The author my colleague, and probably the most talented developer I know isn’t replacing HDF5 with a ‘proprietary binary format’: What is stored in this file? HDF5 gets rid of all this. A full list of file access modes and their meanings is at File Objects. It saturated 1Gbps connection pretty close to its maximum expected capacity.

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Hi Xunlei, On Apr 14,at 2: Based on our observation, there is one data set, mydataset in the file. Type this command into a Terminal or Command Prompt. A crash may result in corruption but there is no srteam risk of corruption. I started using HDF5 once exactly for this reason and it was overkill.

I think it’s reasonable to be very upset if you have a container file and adding new named chunks to the hdr5 has the possibility of causing the old data to become unreadable. As for sanity checks, like checking that probabilities stored in a dataset sum up to 1. This is a lot more complex than it could be, but that is the nature of HDF5 very low level, very powerful.

Trackpy implements a generic interface that could be used to store and retrieve particle tracking data in any file format. Instead, he merely jdf5 the text to hff5 any specific numbers, and he didn’t add any inline text indicating that the post had been edited. For more, see Groups.


While it’s true that you lose atomicity with this, it can both burn you and help you: Message Edited by DFGray on I hdc5 nowadays researchers have to spend million dollar on a electron microscope to look at anything and have to depend on HDF5 to deal with any data.

If the “parallel access” refers to threading, HDF has a thread safe feature that you need to enable when building the code. Alembic, a data hdf format for 3D graphics, especially high end VFX, also initially started with HDF5 but found it to have low performnance and was generally a bottleneck especially in multithreaded contexts.

It all depends what your aims are. More over, if your app crashed, what good is the data?

HDF5 file as a binary stream ?

You can still use binary formats without HDF5, just write the memory buffer of floats to disk directly skipping text format. It is very tricky to build something that works reliably across all systems, but, thankfully, filesystem designers have done that job for us.

Works flawlessly with terabytes of data. I imagine a weak coupling system for scientific applications. I deal with binary data all the time and I just use fwrite in C and pack in Perl, and a text readme in vim explaining the simple format.

Moving away from HDF5 | Hacker News

If your users will rarely need to do this, you could just store the entire folder hierarchy in a. To extend it to any format, write a class subclassing trackpy.


From the discussion that has taken place it seems these two would be of interest. For more, see File Objects and Datasets. HDF5 supports parallelism from distinct programs, but its multithreaded story was is? Can also pipe tar directly to something like nc.

Nope, I was very confused for a second. Before I do so, could you please help me to update the mechanism?

And filesystems are now at a point where they’re very good at storing arbitrary blobs of data which wasn’t the case when HDF was founded. Maybe if you’re lucky you can stick with something that looks like FITS.

HDF provides command-line tools like h5dump and h5diff, so you can dump HDF5 file to text and pipe it into standard and non-standard unix tools [1]. I’ve used HDF5 weekly for the last 5 years and so have my associates and its been wonderful. Perhaps if your project has spectacularly complex data storage requirements as to your examples: