Changes between Version 13 and Version 14 of cypress/R

Timestamp:

08/22/17 20:57:20 (7 years ago)

Author:

fuji

Comment:

—

cypress/R

@@ -101 +101 @@
 library(doParallel)
 
-# use the environment variable SLURM_NTASKS_PER_NODE to set the number of cores
-registerDoParallel(cores=(Sys.getenv("SLURM_NTASKS_PER_NODE")))
+# use the environment variable SLURM_CPUS_PER_TASK to set the number of cores
+registerDoParallel(cores=(Sys.getenv("SLURM_CPUS_PER_TASK")))
 
 # Bootstrapping iteration example
@@ -132 +132 @@
 #SBATCH --time=00:01:00         # WallTime
 #SBATCH --nodes=1               # Number of Nodes
-#SBATCH --ntasks-per-node=16    # Number of Tasks per Node
+#SBATCH --ntasks-per-node=1    # Number of Tasks per Node
+#SBATCH --cpus-per-task=16      # Number of threads per task (OMP threads)
 
 module load R/3.1.2
 
-Rscript bootstrap.R
+Rscript bootstrap.R $SLURM_CPUS_PER_TASK 
 }}}
 
@@ -148 +149 @@
 args<-commandArgs(TRUE)
 
-# use the environment variable SLURM_NTASKS_PER_NODE to set the number of cores
+# use the environment variable SLURM_CPUS_PER_TASK to set the number of cores
 registerDoParallel(cores=(as.integer(args[1])))
 
@@ -179 +180 @@
 #SBATCH --time=00:01:00         # WallTime
 #SBATCH --nodes=1               # Number of Nodes
-#SBATCH --ntasks-per-node=16    # Number of Tasks per Node
+#SBATCH --ntasks-per-node=1    # Number of Tasks per Node
+#SBATCH --cpus-per-task=16      # Number of threads per task (OMP threads)
 
 module load R/3.1.2
 
-Rscript bootstrapWargs.R $SLURM_TASKS_PER_NODE
+Rscript bootstrapWargs.R $SLURM_CPUS_PER_TASK 
 }}}