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:
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://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/snoweye/pbdmpi/issues
Last updated 3 months agofrom:b986e9b7c2. Checks:OK: 1 FAILURE: 1. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 31 2024 |
R-4.5-linux-x86_64 | FAILURE | Nov 02 2024 |
Exports:.mpiopt_initaddr.mpi.comm.ptrallgatherallreduceanysourceanytagarrange.mpi.aptsbarrierbcastcomm.abortcomm.acceptcomm.allcomm.allcommoncomm.allcommon.integercomm.allpairscomm.anycomm.as.gbdcomm.balance.infocomm.c2fcomm.catcomm.chunkcomm.connectcomm.disconnectcomm.distcomm.dist.commoncomm.dist.gbdcomm.dupcomm.end.seedcomm.freecomm.get.streamscomm.is.nullcomm.lengthcomm.load.balancecomm.localrankcomm.match.argcomm.maxcomm.meancomm.mincomm.pairwisecomm.pairwise.commoncomm.pairwise.gbdcomm.printcomm.rangecomm.rankcomm.read.csvcomm.read.csv2comm.read.tablecomm.reset.seedcomm.Rprofcomm.sdcomm.seed.statecomm.set.errhandlercomm.set.seedcomm.set.streamcomm.sizecomm.sortcomm.sort.defaultcomm.sort.doublecomm.sort.integercomm.splitcomm.stopcomm.stopifnotcomm.sumcomm.timercomm.unload.balancecomm.varcomm.warningcomm.warningscomm.whichcomm.which.maxcomm.which.mincomm.writecomm.write.csvcomm.write.csv2comm.write.tableexecmpifinalizegatherget.confget.jidget.libget.mpi.comm.ptrget.sourcetagget.sysenvinfo.c2finfo.createinfo.freeinfo.setinitintercomm.createintercomm.mergeiprobeirecvis.comm.nullis.finalizedisendpbd_optpbdApplypbdLapplypbdSapplyport.closeport.openproberecvreducerunmpiscattersendsendrecvsendrecv.replaceserv.lookupserv.publishserv.unpublishspmd.allcheck.typespmd.allgather.arrayspmd.allgather.defaultspmd.allgather.doublespmd.allgather.integerspmd.allgather.objectspmd.allgather.rawspmd.allgatherv.defaultspmd.allgatherv.doublespmd.allgatherv.integerspmd.allgatherv.rawspmd.allreduce.arrayspmd.allreduce.defaultspmd.allreduce.doublespmd.allreduce.floatspmd.allreduce.float32spmd.allreduce.integerspmd.allreduce.logicalspmd.allreduce.objectspmd.alltoall.doublespmd.alltoall.integerspmd.alltoall.rawspmd.alltoallv.doublespmd.alltoallv.integerspmd.alltoallv.rawspmd.anysourcespmd.anytagspmd.barrierspmd.bcast.arrayspmd.bcast.defaultspmd.bcast.doublespmd.bcast.integerspmd.bcast.messagespmd.bcast.objectspmd.bcast.rawspmd.bcast.stringspmd.check.type.recvspmd.check.type.sendspmd.comm.abortspmd.comm.acceptspmd.comm.c2fspmd.comm.catspmd.comm.connectspmd.comm.disconnectspmd.comm.dupspmd.comm.freespmd.comm.get.parentspmd.comm.is.nullspmd.comm.localrankspmd.comm.printspmd.comm.rankspmd.comm.set.errhandlerspmd.comm.sizespmd.comm.spawnspmd.comm.splitSPMD.CTSPMD.DTspmd.finalizespmd.gather.arrayspmd.gather.defaultspmd.gather.doublespmd.gather.integerspmd.gather.objectspmd.gather.rawspmd.gatherv.defaultspmd.gatherv.doublespmd.gatherv.integerspmd.gatherv.rawspmd.get.countspmd.get.processor.namespmd.get.sourcetagspmd.hostinfospmd.info.c2fspmd.info.createspmd.info.freespmd.info.setspmd.initspmd.intercomm.createspmd.intercomm.mergeSPMD.IOspmd.iprobespmd.irecv.defaultspmd.irecv.doublespmd.irecv.integerspmd.irecv.rawspmd.is.comm.nullspmd.is.finalizedspmd.is.managerspmd.isend.defaultspmd.isend.doublespmd.isend.integerspmd.isend.rawSPMD.OPspmd.port.closespmd.port.openspmd.probespmd.recv.defaultspmd.recv.doublespmd.recv.integerspmd.recv.rawspmd.reduce.arrayspmd.reduce.defaultspmd.reduce.doublespmd.reduce.floatspmd.reduce.float32spmd.reduce.integerspmd.reduce.logicalspmd.reduce.objectspmd.scatter.arrayspmd.scatter.defaultspmd.scatter.doublespmd.scatter.integerspmd.scatter.objectspmd.scatter.rawspmd.scatterv.defaultspmd.scatterv.doublespmd.scatterv.integerspmd.scatterv.rawspmd.send.defaultspmd.send.doublespmd.send.integerspmd.send.rawspmd.sendrecv.defaultspmd.sendrecv.doublespmd.sendrecv.integerspmd.sendrecv.rawspmd.sendrecv.replace.defaultspmd.sendrecv.replace.doublespmd.sendrecv.replace.integerspmd.sendrecv.replace.rawspmd.serv.lookupspmd.serv.publishspmd.serv.unpublishSPMD.TPspmd.waitspmd.waitallspmd.waitanyspmd.waitsometask.pulltask.pull.managertask.pull.workerswaitwaitallwaitanywaitsome
Dependencies:float
Readme and manuals
Help Manual
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 |