<p><b>dwj07@fsu.edu</b> 2011-12-16 15:44:19 -0700 (Fri, 16 Dec 2011)</p><p><br>
        -- BRANCH COMMIT --<br>
<br>
        Fixing some small bugs related to testing on hopper.<br>
</p><hr noshade><pre><font color="gray">Modified: branches/ocean_projects/ocean_test_cases_staging/ocean/hopper_submit_template.sh
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/hopper_submit_template.sh        2011-12-16 17:44:03 UTC (rev 1259)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/hopper_submit_template.sh        2011-12-16 22:44:19 UTC (rev 1260)
@@ -3,8 +3,6 @@
 #PBS -q regular 
 #PBS -l walltime=20:00
 #PBS -l mppwidth=num_procs 
-#PBD -o stdout.out
-#PBD -e stderr.err
 cd  working_dir
 
-aprun -n num_procs ocean_model_executable
+aprun -n num_procs ocean_model.exe

Modified: branches/ocean_projects/ocean_test_cases_staging/ocean/lobo_submit_template.sh
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/lobo_submit_template.sh        2011-12-16 17:44:03 UTC (rev 1259)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/lobo_submit_template.sh        2011-12-16 22:44:19 UTC (rev 1260)
@@ -3,7 +3,5 @@
 #MSUB -l walltime=20:00
 #MSUB -l nodes=num_nodes:ppn=procs_per_node
 #MSUB -d working_dir
-#MSUB -o stdout.out
-#MSUB -e stderr.err
 
 mpirun -np num_procs ./ocean_model.exe

Modified: branches/ocean_projects/ocean_test_cases_staging/ocean/oceanTestCases.sh
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/oceanTestCases.sh        2011-12-16 17:44:03 UTC (rev 1259)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/oceanTestCases.sh        2011-12-16 22:44:19 UTC (rev 1260)
@@ -174,7 +174,7 @@
                 ## Get final kinetic energy, total run time, and run duration
                 ## from run directory
                 KE=`cat ${RUN}/stats_max.txt | tail -n 1 | awk '{print $7}'`
-                TIME=`grep &quot;total time&quot; ${RUN}/stdout.out | awk '{print $4}' | head -n 1`
+                TIME=`grep &quot;total time&quot; ${RUN}/log.0000.out | awk '{print $4}' | head -n 1`
                 DURATION=`grep &quot;config_run_duration&quot; ${RUN}/namelist.input`
 
                 ## Determine spacing in kilometers
@@ -242,7 +242,7 @@
 fi
 
 ## Check to see if pmetis is in path, as it is supposed to be. If not exit
-which pmets 1&gt; /dev/null 2&gt; err
+which pmetis 1&gt; /dev/null 2&gt; err
 PMETIS_CHECK=`grep &quot;no pmetis in&quot; err`
 rm err
 

Modified: branches/ocean_projects/ocean_test_cases_staging/ocean/overflow/basin_src/basin-template.F
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/overflow/basin_src/basin-template.F        2011-12-16 17:44:03 UTC (rev 1259)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/overflow/basin_src/basin-template.F        2011-12-16 22:44:19 UTC (rev 1260)
@@ -977,8 +977,8 @@
     kmt = nVertLevelsMOD
 
     do iCell = 1,nCells
-      levels = tanh((40000-yCell(iCell))/6000)*(nVertLevelsMOD*(3.0/8.0)) + (nVertLevelsMOD*(3.0/8.0))
-      levels = tanh((40000-yCell(iCell))/3000)*(nVertLevelsMOD*(3.0/8.0)) + (nVertLevelsMOD*(3.0/8.0))
+      levels = tanh((30000-yCell(iCell))/6000)*(nVertLevelsMOD*(3.0/8.0)) + (nVertLevelsMOD*(3.0/8.0))
+      levels = tanh((30000-yCell(iCell))/3000)*(nVertLevelsMOD*(3.0/8.0)) + (nVertLevelsMOD*(3.0/8.0))
 
       kmt(iCell) = nVertLevelsMOD - levels
     enddo

Modified: branches/ocean_projects/ocean_test_cases_staging/ocean/overflow/basin_src/basin.F
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/overflow/basin_src/basin.F        2011-12-16 17:44:03 UTC (rev 1259)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/overflow/basin_src/basin.F        2011-12-16 22:44:19 UTC (rev 1260)
@@ -61,7 +61,7 @@
 real, dimension(40) :: dz
 
