Molecular Dynamics a Next Frontier for FPGA Acceleration

Molecular dynamics codes have a wide range of uses across scientific research and represent a target base for a variety of accelerators and approaches, from GPUs to custom ASICs. The iterative nature of these codes on a CPU alone can require massive amounts of compute time for relatively simple simulations, thus the push is strong to find ways to bolster performance.

It is not practical for all users to make use of a custom ASIC (as exists on domain specific machines like those from D.E. Shaw, for instance). Accordingly, this community has looked to a mid-way step between general purpose processors and accelerators and custom hardware—the FPGA. Researchers have been targeting FPGAs to speed the time and boost complexity of molecular dynamics codes for several years, but more mainstream success has been limited by the programmatic complexity. Higher level tools, including OpenCL have added a new base of users for FPGAs on the molecular dynamics front and while the performance might be less than with more low-level tooling, it is catching on.

As it stands now, all of the major molecular dynamics software packages have been ported to CUDA for use on GPU for acceleration, which from the base of research since 2010 (as an ideal starting point) shows has taken off. In that time, the performance and programming capabilities of FPGAs has also been bolstered and with more approachable interfaces for design and implementation via OpenCL, reconfigurable devices could see far more adoption than before—although likely not equivalent to the GPU.

FPGAs, like molecular dynamics codes, have been around for decades and changed relatively little in terms of their core architectures. However, due to increases in performance and usability of the hardware to match standard MD algorithms, there are new possibilities ahead. This area might not be a new frontier since research has been ongoing–but it certainly represents a refreshed opportunity.

“ASICs are out of reach for most researchers, although their performance is quite excellent,” notes a team of researchers at Tohoku University in Japan. The group recently developed an FPGA accelerator approach to molecular dynamics simulations using OpenCL. “Although the cost is extremely small compared to ASICs, the design time is still very large.” They point to challenges using HDL and issues around algorithm changes and update, which often require a redesign of the FPGA architecture each time. To get around these barriers, the team focused on using OpenCL, the open source toolset that has all elements to manage the FPGA. Although OpenCL does not provide the same close-to-hardware capabilities of the FPGA, leaving performance on the table, it is a promising toolset for molecular dynamics simulations because changes and updates can be made quicker than retooling via raw HDL—a time consuming task that requires deep expertise.

Even with the performance hit of using a higher level interface like OpenCL for FPGA acceleration, the Japanese research team says that with the Altera offline compiler (working with a Stratix V) they were able to get a 4.6X boost compared to a CPU-only implementation by using only 36% of the FPGA’s resources. Working ahead, they found a theoretical max of 18.4X speedup if 80% of the Stratix V resources could be used, which they say is equivalent to what would be gained with an HDL designed custom accelerator.

“Since the architecture is completely designed by software, the same program code can be reused by recompiling it for any OpenCL capable FPGA board,” the team notes, adding that they can also implement changes to the algorithm by updating and recompiling within a few hours—a far cry from what they would experience with HDL. The problem, however, is one that goes beyond software. “The data transfers between CPU and FPGA are still an issue. This can be solved by future SoC based FPGA boards that contain a multicore CPU and FPGA on the same chip.” Of course, this is something that Intel has been clear about delivering in the next few years in the wake of their Altera acquisition. With this, “the PCIe based data transfers can be replaced by much faster on-board data transfers and the use of shared memory can completely eliminate data transfers.” For now, the team is focused on their system that can be connected into multiple nodes for a cluster to cut down processing time.

With added capabilities coming in new Xilinx hardware and of course, as mentioned previously, the coming integration of CPU and FPGA on the same device, we can expect to see growing interest in non-GPU or ASIC acceleration of molecular dynamics simulations. This is enabled by higher level interfaces, including OpenCL, and growing interest in general in what FPGAs have to offer—something that is happening in enterprise analytics, machine learning, and other areas after recent news around successes at Microsoft (with its Catapult boards used to power Bing search) and other use cases in bioinformatics and other areas.