R/parallel – speeding up bioinformatics analysis with R
© Vera et al; licensee BioMed Central Ltd. 2008
Received: 16 June 2008
Accepted: 22 September 2008
Published: 22 September 2008
R is the preferred tool for statistical analysis of many bioinformaticians due in part to the increasing number of freely available analytical methods. Such methods can be quickly reused and adapted to each particular experiment. However, in experiments where large amounts of data are generated, for example using high-throughput screening devices, the processing time required to analyze data is often quite long. A solution to reduce the processing time is the use of parallel computing technologies. Because R does not support parallel computations, several tools have been developed to enable such technologies. However, these tools require multiple modications to the way R programs are usually written or run. Although these tools can finally speed up the calculations, the time, skills and additional resources required to use them are an obstacle for most bioinformaticians.
We have designed and implemented an R add-on package, R/parallel, that extends R by adding user-friendly parallel computing capabilities. With R/parallel any bioinformatician can now easily automate the parallel execution of loops and benefit from the multicore processor power of today's desktop computers. Using a single and simple function, R/parallel can be integrated directly with other existing R packages. With no need to change the implemented algorithms, the processing time can be approximately reduced N-fold, N being the number of available processor cores.
R/parallel saves bioinformaticians time in their daily tasks of analyzing experimental data. It achieves this objective on two fronts: first, by reducing development time of parallel programs by avoiding reimplementation of existing methods and second, by reducing processing time by speeding up computations on current desktop computers. Future work is focused on extending the envelope of R/parallel by interconnecting and aggregating the power of several computers, both existing office computers and computing clusters.
In recent years, R  has gained a large user community in bioinformatics thanks to its simple but powerful data analysis language. Growing repositories like Bioconductor  and CRAN  assist bioinformaticians with hundreds of free analytical methods and tools. These user-contributed methods are easily reused and adapted to each particular experiment for analysis of biological data. Examples of often reused and adapted methods are, respectively, the packages tilingArray  and affyGG . However, while data generated in experiments previously fitted on a CD-ROM, nowadays, using new equipments, hardly fit on a single DVD-ROM. As a consequence of the post-genomic explosion of data, the demand of computational power is increasing continuously and solutions to keep the processing pace of high-throughput devices are required. A common approach in many bioinformatics fields like genomics, transcriptomics and metabolomics, where large sequential data sets are analyzed, is the use of parallel computing technologies .
Using R together with parallel computing is not a trivial task as the language does not provide mechanisms to support it natively. To compensate for this lack, several tools have been developed with different degrees of success. Early contributions to parallel computing in R were based on available general purpose parallel computing frameworks like MPI  and PVM . Examples of these R libraries are rmpi  and rpvm . These libraries provide low level programming interfaces, the complexity of which hinders a wider use of them. In order to hide such complexity, packages like NetWorkSpaces , snow  or taskPR  were created. They provide a higher level of abstraction, encapsulating the previous libraries (i.e. rmpi, rpvm) in simpler libraries and providing sufficient flexibility for the average type of programs coded in R. Additional development has been carried out with the framework pR . It adds several modules to automate the parallelization of any R program. This feature is very important since programmers do not need to think "in parallel" when coding their R scripts, and anyone without previous knowledge of parallel computing can benefit from its advantages. However, while the programming model has been simplified during the last years, the dependency on external frameworks and dedicated resources is still a major obstacle for many bioinformaticians (e.g. pR depends on a complex installation to access a cluster of MPI enabled servers). These solutions are well suited for research groups with access to dedicated infrastructures (e.g. computing clusters managed by skilled technicians) and/or enough time to invest in the development of ad hoc parallel programs. However, when these requirements are not met, solutions based on self-contained tools (e.g. squid for Perl ), capable of running in common desktop computers, are the preferred choice.
In this paper we present an R add-on package for parallel computing: R/parallel. To use it, the programmer does not need to change his algorithm nor install and maintain any additional software as the R/parallel package is self-contained and capable of using current multicore processor desktop computers. It easily and effectively enables the automatic parallelization of loops without data dependencies , thus bringing the benefits of parallel computing within the reach of any bioinformatician using R. Its design allows its direct use with current bioinformatics analysis tools such as R/qtl , MetaNetwork  or affyGG  for analysis of genome-wide gene expression data.
The implementation of R/parallel has been carried out with the objective of increasing the performance of R by means of parallel computing while minimizing the requirements to use it. This section explains the design decisions made to speed up R programs while overcoming the common problems experienced by bioinformaticians with previous parallel computing solutions.
