Merge branch 'dev_issue811'

Bounds assertion for C isotopes when threading is on Previously, the bounds of c13 and c14 in subroutines TruncateCStates and TruncateCandNStates were not checked when threading was on. This PR allows us to handle c13 and c14 arrays like everything else in CTSM including (bounds checking). This PR resolves issue ESCOMP#811
billsacks · Feb 20, 2020 · 95fc9e1 · 95fc9e1
2 parents 5cc4ede + ece16d8
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diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
@@ -432,7 +432,7 @@
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
-      <option name="wallclock">0:20:00</option>
+      <option name="wallclock">00:20:00</option>
       <option name="comment"  >Do a test with RTM and flooding on as that also impacts CLM code</option>
     </options>
   </test>
@@ -740,7 +740,7 @@
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm">
         <options>
-          <option name="wallclock">0:30:00</option>
+          <option name="wallclock">00:30:00</option>
           <option name="comment">Want an ERP test covering some non-default irrigation options. Long enough so that we're likely to exercise the various groundwater irrigation code.</option>
         </options>
       </machine>
@@ -1646,7 +1646,7 @@
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm">
         <options>
-          <option name="wallclock">0:20:00</option>
+          <option name="wallclock">00:20:00</option>
           <option name="comment">Debug test covering some non-default irrigation options.</option>
         </options>
       </machine>
@@ -1657,7 +1657,7 @@
 
       <machine name="izumi" compiler="intel" category="aux_clm">
         <options>
-          <option name="wallclock">0:30:00</option>
+          <option name="wallclock">00:30:00</option>
           <option name="comment">Include a tracer consistency check in debug mode.</option>
         </options>
       </machine>
@@ -1669,7 +1669,7 @@
 
       <machine name="cheyenne" compiler="intel" category="aux_clm">
         <options>
-          <option name="wallclock">0:30:00</option>
+          <option name="wallclock">00:30:00</option>
           <option name="comment">A debug ERP test of the NWP configuration with active BGC and CROP.</option>
         </options>
       </machine>
@@ -1680,7 +1680,7 @@
     <machines>
       <machine name="cheyenne" compiler="gnu" category="aux_clm">
         <options>
-          <option name="wallclock">0:30:00</option>
+          <option name="wallclock">00:30:00</option>
           <option name="comment">Ensure that turning on water tracers doesn't change answers. Cold start for now, until we can use initial conditions from a non-isotope case in an isotope case; once we can do that, this should be changed to not be cold start (e.g., 5-day decStart transient test: see also https://github.com/ESCOMP/ctsm/issues/495#issuecomment-516619853).</option>
         </options>
       </machine>
@@ -1691,7 +1691,7 @@
 
       <machine name="cheyenne" compiler="intel" category="aux_clm">
         <options>
-          <option name="wallclock">0:30:00</option>
+          <option name="wallclock">00:30:00</option>
           <option name="comment">Include a debug ERP test of the NWP configuration.</option>
         </options>
       </machine>
@@ -1703,7 +1703,7 @@
 
       <machine name="cheyenne" compiler="gnu" category="aux_clm">
         <options>
-          <option name="wallclock">0:30:00</option>
+          <option name="wallclock">00:30:00</option>
           <option name="comment">Include a short smoke test covering the nldas2 grid and the I2000Ctsm50NwpSpNldasGs compset, which uses NLDAS datm forcing.</option>
         </options>
       </machine>
@@ -1715,7 +1715,7 @@
 
