Message 5 of 7. One reason to use binary formats like HDF5 is to avoid precision loss when storing floating-point values. In fact, I’d say it’s a minor consideration compared to the other points. When data sets become large, beginning-friendly file formats like CSV or Excel become impractical. It saturated 1Gbps connection pretty close to its maximum expected capacity. Details on that transition here:

Uploader: Grole
Date Added: 23 March 2007
File Size: 9.46 Mb
Operating Systems: Windows NT/2000/XP/2003/2003/7/8/10 MacOS 10/X
Downloads: 54744
Price: Free* [*Free Regsitration Required]

Thereby it does not conflict with an MPI application and can be used within some MPI-parallelized code without affecting that one. The idea of a general format serving all research just sounds silly to me.

I’m just getting started with HDF5, and your streaming example should be most helpful. The most fundamental thing to remember when using h5py is:. All the major processors are little endian now.

Moving away from HDF5 | Hacker News

In my previous job we were evaluating HDF5 for implementing a data-store a couple of years ago. Thank you for getting back to me. These are tools that serialize buffers with razor-sharp binary specifications. One reason to use binary formats ndf5 HDF5 is to avoid precision loss when storing floating-point values.


We hope that it can make it easier for researchers hcf5 use different file formats to exchange data. From the standard point of view float is a sequence of bits. We can get by just fine with: HDF5 was never intended be be a container used to stream data into — it was meant for sharing data.

But as it turned out, there were problems with his benchmark. If you want headers, you can define those as text and just use extents to embed the binary data.

It is specifically designed to avoid losing a single bit of informaiton. If the “parallel access” refers to threading, HDF has a thread safe feature that you need to enable when building the code. I have to ask though, why not just make a cached file of your data and onces its done, integrate into the hef5 HDF file?

How do you stream data to a HDF5 file? – Discussion Forums – National Instruments

Nope, I was very confused for a second. Can also pipe tar directly to something like nc. Select a hyperslab on this extended dataspace corresponding to the hhdf5 you will be writing. Message Edited by DFGray on In reply to this post by Giraudon Cyril.


Got an SGI Indigo somewhere in your lab? Some people want stuff in R, some straem Python 2. X Dear Quincey, You wrote: I dont always have matlab available when im in the field, same with python.

We had some strict requirements about data corruption e. You simply don’t need fancy file-systems. Looks like you working from an older version of the API I think the rest of the post without performance complaints is strong enough to stand on its own.

HDF5 file as a binary stream ?

Might one take a peek at that? Another thing that will happen is this: I ended up designing a transactional file format a kind of log-structured file system with data versioning and garbage collection, all stored in a single file from scratch to match our requirements.

With Anaconda or Miniconda:. We have a well-defined set of data we need to keep, including intermediate processing steps.

Author: admin