Section: Software

Molecular Dynamics Simulations

Another interesting scheduling problem is the case of applications sharing (large) files stored in replicated distributed databases. We deal here with a particular instance of the scheduling problem mentioned in Section  6.2.1 . This instance involves applications that require the manipulation of large files, which are initially distributed across the platform.

It may well be the case that some files are replicated. In the target application, all tasks depend upon the whole set of files. The target platform is composed of many distant nodes, with different computing capabilities, and which are linked through an overlay network (to be built). To each node is associated a (local) data repository. Initially, the files are stored in one or several of these repositories. We assume that a file may be duplicated, and thus simultaneously stored on several data repositories, thereby potentially speeding up the next request to access them. There may be restrictions on the possibility of duplicating the files (typically, each repository is not large enough to hold a copy of all the files). The techniques developed in Section  6.1.2.3 will be used to dynamically maintain efficient data structures for handling files.

Our aim is to design a prototype for both maintaining data structures and distributing files and tasks over the network.

This framework occurs for instance in the case of Monte-Carlo applications where the parameters of new simulations depend on the average behavior of the simulations previously performed. The general principle is the following: several simulations (independent tasks) are launched simultaneously with different initial parameters, and then the average behavior of these simulations is computed. Then other simulations are performed with new parameters computed from the average behavior. These parameters are tuned to ensure a much faster convergence of the method. Running such an application on a semi-stable platform is a particular instance of the scheduling problem mentioned in Section  6.2.1 .

We will focus on a particular algorithm picked from Molecular Dynamics: calculation of Potential of Mean Force (PMF) using the technique of Adaptive Bias Force (ABF). This work is done via a collaboration with Juan Elezgaray, IECB, Bordeaux. Here is a quick presentation of this context. Estimating the time needed for a molecule to go through a cellular membrane is an important issue in biology and medicine. Typically, the diffusion time is far too long to be computed with atomistic molecular simulations (the average time to be simulated is of order of 1s and the integration step cannot be chosen larger than 10^-15 , due to the nature of physical interactions). Classical parallel approaches, based on domain decomposition methods, lead to very poor results due to the number of barriers. Another method to estimate this time is by calculating the PMF of the system, which is in this context the average force the molecule is subject to at a given position within or around the membrane. Recently, Darve et al.  [79] presented a new method, called ABF, to compute the PMF. The idea is to run a small number of simulations to estimate the PMF, and then add to the system a force that cancels the estimated PMF. With this new force, new simulations are performed starting from different configurations (distributed over the computing platform) of the system computed during the previous simulations and so on. Iterating this process, the algorithm converges quite quickly to a good estimation of the PMF with a uniform sampling along the axis of diffusion. This application has been implemented and integrated to the famous molecular dynamics software NAMD  [110] .

Our aim is to propose a distributed implementation of ABF method using NAMD. It is worth noting that NAMD is designed to run on high-end parallel platforms or clusters, but not to run efficiently on instable and distributed platforms. The different problems to be solved in order to design this application are the following:

• Since we need to start a simulation from a valid configuration (which can represent several Mbytes) with a particular position of the molecule in the membrane, and these configurations are spread among participating nodes, we need to be able to find and to download such configuration. Therefore, the first task is to find an overlay such that those requests can be handled efficiently. This requires expertise in overlay networks, compact data structures and graph theory. Olivier Beaumont, Nicolas Bonichon, Philippe Duchon, Nicolas Hanusse, Cyril Gavoille and Ralf Klasing will work on this part.

• In our context, each participating node may offer some space for storing some configurations, some bandwidth and some computing power to run simulations. The question arising here is how to distribute the simulations to nodes such that computing power of all nodes are fully used. Since nodes may join and leave the network at any time, redistributions of configurations and tasks between nodes will also be necessary (but all tasks only contribute to update the PMF, so that some tasks may fail without changing the overall result). The techniques designed for content distribution will be used to spread and redistribute the set of configurations over the set of participating nodes. This requires expertise in task scheduling and distributed storage. Olivier Beaumont, Nicolas Bonichon, Philippe Duchon and Lionel Eyraud-Dubois will work on this part.

A prototype of a steering tool for NAMD has been developed in the project, that may be used to validate our approach and that has been tested on GRID'5000 up to 200 processors. This prototype supports the dynamicity of the platform: contributing processors can come and leave. The managment of configurations' location is now performed using a distributed hash table. This was done by integrating the library Bamboo in the prototype. We still have to solve numerical instability.