Control: tags -1 unreproducible Control: severity -1 important Hi Otakar,
Thanks for the nc file, can you also send the files used by gmt? With JEJK_topoC9k_ZABA10mHbpv.nc I can now confirm that the issue is not present in gdal (1.11.2+dfsg-3+b2) on unstable: $ ncdump -h JEJK_topoC9k_ZABA10mHbpv.nc netcdf JEJK_topoC9k_ZABA10mHbpv { dimensions: x = 501 ; y = 601 ; variables: double x(x) ; x:long_name = "x" ; x:actual_range = -546000., -541000. ; double y(y) ; y:long_name = "y" ; y:actual_range = -1073000., -1067000. ; float z(y, x) ; z:long_name = "z" ; z:_FillValue = NaNf ; z:actual_range = 2.38614749908447, 11.5756139755249 ; // global attributes: :Conventions = "COARDS, CF-1.5" ; :title = "Produced by grdreformat" ; :history = "grdreformat CRJK_topoC9c_ZABAGED10m.grd Jesenik_topoC9_ZABAGED10mBpv.nc -R-546000/-541000/-1073000/-1067000" ; :GMT_version = "5.1.2 (r14256) [64-bit]" ; } $ ncdump -k JEJK_topoC9k_ZABA10mHbpv.nc netCDF-4 $ h5dump -n JEJK_topoC9k_ZABA10mHbpv.nc HDF5 "JEJK_topoC9k_ZABA10mHbpv.nc" { FILE_CONTENTS { group / dataset /x dataset /y dataset /z } } $ gdalinfo JEJK_topoC9k_ZABA10mHbpv.nc Driver: netCDF/Network Common Data Format Files: JEJK_topoC9k_ZABA10mHbpv.nc Size is 501, 601 Coordinate System is `' Origin = (-546005.000000000000000,-1066995.000000000000000) Pixel Size = (10.000000000000000,-10.000000000000000) Metadata: NC_GLOBAL#Conventions=COARDS, CF-1.5 NC_GLOBAL#GMT_version=5.1.2 (r14256) [64-bit] NC_GLOBAL#history=grdreformat CRJK_topoC9c_ZABAGED10m.grd Jesenik_topoC9_ZABAGED10mBpv.nc -R-546000/-541000/-1073000/-1067000 NC_GLOBAL#title=Produced by grdreformat x#actual_range={-546000,-541000} x#long_name=x y#actual_range={-1073000,-1067000} y#long_name=y z#_FillValue=nan z#actual_range={2.386147499084473,11.5756139755249} z#long_name=z Corner Coordinates: Upper Left ( -546005.000,-1066995.000) Lower Left ( -546005.000,-1073005.000) Upper Right ( -540995.000,-1066995.000) Lower Right ( -540995.000,-1073005.000) Center ( -543500.000,-1070000.000) Band 1 Block=167x151 Type=Float32, ColorInterp=Undefined NoData Value=nan Metadata: _FillValue=nan actual_range={2.386147499084473,11.5756139755249} long_name=z NETCDF_VARNAME=z $ gmt grdreformat JEJK_topoC9k_ZABA10mHbpv.grd JEJK_topoC9k_ZABA10mHbpv.xnc=nf grdreformat: Error for input file: No such file (JEJK_topoC9k_ZABA10mHbpv.grd) grdreformat: Syntax error: Specify only one input and one output file $ 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 [Cartesian grid] JEJK_topoC9k_ZABA10mHbpv.nc: Grid file format: nf = GMT netCDF format (32-bit float), COARDS, CF-1.5 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 JEJK_topoC9k_ZABA10mHbpv.nc: format: netCDF-4 chunk_size: 167,151 shuffle: on deflation_level: 3 $ gmt grdinfo JEJK_topoC9k_ZABA10mHbpv.nc=gd ERROR 1: nBlockYSize = 151, only 1 supported when reading bottom-up dataset ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: IReadBlock failed at X offset 0, Y offset 0 ERROR 1: nBlockYSize = 151, only 1 supported when reading bottom-up dataset ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: IReadBlock failed at X offset 1, Y offset 0 ERROR 1: nBlockYSize = 151, only 1 supported when reading bottom-up dataset ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: IReadBlock failed at X offset 2, Y offset 0 ERROR 1: nBlockYSize = 151, only 1 supported when reading bottom-up dataset ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: IReadBlock failed at X offset 0, Y offset 1 ERROR 1: nBlockYSize = 151, only 1 supported when reading bottom-up dataset ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: IReadBlock failed at X offset 1, Y offset 1 ERROR 1: nBlockYSize = 151, only 1 supported when reading bottom-up dataset ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: IReadBlock failed at X offset 2, Y offset 1 ERROR 1: nBlockYSize = 151, only 1 supported when reading bottom-up dataset ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: IReadBlock failed at X offset 0, Y offset 2 ERROR 1: nBlockYSize = 151, only 1 supported when reading bottom-up dataset ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: IReadBlock failed at X offset 1, Y offset 2 ERROR 1: nBlockYSize = 151, only 1 supported when reading bottom-up dataset ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: IReadBlock failed at X offset 2, Y offset 2 ERROR 1: nBlockYSize = 151, only 1 supported when reading bottom-up dataset ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: IReadBlock failed at X offset 0, Y offset 3 ERROR 1: nBlockYSize = 151, only 1 supported when reading bottom-up dataset ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: IReadBlock failed at X offset 1, Y offset 3 ERROR 1: nBlockYSize = 151, only 1 supported when reading bottom-up dataset ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: IReadBlock failed at X offset 2, Y offset 3 ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: Failed to compute min/max, no valid pixels found in sampling. JEJK_topoC9k_ZABA10mHbpv.nc: Title: Grid imported via GDAL JEJK_topoC9k_ZABA10mHbpv.nc: Command: JEJK_topoC9k_ZABA10mHbpv.nc: Remark: JEJK_topoC9k_ZABA10mHbpv.nc: Gridline node registration used [Cartesian grid] JEJK_topoC9k_ZABA10mHbpv.nc: Grid file format: gd = Import/export through GDAL 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: 0 z_max: 0 name: z JEJK_topoC9k_ZABA10mHbpv.nc: scale_factor: 1 add_offset: 0 On 20-10-15 07:39, otas wrote: > On Mon, 19 Oct 2015 20:00:06 +0200, Sebastiaan Couwenberg wrote: >> >> I suspect this is not actually an issue in gdal, but caused by the >> recent HDF5 transition to 1.8.15-patch1+docs-4. > > I had the same suspicion on HDF5 libraries (yes, they were upgraded too). > However, after downgrade to libhdf5-8_1.8.13+docs-15 and > libhdf5-cpp-8_1.8.13+docs-15 > on my system nothing changed with gdal, i.e. the same error of gdalinfo. You'll also need to downgrade gdal to the version before the hdf5 rebuild (1.11.2+dfsg-3+b1), and the other packages in the chain too: netcdf (1:4.4.0~rc2-1) & gmt (5.1.2+dfsg1-2). > Besides, NetCDF and HDF5 utils, at least, keep the file format correct > recognition, > see e.g. ncdump -h JEJK_topoC9k_ZABA10mHbpv.nc or h5topng -d z > JEJK_topoC9k_ZABA10mHbpv.nc > > On the other hand, I can just recognize that something in the chain gmt > - libgdal - libnetcdf - libhdf5 went wrong recently (Stretch upgrade at > the begin of October), it may be somehow related to HDF5 transition. hdf5 (1.8.15-patch1+docs-4) migrated to testing on October 5th. If the package downgrades don't resolve the issue, can you report the installed versions of gmt, gdal, netcdf & hdf5? Kind Regards, Bas -- GPG Key ID: 4096R/6750F10AE88D4AF1 Fingerprint: 8182 DE41 7056 408D 6146 50D1 6750 F10A E88D 4AF1