# pbdDMAT v0.5-0

Monthly downloads

## 'pbdR' Distributed Matrix Methods

A set of classes for managing distributed matrices, and
a collection of methods for computing linear algebra and
statistics. Computation is handled mostly by routines from the
'pbdBASE' package, which itself relies on the 'ScaLAPACK' and
'PBLAS' numerical libraries for distributed computing.

## Readme

# pbdDMAT

pbdDMAT is an R package for distributed matrix algebra and statistics computations over MPI.

With few exceptions (ff, bigalgebra, etc.), R does computations in memory. If the memory of a matrix is too large for a single node, then distributing the ownership of the matrix across multiple nodes is an effective strategy in working with such large data.

The pbdDMAT package contains numerous routines to help with the distribution and management of data, as well as functions for summarizing, inspecting, and analyzing distributed matrices.

Often the syntax is identical to serial R, only instead of calling `cov(x)`

on a matrix `x`

, you would call it on a distributed matrix `x`

. This is possible by extensive use of R's S3 and S4 methods.

Much of the numerical linear algebra is powered by the ScaLAPACK library, which is the distributed analogue of LAPACK, used extensively by R.

## Installation

pbdDMAT requires

- A system installation of MPI
- R version 3.0.0 or higher
- The pbdMPI and pbdBASE packages, as well as their dependencies.

Assuming you meet the system dependencies, you can install the stable version from CRAN using the usual `install.packages()`

:

```
install.package("pbdDMAT")
```

The development version is maintained on GitHub, and can easily be installed by any of the packages that offer installations from GitHub:

```
remotes::install_github("RBigData/pbdDMAT")
```

See the vignette for installation troubleshooting.

## Usage

```
# load the package
library(pbdDMAT)
# initialize the specialized MPI communicators
init.grid()
# create a 100x100 distributed matrix object
dx <- ddmatrix(1:100, 10)
# print
dx
print(dx, all=TRUE)
# shut down the communicators and exit
finalize()
```

Save this program as `pbd_example.r`

and run it via:

```
mpirun -np 2 Rscript pbd_example.r
```

Numerous other examples can be found in both the pbdDMAT vignette, as well as the pbdDEMO package and its corresponding vignette.

## Authors

pbdDMAT is authored and maintained by the pbdR core team:

- Drew Schmidt
- Wei-Chen Chen
- George Ostrouchov
- Pragneshkumar Patel

With additional contributions from:

- The R Core team (some wrapper code taken from the base and stats packages)
- ZhaoKang Wang (fixes/improvements to
`apply()`

) - Michael Lawrence (fix for
`as.vector()`

)

## Functions in pbdDMAT

Name | Description | |

chol2inv | Inverse from Choleski (or QR) Decomposition | |

companion | Generate Companion Matrices | |

condnums | Compute or estimate the Condition Number of a Distributed Matrix | |

ddmatrix-print | Printing a Distributed Matrix | |

lm.fit | Fitter for Linear Models | |

matmult | Matrix Multiplication | |

math | Miscellaneous Mathematical Functions | |

isdot | Type Checks, Including NA, NaN, etc. | |

as.ddmatrix | Non-Distributed object to Distributed Object Converters | |

ddmatrix-class | Class ddmatrix | |

sparsity | Sparsity of Matrix Objects | |

Comparators | Logical Comparisons | |

ddmatrix-constructors | Distributed Matrix Creation | |

arithmetic | Arithmetic Operators | |

ddmatrix-svd | Singular Value Decomposition | |

getLocal | getLocal | |

ddmatrix-sumstats | Basic Summary Statistics | |

sd | Covariance and Correlation | |

headsortails | Head and Tail of a Distributed Matrix | |

insert | Directly Insert Into Distributed Matrix Submatrix Slot | |

ddmatrix-apply | Apply Family of Functions | |

qr | QR Decomposition Methods | |

pbdDMAT Control | Some default parameters for pbdDMAT. | |

Hilbert | Generate Hilbert Matrices | |

ddmatrix-chol | Cholesky Factorization | |

redistribute | Distribute/Redistribute matrices across the process grid | |

ddmatrix-norm | Norm | |

as.vector | Distributed object to Vector Converters | |

ddmatrix-eigen | eigen | |

ddmatrix-solve | Solve | |

ddmatrix-summary | Distributed Matrix Summary | |

ddmatrix-prcomp | Principal Components Analysis | |

ddmatrix-lu | LU Factorization | |

sweep | Sweep | |

na | Handle Missing Values in Distributed Matrices | |

transpose | Distributed Matrix Transpose | |

diag-constructors | Distributed Matrix Diagonals | |

isSymmetric | isSymmetric | |

extract | Extract or Replace Parts of a Distributed Matrix | |

covariance | Covariance and Correlation | |

expm | Matrix Exponentiation | |

pbdDMAT-package | Distributed Matrix Methods | |

eigen2 | eigen2 | |

reductions | Arithmetic Reductions: Sums, Means, and Prods | |

rounding | Rounding of Numbers | |

Accessors | Accessor Functions for Distributed Matrix Slots | |

binds | Row and Column binds for Distributed Matrices | |

as.matrix | Distributed object to Matrix Converters | |

as.rowcyclic | Distribute/Redistribute matrices across the process grid | |

ddmatrix-scale | Scale | |

No Results! |

## Vignettes of pbdDMAT

## Last month downloads

## Details

License | GPL (>= 2) |

SystemRequirements | OpenMPI (>= 1.5.4) on Solaris, Linux, Mac, and FreeBSD. MS-MPI (Microsoft HPC Pack 2012) or MPICH2 (>= 1.4.1p1) on Windows. |

LazyLoad | yes |

LazyData | yes |

ByteCompile | yes |

NeedsCompilation | yes |

URL | http://r-pbd.org/ |

BugReports | http://group.r-pbd.org/ |

MailingList | Please send questions and comments regarding pbdR to RBigData@gmail.com |

RoxygenNote | 6.1.0 |

Packaged | 2018-12-11 03:35:21 UTC; mschmid3 |

Repository | CRAN |

Date/Publication | 2018-12-11 09:20:08 UTC |

imports | methods , utils |

depends | pbdBASE (>= 0.5-0) , pbdMPI (>= 0.3-8) , R (>= 3.1.0) , stats |

Contributors | Michael Lawrence, R Core team, Wei-Chen Chen, George Ostrouchov, Pragneshkumar Patel, ZhaoKang Wang, Sebastien Lamy de la Chapelle |

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