPA has GDAL 2.1.0, and quite a lot of changes to the NetCDF driver have been made between those release.

Valgrid reports the following for the gdalinfo command with the gdal & netcdf debug packages installed:

==9254== Invalid read of size 1
==9254== at 0x4C30F62: strlen (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==9254== by 0x53F2EC2: NCDFSafeStrcat(char**, char*, unsigned long*) (netcdfdataset.cpp:6268)
==9254== by 0x53F3124: NCDFGetAttr1(int, int, char const*, double*, char**, int) (netcdfdataset.cpp:6426)
==9254== by 0x53F3DC3: NCDFGetAttr (netcdfdataset.cpp:6449)
==9254== by 0x53F3DC3: netCDFDataset::ReadAttributes(int, int) (netcdfdataset.cpp:4085)
==9254== by 0x53FBCF1: netCDFDataset::Open(GDALOpenInfo*) (netcdfdataset.cpp:4809)
==9254== by 0x554A10C: GDALOpenInternal(GDALOpenInfo&, char const* const*) (gdaldataset.cpp:2314)
==9254== by 0x554A365: GDALOpenInternal(char const*, GDALAccess, char const* const*) (gdaldataset.cpp:2263)
==9254== by 0x402BB4: ??? (in /usr/bin/gdalinfo)
==9254== by 0x642B82F: (below main) (libc-start.c:291)
==9254== Address 0x0 is not stack'd, malloc'd or (recently) free'd
==9254==
==9254==
==9254== Process terminating with default action of signal 11 (SIGSEGV)
==9254== Access not within mapped region at address 0x0
==9254== at 0x4C30F62: strlen (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==9254== by 0x53F2EC2: NCDFSafeStrcat(char**, char*, unsigned long*) (netcdfdataset.cpp:6268)
==9254== by 0x53F3124: NCDFGetAttr1(int, int, char const*, double*, char**, int) (netcdfdataset.cpp:6426)
==9254== by 0x53F3DC3: NCDFGetAttr (netcdfdataset.cpp:6449)
==9254== by 0x53F3DC3: netCDFDataset::ReadAttributes(int, int) (netcdfdataset.cpp:4085)
==9254== by 0x53FBCF1: netCDFDataset::Open(GDALOpenInfo*) (netcdfdataset.cpp:4809)
==9254== by 0x554A10C: GDALOpenInternal(GDALOpenInfo&, char const* const*) (gdaldataset.cpp:2314)
==9254== by 0x554A365: GDALOpenInternal(char const*, GDALAccess, char const* const*) (gdaldataset.cpp:2263)
==9254== by 0x402BB4: ??? (in /usr/bin/gdalinfo)
==9254== by 0x642B82F: (below main) (libc-start.c:291)
==9254== If you believe this happened as a result of a stack
==9254== overflow in your program's main thread (unlikely but
==9254== possible), you can try to increase the size of the
==9254== main thread stack using the --main-stacksize= flag.
==9254== The main thread stack size used in this run was 8388608.
==9254==
==9254== HEAP SUMMARY:
==9254== in use at exit: 1,789,968 bytes in 6,243 blocks
==9254== total heap usage: 11,605 allocs, 5,362 frees, 2,340,923 bytes allocated
==9254==
==9254== LEAK SUMMARY:
==9254== definitely lost: 0 bytes in 0 blocks
==9254== indirectly lost: 0 bytes in 0 blocks
==9254== possibly lost: 0 bytes in 0 blocks
==9254== still reachable: 1,789,968 bytes in 6,243 blocks
==9254== of which reachable via heuristic:
==9254== length64 : 56,956 bytes in 61 blocks
==9254== newarray : 288 bytes in 16 blocks
==9254== ...

[Bas Couwenberg (sebastic)]

GDAL 2.1.0 adds support for the NetCDF4 datatypes used in the dataset.

[Marcos Sánchez Provencio (rapto)]

Thank you very much; we'll use the unstable ppa. Do you know any reason for the "stable" ubuntugis ppa not offering xenial packages?

[Angelos Tzotsos (gcpp-kalxas)]

We are in the process of moving the unstable packages to stable.

[Bas Couwenberg (sebastic)]

Because UbuntuGIS has a lack of manpower.

There are plans to copy the packages from ubuntugis-unstable to -stable for trusty at least:

 https://lists.osgeo.org/pipermail/ubuntu/2016-October/001528.html