Package: pbdMPI 0.5-2

pbdMPI: R Interface to MPI for HPC Clusters (Programming with Big Data Project)

A simplified, efficient, interface to MPI for HPC clusters. It is a derivation and rethinking of the Rmpi package. pbdMPI embraces the prevalent parallel programming style on HPC clusters. Beyond the interface, a collection of functions for global work with distributed data and resource-independent RNG reproducibility is included. It is based on S4 classes and methods.

Authors:Wei-Chen Chen [aut, cre], George Ostrouchov [aut], Drew Schmidt [aut], Pragneshkumar Patel [aut], Hao Yu [aut], Christian Heckendorf [ctb], Brian Ripley [ctb], R Core team [ctb], Sebastien Lamy de la Chapelle [aut]

pbdMPI_0.5-2.tar.gz

pbdMPI_0.5-2.tar.gz(r-4.5-noble)pbdMPI_0.5-2.tar.gz(r-4.4-noble)
pbdMPI.pdf |pbdMPI.html✨
pbdMPI/json (API)

# Install 'pbdMPI' in R:

install.packages('pbdMPI', repos = c('https://snoweye.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/snoweye/pbdmpi/issues

Uses libs:

openmpi– High performance message passing library

On CRAN:

258 exports 2 stars 2.17 score 1 dependencies 3 dependents 2 mentions 182 scripts 773 downloads

Last updated 2 days agofrom:011d909465. Checks:OK: 1 FAILURE: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 16 2024
R-4.5-linux-x86_64	FAILURE	Sep 18 2024

Exports:.mpiopt_init addr.mpi.comm.ptr allgather allreduce anysource anytag arrange.mpi.apts barrier bcast comm.abort comm.accept comm.all comm.allcommon comm.allcommon.integer comm.allpairs comm.any comm.as.gbd comm.balance.info comm.c2f comm.cat comm.chunk comm.connect comm.disconnect comm.dist comm.dist.common comm.dist.gbd comm.dup comm.end.seed comm.free comm.get.streams comm.is.null comm.length comm.load.balance comm.localrank comm.match.arg comm.max comm.mean comm.min comm.pairwise comm.pairwise.common comm.pairwise.gbd comm.print comm.range comm.rank comm.read.csv comm.read.csv2 comm.read.table comm.reset.seed comm.Rprof comm.sd comm.seed.state comm.set.errhandler comm.set.seed comm.set.stream comm.size comm.sort comm.sort.default comm.sort.double comm.sort.integer comm.split comm.stop comm.stopifnot comm.sum comm.timer comm.unload.balance comm.var comm.warning comm.warnings comm.which comm.which.max comm.which.min comm.write comm.write.csv comm.write.csv2 comm.write.table execmpi finalize gather get.conf get.jid get.lib get.mpi.comm.ptr get.sourcetag get.sysenv info.c2f info.create info.free info.set init intercomm.create intercomm.merge iprobe irecv is.comm.null is.finalized isend pbd_opt pbdApply pbdLapply pbdSapply port.close port.open probe recv reduce runmpi scatter send sendrecv sendrecv.replace