{lang}[foss/2021.07] R v4.1.1

easybuild/easyconfigs/r/R/DMCfun-2.0.0_fix-parallel-detect.patch

@@ -0,0 +1,38 @@
+# parallal::detectCores() detects physical cores and not available cores. It is ususally problem in queue systems
+# like PBS or Slurm. This patch gives solution for that problem for PBS and with Slurm with PBS compatibility switched
+# on. For other queue systems, a different solutiom might needed.
+# April 13th 2021 by B. Hajgato (UGent)
+# Updated for 2.0.0 by Simon Branford (University of Birmingham)
+diff -ru DMCfun.orig/MD5 DMCfun/MD5
+--- DMCfun.orig/MD5	2021-01-10 18:50:10.000000000 +0100
++++ DMCfun/MD5	2021-04-13 09:31:31.242654188 +0200
+@@ -4,7 +4,7 @@
+ a835c7e49694b2c835c438362b16946f *R/DMCfun.R
+ 034299149a3219bf581d440b19d94fbb *R/RcppExports.R
+ 7d89e703313977e0f0390c301ba41719 *R/dmcData.R
+-a3141dac9d27d87db3494c293328358d *R/dmcFit.R
++afbe1e78cad3156de24ae67dd94153c0 *R/dmcFit.R
+ 2c816b9074882e79af599451d079723d *R/dmcSim.R
+ 9acbbd1c38bace26bed9c6a50f7c82ea *R/methods.R
+ 169bfcbfb92b758fb0dd18e481711aa8 *R/plot.R
+diff -ru DMCfun.orig/R/dmcFit.R DMCfun/R/dmcFit.R
+--- DMCfun.orig/R/dmcFit.R	2020-12-03 18:53:03.000000000 +0100
++++ DMCfun/R/dmcFit.R	2021-04-13 09:28:47.506520017 +0200
+@@ -159,7 +159,7 @@
+     if (nzchar(chk) && (chk == "true")) {
+       num_cores <- 2L
+     } else {
+-      num_cores <- parallel::detectCores() / 2
++      num_cores <- as.numeric(Sys.getenv("SLURM_CPUS_ON_NODE", Sys.getenv("PBS_NUM_PPN", parallel::detectCores() / 2)))
+     }
+
+     # Older code (pre June 2020) used doSNOW progress bar 
+@@ -297,7 +297,7 @@
+   if (nzchar(chk) && (chk == "true")) {
+     num_cores <- 2L
+   } else {
+-    num_cores <- parallel::detectCores() / 2
++    num_cores <- as.numeric(Sys.getenv("SLURM_CPUS_ON_NODE", Sys.getenv("PBS_NUM_PPN", parallel::detectCores() / 2)))
+   }
+   cl <- parallel::makeCluster(num_cores)
+   invisible(parallel::clusterExport(cl = cl, varlist=c("dmcSim", "calculateCostValue")))