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GDAL provider unable to open .bag / .hdf5 file in QGIS #1428

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rossoe opened this issue Apr 7, 2019 · 37 comments
Closed

GDAL provider unable to open .bag / .hdf5 file in QGIS #1428

rossoe opened this issue Apr 7, 2019 · 37 comments

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@rossoe
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rossoe commented Apr 7, 2019

Expected behavior and actual behavior.

I'm unsure if this is purely a GDAL bug or QGIS related issue?

I expected to be able to open the below type file within QGIS:

Example .bag file to test:
https://data.ngdc.noaa.gov/platforms/ocean/nos/coast/H12001-H14000/H12656/BAG/H12656_MB_50cm_MLLW_27of31.bag

But it will not load - see below attempts

Steps to reproduce the problem.

Start QGIS - Top Menu > Layer > Data Source Manager
Add layer via Raster selection

Fails with following error:

Invalid Layer: GDAL provider Cannot open GDAL dataset C:\Users\rosso\Downloads\H12656_MB_50cm_MLLW_27of31.bag: C:\Users\rosso\Downloads\H12656_MB_50cm_MLLW_27of31.bag' not recognized as a supported file format. Raster layer Provider is not valid (provider: gdal, URI: C:\Users\rosso\Downloads\H12656_MB_50cm_MLLW_27of31.bag

Also attempted by running command via python console:
os.system(r'''gdal_translate -of AAIGrid E:/Users/rosso/GIS/GlobalMapper/H12656_MB_50cm_MLLW_27of31.bag E:/Users/rosso/GIS/GlobalMapper/final.asc''')
But that fails to run & console spits out:

HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 0:
#000: C:\src\osgeo4w\hdf5\src\H5P.c line 253 in H5Pcreate(): not a property list class
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 0:
#000: C:\src\osgeo4w\hdf5\src\H5Pfapl.c line 829 in H5Pset_driver(): not a property list
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 0:
#000: C:\src\osgeo4w

Tried to run via Raster 'Translate' QGIS GUI:

_core.QgsProcessingException: Could not load source layer for INPUT: E:/Users/rosso/GIS/GlobalMapper/2006 HI1156 Hampstead Ledge to Stansore Point 2m SB.bag not found
Traceback (most recent call last):
File "F:/OSGEO41/apps/qgis/./python/plugins\processing\algs\gdal\GdalAlgorithmDialog.py", line 140, in parametersHaveChanged
commands = self.alg.getConsoleCommands(parameters, context, feedback, executing=False)
File "F:/OSGEO4
1/apps/qgis/./python/plugins\processing\algs\gdal\translate.py", line 120, in getConsoleCommands
raise QgsProcessingException(self.invalidRasterError(parameters, self.INPUT))
_core.QgsProcessingException: Could not load source layer for INPUT: E:/Users/rosso/GIS/GlobalMapper/2006 HI1156 Hampstead Ledge to Stansore Point 2m SB.bag not found

Python version: 3.7.0 (v3.7.0:1bf9cc5093, Jun 27 2018, 04:59:51) [MSC v.1914 64 bit (AMD64)]
QGIS version: 3.6.1-Noosa Noosa, 2468226bc9

Python Path:
F:/OSGEO41/apps/qgis/./python
C:/Users/rosso/AppData/Roaming/QGIS/QGIS3\profiles\default/python
C:\qgis-plugins\qgis-otb-plugin
C:/Users/rosso/AppData/Roaming/QGIS/QGIS3\profiles\default/python/plugins
F:/OSGEO4
1/apps/qgis/./python/plugins
F:\OSGeo4W64\bin\python37.zip
F:\OSGEO41\apps\Python37\DLLs
F:\OSGEO4
1\apps\Python37\lib
F:\OSGeo4W64\bin
F:\OSGEO41\apps\Python37
F:\OSGEO4
1\apps\Python37\lib\site-packages
F:\OSGEO41\apps\Python37\lib\site-packages\win32
F:\OSGEO4
1\apps\Python37\lib\site-packages\win32\lib
F:\OSGEO4~1\apps\Python37\lib\site-packages\Pythonwin
C:/Users/rosso/AppData/Roaming/QGIS/QGIS3\profiles\default/python

Operating system

Windows 10

GDAL version and provenance

Compiled against GDAL/OGR - 2.4.1
QGIS - 3.6.1-Noosa

@rouault
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rouault commented Apr 8, 2019

Works for me on Linux with GDAL 2.4.1 and libhdf5 1.8.16.
Perhaps an issue with the HDF5 lib from OSGeo4W

@rossoe
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rossoe commented Apr 8, 2019

Yes my Ubuntu QGIS handles the .bag files fine. Just Win 10! So where would one raise bug for libhdf5? On QGIS issue tracker?

