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0.3-5 on CRAN
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| Package: pbdMPI | ||
| Version: 0.3-4 | ||
| Date: 2018-01-03 | ||
| Version: 0.3-5 | ||
| Date: 2018-02-25 | ||
| Title: Programming with Big Data -- Interface to MPI | ||
| Authors@R: c(person("Wei-Chen", "Chen", role = c("aut", "cre"), email = | ||
| "[email protected]"), | ||
|
|
@@ -27,7 +27,7 @@ SystemRequirements: OpenMPI (>= 1.5.4) on Solaris, Linux, Mac, and | |
| Pack 2012 R2 MS-MPI Redistributable Package) on Windows. | ||
| License: Mozilla Public License 2.0 | ||
| URL: http://r-pbd.org/ | ||
| BugReports: http://group.r-pbd.org/ | ||
| BugReports: https://github.com/snoweye/pbdMPI/issues | ||
| MailingList: Please send questions and comments regarding pbdR to | ||
| [email protected] | ||
| NeedsCompilation: yes | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,130 @@ | ||
| ### Utility | ||
|
|
||
| execmpi <- function(spmd.code = NULL, spmd.file = NULL, | ||
| mpicmd = NULL, nranks = 2L, verbose = TRUE){ | ||
| ### Check # of ranks. | ||
| nranks <- as.integer(nranks) | ||
| if(nranks <= 0){ | ||
| stop("argument 'nranks' must be a integer and greater than 0.") | ||
| } | ||
|
|
||
| ### Input checks | ||
| if(! is.null(spmd.code)){ | ||
| if(!is.character(spmd.code)){ | ||
| stop("argument 'spmd.code' must be a character string") | ||
| } else if(length(spmd.code) == 0){ | ||
| stop("argument 'spmd.code' must be a non-empty character string") | ||
| } else if (length(spmd.code) > 1){ | ||
| warning("spmd.code has length > 1; only the first element will be used") | ||
| spmd.code <- spmd.code[1L] | ||
| } | ||
|
|
||
| ### Dump spmd.code to a temp file, execute | ||
| spmd.file <- tempfile() | ||
| on.exit(unlink(spmd.file)) | ||
| conn <- file(spmd.file, open = "wt") | ||
| writeLines(spmd.code, conn) | ||
| close(conn) | ||
| } else{ | ||
| if(is.null(spmd.file)){ | ||
| stop("Either spmd.code or spmd.file should be provided.") | ||
| } | ||
| } | ||
| if(! file.exists(spmd.file)){ | ||
| stop("spmd.file does not exist.") | ||
| } | ||
|
|
||
| ### Find MPI executable. | ||
| if(is.null(mpicmd)){ | ||
| if(Sys.info()[['sysname']] == "Windows"){ | ||
| mpicmd <- try(system("mpiexec", intern = TRUE), silent = TRUE) | ||
| if(class(mpicmd) == "try-error"){ | ||
| warning("No MPI executable can be found from PATH.") | ||
| return(invisible(NULL)) | ||
| } else{ | ||
| mpicmd <- "mpiexec" | ||
| } | ||
| } else{ | ||
| mpicmd <- system("which mpiexec", intern = TRUE) | ||
| if(! is.null(attr(mpicmd, "status"))){ | ||
| mpicmd <- system("which mpirun", intern = TRUE) | ||
| if(! is.null(attr(mpicmd, "status"))){ | ||
| mpicmd <- system("which orterun", intern = TRUE) | ||
| if(! is.null(attr(mpicmd, "status"))){ | ||
| mpicmd <- get.conf("MPIEXEC") | ||
| if(mpicmd == ""){ | ||
| mpicmd <- get.conf("MPIRUN") | ||
| if(mpicmd == ""){ | ||
| mpicmd <- get.conf("ORTERUN") | ||
| if(mpicmd == ""){ | ||
| warning("No MPI executable can be found.") | ||
| return(invisible(NULL)) | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
|
||
| ### Find Rscript. | ||
| if(Sys.info()[['sysname']] == "Windows"){ | ||
| rscmd <- paste(Sys.getenv("R_HOME"), "/bin", Sys.getenv("R_ARCH_BIN"), | ||
| "/Rscript", sep = "") | ||
| } else{ | ||
| rscmd <- paste(Sys.getenv("R_HOME"), "/bin/Rscript", sep = "") | ||
| } | ||
|
|
||
| ### Make a cmd. | ||
| if(Sys.info()[['sysname']] == "Windows"){ | ||
| cmd <- paste(mpicmd, "-np", nranks, rscmd, spmd.file, sep = " ") | ||
| ### Redirect to log.file will get the message below and fail. | ||
| ### The process cannot access the file because it is being used by | ||
| ### another process. | ||
| } else{ | ||
