Give users more info and control over key run commands

scripts/Tools/preview_run

@@ -0,0 +1,63 @@
+#!/usr/bin/env python
+
+"""
+Script to query key CIME shell commands (mpirun and batch submission).
+
+To force a certain mpirun command, use:
+./xmlchange MPI_RUN_COMMAND $your_cmd
+
+To force a certain qsub command, use:
+./xmlchange --subgroup=case.run BATCH_COMMAND $your_cmd
+"""
+
+from standard_script_setup import *
+
+from CIME.case import Case
+
+###############################################################################
+def parse_command_line(args, description):
+###############################################################################
+    parser = argparse.ArgumentParser(
+        usage="""\n%s [--verbose]
+OR
+%s --help
+OR
+%s --test
+
+\033[1mEXAMPLES:\033[0m
+    \033[1;32m# Run the tool \033[0m
+    > %s
+""" % ((os.path.basename(args[0]), ) * 4),
+        description=description,
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter
+    )
+
+    parser.add_argument("caseroot", nargs="?", default=os.getcwd(),
+                        help="Case directory to build")
+
+    args = parser.parse_args(args[1:])
+
+    return args.caseroot
+
+###############################################################################
+def _main_func(description):
+###############################################################################
+    if "--test" in sys.argv:
+        test_results = doctest.testmod(verbose=True)
+        sys.exit(1 if test_results.failed > 0 else 0)
+
+    caseroot = parse_command_line(sys.argv, description)
+
+    logging.disable(logging.CRITICAL)
+
+    with Case(caseroot, read_only=False) as case:
+        print "BATCH SUBMIT:"
+        job = "case.test" if case.get_value("TEST") else "case.run"
+        job_id_to_cmd = case.submit_jobs(dry_run=True, job=job)
+        for job_id, cmd in job_id_to_cmd:
+            print "   ", job_id, "->", case.get_resolved_value(cmd)
+        print
+        print "MPIRUN:", case.get_resolved_value(case.get_mpirun_cmd())
+
+if __name__ == "__main__":
+    _main_func(__doc__)

scripts/lib/CIME/XML/env_batch.py

@@ -281,7 +281,7 @@ def get_submit_args(self, case, job):
 
         return submitargs
 
-    def submit_jobs(self, case, no_batch=False, job=None, batch_args=None):
+    def submit_jobs(self, case, no_batch=False, job=None, batch_args=None, dry_run=False):
         alljobs = self.get_jobs()
         startindex = 0
         jobs = []
@@ -299,16 +299,23 @@ def submit_jobs(self, case, no_batch=False, job=None, batch_args=None):
                 if prereq is None or job == firstjob:
                     prereq = True
                 else:
+                    if dry_run:
+                        # Assume build is complete
+                        prereq = prereq.replace("$BUILD_COMPLETE", "True")
                     prereq = case.get_resolved_value(prereq)
                     prereq = eval(prereq)
             except:
                 expect(False,"Unable to evaluate prereq expression '%s' for job '%s'"%(self.get_value('prereq',subgroup=job), job))
+
             if prereq:
-                jobs.append((job,self.get_value('dependency', subgroup=job)))
+                jobs.append((job, self.get_value('dependency', subgroup=job)))
+
             if self.batchtype == "cobalt":
                 break
 
         depid = {}
+        jobcmds = []
+
         for job, dependency in jobs:
             if dependency is not None:
                 deps = dependency.split()
@@ -331,16 +338,21 @@ def submit_jobs(self, case, no_batch=False, job=None, batch_args=None):
             if slen == 0:
                 jobid = None
 
-            logger.warn("job is %s"%job)
-            depid[job] = self.submit_single_job(case, job, jobid, no_batch=no_batch, batch_args=batch_args)
+            logger.warn("job is %s" % job)
+            result = self._submit_single_job(case, job, jobid, no_batch=no_batch, batch_args=batch_args, dry_run=dry_run)
+            batch_job_id = str(alljobs.index(job)) if dry_run else result
+            depid[job] = batch_job_id
+            jobcmds.append( (job, result) )
             if self.batchtype == "cobalt":
                 break
 
-        return sorted(list(depid.values()))
+        if dry_run:
+            return jobcmds
+        else:
+            return sorted(list(depid.values()))
 
-    def submit_single_job(self, case, job, depid=None, no_batch=False, batch_args=None):
+    def _submit_single_job(self, case, job, depid=None, no_batch=False, batch_args=None, dry_run=False):
         logger.warn("Submit job %s"%job)
-        caseroot = case.get_value("CASEROOT")
         batch_system = self.get_value("BATCH_SYSTEM", subgroup=None)
         if batch_system is None or batch_system == "none" or no_batch:
             # Import here to avoid circular include
@@ -351,20 +363,17 @@ def submit_single_job(self, case, job, depid=None, no_batch=False, batch_args=No
 
             logger.info("Starting job script %s" % job)
 
