Implements the prereq argument for case.submit, allowing the user to …

…specify jobs which should finish (not necessarily successfully) before running the current job

scripts/Tools/case.submit

@@ -61,24 +61,23 @@ OR
 
     args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
-    CIME.utils.expect(args.prereq is None, "--prereq not currently supported")
-
-    return args.test, args.caseroot, args.job, args.no_batch, args.resubmit, \
-        args.skip_preview_namelist, args.mail_user, args.mail_type, \
+    return args.test, args.caseroot, args.job, args.no_batch, args.prereq, \
+        args.resubmit, args.skip_preview_namelist, args.mail_user, args.mail_type, \
         args.batch_args
 
 ###############################################################################
 def _main_func(description):
 ###############################################################################
-    test, caseroot, job, no_batch, resubmit, skip_pnl, \
+    test, caseroot, job, no_batch, prereq, resubmit, skip_pnl, \
         mail_user, mail_type, batch_args = parse_command_line(sys.argv, description)
     if test:
         test_results = doctest.testmod(verbose=True)
         sys.exit(1 if test_results.failed > 0 else 0)
 
     with Case(caseroot, read_only=False) as case:
-        submit(case, job=job, no_batch=no_batch, resubmit=resubmit, skip_pnl=skip_pnl,
-               mail_user=mail_user, mail_type=mail_type, batch_args=batch_args)
+        submit(case, job=job, no_batch=no_batch, prereq=prereq, resubmit=resubmit,
+               skip_pnl=skip_pnl, mail_user=mail_user, mail_type=mail_type,
+               batch_args=batch_args)
 
 if __name__ == "__main__":
     _main_func(__doc__)

scripts/lib/CIME/XML/env_batch.py

@@ -20,7 +20,6 @@ def __init__(self, case_root=None, infile="env_batch.xml"):
         """
         initialize an object interface to file env_batch.xml in the case directory
         """
-        self.prereq_jobid = None
         self.batchtype = None
         # This arbitrary setting should always be overwritten
         self._default_walltime = "00:20:00"
@@ -319,9 +318,9 @@ def get_submit_args(self, case, job):
 
         return submitargs
 
-    def submit_jobs(self, case, no_batch=False, job=None, skip_pnl=False,
-                    mail_user=None, mail_type='never', batch_args=None,
-                    dry_run=False):
+    def submit_jobs(self, case, no_batch=False, job=None, user_prereq=None,
+                    skip_pnl=False, mail_user=None, mail_type='never',
+                    batch_args=None, dry_run=False):
         alljobs = self.get_jobs()
         startindex = 0
         jobs = []
@@ -358,25 +357,16 @@ def submit_jobs(self, case, no_batch=False, job=None, skip_pnl=False,
                 deps = dependency.split()
             else:
                 deps = []
-            jobid = ""
-            if self.prereq_jobid is not None:
-                jobid = self.prereq_jobid
+            dep_jobs = []
+            if user_prereq is not None:
+                dep_jobs.append(user_prereq)
             for dep in deps:
                 if dep in depid.keys() and depid[dep] is not None:
-                    jobid += " " + str(depid[dep])
-#TODO: doubt these will be used
-#               elif dep == "and":
-#                   jobid += " && "
-#               elif dep == "or":
-#                   jobid += " || "
+                    dep_jobs.append(str(depid[dep]))
 
-
-            slen = len(jobid)
-            if slen == 0:
-                jobid = None
-
-            logger.warn("job is {}".format(job))
-            result = self._submit_single_job(case, job, jobid,
+            logger.info("job {} depends on {}".format(job, dep_jobs))
+            result = self._submit_single_job(case, job,
+                                             dep_jobs=dep_jobs,
                                              no_batch=no_batch,
                                              skip_pnl=skip_pnl,
                                              mail_user=mail_user,
@@ -394,7 +384,7 @@ def submit_jobs(self, case, no_batch=False, job=None, skip_pnl=False,
         else:
             return sorted(list(depid.values()))
 
-    def _submit_single_job(self, case, job, depid=None, no_batch=False,
+    def _submit_single_job(self, case, job, dep_jobs=None, no_batch=False,
                            skip_pnl=False, mail_user=None, mail_type='never',
                            batch_args=None, dry_run=False):
         logger.warn("Submit job {}".format(job))
@@ -418,9 +408,15 @@ def _submit_single_job(self, case, job, depid=None, no_batch=False,
         if args_override:
             submitargs = args_override
 
