Adding cores transmission mechanism for the R script

benchmark_lbm_seq.R

@@ -9,6 +9,14 @@ library(blockmodels)
 library(here)
 library(microbenchmark)
 
+args <- commandArgs(trailingOnly = TRUE)
+mode <- args[1]
+nb_cores <- as.integer(args[2])
+
+options(parallelly.availableCores.custom = function() {
+    max(1L, nb_cores)
+})
+
 data_folder <- here("results", "lbm-seq")
 
 the_data <- import_biom("data/mach/kinetic.biom")
@@ -22,7 +30,7 @@ if (!dir.exists(tmp_folder)) {
 
 per_taxa_networks <- collapse_otu_at_taxo(the_data)
 
-mode <- commandArgs(trailingOnly = TRUE)
+
 switch(mode,
     "seq" = {
         message("Will use SEQ")

sge_scripts/benchmark_lbm_seq.sh

@@ -5,7 +5,7 @@
 #$ -m besa
 #$ -q long.q
 #$ -t 1-12
-#$ -pe thread 128
+#$ -pe thread 64
 #$ -M louis.lacoste+migale@agroparistech.fr
 #$ -o logs/$JOB_NAME
 #$ -e logs/$JOB_NAME
@@ -40,4 +40,9 @@ case $ARGID in
     ;;
 esac
 
-Rscript "${APPLICATIONS_DIR}/benchmark_lbm_seq.R" $MODE &>> logs/$JOB_NAME.$SGE_TASK_ID
+readonly NB_CORES=$(sed -n 's/^#\$ -pe thread \(.*\)/\1/p' -- "$0")
+
+
+echo -n "Model will be $MODE with $NB_CORES"
+
+Rscript "${APPLICATIONS_DIR}/benchmark_lbm_seq.R" $MODE $NB_CORES &>> logs/$JOB_NAME.$SGE_TASK_ID