Ah yes, after taking a quick glance at the source of h5ls I see why this doesn't help any. H5ls tries to open the file using each of the available file drivers until it is successful or exhausts the list. Since it expects failures to occur when attempting to open the file with an incorrect file driver, it explicitly disables the error stack during file open and this is why you won't see the error stack for the true failure. Not a very elegant solution, but I can see why it was done.
If you are familiar with editing the HDF5 source code and rebuilding, I can show you where the issue is at in the source code for h5ls. Otherwise, I may need to think about the best way to upload a large file somewhere so that we might have a look at the file. ________________________________ From: Hdf-forum <[email protected]> on behalf of Roger Leigh <[email protected]> Sent: Friday, January 5, 2018 11:30 AM To: [email protected] Subject: Re: [Hdf-forum] A number of small problems On 05/01/2018 16:39, Jordan Henderson wrote: Thanks for the detailed explanations, Jordan. All understood and appreciated. > For your last question, this is likely a side effect of an elusive bug > that has also existed in HDFView for a while now. The root cause hasn't > yet been discovered but it has been noticed that occasionally simply > opening a file and closing it at a later time seems to show that some > modification has been made to the HDF file. I imagine that the change it > is making to the file is something metadata-related which would explain > why killing the process corrupts the file. Could you possibly rerun h5ls > on the corrupted file with the additional "--enable-error-stack" > command-line parameter so that we can at least capture and keep a record > of the specific error that HDF5 is running into when it tries to open > the file? This may be very helpful in debugging the root problem. This isn't showing any extra detail I'm afraid: % h5ls -r --enable-error-stack idr016-orig.h5 / Group /Images Dataset {69120/Inf} /Objects Dataset {5880380/Inf} % h5ls -r --enable-error-stack idr016-broken.h5 idr016-broken.h5: unable to open file % h5ls --enable-error-stack idr016-broken.h5 idr016-broken.h5: unable to open file Kind regards, Roger The University of Dundee is a registered Scottish Charity, No: SC015096 _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5
_______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5
