Skip to Content.
Sympa Menu

h5part - [H5part] SVN access available for contributions?

h5part AT

Subject: H5Part development and discussion

List archive

[H5part] SVN access available for contributions?

Chronological Thread 
  • From: John Biddiscombe <biddisco AT>
  • To: h5part AT
  • Subject: [H5part] SVN access available for contributions?
  • Date: Wed, 24 Jan 2007 10:46:00 +0100
  • List-archive: <>
  • List-id: H5Part development and discussion <>

Dear H5Part users,

I'd like, if I may, to access the svn repository so that I can
a) update my copy of H5Part which is no doubt quite old
b) potentially contribute some improvements which I'll list below for your scrutiny

1) I found that reading particles into {x,y,z} arrays rather than into {x}, {y}, {z} separately was desirable from a visualization point of view so I have added some logic to my own code which handles the memory space issues around this. Also when writing data which is stored as an N-component vector field stored as {v0,v1,} rather than N separate arrays.
I have found that to facilitate the display of data using any scalar field as the x,y,z coordinate it's nice to be able to write coordinate or vector fields as single component datasets (as is currently done with H5Part), but read them back in as a vector array again. I also find a lot of data with vector fields as u,v,w in separate arrays and wish to recombine these into a single {u,v,w} array.

2) With reference to the above, when reading N components into a single vector field, one wishes to supply an array of names. for example, the default H5Part "x","y","z" names are used for coordinate variables, but If the vector field :"velocity" is written to file as "velocity_0", "velocity_1", velocity_2" (for 3D), I may wish to read them back as the coordinate array later, so supplying an array of names (e.g. "x", "velocity_2", "y") to a read function allows one to arbitrarily map datasets onto components.

3) the H5Part naming convention uses "Particles1" "Particles2" etc as the group names (renamed I understand in later versions to steps1,2 or similar). I would prefer to use an attribute attached at the top level which would be a standard string preserved for all time
"ParticleTimeStepName" this attribute would be set to "Particles" in earlier files and "steps" in later version. Additionally, I would like to add a second attribute which would be the FormatString
"ParticleTimeFormatString" by default one would use %i to represent a simple integer, but if %05i were set, then particles would be stored as Particles00001 Particles00002, which makes ascii listings of dataset contents more intuitive as they appear in the numerical order (as opposed to the current particles1 particles10 particles100 particles11 particles12 ....).
Although most simulations use time steps, it is frequently the case that data is dropped due to IO issues and using a Real time value might be desireable (eg 0.005, 0.0075, 0.1 - if time steps are not regular, but rather adaptive- in this case a special array which holds the actual time values should be present
"ParticleTimeValues" where the number of entries should match the number of groups or timesteps

4) Support for other data types is lacking - I regularly use int, short, float, double, byte and even boolean. Since HDF5 support all, so should H5Part. Since the majority of my code is in C++, I have used a combination of templates and macros to allow any data type to be read/written and it works fine. I would like to explore ways of extending this to other languages and adding support in the main h5part interface.

5) One of my emails appears in the archive where I mentioned DEM and SPH data and saw a reply that discussed meshed data. In this context, I was referring to Discrete Element Method particle data and Smoothed Particle Hydrodynamics particle data). I am encouraging users in both these domains to use H5Part as a storage form. They invariably have vector fields - so the use of multi-component scalars is essential. In the case of SPH data various kernel functions exist and I would like to store these as string attributes - I wonder if standard names (like those suggested above) could be chosen for Particle formats and enshrined somewhere so that

my own svn repository of H5Part related material is here should anyone wish to browse it.

Thanks for reading. I'm sure most of these issues have already been dealt with in your most recent versions of H5Part. I would very much like to contribute any that have not.



John Biddiscombe, email:biddisco @
CSCS, Swiss National Supercomputing Centre | Tel: +41 (91) 610.82.07
Via Cantonale, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82

Archive powered by MHonArc 2.6.19.

Top of Page