Merge branch 'mapping-tool' of https://git.wur.nl/glowpa/glowpa-model into mapping-tool

Model scripts/GloWPa.R

@@ -58,8 +58,8 @@ glowpa.run <- function(scenario,human_data,isoraster,popurban,poprural,wwtp_inpu
   # merge defaults for scenario with scenario
   result = withCallingHandlers({
     SCENARIO <<- glowpa.get.params(scenario)
-    log_file <- file.path(SCENARIO$model_output,sprintf("logs/log_run%s_pid%s.txt",SCENARIO$run, Sys.getpid()))
-    logger.init(log_file)
+    LOG_FILE <<- file.path(SCENARIO$model_output,sprintf("logs/log_run%s_pid%s.txt",SCENARIO$run, Sys.getpid()))
+    logger.init(LOG_FILE)
     log_info('Start scenario run with id {SCENARIO$run}')
     params_table <- logger.get.table(SCENARIO)
     log_info('Model started with following params:\n{params_table}')

Model scripts/pathogenflows.R

@@ -23,8 +23,14 @@ pathogenflow.run <- function(pathogen){
   tic("calc pathogenflows loadings")
   # for debugging inside getLoadings
   # loadings <- pathogenflows::getLoadings(onsite_data$urban$child,pathogen_type)
-  cl <- makeCluster(detectCores())
+  cl <- makeCluster(detectCores(),outfile=LOG_FILE)
+  clusterEvalQ(cl, library(pathogenflows))
+  clusterExport(cl, varlist=c("log_info"))
   loadings <- parLapply(cl,unlist(onsite_data,recursive = F),fun = function(x){
+    session_info <- sessionInfo()
+    pid <- Sys.getpid()
+    log_info("pathogenflows pid {pid} : R version: {session_info$R.version$version.string}")
+    log_info("pathogenflows pid {pid} : Library path: {.libPaths()}")
     out <- pathogenflows::getLoadings(x,pathogen_type)
     return(out)
   })