@rouault
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rouault commented Apr 8, 2019

Can you try one of the build at http://gisinternals.com/stable.php and see if gdalinfo works on your bag file ?

@jef-n
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jef-n commented Apr 8, 2019

Works for me on Linux with GDAL 2.4.1 and libhdf5 1.8.16.
Perhaps an issue with the HDF5 lib from OSGeo4W

Or with the version? 1.10.4 vs 1.8.x?

@rouault
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rouault commented Apr 8, 2019

Not exactly 1.10.4, but Ubuntu 18.04 has 1.10.0 and BAG autotest work on it : https://api.travis-ci.com/v3/job/190978363/log.txt

@giumas
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giumas commented Apr 9, 2019

Using the southern_hemi_false_northing.bag and gdalinfo in the OSGeo4W64 shell:

C:\>gdalinfo --version
GDAL 2.4.1, released 2019/03/15

C:\>gdalinfo C:\code\cpp\gdal\autotest\gdrivers\data\southern_hemi_false_northing.bag
HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 0:
  #000: C:\src\osgeo4w\hdf5\src\H5P.c line 253 in H5Pcreate(): not a property list class
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 0:
  #000: C:\src\osgeo4w\hdf5\src\H5Pfapl.c line 829 in H5Pset_driver(): not a property list
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 0:
  #000: C:\src\osgeo4w\hdf5\src\H5F.c line 509 in H5Fopen(): unable to open file
    major: File accessibilty
    minor: Unable to open file
  #001: C:\src\osgeo4w\hdf5\src\H5Fint.c line 1400 in H5F__open(): unable to open file
    major: File accessibilty
    minor: Unable to open file
  #002: C:\src\osgeo4w\hdf5\src\H5Fint.c line 1513 in H5F_open(): unable to retrieve VFL class
    major: File accessibilty
    minor: Can't get value
  #003: C:\src\osgeo4w\hdf5\src\H5FD.c line 378 in H5FD_get_class(): can't find object for ID
    major: Object atom
    minor: Unable to find atom information (already closed?)
HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 0:
  #000: C:\src\osgeo4w\hdf5\src\H5P.c line 1518 in H5Pclose(): not a property list
    major: Invalid arguments to routine
    minor: Inappropriate type
ERROR 4: `C:\code\cpp\gdal\autotest\gdrivers\data\southern_hemi_false_northing.bag' not recognized as a supported file format.
gdalinfo failed - unable to open 'C:\code\cpp\gdal\autotest\gdrivers\data\southern_hemi_false_northing.bag'.

The same error when I downgrade GDAL to 2.4.0 or upgrade to 2.5.0dev.

@rossoe
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rossoe commented Apr 13, 2019

So from the confirmation on the last post, do I take it this is purely a HDF5 issue? if so where should it be reported?

@rouault
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rouault commented Apr 13, 2019

do I take it this is purely a HDF5 issue?

I'm afraid the cause of the problem is not well spotted yet. I believe there are some subtleties how to build HDF5 on Windows

@jef-n I've just built HDF5 1.10.4 on Linux and rebuilt GDAL against and it works fine.
From the above traces, I assume you built yourself hdf5 1.10.4 for osgeo4w. Did you also rebuild libnetcdf against it, and GDAL too (just in case of ABI incompatibility) ?
A simple test to check if the hdf5 build is fine would be to just try compile the following test.c and execute it

#include "hdf5.h"
int main()
{
    H5Pcreate(H5P_FILE_ACCESS);
    return 0;
}

@giumas
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giumas commented Apr 15, 2019

In my case, I did not build hdf5, but have just downloaded it using the OSGeo4W Setup:

osgeo4w-setup-work_2019-04-15_09-57-56

@wwwdavid34
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wwwdavid34 commented Jul 2, 2019

I have the exact same issue with OSGeo4W distribution on both QGIS 3.8.0 and 3.4.9. I was not able to open any HDF5 file. The error log is exactly the same with what @giumas posted.

However, gdalinfo on HDF5 works with OSGeo4W that came with QGIS 3.2, and stopped working after QGIS 3.4 (there is no QGIS 3.3). This might be a hint on finding where the HDF5 library installation on Windows went wrong?

Here is my error log with OSGeo4W shell that came with QGIS 3.8.0.

