I think the rest of the post without performance complaints is strong enough to stand on its own. A full list of file access modes and their meanings is at File Objects. This opens an HDF5 file. What do you mean by putting a “file into a cache system”? We don’t need headers, structured arrays, or any weird esoteric object types. One of the best features of HDF5 is that you can store metadata right next to the data it describes.

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Yes, you can use H5Literate to iterate over all links in a group.

HDF5 file as a binary stream ?

Then feed sstream snapshot to tar maybe apply some mild compression on it depending on your tradeoffs. You’d obviously not expect user to do that by hand and would write strream to do it. So wrong motivation to pick HDF. It’s fair in a crash before the file was saved that new chunks might be bad, but old chunks should be fine.

I have investigated this subject a little more but came across yet more problems.

Quick Start Guide — h5py post0 documentation

How widely supported are the alternatives in the wider ecosystem? If you want portable format, you either have to use text, specify endianess in the format specification or store endianess in the file. You do actually have to read it though to understand slabs, hyperslabs, strides etc.


When it comes to performance, I think the main stram is this: Suppose someone has sent you a HDF5 file, mytestfile. These are tools that serialize buffers with razor-sharp binary specifications. So, at the moment, you need to store the buffer in a file on the receiving side and then open it with a file-oriented VFD sec2, stdio, mpio, hd5.

Hi Quincey, I didn’t get the time test your suggestion until today. I remember when someone dropped the specification on my desk and said, “should be a good read. Endianness generally is fast to convert, just pick a standard for the file format and detect on the platform.

Message 2 of 7. Auto-suggest helps you quickly narrow down your search results by suggesting possible matches as you type. If app crashed, you just use the last checkpoint.

HDF5 file as a binary stream? Attributes are accessed through the attrs proxy object, which again implements the dictionary interface: This is true, but anything can happen while futzing with a file. Below about GB you can do everything in memory.

The most fundamental thing to remember when using h5py is:. However, we are missing the final piece of the puzzle: Or Mac OS Finder. Which one are you using? Filesystems are the worst!


Also, as I said, thex example is a quite optimistic one, we do have cases now with , hddf5 10, arrays, and this is only going to increase in the months to come with the new generation of devices. Amazing tool when it’s in its sweetspot. They come with a lot less baggage than say HDF5. With Anaconda or Miniconda:.

For highest speed you need to convert data to your endianess before first use, update information about endianess inside the file and then work with memory-mapped file. I dont think that HDF5’s fault. However, if you’d like to work on a patch for opening a file from a memory buffer, I’d be happy strezm work with you on how I think you should proceed, etc. When in the field and the system shits the bed, its really easy to open an HDF5 file in HDFview and inspect the file contents.

And H5Dcreate will fail if such data item already exists.