Merge pull request #268 from jedwards4b/pbs_fixes

This commit brings the following changes, * Fixes required for the PBS job scheduler * Fixes to get CIME working on Blues * Minor change to the commit template * Fixes to get gptl timing working on blues * A fix to use compiler as an attribute when selecting mpilib in bless_test_results scripts_regression_tests Test suite: Test baseline: Test namelist changes: Test status: bit for bit Fixes #265 Fixes #266 User interface changes?: Code review: jayesh
CESM-Development · Jul 19, 2016 · 300cdce · 300cdce
2 parents 9a4db4d + aa193c7
commit 300cdce
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Showing 15 changed files with 26 additions and 46 deletions.
diff --git a/.github/PULL_REQUEST_TEMPLATE b/.github/PULL_REQUEST_TEMPLATE
@@ -7,7 +7,7 @@ Test baseline:
 Test namelist changes: 
 Test status: [bit for bit, roundoff, climate changing]
 
-Fixes: [CIME Github issue #]
+Fixes [CIME Github issue #]
 
 User interface changes?: 
 

diff --git a/cime_config/acme/machines/config_batch.xml b/cime_config/acme/machines/config_batch.xml
@@ -87,6 +87,7 @@
       <arg flag="-A" name="PROJECT"/>
     </submit_args>
     <directives>
+      <directive> -V </directive>
       <directive> -N {{ job_id }}</directive>
       <directive default="n"> -r {{ rerunnable }} </directive>
       <!-- <directive> -j oe {{ output_error_path }} </directive> -->

diff --git a/cime_config/acme/machines/config_compilers.xml b/cime_config/acme/machines/config_compilers.xml
@@ -928,6 +928,7 @@ for mct, etc.
   <MPI_PATH MPILIB="mvapich">/blues/gpfs/home/software/spack/opt/spack/linux-x86_64/gcc-5.3.0/mvapich2-2.2b-sdh7nhddicl4sh5mgxjyzxtxox3ajqey</MPI_PATH>
   <MPI_LIB_NAME MPILIB="mvapich">mpi</MPI_LIB_NAME>
   <ADD_SLIBS>$(shell $(NETCDF_PATH)/bin/nc-config --flibs) -llapack -lblas</ADD_SLIBS>
+  <GPTL_CPPDEFS> -DHAVE_NANOTIME -DBIT64 -DHAVE_SLASHPROC -DHAVE_GETTIMEOFDAY</GPTL_CPPDEFS>
   <PIO_FILESYSTEM_HINTS>gpfs </PIO_FILESYSTEM_HINTS>
 </compiler>
 

diff --git a/cime_config/acme/machines/config_machines.xml b/cime_config/acme/machines/config_machines.xml
@@ -589,11 +589,12 @@
 
 <machine MACH="blues">
          <DESC>ANL/LCRC Linux Cluster</DESC>
-         <NODENAME_REGEX>(blogin|^b\d)</NODENAME_REGEX>
+         <NODENAME_REGEX>b.*.lcrc.anl.gov</NODENAME_REGEX>
          <TESTS>acme_integration</TESTS>
          <COMPILERS>gnu,pgi,intel,nag</COMPILERS>
          <MPILIBS>mvapich,mpich,openmpi,mpi-serial</MPILIBS>
          <CESMSCRATCHROOT>/lcrc/project/$PROJECT/$USER/acme_scratch</CESMSCRATCHROOT>
+	 <SAVE_TIMING_DIR>/lcrc/project/$PROJECT</SAVE_TIMING_DIR>
 	 <RUNDIR>$CESMSCRATCHROOT/$CASE/run</RUNDIR>
 	 <EXEROOT>$CESMSCRATCHROOT/$CASE/bld</EXEROOT>
          <DIN_LOC_ROOT>/home/ccsm-data/inputdata</DIN_LOC_ROOT>

diff --git a/cime_config/acme/machines/template.case.run b/cime_config/acme/machines/template.case.run
@@ -7,12 +7,9 @@ batch directives. Use case.submit from the command line to run your case.
 """
 
 import os, sys
+os.chdir( '{{ caseroot }}')
 
