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