The first aspect taken into account is the desire to minimize user intervention when parallelizing new or existing R programs. The perfect solution should not require any further modification from the programmer. This is achieved with fully automatic parallelizers, which parse the program code, check it for data dependencies and generate a set of independent tasks that can be safely evaluated in separate processors. However, the drawback of this approach is that the parallelizer, a priori, does not know the execution time of each independent task. When a set of tasks are running concurrently, additional overhead and delays are introduced due to additional processing steps (e.g. code replication or task coordination). It is quite likely that a sequence of small fast tasks is parallelized and, despite parallel execution, as a result of the transformation process and additional synchronization, the overall processing time can be increased. To avoid this situation, the design decision made is to let the users indicate which code regions (i.e. loops) they need to speed up. With this information, R/parallel will automatically parallelize its execution to increase the performance.
Another aspect to consider when developing parallel programs is the difficult task of debugging when coding errors arise. When multiple processing units are running concurrently at different steps of a program, the identification of the conditions that triggers a bug and the retrieval of the state of each execution thread is a cumbersome task that should be avoided. To minimize this risk, an objective of the design of this package is the ability to run the sequential (and parallel) version of the R programs without changing any further line of code. By running a program sequentially it is possible to test the correctness of the implemented algorithm and debug using traditional tools. The user can activate the parallel execution just by loading the R/parallel package before performing a calculation. This design decision is also supported by the fact that, as the user program is not functionally dependent on R/parallel, it can always be shared with other bioinformaticians without requiring them to install the package or modify a single line of code.
Internally, R/parallel is designed using a master-worker architecture. The master component runs within the main R instance and distributes the work. The workers run in new processes with new R instances and perform the calculations retrieved from the master. The implementation of the package uses R scripts and C++ objects, taking advantage of both programming worlds. Combining low level operating system calls in C++ to manage processes, threads and inter-process communications (IPC) with the intrinsic features of R, like the capability of retrieving or creating functions at runtime (a feature known as "computing on the language" ), it has been possible to build a generic solution able to automatically transform a sequential loop and parallelize its execution.
Using the tool
Typical bioinformatics cases where parallel computations are more often used are permutation tests or heuristic searches of multivariate spaces where, due to time constraints, the best result has to be computed before a deadline. The case 2A illustrates the increase of completed analyses (i.e permutation tests) by using all the available processing units. The function qtlThreshold.sma from the package affyGG is used with a quad-core processor to analyze a large number of permuted data sets using the same statistical analysis to compute (approximate) significance thresholds. Incrementing the number of parallel processes (i.e. workers) the usage of more cores has been enabled and therefore the overall performance has increased. The case 2B illustrates the decrease of the total execution time after parallelizing a problem. The function qtlMap.xProbe from the package affyGG is used with a single-core processor to compute the same statistical analysis over large data sets. In this case, due to the way memory is managed in R with linked lists and as a result of partitioning, small and faster tasks (with faster data indexing) are created. Therefore, in cases like this, even with a single processing unit, the total execution time is reduced.
The case 2C, where the function qtlMap.xProbe is used this time with a dual-core processor, illustrates the problem of processor overloading and how to address it. An inconvenience when the processor load is 100% (i.e. the computer is overloaded) is that ready-to-run processes have to wait for the processor(s) to be run. This delay leads to downgraded response times in interactive programs that makes it hard, if not impossible, to keep working with the computer when simultaneously running intensive calculations. Fortunately, common office applications on today's desktop computers rarely claim more than 1% of the processor . Therefore, by giving up a small percentage of the processor, it is possible to keep using the computer for other tasks, while the ongoing calculation only takes slightly more time.
R/parallel, as shown, saves time to bioinformaticians in their daily tasks of analyzing experimental data. It effectively removes the most common obstacles encountered by bioinformaticians approaching parallel computing in R, like complex programming models or external dependencies on hard-to-maintain software frameworks. R/parallel is an easy-to-use R package which allows any programmer to parallelize their loops in a matter of minutes. The results demonstrate that R/parallel efficiently increases the performance of R when running parallel computations in current multicore processor desktop computer. As a consequence, bioinformaticians are able to approach reducing the processing time of a growing number of analytical methods by N-fold, N being the number of present cores in their computers.
Future work is focused on extending the functional and performance capabilities of R/parallel.