serv.lookup serv.publish serv.unpublish spmd.allcheck.type spmd.allgather.array spmd.allgather.default spmd.allgather.double spmd.allgather.integer spmd.allgather.object spmd.allgather.raw spmd.allgatherv.default spmd.allgatherv.double spmd.allgatherv.integer spmd.allgatherv.raw spmd.allreduce.array spmd.allreduce.default spmd.allreduce.double spmd.allreduce.float spmd.allreduce.float32 spmd.allreduce.integer spmd.allreduce.logical spmd.allreduce.object spmd.alltoall.double spmd.alltoall.integer spmd.alltoall.raw spmd.alltoallv.double spmd.alltoallv.integer spmd.alltoallv.raw spmd.anysource spmd.anytag spmd.barrier spmd.bcast.array spmd.bcast.default spmd.bcast.double spmd.bcast.integer spmd.bcast.message spmd.bcast.object spmd.bcast.raw spmd.bcast.string spmd.check.type.recv spmd.check.type.send spmd.comm.abort spmd.comm.accept spmd.comm.c2f spmd.comm.cat spmd.comm.connect spmd.comm.disconnect spmd.comm.dup spmd.comm.free spmd.comm.get.parent spmd.comm.is.null spmd.comm.localrank spmd.comm.print spmd.comm.rank spmd.comm.set.errhandler spmd.comm.size spmd.comm.spawn spmd.comm.split SPMD.CT SPMD.DT spmd.finalize spmd.gather.array spmd.gather.default spmd.gather.double spmd.gather.integer spmd.gather.object spmd.gather.raw spmd.gatherv.default spmd.gatherv.double spmd.gatherv.integer spmd.gatherv.raw spmd.get.count spmd.get.processor.name spmd.get.sourcetag spmd.hostinfo spmd.info.c2f spmd.info.create spmd.info.free spmd.info.set spmd.init spmd.intercomm.create spmd.intercomm.merge SPMD.IO spmd.iprobe spmd.irecv.default spmd.irecv.double spmd.irecv.integer spmd.irecv.raw spmd.is.comm.null spmd.is.finalized spmd.is.manager spmd.isend.default spmd.isend.double spmd.isend.integer spmd.isend.raw SPMD.OP spmd.port.close spmd.port.open spmd.probe spmd.recv.default spmd.recv.double spmd.recv.integer spmd.recv.raw spmd.reduce.array spmd.reduce.default spmd.reduce.double spmd.reduce.float spmd.reduce.float32 spmd.reduce.integer spmd.reduce.logical spmd.reduce.object spmd.scatter.array spmd.scatter.default spmd.scatter.double spmd.scatter.integer spmd.scatter.object spmd.scatter.raw spmd.scatterv.default spmd.scatterv.double spmd.scatterv.integer spmd.scatterv.raw spmd.send.default spmd.send.double spmd.send.integer spmd.send.raw spmd.sendrecv.default spmd.sendrecv.double spmd.sendrecv.integer spmd.sendrecv.raw spmd.sendrecv.replace.default spmd.sendrecv.replace.double spmd.sendrecv.replace.integer spmd.sendrecv.replace.raw spmd.serv.lookup spmd.serv.publish spmd.serv.unpublish SPMD.TP spmd.wait spmd.waitall spmd.waitany spmd.waitsome task.pull task.pull.manager task.pull.workers wait waitall waitany waitsome