-_CIMEROOT = os.environ.get("CIMEROOT")
-if _CIMEROOT is None:
-    raise SystemExit("ERROR: must set CIMEROOT environment variable")
-
-_LIBDIR = os.path.join(_CIMEROOT, "scripts", "Tools")
+_LIBDIR = os.path.join("{{ cimeroot }}", "scripts", "Tools")
 sys.path.append(_LIBDIR)
 
 from standard_script_setup          import *

diff --git a/cime_config/acme/machines/template.case.test b/cime_config/acme/machines/template.case.test
@@ -6,12 +6,9 @@ by case.submit when on batch system. This script only exists as a way of providi
 batch directives. Use case.submit from the command line to run your case.
 """
 import os, sys
+os.chdir( '{{ caseroot }}')
 
-_CIMEROOT = os.environ.get("CIMEROOT")
-if _CIMEROOT is None:
-    raise SystemExit("ERROR: must set CIMEROOT environment variable")
-
-_LIBDIR = os.path.join(_CIMEROOT, "scripts", "Tools")
+_LIBDIR = os.path.join("{{ cimeroot }}", "scripts", "Tools")
 sys.path.append(_LIBDIR)
 
 from standard_script_setup import *

diff --git a/cime_config/acme/machines/template.lt_archive b/cime_config/acme/machines/template.lt_archive
@@ -8,11 +8,9 @@ batch directives. Use case.submit from the command line to run your case.
 
 import sys
 import os
-_CIMEROOT = os.environ.get("CIMEROOT")
-if _CIMEROOT is None:
-    raise SystemExit("ERROR: must set CIMEROOT environment variable")
+os.chdir( '{{ caseroot }}' )
 
-_LIBDIR = os.path.join(_CIMEROOT, "scripts", "Tools")
+_LIBDIR = os.path.join("{{ cimeroot }}", "scripts", "Tools")
 sys.path.append(_LIBDIR)
 
 from standard_script_setup          import *

diff --git a/cime_config/acme/machines/template.st_archive b/cime_config/acme/machines/template.st_archive
@@ -7,11 +7,9 @@ batch directives. Use case.submit from the command line to run your case.
 """
 
 import sys, os, time
-_CIMEROOT = os.environ.get("CIMEROOT")
-if _CIMEROOT is None:
-    raise SystemExit("ERROR: must set CIMEROOT environment variable")
+os.chdir( '{{ caseroot }}')
 
-_LIBDIR = os.path.join(_CIMEROOT, "scripts", "Tools")
+_LIBDIR = os.path.join("{{ cimeroot }}", "scripts", "Tools")
 sys.path.append(_LIBDIR)
 
 from standard_script_setup          import *

diff --git a/cime_config/cesm/machines/template.case.run b/cime_config/cesm/machines/template.case.run
@@ -7,12 +7,9 @@ batch directives. Use case.submit from the command line to run your case.
 """
 
 import os, sys
+os.chdir( '{{ caseroot }}')
 
-_CIMEROOT = os.environ.get("CIMEROOT")
-if _CIMEROOT is None:
-    raise SystemExit("ERROR: must set CIMEROOT environment variable")
-
-_LIBDIR = os.path.join(_CIMEROOT, "scripts", "Tools")
+_LIBDIR = os.path.join("{{ cimeroot }}", "scripts", "Tools")
 sys.path.append(_LIBDIR)
 
 from standard_script_setup          import *

diff --git a/cime_config/cesm/machines/template.case.test b/cime_config/cesm/machines/template.case.test
@@ -6,12 +6,9 @@ by case.submit when on batch system. This script only exists as a way of providi
 batch directives. Use case.submit from the command line to run your case.
 """
 import os, sys
+os.chdir( '{{ caseroot }}')
 
