Addition of reservation to bsub headers. (#367)

maestrowf/interfaces/script/lsfscriptadapter.py

@@ -75,15 +75,18 @@ def __init__(self, **kwargs):
         self.add_batch_parameter("bank", kwargs.pop("bank"))
         self.add_batch_parameter("queue", kwargs.pop("queue"))
         self.add_batch_parameter("nodes", kwargs.pop("nodes", "1"))
+        reservation = kwargs.get("reservation", None)
+        if reservation:
+            self.add_batch_parameter("reservation", reservation)
 
-        self._exec = "#!/bin/bash"
         self._header = {
             "nodes": "#BSUB -nnodes {nodes}",
             "queue": "#BSUB -q {queue}",
             "bank": "#BSUB -G {bank}",
             "walltime": "#BSUB -W {walltime}",
             "job-name": "#BSUB -J {job-name}",
             "output": "#BSUB -o {output}",
+            "reservation": "#BSUB -U {reservation}",
             "error": "#BSUB -e {error}",
         }
 
@@ -95,7 +98,7 @@ def __init__(self, **kwargs):
             "reservation":  "-J",
         }
 
-        self._extension = ".lsf.sh"
+        self._extension = "lsf.sh"
 
     def get_header(self, step):
         """
@@ -105,16 +108,23 @@ def get_header(self, step):
         :returns: A string of the header based on internal batch parameters and
                   the parameter step.
         """
-        run = dict(step.run)
         batch_header = dict(self._batch)
-        batch_header["nodes"] = run.pop("nodes", self._batch["nodes"])
+        batch_header["nodes"] = step.run.get("nodes", self._batch["nodes"])
         batch_header["job-name"] = step.name.replace(" ", "_")
         batch_header["output"] = "{}.%J.out".format(batch_header["job-name"])
         batch_header["error"] = "{}.%J.err".format(batch_header["job-name"])
 
+        # Updte the batch header with the values from the step's resources
+        batch_header.update(
+            {
+                resource: value for (resource, value) in step.run.items()
+                if value
+            }
+        )
+
         # LSF requires an hour and minutes format. We need to attempt to split
         # and correct if we get something that's coming in as HH:MM:SS
-        walltime = run.pop("walltime")
+        walltime = step.run.get("walltime")
         wt_split = walltime.split(":")
         if len(wt_split) == 3:
             # If wall time is specified in three parts, we'll just calculate
@@ -128,9 +138,10 @@ def get_header(self, step):
 
         batch_header["walltime"] = walltime
 
-        modified_header = [self._exec]
+        modified_header = ["#!{}".format(self._exec)]
         for key, value in self._header.items():
-            modified_header.append(value.format(**batch_header))
+            if key in batch_header:
+                modified_header.append(value.format(**batch_header))
 
         return "\n".join(modified_header)
 
@@ -187,13 +198,6 @@ def submit(self, step, path, cwd, job_map=None, env=None):
                   identiifer.
         """
         args = ["bsub"]
-
-        if "reservation" in self._batch:
-            args += [
-                "-U",
-                self._batch["reservation"]
-            ]
-
         args += ["-cwd", cwd, "<", path]
         cmd = " ".join(args)
         LOGGER.debug("cwd = %s", cwd)