<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Richard,<div><br><div><div>On Jun 4, 2009, at 4:35 AM, Richard Corden wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <div bgcolor="#ffffff" text="#000000"> Hi,<br> <br> After reading this post: "HDF5 Deleting Datasets AND Recovering Space", I thought I'd run h5repack over some of my datasets to see what the affect would be.<br> <br> However, when I run it over one "test" dataset I get the following assertion:<br> <tt><br> h5repack: H5Dscatgath.c:501: H5D_scatgath_read: Assertion `(H5S_select_iter_nelmts(&file_iter)) == (nelmts - smine_start)' failed.<br> Aborted<br> </tt><br> What's interesting is that this only happens if before I close the dataset I call "H5Dset_extent" to the exact number of elements in my dataset. So, for example, if I don't call this function, or if I set the dataset extent to the "size +1", then h5repack runs without an error.<br> <br> My main concern is that I'm not "misusing" the HDF5 format and this problem is only shows (at the moment) by using h5repack.</div></blockquote><div><br></div><span class="Apple-tab-span" style="white-space:pre"> </span>Sounds reasonable to me - could you contact the HDF helpdesk (<a href="mailto:help@hdfgroup.org">help@hdfgroup.org</a>) with a test program that shows the error and we'll verify it and try to get it fixed.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Thanks,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Quincey</div><div><br><blockquote type="cite"><div bgcolor="#ffffff" text="#000000"><br> <br> <br> The command I'm using:<br> <blockquote><tt>h5repack -v -f GZIP=1 file1.qa file2.qa</tt><br> </blockquote> And the output of the run is:<br> <br> <blockquote><tt>Objects to modify layout are...</tt><br> <tt>Objects to apply filter are...</tt><br> <tt> All with GZIP, parameter 1</tt><br> <tt>Making file <file2.qa>...</tt><br> <tt>-----------------------------------------</tt><br> <tt> Type Filter (Compression) Name</tt><br> <tt>-----------------------------------------</tt><br> <tt> group /</tt><br> <tt> group /analysis</tt><br> <tt> group /analysis/filenames</tt><br> <tt> dset /analysis/filenames/filenames</tt><br> <tt> group /analysis/locations</tt><br> <tt>h5repack: H5Dscatgath.c:501: H5D_scatgath_read: Assertion `(H5S_select_iter_nelmts(&file_iter)) == (nelmts - smine_start)' failed.</tt><br> <tt>Aborted</tt><br> </blockquote> <br> Here's the contents of '/analysis/locations/locations' which at least from the output above, appears to be where the problem occurs:<br> <br> <br> <tt> GROUP "locations" {<br> DATASET "locations" {<br> DATATYPE H5T_COMPOUND {<br> H5T_STD_U64LE "filename";<br> H5T_STD_I32LE "line";<br> H5T_STD_I32LE "column";<br> H5T_STD_U64LE "incl_from";<br> H5T_STD_I32LE "hash_line_file";<br> H5T_STD_I32LE "hash_line_line";<br> H5T_REFERENCE "properties";<br> }<br> DATASPACE SIMPLE { ( 1 ) / ( H5S_UNLIMITED ) }<br> DATA {<br> (0): {<br> 0,<br> 184,<br> 183,<br> 18446744073709551615,<br> -1,<br> -1,<br> NULL<br> }<br> }<br> }<br> }</tt><br> <br> Thanks for your help.<br> <br> Regards,<br> <br> Richard<br> <br> </div> </blockquote></div><br></div></body></html>