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hdf5

About

HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.

The HDF5 technology suite includes:

  • A versatile data model that can represent very complex data objects and a wide variety of metadata.
  • A completely portable file format with no limit on the number or size of data objects in the collection.
  • A software library that runs on a range of computational platforms, from laptops to massively parallel systems, and implements a high-level API with C, C++, Fortran 90, and Java interfaces.
  • A rich set of integrated performance features that allow for access time and storage space optimizations.
  • Tools and applications for managing, manipulating, viewing, and analyzing the data in the collection.

The HDF5 data model, file format, API, library, and tools are open and distributed without charge.

Building on its 20-year history, The HDF Group offers personalized consulting, training, design, software development, and support services to help clients take full advantage of HDF5 capabilities in addressing their unique data management challenges. (see: HDFGroup.

Version and Availability

Softenv Keys for hdf5 on painter
Machine Version Softenv Key
painter 1.8.2 +hdf5-1.8.2-intel-11.1-mvapich-1.1
painter 1.8.2 +hdf5-1.8.2-intel-11.1-mvapich2-1.4
▶ Display Softenv Keys for hdf5 all clusters
Machine Version Softenv Key
eric 1.8.2 +hdf5-1.8.2-intel-11.1-mvapich-1.1
eric 1.8.2 +hdf5-1.8.2-intel-11.1-mvapich2-1.4
qb 1.8.11 +hdf5-1.8.11-intel-11.1-mvapich-1.1
qb 1.8.2 +hdf5-1.8.2-intel-10.1-mvapich-1.1
qb 1.8.2 +hdf5-1.8.2-intel-10.1-mvapich2-1.4
qb 1.8.2 +hdf5-1.8.2-intel-11.1-mvapich-1.1
qb 1.8.2 +hdf5-1.8.2-intel-11.1-mvapich2-1.4
oliver 1.8.2 +hdf5-1.8.2-intel-11.1-mvapich-1.1
oliver 1.8.2 +hdf5-1.8.2-intel-11.1-mvapich2-1.4
louie 1.8.2 +hdf5-1.8.2-intel-11.1-mvapich-1.1
louie 1.8.2 +hdf5-1.8.2-intel-11.1-mvapich2-1.4
poseidon 1.8.2 +hdf5-1.8.2-intel-11.1-mvapich-1.1
poseidon 1.8.2 +hdf5-1.8.2-intel-11.1-mvapich2-1.4
painter 1.8.2 +hdf5-1.8.2-intel-11.1-mvapich-1.1
painter 1.8.2 +hdf5-1.8.2-intel-11.1-mvapich2-1.4
philip 1.8.2 +hdf5-1.8.2-intel-11.1-mpich-1.2.7p1
supermike2 1.8.10 +hdf5-1.8.10-gcc-4.4.6-openmpi-1.6.2
supermike2 1.8.10 +hdf5-1.8.10-Intel-13.0.0-openmpi-1.6.2
supermike2 1.8.9 +hdf5-1.8.9-Intel-13.0.0-openmpi-1.6.2
▶ Softenv FAQ?

The information here is applicable to LSU HPC and LONI systems.

Softenv

SoftEnv is a utility that is supposed to help users manage complex user environments with potentially conflicting application versions and libraries.

System Default Path

When a user logs in, the system /etc/profile or /etc/csh.cshrc (depending on login shell, and mirrored from csm:/cfmroot/etc/profile) calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to set up the default path via the SoftEnv database.

SoftEnv looks for a user's ~/.soft file and updates the variables and paths accordingly.

Viewing Available Packages

Using the softenv command, a user may view the list of available packages. Currently, it can not be ensured that the packages shown are actually available or working on the particular machine. Every attempt is made to present an identical environment on all of the LONI clusters, but sometimes this is not the case.

Example,

$ softenv
These are the macros available:
*   @default
These are the keywords explicitly available:
+amber-8                       Applications: 'Amber', version: 8 Amber is a
+apache-ant-1.6.5              Ant, Java based XML make system version: 1.6.
+charm-5.9                     Applications: 'Charm++', version: 5.9 Charm++
+default                       this is the default environment...nukes /etc/
+essl-4.2                      Libraries: 'ESSL', version: 4.2 ESSL is a sta
+gaussian-03                   Applications: 'Gaussian', version: 03 Gaussia
....
Listing of Available Packages

See Packages Available via SoftEnv on LSU HPC and LONI.

For a more accurate, up to date list, use the softenv command.

Caveats

Currently there are some caveats to using this tool.

  1. packages might be out of sync between what is listed and what is actually available
  2. resoft and soft utilities are not; to update the environment for now, log out and login after modifying the ~/.soft file.
Availability

softenv is available on all LSU HPC and LONI clusters to all users in both interactive login sessions (i.e., just logging into the machine) and the batch environment created by the PBS job scheduler on Linux clusters and by loadleveler on AIX clusters..

Packages Availability

This information can be viewed using the softenv command:

% softenv
Managing Environment with SoftEnv

The file ~/.soft in the user's home directory is where the different packages are managed. Add the +keyword into your .soft file. For instance, ff one wants to add the Amber Molecular Dynamics package into their environment, the end of the .soft file should look like this:

+amber-8

@default

To update the environment after modifying this file, one simply uses the resoft command:

% resoft

Usage

HDF5 is provided as an application programming interface (API) library, so it must be included during an application build process. This can be done with the typical compiler options (-l, -L) using explicit library names and directories, or through the use of wrapper scripts in the place of the usual compiler commands (recommended). Serial or parallel program can be compiled using these wrappers:

  • h5c++ - The C++ compiler wrapper.
  • h5pcc - The C compiler wrapper.
  • h5pfc - The Fortran compiler wrapper.

The actual compilers, and possibly MPI libraries, are selected based on the version of HDF5 selected by the softenv key. For instance, the key:

      +hdf5-1.8.10-gcc-4.4.6-openmpi-1.6.2
    

would have the wrappers for the 1.8.10 version of HDF5 use the GCC 4.4.6 compiler and the OpenMPI 1.6.2 library.

Resources

Last modified: March 25 2014 14:58:11.