Monthly Archives: January 2011

Commentary: The GPU computing fallacy

Modern graphics processors (GPUs) deliver considerably more brute force computational power than traditional processors (CPUs). With NVIDIA’s launch of CUDA, general purpose GPU computing has become greatly simplified, and many research groups around the world have consequently experimented with how one can harvest the power of GPUs to speed up scientific computing.

This is also the case for bioinformatics algorithms. NVIDIA advertises a number of applications that have been adapted to make use of GPUs, including several applications for bioinformatics and life sciences, which supposedly speed up bioinformatics algorithms by an order of magnitude or more.

In this commentary I will focus primarily on two GPU-accelerated versions of NCBI-BLAST, namely CUDA-BLAST and GPU-BLAST. I do so not to specifically criticize these two programs, but because BLAST is the single most commonly used bioinformatics tool and thus a prime example for illustrating whether GPU acceleration of bioinformatics algorithms pays off.

Whereas CUDA-BLAST to the best of my knowledge has not been published in a peer-reviewed journal, GPU-BLAST is described in the following Bioinformatics paper by Vouzis and Sahinidis:

GPU-BLAST: using graphics processors to accelerate protein sequence alignment

Motivation: The Basic Local Alignment Search Tool (BLAST) is one of the most widely used bioinformatics tools. The widespread impact of BLAST is reflected in over 53 000 citations that this software has received in the past two decades, and the use of the word ‘blast’ as a verb referring to biological sequence comparison. Any improvement in the execution speed of BLAST would be of great importance in the practice of bioinformatics, and facilitate coping with ever increasing sizes of biomolecular databases.

Results: Using a general-purpose graphics processing unit (GPU), we have developed GPU-BLAST, an accelerated version of the popular NCBI-BLAST. The implementation is based on the source code of NCBI-BLAST, thus maintaining the same input and output interface while producing identical results. In comparison to the sequential NCBI-BLAST, the speedups achieved by GPU-BLAST range mostly between 3 and 4.

It took me a while to figure out from where the 3-4x speedup came. I eventually found it in Figure 4B of the paper. GPU-BLAST achieves an approximately 3.3x speedup over NCBI-BLAST in only one situation, namely if it is used to perform ungapped sequence similarity searches and only one of six CPU cores is used:

Speedup of GPU-BLAST over NCBI-BLAST as function of number of CPU threads used. Figure by Vouzis and Sahinidis.

The vast majority of use cases for BLAST require gapped alignments, however, in which case GPU-BLAST never achieves even a 3x speedup on the hardware used by the authors. Moreover, nobody concerned about the speed of BLAST would buy a multi-core server and leave all but one core idle. The most relevant speedup is thus the speedup achieved by using all CPU cores and the GPU vs. only the CPU cores, in which case GPU-BLAST achieves only a 1.5x speedup over NCBI-BLAST.

The benchmark by NVIDIA does not fair much better. Their 10x speedup comes from comparing CUDA-BLAST to NCBI-BLAST using only a single CPU core. The moment one compares to NCBI-BLAST running with 4 threads on their quad-core Intel i7 CPU, the speedup drops to 3x. However, the CPU supports hyperthreading. To get the full performance out of it, one should thus presumably run NCBI-BLAST with 8 threads, which I estimate will reduce the speedup of CUDA-BLAST vs. NCBI-BLAST to 2.5x at best.

Even these numbers are not entirely fair. They are based on the 3.5x or 4x speedup that one gets by running a single instance of BLAST with 4 or 6 threads, respectively. The typical situation when the speed of BLAST becomes relevant, however, is when you have a large number of sequences that need to be searched against a database. This is an embarrassingly parallel problem; by partitioning the query sequences and running multiple single-threaded instances of BLAST, you can get a 6x speedup on either platform (personal experience shows that running 8 simultaneous BLAST searches on a quad-core CPU with hyperthreading gives approximately 6x speedup).

It is not just BLAST

Optimists could argue that perhaps BLAST is just one of few bioinformatics problems that do not benefit from GPU computing. However, reading the recent literature, I think that GPU-BLAST is a representative example. Most publications about GPU acceleration of algorithms relevant to bioinformatics report speedups of at most 10x. Typically, this performance number represents the speedup that can be attained relative to a single-threaded version of the program running on the CPU, hence leaving most of the CPU cores standing idle. Not exactly a fair comparison.

