# Presentation: 005202

## Automatic Parallelization for Statistical Computing with pR

** ****Nagiza F. Samatova (**_**[samatovan@ornl.gov](mailto:samatovan@ornl.gov)**__**) **_
** ****Srikanth Yoginath **
** ****Guruprasad Kora**
** ****Xiaosong Ma**
** ****Jiangtian Li**

- DOE SciDAC SDM AHM, December 11-13, 2006

## Statistical Computing with R

**> ****.****PVM.start.pvmd**** ()**
**> ****.PVM.addhosts**** (...)**
**> ****.PVM.config**** ()**

**Statistical Computing with *****R***

**About *****R***** (**_[http://www.r-project.org](http://www.r-project.org/)__[/](http://www.r-project.org/)_**):**
-  Open source, most widely used for statistical analysis and graphics; similar to ***S***.
-  Extensible via dynamically loadable add-on packages.
-  Originally developed by R. Gentleman and R. Ihaka.

**Towards Enabling Parallel Computing in *****R*****:**

*** ******snow*** (Luke Tierney): general API on top of message passing routines to provide high-level (*parallel apply*) commands; mostly demonstrated for ***embarrassingly parallel*** applications.

*** ******rpvm****** ***(Na Li and Tony Rossini): ***R*** interface to ***PVM***; requires knowledge of parallel programming.

-  ***Rmpi*** (Hao Yu): ***R*** interface to ***LAM-MPI***.

## Task and Data Parallelism in pR

## Software Stack for pR

## pR in Use 

**Across Science Applications:**
-  **Biology**: Quantitative Proteomics (B. Hettich, G. Hurst, C. Harwood, C. Pan)
-  **Climate**: Analysis of Extreme Events (M. Branstetter, A. Ganguly, S. Khan)
-  **GIS**: GRASS+pR (G. Fann, B. Budhend)
-  **Fusion**: Distributed PCA (G. Ostrouchov)

## Near-Term Future Plans

**Release of *****automatic***** task-parallel component in pR**
**Exploit the use of Global Arrays (as opposed to Data Bank Cluster Manager) for distributed and shared memory management in pR**
**Provide basic parallel I/O (pNetCDF and ROMIO) hooks to pR**
**Identify requirements and demonstrate the use across other applications: fusion (S. Klasky), combustion (J. Chen), climate (J. Drake), nanoscience (P. Rack)**

## Recent Publications & Software

**Samatova NF, Yoginath S, Kora G, Bauer D, http://www.aspect-sdm.org/Parallel-R  or **_**[http://cran.r-project.org/mirrors.html](http://cran.r-project.org/mirrors.html)**_**.**
**Samatova NF, Branstetter M, Ganguly AR, Hettich R, Khan S, Kora G, Li J, Ma X, Pan C, Shoshani A, Yoginath S, *****Journal of Physics*****: Conference Series 46 (2006) 505–509.**
**Yoginath S, Samatova NF, Bauer D, Kora G, Fann G, Geist A, In *****Proceedings of the 18th International Conference on Parallel and Distributed Computing Systems***** (PDCS-2005), September 12 - 14, 2005, Las Vegas, Nevada.**
**Pan C, Kora G, McDonald WH, Tabb DL, VerBerkmoes NC, Hurst GB, Pelletier DA, Samatova NF, Hettich RL, *****Anal Chem*****. 2006 Oct 15;78(20):7121-31. **
**Pan C, Kora G, Tabb DL, Pelletier DA, McDonald WH, Hurst GB, Hettich RL, Samatova NF, *****Anal Chem*****. 2006 Oct 15;78(20):7110-20. **
**Ostrouchov G, Samatova NF, *****IEEE Transactions on Pattern Analysis and Machine Intelligence*****, 27:1340-1343, 2005.**
**Park B.-H, Ostrouchov G, Samatova NF, *****Computational Statistics and Data Analysis*****, 2007 (accepted).**
**Sisneros R, Jones C, Huang J, Gao H, Park BH, Samatova NF, *****IEEE Transactions on Visualization and Computer Graphics*****, 2007 (second revision).**
**Qu YM, Ostrouchov G, Yoginath S, Samatova NF, *****Journal of Computational and Graphical Statistics*****, 2007 (second revision).**