-        if depid is not None:
+        if dep_jobs is not None and len(dep_jobs) > 0:
+            logger.info("dependencies: {}".format(dep_jobs))
             dep_string = self.get_value("depend_string", subgroup=None)
-            dep_string = dep_string.replace("jobid",depid.strip()) # pylint: disable=maybe-no-member
+            separator_string = self.get_value("depend_separator", subgroup=None)
+            expect("jobid" in dep_string, "depend_string is missing jobid for prerequisite jobs")
+            dep_ids_str = str(dep_jobs[0])
+            for dep_id in dep_jobs[1:]:
+                dep_ids_str += separator_string + str(dep_id)
+            dep_string = dep_string.replace("jobid",dep_ids_str.strip()) # pylint: disable=maybe-no-member
             submitargs += " " + dep_string
 
         if batch_args is not None:

scripts/lib/CIME/case.py

@@ -1236,11 +1236,11 @@ def create_clone(self, newcase, keepexe=False, mach_dir=None, project=None, cime
 
         return newcase
 
-    def submit_jobs(self, no_batch=False, job=None, skip_pnl=False,
+    def submit_jobs(self, no_batch=False, job=None, prereq=None, skip_pnl=False,
                     mail_user=None, mail_type='never', batch_args=None,
                     dry_run=False):
         env_batch = self.get_env('batch')
-        return env_batch.submit_jobs(self, no_batch=no_batch, job=job,
+        return env_batch.submit_jobs(self, no_batch=no_batch, job=job, user_prereq=prereq,
                                      skip_pnl=skip_pnl, mail_user=mail_user,
                                      mail_type=mail_type, batch_args=batch_args,
                                      dry_run=dry_run)

scripts/lib/CIME/case_submit.py

@@ -15,8 +15,8 @@
 
 logger = logging.getLogger(__name__)
 
-def _submit(case, job=None, resubmit=False, no_batch=False, skip_pnl=False,
-            mail_user=None, mail_type='never', batch_args=None):
+def _submit(case, job=None, no_batch=False, prereq=None, resubmit=False,
+            skip_pnl=False, mail_user=None, mail_type='never', batch_args=None):
     caseroot = case.get_value("CASEROOT")
 
     if job is None:
@@ -65,13 +65,13 @@ def _submit(case, job=None, resubmit=False, no_batch=False, skip_pnl=False,
     case.flush()
 
     logger.warn("submit_jobs {}".format(job))
-    job_ids = case.submit_jobs(no_batch=no_batch, job=job, skip_pnl=skip_pnl,
-                               mail_user=mail_user, mail_type=mail_type,
-                               batch_args=batch_args)
+    job_ids = case.submit_jobs(no_batch=no_batch, job=job, prereq=prereq,
+                               skip_pnl=skip_pnl, mail_user=mail_user,
+                               mail_type=mail_type, batch_args=batch_args)
     logger.info("Submitted job ids {}".format(job_ids))
 
-def submit(case, job=None, resubmit=False, no_batch=False, skip_pnl=False,
-           mail_user=None, mail_type='never', batch_args=None):
+def submit(case, job=None, no_batch=False, prereq=None, resubmit=False,
+           skip_pnl=False, mail_user=None, mail_type='never', batch_args=None):
     if case.get_value("TEST"):
         caseroot = case.get_value("CASEROOT")
         casebaseid = case.get_value("CASEBASEID")
@@ -86,8 +86,10 @@ def submit(case, job=None, resubmit=False, no_batch=False, skip_pnl=False,
                 ts.set_status(SUBMIT_PHASE, TEST_PASS_STATUS)
 
     try:
-        functor = lambda: _submit(case, job, resubmit, no_batch, skip_pnl,
-                                  mail_user, mail_type, batch_args)
+        functor = lambda: _submit(case, job=job, no_batch=no_batch, prereq=prereq,
+                                  resubmit=resubmit, skip_pnl=skip_pnl,
+                                  mail_user=mail_user, mail_type=mail_type,
+                                  batch_args=batch_args)
         run_and_log_case_status(functor, "case.submit", caseroot=case.get_value("CASEROOT"))
     except:
         # If something failed in the batch system, make sure to mark