Real Mission Critical

Mark Stone — Mon, 01 Jun 2009 16:15:00 GMT

The 1.0 release of WinBioinfTools might seem like a modest event; as of this writing, the project has
44 downloads. High Performance Computing (HPC) is a small community, granted, and the number of HPC
applications for bioinformatics is a small subset of that. Let's not confuse popularity with importance,
however.

We use the phrase "mission critical" very frequently and somewhat casually within software development. In
talking to a friend about the swine flu outbreak, I was reminded that the phrase has its origin in
military history: an aspect of a mission so critical that failure in that aspect would result in the
loss of life. In the developing world where medical infrastructure can be a fragile thing, information about
the origins or genetic makeup of a virus can be vital. It can be mission critical.

Historically, the developing world has been dependent on developed western countries to do their research for them.
Open source is beginning to level that playing field, though. Using a cluster environment and software
projects like CoCoNUT for gene sequencing and comparison, even university research centers with modest x86
server environments can play in the HPC space. This is important because the research priorities for a
university in a developing country may be very different from the research priorities of a major western
research university. At its best, this is exactly the kind of lowering of barriers to entry that open
source should facilitate.

For all its value, CoCoNUT has two significant limitations. Its license is an academic license, not a fully
open source license. And it runs only on Linux/Unix systems. The latter is particularly important. Research
scientists are not IT professionals, and they should not have to care about the underlying platform on which
their software runs. The spirit of open source is to make software as widely available as possible, and there
is no way to meet that spirit without including Windows Server among the target platforms. Mission critical
demands no less.

So WinBioinfTools makes important steps forward on both fronts. The team at Nile University has released a
GPL-licensed project that "contains a number of programs for Bioinformatics running over Windows Cluster running
Windows HPC server 2008. The current version includes the CoCoNUT system for pairwise genome comparison,
parallel global sequence alignment, and parallel BLAST."

This is a great example of a local software community using open source to make their needs a priority,
and delivering a project that will benefit local software communities in other developing countries with
similar needs. WinBioinfTools puts us one step closer to making scientific computing software platform
neutral, and closer to making Windows Server a first class citizen in the open source world of HPC.

Brazilian Students Set Their Own Course

Mark Stone — Mon, 16 Mar 2009 19:05:00 GMT

I’m going to tell a story that starts in Indiana, but really it’s about Brazil.

Once upon a time “scientific computing” was nearly synonymous with “Fortran”. Today, though, just about any high level language can be used to write High Performance Computing (HPC) applications. These days that language choice also includes C#.

At Indiana University, the Open Systems Lab has pioneered work to implement Message Passing Interface (MPI) support for .Net, so that MPI applications can be written in C#. The project is MPI.Net, and you can find it on Codeplex. It is open source, about three years old, has reached a 1.0 release, and is compatible with two other important open source projects, OpenMPI and Mono. The principle developers behind the project are Andrew Lumsdaine at Indiana University and his former student, Douglas Gregor, who is now on the faculty of Rensselear Polytechnic Institute.

This is the kind of open source work that’s really exciting to see because of the way it expands choices for the developer and the end user. A C# developer should not be closed off from writing HPC applications if that’s what they want to do. And a research scientist should not have to think about whether their lab is running Linux or Windows Server. Both of these individuals are working enough layers above the operating system that somebody else’s operating system choice should not be a constraint.

So I was very excited to learn that students in Brazil at Federal University of Rio Grande do Sul were doing work on MPI, and excited to talk with them about their work. One of their projects is MPI#, also open source and also hosted on Codeplex.

MPI# builds on top of the work of MPI.Net, adding some functionality not yet present in MPI.Net. Specifically, quoting from the project description:

The goals of this project would be to build upon MPI.NET in order to complement it with the features that are missing, mainly regarding collective communication. Either they could benefit from C# native support for such communication, either they could be programmed on top of the provided MPISend/MPIRecv encapsulations. C# and .NET features such as fault tolerance or dynamicity support would be studied, in other to turn the MPI# implementation robust in large, dynamic and heterogeneous platforms.

Two of the students working on MPI# are Ismael Stangherlini and Fernando Afonso. They are graduate students in computer science, working on projects affiliated with the Brazilian Interoperability and Open Source Software Development Nucleous. When I talked to them about their work on MPI# I was curious what their communication with Indiana University had been like. Their response: they had never been in contact with Indiana University; they simply downloaded the code for MPI.Net and started working on their own.

That’s the magic of open source: that they can, in fact, just download the code on their own and start coding against it. They may make an important contribution to MPI.Net. Or their code may be entirely disregarded. Or they may move on to other projects and somebody else may or may not pick up where they left off. At this stage it’s too early to tell. But the fact that all of these scenarios are possible demonstrates why, as a methodology, open source is so nimble and adaptive. A top-down product development process, or a top-down standards development process can only execute on the innovations envisioned by the few at the top, and at the speed of the slowest decision-makers in the process. But a bottom-up open source process enables every innovation that anyone at the grass roots level can see.

Port 25: The Open Source Community at Microsoft : Interop, HPC

Real Mission Critical

Brazilian Students Set Their Own Course