Bug#802321: gdal-bin: NetCDF-4 / HDF5 support broken in recent gdal

[otas]

 Hi Bas,

 On Mon, 19 Oct 2015 20:00:06 +0200, Sebastiaan Couwenberg wrote:
> Do you have another testing machine perhaps that hasn't been updated 
> yet?
>
 Unfortunately not.

 The issue is related to GMT 5.1.2 I'm using "in production" on my 
 system (Debian Stretch). I have a MS Windows computer too with GMT 5.1, 
 where the issue with NetCDF-4 format is not present.

 Under wheezy, there is GMT 4.5.7 which is not so far dependent on gdal.
 So I can issue under wheezy (on the same sample grid)

 $ GMT grdinfo JEJK_topoC9k_ZABA10mHbpv.nc
 JEJK_topoC9k_ZABA10mHbpv.nc: Title: Produced by grdreformat
 JEJK_topoC9k_ZABA10mHbpv.nc: Command: grdreformat 
 CRJK_topoC9c_ZABAGED10m.grd Jesenik_topoC9_ZABAGED10mBpv.nc 
 -R-546000/-541000/-1073000/-1067000
 JEJK_topoC9k_ZABA10mHbpv.nc: Remark:
 JEJK_topoC9k_ZABA10mHbpv.nc: Gridline node registration used
 JEJK_topoC9k_ZABA10mHbpv.nc: Grid file format: nf (# 18) GMT netCDF 
 format (float)  (COARDS-compliant) [DEFAULT]
 JEJK_topoC9k_ZABA10mHbpv.nc: x_min: -546000 x_max: -541000 x_inc: 10 
 name: x nx: 501
 JEJK_topoC9k_ZABA10mHbpv.nc: y_min: -1073000 y_max: -1067000 y_inc: 10 
 name: y ny: 601
 JEJK_topoC9k_ZABA10mHbpv.nc: z_min: 2.38614749908 z_max: 11.5756139755 
 name: z
 JEJK_topoC9k_ZABA10mHbpv.nc: scale_factor: 1 add_offset: 0

 without any problem, because GMT4 applies directly own internal 
 routines (or netcdf library functions) to recognize and import NetCDF-4 
 raster data. However, the forced use of gdal input routines in GMT4 
 brings a problem again (under wheezy):

 $ GMT grdinfo JEJK_topoC9k_ZABA10mHbpv.nc=gd

 terminates with SIGSEGV.

 Take a closer look at gdal:

 $ gdalinfo JEJK_topoC9k_ZABA10mHbpv.nc
 HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 140136550176640:
   #000: ../../../src/H5Ddeprec.c line 231 in H5Dopen1(): not found
     major: Dataset
     minor: Object not found
   #001: ../../../src/H5Gloc.c line 430 in H5G_loc_find(): can't find 
 object
     major: Symbol table
     minor: Object not found
   #002: ../../../src/H5Gtraverse.c line 861 in H5G_traverse(): internal 
 path traversal failed
     major: Symbol table
     minor: Object not found
   #003: ../../../src/H5Gtraverse.c line 641 in H5G_traverse_real(): 
 traversal operator failed
     major: Symbol table
     minor: Callback failed
   #004: ../../../src/H5Gloc.c line 385 in H5G_loc_find_cb(): object 
 'xx' doesn't exist
     major: Symbol table
     minor: Object not found
 HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 140136550176640:
   #000: ../../../src/H5D.c line 391 in H5Dclose(): not a dataset
     major: Invalid arguments to routine
     minor: Inappropriate type
 HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 140136550176640:
   #000: ../../../src/H5Ddeprec.c line 231 in H5Dopen1(): not found
     major: Dataset
     minor: Object not found
   #001: ../../../src/H5Gloc.c line 430 in H5G_loc_find(): can't find 
 object
     major: Symbol table
     minor: Object not found
   #002: ../../../src/H5Gtraverse.c line 861 in H5G_traverse(): internal 
 path traversal failed
     major: Symbol table
     minor: Object not found
   #003: ../../../src/H5Gtraverse.c line 641 in H5G_traverse_real(): 
 traversal operator failed
     major: Symbol table
     minor: Callback failed
   #004: ../../../src/H5Gloc.c line 385 in H5G_loc_find_cb(): object 
 'yy' doesn't exist
     major: Symbol table
     minor: Object not found
 HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 140136550176640:
   #000: ../../../src/H5D.c line 391 in H5Dclose(): not a dataset
     major: Invalid arguments to routine
     minor: Inappropriate type
 HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 140136550176640:
   #000: ../../../src/H5Ddeprec.c line 231 in H5Dopen1(): not found
     major: Dataset
     minor: Object not found
   #001: ../../../src/H5Gloc.c line 430 in H5G_loc_find(): can't find 
 object
     major: Symbol table
     minor: Object not found
   #002: ../../../src/H5Gtraverse.c line 861 in H5G_traverse(): internal 
 path traversal failed
     major: Symbol table
     minor: Object not found
   #003: ../../../src/H5Gtraverse.c line 641 in H5G_traverse_real(): 
 traversal operator failed
     major: Symbol table
     minor: Callback failed
   #004: ../../../src/H5Gloc.c line 385 in H5G_loc_find_cb(): object 
 'zz' doesn't exist
     major: Symbol table
     minor: Object not found
 HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 140136550176640:
   #000: ../../../src/H5D.c line 391 in H5Dclose(): not a dataset
     major: Invalid arguments to routine
     minor: Inappropriate type
 HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 140136550176640:
   #000: ../../../src/H5Ddeprec.c line 231 in H5Dopen1(): not found
     major: Dataset
     minor: Object not found
   #001: ../../../src/H5Gloc.c line 430 in H5G_loc_find(): can't find 
 object
     major: Symbol table
     minor: Object not found
   #002: ../../../src/H5Gtraverse.c line 861 in H5G_traverse(): internal 
 path traversal failed
     major: Symbol table
     minor: Object not found
   #003: ../../../src/H5Gtraverse.c line 641 in H5G_traverse_real(): 
 traversal operator failed
     major: Symbol table
     minor: Callback failed
   #004: ../../../src/H5Gloc.c line 385 in H5G_loc_find_cb(): object 
 'zz' doesn't exist
     major: Symbol table
     minor: Object not found
 HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 140136550176640:
   #000: ../../../src/H5D.c line 437 in H5Dget_space(): not a dataset
     major: Invalid arguments to routine
     minor: Inappropriate type
 HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 140136550176640:
   #000: ../../../src/H5S.c line 752 in H5Sget_simple_extent_ndims(): 
 not a dataspace
     major: Invalid arguments to routine
     minor: Inappropriate type
 ERROR 1: CPLMalloc(-8): Silly size requested.

 Neoprávněný přístup do paměti (SIGSEGV)

 ----

 Since this issue is related to wheezy (and obsolete gdal), I do not 
 report it as a bug, but it is one more think that made me suspicious 
 about present gdal.

 Regards,

 Otakar