Fix issues with large external data files #4843
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Merge - To 1.14
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Co-authored-by: Neil Fortner <[email protected]>
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* Fix issues with large external data files (#4843) (#4847) * Fixed a memory leak from H5FL_blk_malloc (#4882) In H5F__accum_reset(), when H5F__accum_flush() failed, the freeing of f_sh->accum.buf was never reached, causing resource leak. @fortnern added the third argument to H5F__accum_reset() so we can free f_sh->accum.buf when we close the file, that is, when H5F__accum_reset() is called from the H5F__dest() route, and can leave the accumulator in place otherwise. * Added an entry for the GH-4585 fix (#4889) * Fix an incorrect returned value by H5LTfind_dataset() (#4869) H5LTfind_dataset() returns true for non-existing datasets because it only compares up to the length of the searched string, such as "Day" vs "DayNight" (issue GH-4780). This PR applied the user's patch and added tests. * Fix minor spelling in documentation (#4870) --------- Co-authored-by: Neil Fortner <[email protected]> Co-authored-by: bmribler <[email protected]>
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* Fix issues with large external data files (#4843) (#4847) * Fixed a memory leak from H5FL_blk_malloc (#4882) In H5F__accum_reset(), when H5F__accum_flush() failed, the freeing of f_sh->accum.buf was never reached, causing resource leak. @fortnern added the third argument to H5F__accum_reset() so we can free f_sh->accum.buf when we close the file, that is, when H5F__accum_reset() is called from the H5F__dest() route, and can leave the accumulator in place otherwise. * Added an entry for the GH-4585 fix (#4889) * Fix an incorrect returned value by H5LTfind_dataset() (#4869) H5LTfind_dataset() returns true for non-existing datasets because it only compares up to the length of the searched string, such as "Day" vs "DayNight" (issue GH-4780). This PR applied the user's patch and added tests. * Fix minor spelling in documentation (#4870) * Updated Platforms tested in RELEASE.txt Incremented version subrelease to -3.
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* Fix issues with large external data files (#4843) (#4847) * Fixed a memory leak from H5FL_blk_malloc (#4882) In H5F__accum_reset(), when H5F__accum_flush() failed, the freeing of f_sh->accum.buf was never reached, causing resource leak. @fortnern added the third argument to H5F__accum_reset() so we can free f_sh->accum.buf when we close the file, that is, when H5F__accum_reset() is called from the H5F__dest() route, and can leave the accumulator in place otherwise. * Added an entry for the GH-4585 fix (#4889) * Fix an incorrect returned value by H5LTfind_dataset() (#4869) H5LTfind_dataset() returns true for non-existing datasets because it only compares up to the length of the searched string, such as "Day" vs "DayNight" (issue GH-4780). This PR applied the user's patch and added tests. * Fix minor spelling in documentation (#4870) * Set release version 1.14.5 and release date to 2024-09-30.
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The code for reading and writing external raw data files does not account for the case where a single call to read() or write() does not process all the bytes in the request. This can cause errors when dealing with large external files. Modified this code to call read() or write() in a loop until all bytes are processed. This code is partly taken from H5FDsec2.c. In the future we should consider having the external dataset code run through the H5FD layer to avoid these sorts of issues in the future (and add additional flexibility to the external dataset feature). Fixes #4216 and h5py/h5py#2394