GDAL 2.4.1, released 2019/03/15

C:\>gdalinfo GDNBO-SVDNB_npp_d20190630_t1855493_e1901296_b39759_c20190701191715059163_noac_ops.h5
HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 0:
  #000: C:\src\osgeo4w\hdf5\src\H5P.c line 253 in H5Pcreate(): not a property list class
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 0:
  #000: C:\src\osgeo4w\hdf5\src\H5Pfapl.c line 829 in H5Pset_driver(): not a property list
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 0:
  #000: C:\src\osgeo4w\hdf5\src\H5F.c line 509 in H5Fopen(): unable to open file
    major: File accessibilty
    minor: Unable to open file
  #001: C:\src\osgeo4w\hdf5\src\H5Fint.c line 1400 in H5F__open(): unable to open file
    major: File accessibilty
    minor: Unable to open file
  #002: C:\src\osgeo4w\hdf5\src\H5Fint.c line 1513 in H5F_open(): unable to retrieve VFL class
    major: File accessibilty
    minor: Can't get value
  #003: C:\src\osgeo4w\hdf5\src\H5FD.c line 378 in H5FD_get_class(): can't find object for ID
    major: Object atom
    minor: Unable to find atom information (already closed?)
HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 0:
  #000: C:\src\osgeo4w\hdf5\src\H5P.c line 1518 in H5Pclose(): not a property list
    major: Invalid arguments to routine
    minor: Inappropriate type
ERROR 4: `GDNBO-SVDNB_npp_d20190630_t1855493_e1901296_b39759_c20190701191715059163_noac_ops.h5' not recognized as a supported file format.
gdalinfo failed - unable to open 'GDNBO-SVDNB_npp_d20190630_t1855493_e1901296_b39759_c20190701191715059163_noac_ops.h5'.```

@sbahtiyar
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I have the same issue here with QGIS 3.8.0 on Win 10.

The error log when gdalinfo called from OSGeo4W Shell:

gdalinfo --version
GDAL 2.4.1, released 2019/03/15

gdalinfo sample.h5
HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 0:
#000: C:\src\osgeo4w\hdf5\src\H5P.c line 253 in H5Pcreate(): not a property list class
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 0:
#000: C:\src\osgeo4w\hdf5\src\H5Pfapl.c line 829 in H5Pset_driver(): not a property list
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 0:
#000: C:\src\osgeo4w\hdf5\src\H5F.c line 509 in H5Fopen(): unable to open file
major: File accessibilty
minor: Unable to open file
#1: C:\src\osgeo4w\hdf5\src\H5Fint.c line 1400 in H5F__open(): unable to open file
major: File accessibilty
minor: Unable to open file
#2: C:\src\osgeo4w\hdf5\src\H5Fint.c line 1513 in H5F_open(): unable to retrieve VFL class
major: File accessibilty
minor: Can't get value
#3: C:\src\osgeo4w\hdf5\src\H5FD.c line 378 in H5FD_get_class(): can't find object for ID
major: Object atom
minor: Unable to find atom information (already closed?)
HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 0:
#000: C:\src\osgeo4w\hdf5\src\H5P.c line 1518 in H5Pclose(): not a property list
major: Invalid arguments to routine
minor: Inappropriate type
ERROR 4: sample.h5 not recognized as a supported file format.
gdalinfo failed - unable to open sample.h5.

@allixender
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Same with I have the same issue here with QGIS 3.8.3 on Win 10 x64. (gdal 2.4.1, hdf 1.10.4)

HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 0:
  #000: C:\src\osgeo4w\hdf5\src\H5P.c line 1518 in H5Pclose(): not a property list
    major: Invalid arguments to routine
    minor: Inappropriate type
ERROR 4: `AMSR_U2_L3_SeaIce25km_R02_20191002.he5' not recognized as a supported file format.
gdalinfo failed - unable to open 'AMSR_U2_L3_SeaIce25km_R02_20191002.he5'.

@rouault rouault changed the title GDAL provider unable to open .bag file in QGIS GDAL provider unable to open .bag / .hdf5 file in QGIS Nov 13, 2019
@jef-n
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jef-n commented Nov 13, 2019

Built 1.10.5 - same error on gdalinfo - just before the a crash. rebuilding netcdf and GDAL…

@SrNetoChan
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SrNetoChan commented Dec 2, 2019

Any news about this?

@Dave-Allured
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HDF5 was recently notorious for changing their ABI (application binary interface) frequently in ways that broke library binary compatibility. The messages above strongly suggest this is the current problem. Simply stated, the quick fix is to recompile anything that calls HDF5 directly. This includes gdal and netcdf, among other things. These must be recompiled against the HDF5 headers matching your currently installed HDF5 library.