-            # Hack until all testcases are ported to python
-            testcase = case.get_value("TESTCASE")
-            cimeroot = get_cime_root()
-            testscript = os.path.join(cimeroot, "scripts", "Testing", "Testcases", "%s_script" % testcase)
-            if job == "case.test" and testcase is not None and os.path.exists(testscript):
-                run_cmd_no_fail("%s --caseroot %s" % (os.path.join(".", job), caseroot))
-            else:
-                # This is what we want longterm
+            function_name = job.replace(".", "_")
+            if not dry_run:
                 function_name = job.replace(".", "_")
                 locals()[function_name](case)
 
             return
 
         submitargs = self.get_submit_args(case, job)
+        args_override = self.get_value("BATCH_COMMAND", subgroup=job)
+        if args_override:
+            submitargs = args_override
 
         if depid is not None:
             dep_string = self.get_value("depend_string", subgroup=None)
@@ -383,11 +392,14 @@ def submit_single_job(self, case, job, depid=None, no_batch=False, batch_args=No
             if  string is not None:
                 submitcmd += string + " "
 
-        logger.info("Submitting job script %s"%submitcmd)
-        output = run_cmd_no_fail(submitcmd, combine_output=True)
-        jobid = self.get_job_id(output)
-        logger.info("Submitted job id is %s"%jobid)
-        return jobid
+        if dry_run:
+            return submitcmd
+        else:
+            logger.info("Submitting job script %s"%submitcmd)
+            output = run_cmd_no_fail(submitcmd, combine_output=True)
+            jobid = self.get_job_id(output)
+            logger.info("Submitted job id is %s"%jobid)
+            return jobid
 
     def get_batch_system_type(self):
         nodes = self.get_nodes("batch_system")
@@ -445,7 +457,7 @@ def get_all_queues(self):
 
     def get_nodes(self, nodename, attributes=None, root=None, xpath=None):
         if nodename in ("JOB_WALLCLOCK_TIME", "PROJECT", "PROJECT_REQUIRED",
-                        "JOB_QUEUE"):
+                        "JOB_QUEUE", "BATCH_COMMAND"):
             nodes = EnvBase.get_nodes(self, "entry", attributes={"id":nodename},
                                         root=root, xpath=xpath)
         else:

scripts/lib/CIME/case.py

@@ -862,6 +862,7 @@ def _create_caseroot_tools(self):
                      os.path.join(toolsdir, "lt_archive.sh"),
                      os.path.join(toolsdir, "getTiming"),
                      os.path.join(toolsdir, "save_provenance"),
+                     os.path.join(toolsdir, "preview_run"),
                      os.path.join(machines_dir,"Makefile"),
                      os.path.join(machines_dir,"mkSrcfiles"),
                      os.path.join(machines_dir,"mkDepends")]
@@ -1062,9 +1063,9 @@ def create_clone(self, newcase, keepexe=False, mach_dir=None, project=None, cime
 
         return newcase
 
-    def submit_jobs(self, no_batch=False, job=None, batch_args=None):
+    def submit_jobs(self, no_batch=False, job=None, batch_args=None, dry_run=False):
         env_batch = self.get_env('batch')
-        return env_batch.submit_jobs(self, no_batch=no_batch, job=job, batch_args=batch_args)
+        return env_batch.submit_jobs(self, no_batch=no_batch, job=job, batch_args=batch_args, dry_run=dry_run)
 
     def get_mpirun_cmd(self, job="case.run"):
         env_mach_specific = self.get_env('mach_specific')
@@ -1073,28 +1074,33 @@ def get_mpirun_cmd(self, job="case.run"):
         run_misc_suffix = "" if run_misc_suffix is None else run_misc_suffix
         run_suffix = run_exe + run_misc_suffix
 
-        # Things that will have to be matched against mpirun element attributes
-        mpi_attribs = {
-            "compiler" : self.get_value("COMPILER"),
-            "mpilib"   : self.get_value("MPILIB"),
-            "threaded" : self.get_build_threaded(),
-            "unit_testing" : False
-            }
-
-        executable, args = env_mach_specific.get_mpirun(self, mpi_attribs, job=job)
+        mpirun_cmd_override = self.get_value("MPI_RUN_COMMAND")
 
