{"action":"created","issue":{"url":"https://api.github.com/repos/h5py/h5py/issues/1036","repository_url":"https://api.github.com/repos/h5py/h5py","labels_url":"https://api.github.com/repos/h5py/h5py/issues/1036/labels{/name}","comments_url":"https://api.github.com/repos/h5py/h5py/issues/1036/comments","events_url":"https://api.github.com/repos/h5py/h5py/issues/1036/events","html_url":"https://github.com/h5py/h5py/issues/1036","id":323305095,"number":1036,"title":"Cannot open HDF file created in H5Py in any other package","user":{"login":"mhearne-usgs","id":303058,"avatar_url":"https://avatars1.githubusercontent.com/u/303058?v=4","gravatar_id":"","url":"https://api.github.com/users/mhearne-usgs","html_url":"https://github.com/mhearne-usgs","followers_url":"https://api.github.com/users/mhearne-usgs/followers","following_url":"https://api.github.com/users/mhearne-usgs/following{/other_user}","gists_url":"https://api.github.com/users/mhearne-usgs/gists{/gist_id}","starred_url":"https://api.github.com/users/mhearne-usgs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mhearne-usgs/subscriptions","organizations_url":"https://api.github.com/users/mhearne-usgs/orgs","repos_url":"https://api.github.com/users/mhearne-usgs/repos","events_url":"https://api.github.com/users/mhearne-usgs/events{/privacy}","received_events_url":"https://api.github.com/users/mhearne-usgs/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-05-15T17:05:05Z","updated_at":"2018-05-16T04:15:53Z","closed_at":null,"author_association":"NONE","body":"Operating System:\r\nOSX 10.12.6\r\n\r\nPython Version:\r\nPython 3.5.5\r\n\r\nPython Acquired:\r\nMiniconda on OSX\r\n\r\nH5Py Version:\r\n2.7.1\r\n\r\nHDF5 Version:\r\n1.8.17\r\n\r\nStack Trace:\r\nAs noted in the title, the problem doesn't seem to be in H5Py, but rather in every other HDF5-related tool I try.  I've created a large (14M) HDF5 file using my own class hierarchy based on H5Py, which I can read/write just fine using those classes. However, when trying to open that file using either h5dump on the command line or the Java HDFView tool I get the error below.\r\n\r\nh5dump error: unable to open file \"shake_result.hdf\"\r\n\r\nI'm attaching a text file with the results of running \"h5dump --enable-error-stack shake_result.hdf\".\r\n[h5dump_results.txt](https://github.com/h5py/h5py/files/2005953/h5dump_results.txt)\r\n\r\n\r\nI've tried using my classes to create a smaller example, but none of them seemed to reproduce the error.  The file in question can be found here:\r\n\r\nftp://ftpint.usgs.gov/pub/cr/co/golden/hearne/shake_result.hdf\r\n\r\nIf it is helpful, I tried reading the file in Matlab as well, and the error I get in there looks like this:\r\nError using hdf5infoc\r\nCall to HDF5 library failed (open_group): \"Unable to open group: /__arrays__\".\r\n\r\nThe HDF file is organized into groups by (sort of) data type: strings, dictionaries, lists, pandas dataframes, numpy arrays, etc. Each group is named as you see above with two leading and trailing underscores. Each thing (string, array, etc.) is stored as a dataset with its own name inside the appropriate group, with appropriate serialization techniques applied as needed.\r\n"},"comment":{"url":"https://api.github.com/repos/h5py/h5py/issues/comments/389389210","html_url":"https://github.com/h5py/h5py/issues/1036#issuecomment-389389210","issue_url":"https://api.github.com/repos/h5py/h5py/issues/1036","id":389389210,"user":{"login":"aragilar","id":1281144,"avatar_url":"https://avatars2.githubusercontent.com/u/1281144?v=4","gravatar_id":"","url":"https://api.github.com/users/aragilar","html_url":"https://github.com/aragilar","followers_url":"https://api.github.com/users/aragilar/followers","following_url":"https://api.github.com/users/aragilar/following{/other_user}","gists_url":"https://api.github.com/users/aragilar/gists{/gist_id}","starred_url":"https://api.github.com/users/aragilar/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aragilar/subscriptions","organizations_url":"https://api.github.com/users/aragilar/orgs","repos_url":"https://api.github.com/users/aragilar/repos","events_url":"https://api.github.com/users/aragilar/events{/privacy}","received_events_url":"https://api.github.com/users/aragilar/received_events","type":"User","site_admin":false},"created_at":"2018-05-16T04:15:53Z","updated_at":"2018-05-16T04:15:53Z","author_association":"CONTRIBUTOR","body":"It may be that the Java app and Matlab are using older versions of HDF5, can you check what versions they are using?"}}
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