There are limited ABI compatibility reports for HDF5. The current version 1.10.5 has reportedly good backward compatibility to 1.10.4 and 1.10.3. I recommend recompiling anything that was built against 1.10.2 or older. All 1.8 builds are completely ABI incompatible with all 1.10 versions.

https://portal.hdfgroup.org/display/support/HDF5%201.10.5#compatibility1104

@rossoe
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rossoe commented Dec 4, 2019

Our company is having to revert back from 3.10 to 3.4 as it's essential to be able to manage .bag files. It's unlikely we can take advantage of quick fix mentioned above re recompile due to security policies!

I just raised a similar ticket on QGIS github:
qgis/QGIS#33229

In case anything can be done to compile compatible versions into official release.

@Dave-Allured
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Dave-Allured commented Dec 7, 2019

CANCELLED: ((( New info. I can reproduce this problem, or one like it, on Mac OS 10.14.6 (Mojave). So it looks like this is not just a Windows build problem any more. )))

Rest of comment deleted by author. This comment was a mistake. I did not have the HDF5/BAG driver installed at this time on my Mac version of GDAL.

@Dave-Allured
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Please ignore my previous comment. I did not have the HDF5 driver installed. After rebuilding properly, GDAL 3.0.1 on Mac handles this .bag file correctly. Sorry for the confusion.

mac56:~/hdf5/issues/1202 28> ls -go H12656_MB_50cm_MLLW_27of31.bag 
-rw-r--r--  1   15373048 Nov  1  2016 H12656_MB_50cm_MLLW_27of31.bag

mac56:~/hdf5/issues/1202 29> file H12656_MB_50cm_MLLW_27of31.bag 
H12656_MB_50cm_MLLW_27of31.bag: Hierarchical Data Format (version 5) data

mac56:~/hdf5/issues/1202 30> gdalinfo --version
GDAL 3.0.1, released 2019/06/28

mac56:~/hdf5/issues/1202 31> gdalinfo --formats | grep -i -e hdf -e bag
  BAG -raster- (rwv): Bathymetry Attributed Grid
  HDF5 -raster- (rovs): Hierarchical Data Format Release 5
  HDF5Image -raster- (rov): HDF5 Dataset

mac56:~/hdf5/issues/1202 32> gdalinfo H12656_MB_50cm_MLLW_27of31.bag
Driver: BAG/Bathymetry Attributed Grid
Files: H12656_MB_50cm_MLLW_27of31.bag
Size is 1435, 382
Coordinate System is:
BOUNDCRS[
<snip>

@rouault
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rouault commented Jan 3, 2020

@jef-n I've investigated the issue. With GDAL master and OSGeo4W http://download.osgeo.org/osgeo4w/x86_64/release/hdf5/hdf5-1.10.5-1.tar.bz2 + http://download.osgeo.org/osgeo4w/x86_64/release/szip/szip-2.1.1-1.tar.bz2 + Visual Studio 2017, I managed to get a working build that can open the https://data.ngdc.noaa.gov/platforms/ocean/nos/coast/H12001-H14000/H12656/BAG/H12656_MB_50cm_MLLW_27of31.bag file by specifying for nmake.opt:

HDF5_PLUGIN = NO
HDF5_DIR =	c:\dev\hdf5
HDF5_LIB =	$(HDF5_DIR)\lib\hdf5.lib
HDF5_H5_IS_DLL = YES

HDF5_H5_IS_DLL = YES is important. I didn't manage to get linking to succeed otherwise. This is a new setting of GDAL master that activates -DH5_BUILT_AS_DYNAMIC_LIB in frmts/hdf5/makefile.vc . Without it, -D_HDF5USEDLL_ is used and I got linking errors. So I'm not sure how you can manage to get a build at all with GDAL 3.0... I've just backported the support for HDF5_H5_IS_DLL to the 3.0 branch per 0a3365a

I've also just installed a fresh OSGeo4W of GDAL 3.0.2 only and when opening a HDF5 file, I get the following error

The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.10.5, library is 1.10.4

@jef
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jef commented Jan 3, 2020

@rouault i think you mean @jef-n

@rouault
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rouault commented Jan 3, 2020

oops sorry "at jef". I did mean @jef-n to look at #1428 (comment)

@Dave-Allured
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Dave-Allured commented Jan 3, 2020

@roault wrote:

... I've also just installed a fresh OSGeo4W of GDAL 3.0.2 only and when opening a HDF5 file, I get the following error

The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
...
Headers are 1.10.5, library is 1.10.4

Install or fully activate HDF5 1.10.5, then rebuild GDAL. Also rebuild ALL other packages that directly link to HDF5.

