[Top][All Lists]

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [h5md-user] Mandate Variable-length string datatype

From: Konrad Hinsen
Subject: Re: [h5md-user] Mandate Variable-length string datatype
Date: Tue, 24 Sep 2013 11:06:57 +0200

Peter Colberg writes:

 > Abstractions are very hard to get right. To day I have not seen a
 > single C++ interface to HDF5 that is useful beyond the initial goals
 > at its conception.

I am tempted to make some mean comments about C++, but I can just
force myself to shut up ;-)

 > While it is important to have high-level interfaces that guide new
 > H5MD users (e.g., pyh5md), it is equally important to support those
 > users that write high-performance programs using the HDF5 API.

Another nice illustration for the importance of practicalities.

In this particular case, we have

1) String data in trajectories are usually small in amount (I have yet
   to see a use for time-dependent string data), so efficiency of storage
   and access is of secondary importance.

2) In high-level languages such as Python, dealing with any kind of string
   data is easy enough.

The priority in defining the layout for string data should thus be to
reduce the barrier for dealing with H5MD in low-level languages. My
own experience is C, which makes me prefer variable-length strings,
but of course there are other languages to take into consideration.

 > Keeping the choice between fixed- and variable-length strings will
 > simply mean that many writers and readers will not be interoperable,
 > even if they use the same domain-specific data.

Here are the pros and cons as I see them:

 Mandatory string type (either fixed or variable)

  + simplifies software for reading H5MD

 User's choice of string type

  + simplifies software for writing H5MD

  - likely to create incompatibilities because people will write
    H5MD readers with a specific "dialect" in mind

Personally that makes me favor a mandatory single string type.

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen

reply via email to

[Prev in Thread] Current Thread [Next in Thread]