Davis et al. recently published a sobering paper in Bioinformatics in which they made exactly that point:

Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS

Motivation: Bioinformatics researchers have a variety of programming languages and architectures at their disposal, and recent advances in graphics processing unit (GPU) computing have added a promising new option. However, many performance comparisons inflate the actual advantages of GPU technology. In this study, we carry out a realistic performance evaluation of SNPrank, a network centrality algorithm that ranks single nucleotide polymorhisms (SNPs) based on their importance in the context of a phenotype-specific interaction network. Our goal is to identify the best computational engine for the SNPrank web application and to provide a variety of well-tested implementations of SNPrank for Bioinformaticists to integrate into their research.

Results: Using SNP data from the Wellcome Trust Case Control Consortium genome-wide association study of Bipolar Disorder, we compare multiple SNPrank implementations, including Python, Matlab and Java as well as CPU versus GPU implementations. When compared with naïve, single-threaded CPU implementations, the GPU yields a large improvement in the execution time. However, with comparable effort, multi-threaded CPU implementations negate the apparent advantage of GPU implementations.

Kudos for that. They could have published yet another paper with the title “N-fold speedup of algorithm X by GPU computing”. Instead they honestly reported that if one puts the same effort into parallelizing the CPU implementation as it takes to write a massively parallel GPU implementation, one gets about the same speedup.

GPUs cost money

It gets worse. Almost all papers on GPU computing ignore the detail that powerful GPU cards are expensive. It is not surprising that you can make an algorithm run faster by buying a piece of hardware that costs as much if not more than the computer itself. You could have spent that money buying a second computer instead. What matters is not the performance but the price/performance ratio. You do not see anyone publishing papers with titles like “N-fold speed up of algoritm X by using N computers”.

Let us have a quick look at the hardware platforms used for benchmarking the two GPU-accelerated implementations of BLAST. Vouzis and Sahinidis used a server with an Intel Xeon X5650 CPU, which I was able to find for under $3000. For acceleration they used a Tesla C2050 GPU card, which costs another $2500. The hardware necessary to make BLAST ~1.5x faster made the computer ~1.8x more expensive. NVIDIA used a different setup consisting of a server equipped with an Intel i7-920, which I could find for $1500, and two Tesla C1060 GPU cards costing $1300 each. In other words, they used a 2.7x more expensive computer to make BLAST 2.5x faster at best. The bottom line is that the increase in hardware costs outstripped the speed increase in both cases.

But what about the energy savings?

… I hear the die-hard GPU-computing enthusiasts cry. One of the selling arguments for GPU computing is that GPUs are much more energy efficient than CPUs. I will not question the fact that the peak Gflops delivered by a GPU exceeds that of CPUs using the same amount of energy. But does this theoretical number translate into higher energy efficiency when applied to a real-world problem such as BLAST?

The big fan on an NVIDIA Tesla GPU card is not there for show. (Picture from NVIDIA’s website.)

As anyone who has build a gaming computer in recent years can testify, modern day GPUs use as much electrical power as a CPU if not more. NVIDIA Tesla Computing Processors are no exception. The two Tesla C1060 cards in the machine used by NVIDIA to benchmark CUDA-BLAST use 187.7 Watts each, or 375.6 Watts in total. By comparison a basic Intel i7 system like the one used by NVIDIA uses less than 200 Watts. The two Tesla C1060 cards thus triple the power consumption while delivering at most 2.5 times the speed. Similarly, the single Tesla C2050 card used by Vouzis and Sahinidis uses 238 Watts, which is around the same as the power requirement of their base hexa-core Intel Xeon system, thereby doubling the power consumption for less than a 1.5-fold speedup. In other words, using either of the two GPU-accelerated versions of BLAST appears to be less energy efficient than using NCBI-BLAST.


Many of the claims regarding speedup of various bioinformatics algorithms using GPU computing are based on faulty comparisons. Typically, the massively parallel GPU implementation of an algorithm is compared to a serial version that makes use of only a fraction of the CPU’s compute power. Also, the considerable costs associated with GPU computing processors, both in terms of initial investment and power consumption, are usually ignored. Once all of this has been corrected for, GPU computing presently looks like a very bad deal.

There is a silver lining, though. First, everyone uses very expensive Tesla boards in order to achieve the highest possible speedup over the CPU implementations, whereas high-end gaming graphics cards might provide better value for money. However, the evidence for this remains to be seen. Second, certain specific problems such as molecular dynamics probably benefit more from GPU acceleration than BLAST does. In that case, you should be aware that you are buying hardware to speed up one specific type of analysis rather than bioinformatics analyses in general. Third, it is difficult to make predictions – especially about the future. It is possible that future generations of GPUs will change the picture, but that is no reason for buying expensive GPU accelerators today.

The message then is clear. If you are a bioinformatician who likes to live on the bleeding edge while wasting money and electricity, get a GPU compute server. If on the other hand you want something generally useful and well tested and quite a lot faster than a GPU compute server … get yourself some computers.