-_CIMEROOT = os.environ.get("CIMEROOT")
-if _CIMEROOT is None:
-    raise SystemExit("ERROR: must set CIMEROOT environment variable")
-
-_LIBDIR = os.path.join(_CIMEROOT, "scripts", "Tools")
+_LIBDIR = os.path.join("{{ cimeroot }}", "scripts", "Tools")
 sys.path.append(_LIBDIR)
 
 from standard_script_setup import *

diff --git a/cime_config/cesm/machines/template.lt_archive b/cime_config/cesm/machines/template.lt_archive
@@ -8,11 +8,9 @@ batch directives. Use case.submit from the command line to run your case.
 
 import sys
 import os
-_CIMEROOT = os.environ.get("CIMEROOT")
-if _CIMEROOT is None:
-    raise SystemExit("ERROR: must set CIMEROOT environment variable")
+os.chdir( '{{ caseroot }}' )
 
-_LIBDIR = os.path.join(_CIMEROOT, "scripts", "Tools")
+_LIBDIR = os.path.join("{{ cimeroot }}", "scripts", "Tools")
 sys.path.append(_LIBDIR)
 
 from standard_script_setup          import *

diff --git a/cime_config/cesm/machines/template.st_archive b/cime_config/cesm/machines/template.st_archive
@@ -7,11 +7,9 @@ batch directives. Use case.submit from the command line to run your case.
 """
 
 import sys, os, time
-_CIMEROOT = os.environ.get("CIMEROOT")
-if _CIMEROOT is None:
-    raise SystemExit("ERROR: must set CIMEROOT environment variable")
+os.chdir( '{{ caseroot }}')
 
-_LIBDIR = os.path.join(_CIMEROOT, "scripts", "Tools")
+_LIBDIR = os.path.join("{{ cimeroot }}", "scripts", "Tools")
 sys.path.append(_LIBDIR)
 
 from standard_script_setup          import *
@@ -61,7 +59,6 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
 ###############################################################################
 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)

diff --git a/scripts/Tools/bless_test_results b/scripts/Tools/bless_test_results
@@ -179,8 +179,9 @@ def bless_test_results(baseline_name, test_root, compiler, test_id=None, namelis
     baseline_area = os.path.join(baseline_root, baseline_tag)
 
     # The env_mach_specific script may need these to be defined
-    os.environ["COMPILER"] = _MACHINE.get_default_compiler() # this MUST match compiler that cprnc was built with
-    os.environ["MPILIB"] = _MACHINE.get_default_MPIlib()
+    compiler = _MACHINE.get_default_compiler() # this MUST match compiler that cprnc was built with
+    os.environ["COMPILER"]  = compiler
+    os.environ["MPILIB"] = _MACHINE.get_default_MPIlib(attributes={"compiler":compiler})
 
     broken_blesses = []
     for test_status_file in test_status_files:

diff --git a/utils/python/CIME/XML/env_batch.py b/utils/python/CIME/XML/env_batch.py
@@ -420,9 +420,6 @@ def submit_single_job(self, case, job, depid=None, no_batch=False):
             if  string is not None:
                 submitcmd += string + " "
 
-        if self.batchtype == "pbs":
-            submitcmd += " -F \"--caseroot %s\""%caseroot
-
         logger.info("Submitting job script %s"%submitcmd)
         output = run_cmd(submitcmd)
         jobid = self.get_job_id(output)

diff --git a/utils/python/CIME/case_run.py b/utils/python/CIME/case_run.py
@@ -156,10 +156,10 @@ def save_timing_setup_acme(case, lid):
         return
 
     timing_dir = case.get_value("SAVE_TIMING_DIR")
-    if timing_dir is None:
+    if timing_dir is None or timing_dir == 'UNSET':
         logger.warning("ACME requires SAVE_TIMING_DIR to be set in order to save timings. Skipping save timings")
         return
-
+    logger.warn("timing dir is %s"%timing_dir)
     rundir = case.get_value("RUNDIR")
     caseroot = case.get_value("CASEROOT")
     cimeroot = case.get_value("CIMEROOT")