pbdBASE v0.5-0

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Programming with Big Data -- Base Wrappers for Distributed Matrices

An interface to and extensions for the 'PBLAS' and 'ScaLAPACK' numerical libraries. This enables R to utilize distributed linear algebra for codes written in the 'SPMD' fashion. This interface is deliberately low-level and mimics the style of the native libraries it wraps. For a much higher level way of managing distributed matrices, see the 'pbdDMAT' package.

Readme

pbdBASE

pbdBASE is a set of bindings to and extensions for the distributed linear algebra libraries BLACS, PBLAS, and ScaLAPACK. The package is very low-level, and unless you are very familiar with these libraries (or even if you are...), you are instead recommended to see the pbdDMAT and pbdDEMO packages.

Installation

pbdBASE requires:

  • A system installation of MPI
  • R version 3.0.0 or higher
  • The pbdSLAP and pbdMPI 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("pbdBASE")

The development version is maintained on GitHub:

remotes::install_github("RBigData/pbdBASE")

See the vignette for installation troubleshooting.

Functions in pbdBASE

Name Description
base.indxg2p indxg2p
base.descinit descinit
base.matexp matexp
base.dhilbmk dhilbmk
base.nbd Next Best Divisor
base.pdclvar Column Variances
base.numroc numroc
base.pdhilbmk pdhilbmk
base.rl2insert R-like Matrix-Vector Insertion
base.pdmkcpn1 pdmkcpn1
base.crossprod crossprod
base.pdmvsum R-like Matrix-Vector Sum
base.blacs_gridinit Creating Grid From A System Context
BASE Global Environment Global Environment for the pbdBASE Package
base.maxdim maxdim
base.minctxt Get BLACS Context Grid Information
base.dallreduce dallreduce
base.rpdgesvd rpdgesvd
base.pdsweep pdsweep
base.rpdgetrf rpdgetrf
base.dim0 maxdim
base.rpdgecon rpdgecon
base.procgrid procgrid
base.rpdgelqf rpdgelqf
base.rpdgels rpdgels
base.ownany Determining Local Ownership of a Distributed Matrix
base.rpdlaprnt rpdlaprnt
base.rpdorglq rpdorglq
base.free_blacs_system_handle Free Blacs System Handle
blacsexit BLACS Exit
base.p_matpow_by_squaring_wrap p_matpow_by_squaring_wrap
base.rpdorgqr rpdorgqr
base.rpdgemm rpdgemm
base.rpdgemr2d rpdgemr2d
base.p_matexp_pade_wrap p_matexp_pade_wrap
base.rpdtrcon rpdtrcon
base.redist base.redist
base.rpdormqr rpdormqr
base.igsum2d BLACS Sums
blacs_apts Functions to set and get BLACS_APTS
base.pdchtri pdchtri
base.rl2blas Level 2 R-like BLAS
coords Local to Global/Global to Local Indexing
base.rcolcpy R Column Copy
base.rrowcpy R Row Copy
base.rpdgeqpf rpdgeqpf
base.rcolcpy2 R Column Copy-2
gridinit blacs_init
base.rpdgetri rpdgetri
gridexit gridexit
InitGrid Initialize Process Grid
base.valid_context BLACS Context Validation
gridinfo Get BLACS Context Grid Information
base.rpdlange rpdlange
l2g_coord l2g_coord
base.mksubmat (Un)Distribute
base.rpdgesv rpdgesv
base.rpdsyevx rpdsyevx
base.rpdtran rpdtran
base.igamx2d BLACS Max
base.dgamx2d BLACS Min
base.dgesd2d BLACS Point to Poin
finalizer Finalizer
g2lcoord g2lcoord
base.rpdpotrf rpdpotrf
g2l_coord g2l_coord
base.rpdsyevr rpdsyevr
get.comm.from.ICTXT Getting Communicator From BLACS Context
numroc2 numroc2
base.rrowcpy2 R Row Copy-2
base.tri2zero tri2zero
pbdBASE-package ScaLAPACK Wrappers and Utilities
coordspair Global to Local/Local to Global Pair Indexing
diag diag
pcoords Interchange Between Process Number and BLACS Coordinates
sys2blacs.handle Context Within a Given Communicator
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Vignettes of pbdBASE

Name
include/00-acknowledgement.tex
include/00-copyright.tex
include/01-abstract.tex
include/01-introduction.tex
include/02-use.tex
include/pbdBASE.bib
include/preamble.tex
include/titlepage.tex
build_pdf.sh
pbdBASE-guide.Rnw
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Details

Type Package
License Mozilla Public License 2.0
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 6.0.1
Packaged 2018-12-02 23:24:18 UTC; mschmid3
Repository CRAN
Date/Publication 2018-12-08 15:00:03 UTC

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