Dependencies:float

pbdMPI-guide

Rendered frompbdMPI-guide.Rnwusingutils::Sweaveon Sep 16 2024.

Last update: 2016-12-17
Started: 2013-07-03

Help page	Topics
R Interface to MPI (Programming with Big Data in R Project)	pbdMPI-package pbdMPI
All Ranks Gather Objects from Every Rank	allgather allgather,ANY,ANY,integer-method allgather,ANY,missing,integer-method allgather,ANY,missing,missing-method allgather,integer,integer,integer-method allgather,integer,integer,missing-method allgather,numeric,numeric,integer-method allgather,numeric,numeric,missing-method allgather,raw,raw,integer-method allgather,raw,raw,missing-method allgather-methods allgatherv
All Ranks Receive a Reduction of Objects from Every Rank	allreduce allreduce,ANY,missing-method allreduce,float32,float32-method allreduce,integer,integer-method allreduce,logical,logical-method allreduce,numeric,numeric-method allreduce-method
All to All	alltoall spmd.alltoall.double spmd.alltoall.integer spmd.alltoall.raw spmd.alltoallv.double spmd.alltoallv.integer spmd.alltoallv.raw
Parallel Apply and Lapply Functions	pbdApply pbdLapply pbdSapply
A Rank Broadcast an Object to Every Rank	bcast bcast,ANY-method bcast,integer-method bcast,numeric-method bcast,raw-method bcast-method
comm.chunk	comm.chunk
Communicator Functions	barrier comm.abort comm.accept comm.c2f comm.connect comm.disconnect comm.dup comm.free comm.is.null comm.localrank comm.rank comm.size comm.split finalize init intercomm.create intercomm.merge is.finalized port.close port.open serv.lookup serv.publish serv.unpublish
A Rank Gathers Objects from Every Rank	gather gather,ANY,ANY,integer-method gather,ANY,missing,integer-method gather,ANY,missing,missing-method gather,integer,integer,integer-method gather,integer,integer,missing-method gather,numeric,numeric,integer-method gather,numeric,numeric,missing-method gather,raw,raw,integer-method gather,raw,raw,missing-method gather-methods gatherv
Functions to Get MPI and/or pbdMPI Configures Used at Compiling Time	get.conf get.lib get.sysenv
Divide Job ID by Ranks	get.jid
Global All Pairs	comm.allpairs
Global Any and All Functions	comm.all comm.allcommon comm.any
Global As GBD Function	comm.as.gbd
Global Balance Functions	comm.balance.info comm.load.balance comm.unload.balance
Global Base Functions	comm.length comm.mean comm.sd comm.sum comm.var
Global Distance for Distributed Matrices	comm.dist
Global Argument Matching	comm.match.arg
Global Pairwise Evaluations	comm.pairwise
Global Print and Cat Functions	comm.cat comm.print
Global Range, Max, and Min Functions	comm.max comm.min comm.range
Global Reading Functions	comm.read.csv comm.read.csv2 comm.read.table
A Rprof Function for SPMD Routines	comm.Rprof
Global Quick Sort for Distributed Vectors or Matrices	comm.sort
Global Stop and Warning Functions	comm.stop comm.stopifnot comm.warning comm.warnings
A Timing Function for SPMD Routines	comm.timer
Global Which Functions	comm.which comm.which.max comm.which.min
Global Writing Functions	comm.write comm.write.csv comm.write.csv2 comm.write.table
Info Functions	info.c2f info.create info.free info.set
A Rank Receives (Nonblocking) an Object from the Other Rank	irecv irecv,ANY-method irecv,integer-method irecv,numeric-method irecv,raw-method irecv-method
Check if a MPI_COMM_NULL	is.comm.null
A Rank Send (Nonblocking) an Object to the Other Rank	isend isend,ANY-method isend,integer-method isend,numeric-method isend,raw-method isend-method
Set or Get MPI Array Pointers in R	arrange.mpi.apts
Functions for Get/Print MPI_COMM Pointer (Address)	addr.mpi.comm.ptr get.mpi.comm.ptr
Probe Functions	iprobe probe
A Rank Receives (Blocking) an Object from the Other Rank	recv recv,ANY-method recv,integer-method recv,numeric-method recv,raw-method recv-method
A Rank Receive a Reduction of Objects from Every Rank	reduce reduce,ANY,missing-method reduce,float32,float32-method reduce,integer,integer-method reduce,logical,logical-method reduce,numeric,numeric-method reduce-method
A Rank Scatter Objects to Every Rank	scatter scatter,ANY,ANY,integer-method scatter,ANY,missing,integer-method scatter,ANY,missing,missing-method scatter,integer,integer,integer-method scatter,integer,integer,missing-method scatter,numeric,numeric,integer-method scatter,numeric,numeric,missing-method scatter,raw,raw,integer-method scatter,raw,raw,missing-method scatter-method
Parallel random number generation with reproducible results	comm.end.seed comm.get.streams comm.reset.seed comm.seed.state comm.set.seed comm.set.stream
A Rank Send (blocking) an Object to the Other Rank	send send,ANY-method send,integer-method send,numeric-method send,raw-method send-method
Send and Receive an Object to and from Other Ranks	sendrecv sendrecv,ANY,ANY-method sendrecv,integer,integer-method sendrecv,numeric,numeric-method sendrecv,raw,raw-method sendrecv-method
Send and Receive an Object to and from Other Ranks	sendrecv.replace sendrecv.replace,ANY-method sendrecv.replace,integer-method sendrecv.replace,numeric-method sendrecv.replace,raw-method sendrecv.replace-method
Set Global pbdR Options	pbd_opt
Functions to Obtain source and tag	anysource anytag get.sourcetag
Default control in pbdMPI.	.pbd_env
Sets of controls in pbdMPI.	.mpiopt_init SPMD.CT SPMD.DT SPMD.IO SPMD.OP SPMD.TP
Functions for Task Pull Parallelism	task.pull task.pull.manager task.pull.workers
Execute MPI code in system	execmpi runmpi
Wait Functions	wait waitall waitany waitsome

Package: pbdMPI 0.5-2

pbdMPI: R Interface to MPI for HPC Clusters (Programming with Big Data Project)

pbdMPI-guide

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