Technical Insights

Elena Pourmal, The HDF Group What happened to my compression? One of the most powerful features of HDF5 is the ability to compress or otherwise modify, or “filter,” your data during I/O. By far, the most common user-defined filters are ones that perform data compression.  As you know, there are many compression options. There are filters provided by the HDF5 library (“predefined filters,”) which include several types of filters for data compression, data shuffling and checksum. Users can implement their own “user-defined filters” and employ them with the HDF5 library. [caption id="attachment_10741" align="alignright" width="300"] Cars in a 1973 Philadelphia junkyard – image from National Archives and Records Administration[/caption] While the programming model and usage of the compression filters is straightforward, it is possible for...

...we focus on how far we can push our personal computing devices with Spark. It consists of 7,850 HDF-EOS5 files covering 27 years and totals about 120 GB. We use a driver script, which reads a dataset of interest from each file in the collection, computes per-file quantities of interest, and gathers them in a CSV file for visualization. The processing time on our reference tablet machine for 3.5 years of data using 4 logical processors was about 10 seconds....

Mohamad Chaarawi, The HDF Group

First in a series: parallel HDF5

What costs applications a lot of time and resources rather than doing actual computation?  Slow I/O.  It is well known that I/O subsystems are very slow compared to other parts of a computing system.  Applications use I/O to store simulation output for future use by analysis applications, to checkpoint application memory to guard against system failure, to exercise out-of-core techniques for data that does not fit in a processor’s memory, and so on.  I/O middleware libraries, such as HDF5, provide application users with a rich interface for I/O access to organize their data and store it efficiently.  A lot of effort is invested by such I/O libraries to reduce or completely hide the cost of I/O from applications.

Parallel I/O is one technique used to access data on disk simultaneously from different application processes to maximize bandwidth and speed things up. There are several ways to do parallel I/O, and I will highlight the most popular methods that are in use today.

Blue Waters supercomputer at the National Center for Supercomputing Applications, University of Illinois, Urbana-Champaign campus. Blue Waters is supported by the National Science Foundation and the University of Illinois.

First, to leverage parallel I/O, it is very important that you have a parallel file system;

HDF Group has just announced “HDF Server” - a freely available service that enables remote access to HDF5 content using a RESTful API. In our scenario, using HDF Server, we upload our Monopoly simulation results to the server and then interested parties can make requests for any desired content to the server - no file size issues, no downloading entire files...

Quincey Koziol, The HDF Group

Oil Rig, Rice oil and gas

Photo from nasa.gov

Perhaps the original producers of “big data,” the oil & gas (O&G) industry held its eighth annual High-Performance Computing (HPC) workshop in early March. Hosted by Rice University, the workshop brings in attendees from both the HPC and petroleum industries.

Jan Odegard, the workshop organizer, invited me to the workshop to give a tutorial and short update on HDF5.

The workshop (#oghpc) has grown a great deal during the last few years and now has more than 500 people attending, with preliminary attendance numbers for this year’s workshop over 575 people (even in a “down” year for the industry).  In fact, Jan’s pushing it to a “conference” next year, saying, “any workshop with more attendees than Congress is really a conference.” But it’s still a small enough crowd and venue that most people know each other well, both on the Oil & Gas and HPC sides.

The workshop program had two main tracks, one on HPC-oriented technologies that support the industry, and one on oil & gas technologies and how they can leverage HPC.  The HPC track is interesting, but mostly “practical” and not research-oriented, unlike, for example, the SC technical track. The oil & gas track seems more research-focused, in ways that can enable the industry to be more productive.

I gave an hour and a half tutorial on developing and tuning parallel HDF5 applications, which