I looked into this in a little more detail. HDF5 does not support drop-in ABI compatibility for ANY recent versions. Therefore, every time the HDF5 library is updated, ALL packages that have direct dependencies on HDF5 must be rebuilt.

There is an environmental variable kludge mentioned in the error message. I consider this kludge incredibly dangerous, and it should never have been made public. Do not use! Danger Will Robinson!

@Dave-Allured
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I said "rebuild GDAL". You may need to go all the way back to GDAL configure or Cmake equivalent, to fully accomplish the correct linkage to the currently installed HDF5 version. Not being a configure expert, I am not sure this is needed, so I would do it anyway, just to be safe.

The same is true for any other packages with direct HDF5 dependency.

@Dave-Allured
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Headers are 1.10.5, library is 1.10.4

This message in this context is also diagnostic of a mix-up of two different installed HDF5 library versions. Check both header files and libraries for multiple installed versions. In the case of HDF5, it may be necessary to purge all but a single version of each include and library file.

There are proper ways for multiple installed library versions to co-exist. I am not sure that HDF5 in its current state is capable of such support.

@rouault
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rouault commented Jan 3, 2020

I said "rebuild GDAL"

I know how to build GDAL, thanks ;-) My comment was a note for @jef-n that there's something fishy in the OSGeo4W setup. I did finally manage to force installation of 1.10.5 in the OSGeo4W installer (1.10.4 is installed by default because in setup.ini 1.10.5 is in the [test] section), but then I'm hitting the issue raised by others regarding 'H5Pcreate(): not a property list class').
Hopefully my above note about building GDAL with HDF5_H5_IS_DLL = YES (with 0a3365a applied) will fix the issue for OSGeo4W. At least that makes things to work correctly in my custom build.

@Dave-Allured
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I know how to build GDAL, thanks ;-)

Yes of course. I was only trying to emphasize the version issues and due caution. I am glad you got your custom build working.

@Dave-Allured
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Is H5Pclose(): not a property list still an issue for anyone? If so, could you please confirm that no shell or wrapper is setting the variable HDF5_DISABLE_VERSION_CHECK before running gdalinfo?

If that is confirmed, then I think it will be time to ask HDF5 support for an interpretation of the message stack related to 'H5Pcreate(): not a property list class'.

@jef-n
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jef-n commented Jan 24, 2020

Try gdal-3.0.3-2 please.

@rouault
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rouault commented Jan 24, 2020

For people not installing qgis-full, I believe they must explicitly install the gdal-hdf5 package now.

@jef-n
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jef-n commented Jan 24, 2020

For people not installing qgis-full, I believe they must explicitly install the gdal-hdf5 package now.

correct - same as other for plugins (ecw, mrsid, sosi, oracle, mss, filegdb)

@rouault
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rouault commented Jan 24, 2020

Did you hit a stumbling point in trying to built it as a non-plugin driver? I did manage in #1428 (comment) to have a build with the HDF5 driver built-in (but I didn't try with other drivers such as netCDF etc)

@jef-n
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jef-n commented Jan 24, 2020

Did you hit a stumbling point in trying to built it as a non-plugin driver? I did manage in #1428 (comment) to have a build with the HDF5 driver built-in (but I didn't try with other drivers such as netCDF etc)

No. I didn't try. It would probably have worked in the first place - if I had used /DH5_BUILT_AS_DYNAMIC_LIB as intended, but I used /DDH5_BUILT_AS_DYNAMIC_LIB instead - probably a copy & paste error. I noticed when I changed to HDF5_PLUGIN just now.

@rossoe
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rossoe commented Jan 24, 2020

Re:

install the gdal-hdf5 package

Is that easy enough to do within a Windows OS? via OSGeo4W for example?

@rouault
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rouault commented Jan 24, 2020

via OSGeo4W for example?

I don't have a Windows VM running, but from memory, in the osgeo4w-installer select Advanced install or something similar, and then you can select individual packages. There is one that should be called "gdal-hdf5"

@rossoe
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rossoe commented Jan 24, 2020

Indeed there is:
image

@jeroendenhertog
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I'm having similar problems using gdal 3.0.4 / QGis 3.12.1.
When I run gdalinfo, the corner coordinates of the BAG file are all the same. It seems that the horizontal and vertical resolution are not read from the bag file properly. I tested with the sample bag files on opennavsurf.org: http://www.opennavsurf.org/examples/H12617_MB_1m_MLLW_1of2.bag

@rouault
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rouault commented Apr 5, 2020

Closing. Was a binary build issue, not a source one

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