| log.file <- tempfile() | ||
| on.exit(unlink(log.file), add = TRUE) | ||
| cmd <- paste(mpicmd, "-np", nranks, rscmd, spmd.file, | ||
| ">", log.file, "2>&1 & echo \"PID=$!\" &", sep = " ") | ||
| } | ||
| if(verbose){ | ||
| cat(">>> MPI command:\n", cmd, "\n", sep = "") | ||
| } | ||
|
|
||
| ### Run the cmd. | ||
| if(Sys.info()[['sysname']] == "Windows"){ | ||
| ret <- system(cmd, intern = TRUE, ignore.stdout = FALSE, | ||
| ignore.stderr = FALSE, wait = TRUE) | ||
| } else{ | ||
| tmp <- system(cmd, intern = TRUE, ignore.stdout = FALSE, | ||
| ignore.stderr = FALSE, wait = FALSE) | ||
| if(verbose){ | ||
| cat(">>> MPI PID:\n", paste(tmp, collapse = "\n"), "\n", sep = "") | ||
| } | ||
|
|
||
| ### Check if the job is finished, otherwise wait for it. | ||
| pid <- gsub("^PID=(.*)$", "\\1", tmp) | ||
| cmd.pid <- paste("ps -p", pid, sep = " ") | ||
| while(TRUE){ | ||
| tmp.pid <- suppressWarnings(system(cmd.pid, intern = TRUE)) | ||
| if(is.null(attr(tmp.pid, "status"))){ | ||
| Sys.sleep(1) | ||
| } else{ | ||
| break | ||
| } | ||
| } | ||
| } | ||
|
|
||
| ### Get the output from the log file. | ||
| if(Sys.info()[['sysname']] != "Windows"){ | ||
| ret <- readLines(log.file) | ||
| } | ||
| if(verbose){ | ||
| cat(">>> MPI results:\n", paste(ret, collapse = "\n"), "\n", sep = "") | ||
| } | ||
|
|
||
| ### Return | ||
| invisible(ret) | ||
| } # End of execmpi(). | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,56 @@ | ||
| # DO NOT CHANGE the "init" and "install" sections below | ||
|
|
||
| # Download script file from GitHub | ||
| init: | ||
| ps: | | ||
| $ErrorActionPreference = "Stop" | ||
| Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1" | ||
| Import-Module '..\appveyor-tool.ps1' | ||
| install: | ||
| - ps: Bootstrap | ||
| - cd .. | ||
| ### Install HPC Pack 2012 R2 Update 3 SDK | ||
| # - ps: (New-Object Net.WebClient).DownloadFile("https://download.microsoft.com/download/7/B/5/7B582B17-AF1E-454A-B86B-E6733010EB47/sdk_x64.msi", "sdk_x64.msi") | ||
| # - ps: msiexec /i sdk_x64.msi /quiet /qn /norestart /log install.log PROPERTY1=value1 PROPERTY2=value2 | ||
| ### Install MS-MPI v9.0 | ||
| - ps: Start-FileDownload 'https://download.microsoft.com/download/2/E/C/2EC96D7F-687B-4613-80F6-E10F670A2D97/msmpisetup.exe' | ||
| - MSMpiSetup.exe -unattend | ||
| - dir "C:\Program Files\Microsoft MPI" | ||
| - dir "C:\Program Files\Microsoft MPI\Bin" | ||
| ### Install MS-MPI v9.0 SDK | ||
| - ps: Start-FileDownload 'https://download.microsoft.com/download/2/E/C/2EC96D7F-687B-4613-80F6-E10F670A2D97/msmpisdk.msi' | ||
| - msmpisdk.msi /passive | ||
| - dir "C:\Program Files (x86)\Microsoft SDKs\MPI" | ||
| - dir "C:\Program Files (x86)\Microsoft SDKs\MPI\Include" | ||
| - dir "C:\Program Files (x86)\Microsoft SDKs\MPI\Lib" | ||
| ### Set PATH | ||
| - set MPI_EXEC=C:\Program Files\Microsoft MPI | ||
| - set MPI_ROOT=C:\Program Files (x86)\Microsoft SDKS\MPI | ||
| - set PATH=%MPI_EXEC%\Bin;%PATH% | ||
| ### Check MS-MPI | ||
| - mpiexec -help | ||
| # - mpiexec -help2 | ||
| # - mpiexec -help3 | ||
|
|
||
| environment: | ||
| global: | ||
| WARNINGS_ARE_ERRORS: | ||
| RTOOLS_VERSION: 34 | ||
| USE_RTOOLS: true | ||
|
|
||
| matrix: | ||
| - R_VERSION: release | ||
| R_ARCH: x64 | ||
|
|
||
| build_script: | ||
| - cd pbdMPI | ||
| - travis-tool.sh install_deps | ||
| - cd .. | ||
| - R CMD build --no-build-vignettes --no-manual --no-resave-data pbdMPI | ||
| - R CMD INSTALL pbdMPI*.tar.gz | ||
| - R CMD check pbdMPI*.tar.gz --as-cran --no-manual --no-vignettes --no-clean | ||
| - dir pbdMPI.Rcheck | ||
| # - type pbdMPI.Rcheck\00check.log | ||
| - type pbdMPI.Rcheck\pbdMPI-Ex_x64.Rout | ||
|
|
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