Copy all run and out dirs at once, not in for-loop

CHANGELOG.md

@@ -46,6 +46,7 @@ convert data for a single PFT fixed (#1329, #2974, #2981)
   Note that both `units` and `udunits2` interface with the same underlying
   compiled code, so the `udunits2` *system library* is still required.
   (#2989; @nanu1605)
+- Occasionally some run directories were not getting copied over to remote hosts.  This should be fixed now (#3025)
 
 ### Changed
 

base/workflow/R/start_model_runs.R

@@ -79,28 +79,35 @@ start_model_runs <- function(settings, write = TRUE, stop.on.error = TRUE) {
   jobfile <- NULL
   firstrun <- NULL
 
+  #Copy all run directories over if not local
+  if (!is_local) {
+    # Set up outdir
+    PEcAn.remote::remote.execute.cmd(
+      host = settings$host,
+      cmd = "mkdir",
+      args = c(
+        "-p",
+        dirname(settings$host$outdir))) 
+    # copy over out directories
+    PEcAn.remote::remote.copy.to(
+      host = settings$host,
+      src = file.path(settings$outdir, "out"),
+      dst = dirname(settings$host$outdir) 
+    )
+    # copy over run directories
+    PEcAn.remote::remote.copy.to(
+      host = settings$host,
+      src = settings$rundir, 
+      dst = dirname(settings$host$rundir), 
+      delete = TRUE)
+  }
+
   # launch each of the jobs
   for (run in run_list) {
     run_id_string <- format(run, scientific = FALSE)
     # write start time to database
     PEcAn.DB::stamp_started(con = dbcon, run = run)
 
-    # if running on a remote cluster, create folders and copy any data
-    # to remote host
-    if (!is_local) {
-      PEcAn.remote::remote.execute.cmd(
-        host = settings$host,
-        cmd = "mkdir",
-        args = c(
-          "-p",
-          file.path(settings$host$outdir, run_id_string)))
-      PEcAn.remote::remote.copy.to(
-        host = settings$host,
-        src = file.path(settings$rundir, run_id_string),
-        dst = settings$host$rundir,
-        delete = TRUE)
-    }
-
     # check to see if we use the model launcer
     if (is_rabbitmq) {
       run_id_string <- format(run, scientific = FALSE)