diff --git a/DESCRIPTION b/DESCRIPTION index 89d68852..952e4b94 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: BiocParallel Type: Package Title: Bioconductor facilities for parallel evaluation -Version: 1.23.1 +Version: 1.23.2 Authors@R: c( person("Bioconductor Package Maintainer", email="maintainer@bioconductor.org", role="cre"), diff --git a/NAMESPACE b/NAMESPACE index 70856542..8017d48a 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -46,6 +46,7 @@ export( batchtoolsTemplate, bpvalidate, bpok, bprunMPIslave, + bprunMPIworker, ## ipcmutex ipcid, ipcremove, ipclock, ipctrylock, ipcunlock, ipclocked, diff --git a/R/SnowParam-utils.R b/R/SnowParam-utils.R index 6ddb65ac..83235e2f 100644 --- a/R/SnowParam-utils.R +++ b/R/SnowParam-utils.R @@ -5,6 +5,11 @@ ### bprunMPIslave <- function() { + .Deprecated("bprunMPIworker") + bprunMPIworker() +} + +bprunMPIworker <- function() { comm <- 1 intercomm <- 2 Rmpi::mpi.comm.get.parent(intercomm) diff --git a/inst/RMPInode.sh b/inst/RMPInode.sh index 1b9abf4d..6ebf9f24 100755 --- a/inst/RMPInode.sh +++ b/inst/RMPInode.sh @@ -5,5 +5,5 @@ ${RPROG:-R} --vanilla < ${OUT:-/dev/null} 2>&1 loadNamespace("Rmpi") loadNamespace("snow") -BiocParallel::bprunMPIslave() +BiocParallel::bprunMPIworker() EOF diff --git a/inst/snow/RMPInode.R b/inst/snow/RMPInode.R index 079d77f7..811b92a8 100755 --- a/inst/snow/RMPInode.R +++ b/inst/snow/RMPInode.R @@ -20,6 +20,6 @@ local({ loadNamespace("Rmpi") loadNamespace("snow") - BiocParallel::bprunMPIslave() + BiocParallel::bprunMPIworker() quit("no") }) diff --git a/inst/unitTests/test_script/test-sge-template.tmpl b/inst/unitTests/test_script/test-sge-template.tmpl index 783b0ff9..90894285 100644 --- a/inst/unitTests/test_script/test-sge-template.tmpl +++ b/inst/unitTests/test_script/test-sge-template.tmpl @@ -22,7 +22,7 @@ ## R settings module load R/3.4.3 -## Export value of DEBUGME environemnt var to slave +## Export value of DEBUGME environemnt var to worker export DEBUGME=<%= Sys.getenv("DEBUGME") %> Rscript -e 'batchtools::doJobCollection("<%= uri %>")' diff --git a/man/bploop.Rd b/man/bploop.Rd index 305f0e67..7562b24d 100644 --- a/man/bploop.Rd +++ b/man/bploop.Rd @@ -9,6 +9,7 @@ \alias{bploop.iterate} \alias{bprunMPIslave} +\alias{bprunMPIworker} \title{Internal Functions for SNOW-style Parallel Evaluation} diff --git a/vignettes/BiocParallel_BatchtoolsParam.Rnw b/vignettes/BiocParallel_BatchtoolsParam.Rnw index 63b7137d..ee59e468 100644 --- a/vignettes/BiocParallel_BatchtoolsParam.Rnw +++ b/vignettes/BiocParallel_BatchtoolsParam.Rnw @@ -192,7 +192,7 @@ cluster. For example, one might use instead: \begin{verbatim} echo 'batchtools::doJobCollection("<%= uri %>")' |\ - ArbitraryRcommand --no-save --slave + ArbitraryRcommand --no-save --no-echo \end{verbatim} If such customization is necessary, we suggest making a local copy of