From df88bb70d827ff62855380303c173fa2dafa592f Mon Sep 17 00:00:00 2001 From: MilanFischer Date: Fri, 12 Apr 2024 23:50:32 +0200 Subject: [PATCH 1/8] Update calibrateMuso.R added workers argument into multisession. --- RBBGCMuso/R/calibrateMuso.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RBBGCMuso/R/calibrateMuso.R b/RBBGCMuso/R/calibrateMuso.R index dd56fc7..3e3678a 100644 --- a/RBBGCMuso/R/calibrateMuso.R +++ b/RBBGCMuso/R/calibrateMuso.R @@ -17,7 +17,7 @@ calibrateMuso <- function(measuredData, parameters =read.csv("parameters.csv", s maxLikelihoodEpc=TRUE, pbUpdate = setTxtProgressBar, outputLoc="./", method="GLUE",lg = FALSE, w=NULL, ...){ - future::plan(future::multisession) + future::plan(future::multisession(workers = numCores)) file.remove(list.files(path = settings$inputLoc, pattern="progress.txt", recursive = TRUE, full.names=TRUE)) file.remove(list.files(path = settings$inputLoc, pattern="preservedCalib.csv", recursive = TRUE, full.names=TRUE)) unlink(file.path(settings$inputLoc,"thread"),recursive=TRUE) From 73ab5d43f339621fb27ce222ea9e1ce445e65f80 Mon Sep 17 00:00:00 2001 From: MilanFischer Date: Sat, 13 Apr 2024 00:19:19 +0200 Subject: [PATCH 2/8] Update calibrateMuso.R numCores redefined --- RBBGCMuso/R/calibrateMuso.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RBBGCMuso/R/calibrateMuso.R b/RBBGCMuso/R/calibrateMuso.R index 3e3678a..575f324 100644 --- a/RBBGCMuso/R/calibrateMuso.R +++ b/RBBGCMuso/R/calibrateMuso.R @@ -17,7 +17,7 @@ calibrateMuso <- function(measuredData, parameters =read.csv("parameters.csv", s maxLikelihoodEpc=TRUE, pbUpdate = setTxtProgressBar, outputLoc="./", method="GLUE",lg = FALSE, w=NULL, ...){ - future::plan(future::multisession(workers = numCores)) + future::plan(future::multisession(workers = numCores), numCores = numCores) file.remove(list.files(path = settings$inputLoc, pattern="progress.txt", recursive = TRUE, full.names=TRUE)) file.remove(list.files(path = settings$inputLoc, pattern="preservedCalib.csv", recursive = TRUE, full.names=TRUE)) unlink(file.path(settings$inputLoc,"thread"),recursive=TRUE) From 9fc504f5c89d01e6ba74c2c5db57a5e5c36d8f4c Mon Sep 17 00:00:00 2001 From: MilanFischer Date: Sat, 13 Apr 2024 00:27:09 +0200 Subject: [PATCH 3/8] Update calibrateMuso.R numCores default value removed --- RBBGCMuso/R/calibrateMuso.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/RBBGCMuso/R/calibrateMuso.R b/RBBGCMuso/R/calibrateMuso.R index 575f324..cb7a807 100644 --- a/RBBGCMuso/R/calibrateMuso.R +++ b/RBBGCMuso/R/calibrateMuso.R @@ -13,11 +13,11 @@ calibrateMuso <- function(measuredData, parameters =read.csv("parameters.csv", s modifyOriginal=TRUE, likelihood, uncertainity = NULL, naVal = NULL, postProcString = NULL, sourceFile=NULL, # bases for musoRand if dependecy group is not fully defined by parameters.csv - thread_prefix="thread", numCores = max(c(parallel::detectCores()-1,1)), pb = txtProgressBar(min=0, max=iterations, style=3), + thread_prefix="thread", numCores, pb = txtProgressBar(min=0, max=iterations, style=3), maxLikelihoodEpc=TRUE, pbUpdate = setTxtProgressBar, outputLoc="./", method="GLUE",lg = FALSE, w=NULL, ...){ - future::plan(future::multisession(workers = numCores), numCores = numCores) + future::plan(future::multisession(workers = numCores)) file.remove(list.files(path = settings$inputLoc, pattern="progress.txt", recursive = TRUE, full.names=TRUE)) file.remove(list.files(path = settings$inputLoc, pattern="preservedCalib.csv", recursive = TRUE, full.names=TRUE)) unlink(file.path(settings$inputLoc,"thread"),recursive=TRUE) From f72e49a4a978a75994ca921a3697cdca101f949c Mon Sep 17 00:00:00 2001 From: MilanFischer Date: Sat, 13 Apr 2024 00:29:20 +0200 Subject: [PATCH 4/8] Update calibrateMuso.R --- RBBGCMuso/R/calibrateMuso.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RBBGCMuso/R/calibrateMuso.R b/RBBGCMuso/R/calibrateMuso.R index cb7a807..3e830bb 100644 --- a/RBBGCMuso/R/calibrateMuso.R +++ b/RBBGCMuso/R/calibrateMuso.R @@ -16,7 +16,7 @@ calibrateMuso <- function(measuredData, parameters =read.csv("parameters.csv", s thread_prefix="thread", numCores, pb = txtProgressBar(min=0, max=iterations, style=3), maxLikelihoodEpc=TRUE, pbUpdate = setTxtProgressBar, outputLoc="./", method="GLUE",lg = FALSE, w=NULL, ...){ - + print(numCores) future::plan(future::multisession(workers = numCores)) file.remove(list.files(path = settings$inputLoc, pattern="progress.txt", recursive = TRUE, full.names=TRUE)) file.remove(list.files(path = settings$inputLoc, pattern="preservedCalib.csv", recursive = TRUE, full.names=TRUE)) From 6e9f31234ed401b6c044cf4ad6c3b83accbb74f9 Mon Sep 17 00:00:00 2001 From: MilanFischer Date: Sat, 13 Apr 2024 00:35:30 +0200 Subject: [PATCH 5/8] Update calibrateMuso.R --- RBBGCMuso/R/calibrateMuso.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/RBBGCMuso/R/calibrateMuso.R b/RBBGCMuso/R/calibrateMuso.R index 3e830bb..5d48e99 100644 --- a/RBBGCMuso/R/calibrateMuso.R +++ b/RBBGCMuso/R/calibrateMuso.R @@ -16,8 +16,8 @@ calibrateMuso <- function(measuredData, parameters =read.csv("parameters.csv", s thread_prefix="thread", numCores, pb = txtProgressBar(min=0, max=iterations, style=3), maxLikelihoodEpc=TRUE, pbUpdate = setTxtProgressBar, outputLoc="./", method="GLUE",lg = FALSE, w=NULL, ...){ - print(numCores) - future::plan(future::multisession(workers = numCores)) + + future::plan(future::multisession(workers = numCores, envir = environment())) file.remove(list.files(path = settings$inputLoc, pattern="progress.txt", recursive = TRUE, full.names=TRUE)) file.remove(list.files(path = settings$inputLoc, pattern="preservedCalib.csv", recursive = TRUE, full.names=TRUE)) unlink(file.path(settings$inputLoc,"thread"),recursive=TRUE) From 5ef318324cfffebc4e174433787bd37b85c1279d Mon Sep 17 00:00:00 2001 From: MilanFischer Date: Sat, 13 Apr 2024 00:38:28 +0200 Subject: [PATCH 6/8] Update calibrateMuso.R --- RBBGCMuso/R/calibrateMuso.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RBBGCMuso/R/calibrateMuso.R b/RBBGCMuso/R/calibrateMuso.R index 5d48e99..b46b6b9 100644 --- a/RBBGCMuso/R/calibrateMuso.R +++ b/RBBGCMuso/R/calibrateMuso.R @@ -17,7 +17,7 @@ calibrateMuso <- function(measuredData, parameters =read.csv("parameters.csv", s maxLikelihoodEpc=TRUE, pbUpdate = setTxtProgressBar, outputLoc="./", method="GLUE",lg = FALSE, w=NULL, ...){ - future::plan(future::multisession(workers = numCores, envir = environment())) + future::plan(future::multisession(workers = 124)) file.remove(list.files(path = settings$inputLoc, pattern="progress.txt", recursive = TRUE, full.names=TRUE)) file.remove(list.files(path = settings$inputLoc, pattern="preservedCalib.csv", recursive = TRUE, full.names=TRUE)) unlink(file.path(settings$inputLoc,"thread"),recursive=TRUE) From e865097472bf18d9c843fda1daafc663b42609f0 Mon Sep 17 00:00:00 2001 From: MilanFischer Date: Sat, 13 Apr 2024 00:51:18 +0200 Subject: [PATCH 7/8] Update calibrateMuso.R Explicitly specify the environment in the multisession call --- RBBGCMuso/R/calibrateMuso.R | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/RBBGCMuso/R/calibrateMuso.R b/RBBGCMuso/R/calibrateMuso.R index b46b6b9..3489e7b 100644 --- a/RBBGCMuso/R/calibrateMuso.R +++ b/RBBGCMuso/R/calibrateMuso.R @@ -13,11 +13,13 @@ calibrateMuso <- function(measuredData, parameters =read.csv("parameters.csv", s modifyOriginal=TRUE, likelihood, uncertainity = NULL, naVal = NULL, postProcString = NULL, sourceFile=NULL, # bases for musoRand if dependecy group is not fully defined by parameters.csv - thread_prefix="thread", numCores, pb = txtProgressBar(min=0, max=iterations, style=3), + thread_prefix="thread", numCores = max(c(parallel::detectCores()-1,1)), pb = txtProgressBar(min=0, max=iterations, style=3), maxLikelihoodEpc=TRUE, pbUpdate = setTxtProgressBar, outputLoc="./", method="GLUE",lg = FALSE, w=NULL, ...){ - future::plan(future::multisession(workers = 124)) + # Explicitly specify the environment in the multisession call + plan <- future::multisession(workers = numCores, envir = environment()) + future::plan(plan) file.remove(list.files(path = settings$inputLoc, pattern="progress.txt", recursive = TRUE, full.names=TRUE)) file.remove(list.files(path = settings$inputLoc, pattern="preservedCalib.csv", recursive = TRUE, full.names=TRUE)) unlink(file.path(settings$inputLoc,"thread"),recursive=TRUE) From 5de8f2a23c6173631f348c03cc2d73d4a403bb4a Mon Sep 17 00:00:00 2001 From: MilanFischer Date: Sat, 13 Apr 2024 00:57:34 +0200 Subject: [PATCH 8/8] Update calibrateMuso.R --- RBBGCMuso/R/calibrateMuso.R | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/RBBGCMuso/R/calibrateMuso.R b/RBBGCMuso/R/calibrateMuso.R index 3489e7b..e02dd54 100644 --- a/RBBGCMuso/R/calibrateMuso.R +++ b/RBBGCMuso/R/calibrateMuso.R @@ -17,9 +17,7 @@ calibrateMuso <- function(measuredData, parameters =read.csv("parameters.csv", s maxLikelihoodEpc=TRUE, pbUpdate = setTxtProgressBar, outputLoc="./", method="GLUE",lg = FALSE, w=NULL, ...){ - # Explicitly specify the environment in the multisession call - plan <- future::multisession(workers = numCores, envir = environment()) - future::plan(plan) + future::plan(future::multisession, workers = numCores) file.remove(list.files(path = settings$inputLoc, pattern="progress.txt", recursive = TRUE, full.names=TRUE)) file.remove(list.files(path = settings$inputLoc, pattern="preservedCalib.csv", recursive = TRUE, full.names=TRUE)) unlink(file.path(settings$inputLoc,"thread"),recursive=TRUE)