       <machine name="cheyenne" compiler="gnu" category="aux_clm">
         <options>
-          <option name="wallclock">0:30:00</option>
+          <option name="wallclock">00:30:00</option>
           <option name="comment">Include a short smoke test covering the nldas2 grid and the I2000Ctsm50NwpSpNldasRsGs compset, which uses NLDAS datm forcing.</option>
         </options>
       </machine>
@@ -1900,7 +1900,7 @@
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm">
         <options>
-          <option name="wallclock">0:30:00</option>
+          <option name="wallclock">00:30:00</option>
           <option name="comment">Include a test of the NUOPC cap</option>
         </options>
       </machine>
@@ -1910,7 +1910,7 @@
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm">
         <options>
-          <option name="wallclock">0:30:00</option>
+          <option name="wallclock">00:30:00</option>
           <option name="comment">Can use this test to determine if there are significant throughput changes, at least for this common and important configuration. Note that this deliberately doesn't have any testmods in order to (1) avoid doing history output (because the timing of output can be very variable, and mixing output timing with other aspects of model time can be confusing), and (2) generally keep the test replicating a production configuration as closely as possible (so, for example, we do NOT set BFBFLAG=TRUE for this test).</option>
         </options>
       </machine>
@@ -1920,7 +1920,7 @@
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm">
         <options>
-          <option name="wallclock">0:30:00</option>
+          <option name="wallclock">00:30:00</option>
           <option name="comment">This test runs CTSM's Fortran unit tests. We're abusing the system test infrastructure to run these, so that a run of the test suite results in the unit tests being run as well. Grid and compset are irrelevant here, except that compset must be one that includes CTSM in order for CIME to find the test definition.</option>
         </options>
       </machine>

diff --git a/doc/ChangeLog b/doc/ChangeLog
@@ -1,4 +1,109 @@
 ===============================================================
+Tag name:  ctsm1.0.dev084
+Originator(s):  negins (Negin Sobhani,UCAR/CSEG,303-497-1224)
+Date: Wed Feb 19 15:05:03 MST 2020
+One-line Summary: Bounds assertion for C isotopes when threading is on
+
+Purpose of changes
+------------------
+
+Previously, the bounds of c13 and c14 in subroutines TruncateCStates and
+TruncateCandNStates were not checked when threading was on. This PR allows us
+to handle c13 and c14 arrays like everything else in CTSM including (bounds
+checking).
+
+This PR resolves issue ESCOMP/ctsm#811
+
+
+Bugs fixed or introduced
+------------------------
+
+Issues fixed (include CTSM Issue #):
+	-ESCOMP/ctsm#811
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions): none
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none
+
+Changes made to namelist defaults (e.g., changed parameter values): none
+
+Changes to the datasets (e.g., parameter, surface or initial files): none
+
+Substantial timing or memory changes: none
+
+Notes of particular relevance for developers: (including Code reviews and testing)
+---------------------------------------------
+NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance): none
+
+Changes to tests or testing: 
+	- There was an issue (wrong wallclock time ) for one of the tests in the test
+	  definitions which got fixed:  (SMS_D_Vnuopc.f10_f10_musgs.I2000Clm50SpRsGs..)
+	- Also, I tried making the wallclocktime for all tests in
+	  cime_config/testdefs/testlist_clm.xml consistent in the format of hh:mm:ss. 
+
+Code reviewed by: Bill Sacks
+
+
+CTSM testing:
+
+ [PASS means all tests PASS and OK means tests PASS other than expected fails.]
+
+  build-namelist tests:
+
+    cheyenne - not run 
+
+  tools-tests (test/tools):
+
+    cheyenne - not run 
+
+  PTCLM testing (tools/shared/PTCLM/test):
+
+    cheyenne - not run 
+
+  python testing (see instructions in python/README.md; document testing done):
+
+    (any machine) - not run 
+
+  regular tests (aux_clm):
+
+    cheyenne ---- OK 
+    izumi ------- PASS
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: NO
+
+Detailed list of changes
+------------------------
+
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/CTSM/pull/923)
+
+===============================================================
+===============================================================
 Tag name:  ctsm1.0.dev083
 Originator(s):  negins (Negin Sobhani,UCAR/CSEG,303-497-1224)
 Date: Thu Feb  6 12:12:26 MST 2020

diff --git a/doc/ChangeSum b/doc/ChangeSum
@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+  ctsm1.0.dev084   negins 02/19/2020 Bounds assertion for C isotopes when threading is on
   ctsm1.0.dev083   negins 02/06/2020 Some BFB Fixes: Resolve issues #683, # 874, #878, # 885, # 745, #838
   ctsm1.0.dev082   oleson 02/01/2020 Rename variables to avoid confusion; fix QSNOEVAP diagnostic
   ctsm1.0.dev081   slevis 01/13/2020 Speed up restart writes