Additional functionalities like support for task parallelism or delayed loading of input data will extend the usability of the package. Additional performance, by expanding R/parallel from a single desktop computer to an office with several desktop computers or even a server farm, is our next milestone to speed up bioinformatics analysis with R.
We encourage any users to share their experiences with the authors to contribute to the extension of R/parallel.
Availability and requirements
Project home page: http://www.rparallel.org
Operating system(s): Windows and Linux
Programming language: R 2.6, C, C++
Other requirements: none
License: GPL for non-profit organizations
Any restrictions to use by non-academics: licence needed
We thank the members of the Groningen Bioinformatics Centre who have helped us testing R/parallel with their own R tasks and providing valuable comments and suggestions.
- Ihaka R, Gentleman R: R: A Language for Data Analysis and Graphics. Journal of Computational and Graphical Statistics 2005, 5(3):299–314. [http://www.jstor.org/pss/1390807]Google Scholar
- Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biology 2004, 5: R80.PubMed CentralView ArticlePubMedGoogle Scholar
- The Comprehensive R Archive Network[http://cran.r-project.org]
- tilingArray – Analysis of high-density oligonucleotide tiling arrays[http://bioconductor.org/packages/2.2/bioc/html/tilingArray.html]
- Alberts R, Vera G, Jansen RC: affyGG: computational protocols for genetical genomics with Affymetrix arrays. Bioinformatics 2008, 24(3):433–434. [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/3/433]View ArticlePubMedGoogle Scholar
- Trelles O: On the parallelisation of bioinformatics applications. Briefings in Bioinformatics 2001, 2(2):181–194. [http://bib.oxfordjournals.org/cgi/content/abstract/2/2/181]View ArticlePubMedGoogle Scholar
- Message Passing Interface (MPI) Forum[http://www.mpi-forum.org/]
- PVM: Parallel Virtual Machines[http://www.csm.ornl.gov/pvm/]
- Rmpi: Interface (Wrapper) to MPI (Message-Passing Interface)[http://www.stats.uwo.ca/faculty/yu/Rmpi]
- rpvm: R interface to PVM (Parallel Virtual Machine)[http://cran.r-project.org/web/packages/rpvm/index.html]
- NetWorkSpaces for R[http://nws-r.sourceforge.net]
- Rossini A, Tierney L, Li N: Simple Parallel Statistical Computing in R. UW Biostatistics Working Paper Series 2003., 193: [http://www.bepress.com/uwbiostat/paper193]Google Scholar
- taskPR: Task-Parallel R Package[http://cran.r-project.org/web/packages/taskPR/index.html]
- Ma X, Li J, Samatova N: Automatic Parallelization of Scripting Languages: Toward Transparent Desktop Parallel Computing. Parallel and Distributed Processing Symposium, 2007. IPDPS 2007. IEEE International 2007, 1–6.View ArticleGoogle Scholar
- Carvalho PC, Glória RV, de Miranda AB, Degrave WM: Squid – a simple bioinformatics grid. BMC Bioinformatics 2005, 6: 197.PubMed CentralView ArticlePubMedGoogle Scholar
- Briggs P: Automatic parallelization. SIGPLAN Not 1996, 31(4):11–15.View ArticleGoogle Scholar
- Broman KW, Wu H, Sen S, Churchill GA: R/qtl: QTL mapping in experimental crosses. Bioinformatics 2003, 19(7):889–890. [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/7/889]View ArticlePubMedGoogle Scholar
- Fu J, Swertz M, Keurentjes JJ, Jansen RC: MetaNetwork: a computational protocol for the genetic study of metabolic networks. Nature Protocols 2007, 2(3):685–694.View ArticlePubMedGoogle Scholar
- R Development Core Team:R Language Definition. The R Foundation for Statistical Computing, Vienna, Austria; 2008. [ISBN 3–900051–13–5] [http://cran.r-project.org/doc/manuals/R-lang.pdf]Google Scholar
- Jansen RC: Interval Mapping of Multiple Quantitative Trait Loci. Genetics 1993, 135: 205–211. [http://www.genetics.org/cgi/content/abstract/135/1/205]PubMed CentralPubMedGoogle Scholar
- Gupta A, Lin B, Dinda PA: Measuring and Understanding User Comfort With Resource Borrowing. 13th IEEE International Symposium on High Performance Distributed Computing (HPDC-13 '04) 2004, 214–224. [http://doi.ieeecomputersociety.org/10.1109/HPDC.2004.21]Google Scholar
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