-        # special case for aprun
-        if executable == "aprun":
-            aprun_cmd, num_nodes = get_aprun_cmd_for_case(self, run_exe)
-            expect(num_nodes == self.num_nodes, "Not using optimized num nodes")
-            return aprun_cmd + " " + run_misc_suffix
+        if mpirun_cmd_override not in ["", None, "UNSET"]:
+            return mpirun_cmd_override + " " + run_exe + " " + run_misc_suffix
         else:
-            mpi_arg_string = " ".join(args.values())
+            # Things that will have to be matched against mpirun element attributes
+            mpi_attribs = {
+                "compiler" : self.get_value("COMPILER"),
+                "mpilib"   : self.get_value("MPILIB"),
+                "threaded" : self.get_build_threaded(),
+                "unit_testing" : False
+                }
+
+            executable, args = env_mach_specific.get_mpirun(self, mpi_attribs, job=job)
+
+            # special case for aprun
+            if executable == "aprun":
+                aprun_cmd, num_nodes = get_aprun_cmd_for_case(self, run_exe)
+                expect(num_nodes == self.num_nodes, "Not using optimized num nodes")
+                return aprun_cmd + " " + run_misc_suffix
+            else:
+                mpi_arg_string = " ".join(args.values())
 
-            if self.get_value("BATCH_SYSTEM") == "cobalt":
-                mpi_arg_string += " : "
+                if self.get_value("BATCH_SYSTEM") == "cobalt":
+                    mpi_arg_string += " : "
 
-            return "%s %s %s" % (executable if executable is not None else "", mpi_arg_string, run_suffix)
+                return "%s %s %s" % (executable if executable is not None else "", mpi_arg_string, run_suffix)
 
     def set_model_version(self, model):
         version = "unknown"

scripts/lib/CIME/case_setup.py

@@ -165,10 +165,7 @@ def _case_setup_impl(case, caseroot, clean=False, test_mode=False, reset=False,
                 input_batch_script  = os.path.join(case.get_value("MACHDIR"), env_batch.get_value('template', subgroup=job))
                 if job == "case.test" and testcase is not None and not test_mode:
                     logger.info("Writing %s script" % job)
-                    testscript = os.path.join(cimeroot, "scripts", "Testing", "Testcases", "%s_script" % testcase)
-                    # Short term fix to be removed when csh tests are removed
-                    if not os.path.exists(testscript):
-                        env_batch.make_batch_script(input_batch_script, job, case, pestot, tasks_per_node, num_nodes, thread_count)
+                    env_batch.make_batch_script(input_batch_script, job, case, pestot, tasks_per_node, num_nodes, thread_count)
                 elif job != "case.test":
                     logger.info("Writing %s script from input template %s" % (job, input_batch_script))
                     env_batch.make_batch_script(input_batch_script, job, case, pestot, tasks_per_node, num_nodes, thread_count)
@@ -203,14 +200,6 @@ def _case_setup_impl(case, caseroot, clean=False, test_mode=False, reset=False,
 
         logger.info("If an old case build already exists, might want to run \'case.build --clean\' before building")
 
-        # Create test script if appropriate
-        # Short term fix to be removed when csh tests are removed
-        if os.path.exists("env_test.xml"):
-            if not os.path.exists("case.test"):
-                logger.info("Starting testcase.setup")
-                run_cmd_no_fail("./testcase.setup -caseroot %s" % caseroot)
-                logger.info("Finished testcase.setup")
-
         # Some tests need namelists created here (ERP) - so do this if are in test mode
         if test_mode or get_model() == "acme":
             logger.info("Generating component namelists as part of setup")

scripts/lib/CIME/utils.py

@@ -259,7 +259,7 @@ def run_cmd_no_fail(cmd, input_str=None, from_dir=None, verbose=None,
     if stat != 0:
         # If command produced no errput, put output in the exception since we
         # have nothing else to go on.
-        errput = output if errput == "" else errput
+        errput = output if not errput else errput
         expect(False, "Command: '%s' failed with error '%s'%s" %
                (cmd, errput, "" if from_dir is None else " from dir '%s'" % from_dir))
 
@@ -1172,7 +1172,7 @@ def run_and_log_case_status(func, phase, caseroot='.'):
     try:
         rv = func()
     except:
-        e = sys.exc_info()[0]
+        e = sys.exc_info()[1]
         append_case_status(phase, "error", msg=("\n%s" % e), caseroot=caseroot)
         raise
     else:

src/drivers/mct/cime_config/config_component.xml

@@ -1899,7 +1899,7 @@
     <default_value>UNSET</default_value>
     <group>run_mpi</group>
     <file>env_run.xml</file>
-    <desc>mpi run command</desc>
+    <desc>override the mpi run command, do not include model executable</desc>
   </entry>
 
   <!-- ===================================================================== -->
@@ -2602,6 +2602,15 @@
    <desc>The machine wallclock setting.  Default determined in config_machines.xml can be overwritten by testing</desc>
  </entry>
 
+  <entry id="BATCH_COMMAND">
+    <type>char</type>
+    <valid_values></valid_values>
+    <default_value></default_value>
+    <group>job_submission</group>
+    <file>env_batch.xml</file>
+    <desc>Override the batch submit command this job. Do not include executable or dependencies</desc>
+  </entry>
+
  <entry id="PROJECT">
    <type>char</type>
    <default_value></default_value>