 ! Step 1: Set the number of Vertical levels
-integer, parameter :: nVertLevelsMOD = 50
+integer, parameter :: nVertLevelsMOD = 100
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 ! basin-mod
@@ -977,8 +977,8 @@
     kmt = nVertLevelsMOD
 
     do iCell = 1,nCells
-      levels = tanh((40000-yCell(iCell))/6000)*(nVertLevelsMOD*(3.0/8.0)) + (nVertLevelsMOD*(3.0/8.0))
-      levels = tanh((40000-yCell(iCell))/3000)*(nVertLevelsMOD*(3.0/8.0)) + (nVertLevelsMOD*(3.0/8.0))
+      levels = tanh((30000-yCell(iCell))/6000)*(nVertLevelsMOD*(3.0/8.0)) + (nVertLevelsMOD*(3.0/8.0))
+      levels = tanh((30000-yCell(iCell))/3000)*(nVertLevelsMOD*(3.0/8.0)) + (nVertLevelsMOD*(3.0/8.0))
 
       kmt(iCell) = nVertLevelsMOD - levels
     enddo

Modified: branches/ocean_projects/ocean_test_cases_staging/ocean/overflow/makeMeshes.sh
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/overflow/makeMeshes.sh        2011-12-16 17:44:03 UTC (rev 1259)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/overflow/makeMeshes.sh        2011-12-16 22:44:19 UTC (rev 1260)
@@ -7,7 +7,7 @@
 
 SPACINGS=&quot;1000&quot;
 VERTLEVS=&quot;50 66 100&quot;
-VERTLEVS=&quot;50&quot;
+VERTLEVS=&quot;100&quot;
 NX=&quot;3&quot;
 TCNAME=&quot;overflow&quot;
 
@@ -16,7 +16,7 @@
 ###############################################################
 REF_TIME_STEP=&quot;10&quot;
 REF_VISC_H=&quot;1000.0&quot;
-REF_VISC_V=&quot;0.0001&quot;
+REF_VISC_V=&quot;10000.0&quot;
 REF_SPACING=&quot;1000.0&quot;
 TOTAL_TIME=&quot;21600&quot; # in seconds
 
@@ -59,7 +59,7 @@
         cat namelist.input.template | sed &quot;s/*NX/${NX}/g&quot; | sed &quot;s/*NY/${NY}/g&quot; | sed &quot;s/*DC/${DC}/g&quot; &gt; namelist.input
         ./periodic_grid
 
-        mv grid.nc ${TCNAME}${NAME}.grid.nc
+        mv grid.nc ${TCNAME}_${NAME}.grid.nc
 done
 
 mv ${TCNAME}*.grid.nc $CUR_DIR/.
@@ -128,7 +128,7 @@
 
                 echo &quot;     Converting ${NAME} mesh to have ${VERTLEV} levels&quot;
 
-                ln -s ${TCNAME}${NAME}.grid.nc grid.nc
+                ln -s ${TCNAME}_${NAME}.grid.nc grid.nc
 
                 ./map &gt; /dev/null
 
@@ -136,18 +136,18 @@
 
                 mkdir -p ${NAME}_${VERTLEV}levs
 
-                mv ocean.nc ${TCNAME}${NAME}_${VERTLEV}levs.grid.nc
-                mv graph.info ${TCNAME}${NAME}_${VERTLEV}levs.graph.info
+                mv ocean.nc ${TCNAME}_${NAME}_${VERTLEV}levs.grid.nc
+                mv graph.info ${TCNAME}_${NAME}_${VERTLEV}levs.graph.info
 
                 for PROC in $PROCS
                 do
                         mkdir -p ${NAME}_${VERTLEV}levs/${PROC}procs
 
-                        pmetis ${TCNAME}${NAME}_${VERTLEV}levs.graph.info $PROC &gt; /dev/null
+                        pmetis ${TCNAME}_${NAME}_${VERTLEV}levs.graph.info $PROC &gt; /dev/null
 
-                        ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/${TCNAME}${NAME}_${VERTLEV}levs.graph.info ${NAME}_${VERTLEV}levs/${PROC}procs/graph.info
-                        ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/${TCNAME}${NAME}_${VERTLEV}levs.graph.info.part.${PROC} ${NAME}_${VERTLEV}levs/${PROC}procs/graph.info.part.${PROC}
-                        ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/${TCNAME}${NAME}_${VERTLEV}levs.grid.nc ${NAME}_${VERTLEV}levs/${PROC}procs/grid.nc
+                        ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/${TCNAME}_${NAME}_${VERTLEV}levs.graph.info ${NAME}_${VERTLEV}levs/${PROC}procs/graph.info
+                        ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/${TCNAME}_${NAME}_${VERTLEV}levs.graph.info.part.${PROC} ${NAME}_${VERTLEV}levs/${PROC}procs/graph.info.part.${PROC}
+                        ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/${TCNAME}_${NAME}_${VERTLEV}levs.grid.nc ${NAME}_${VERTLEV}levs/${PROC}procs/grid.nc
                         ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/namelist.input ${NAME}_${VERTLEV}levs/${PROC}procs/namelist.input
 
                         ## Copy executable to run directory
@@ -163,7 +163,7 @@
                         echo &quot;${CUR_DIR}/${NAME}_${VERTLEV}levs/${PROC}procs&quot; &gt;&gt; run_paths
                 done
 
-                mv ${TCNAME}${NAME}_${VERTLEV}levs* ${NAME}_${VERTLEV}levs/.
+                mv ${TCNAME}_${NAME}_${VERTLEV}levs* ${NAME}_${VERTLEV}levs/.
 
                 ## Generate new namelist.input file for test case
                 cat MPAS-namelist.input.template | sed &quot;s/*VISC_H/${VISC_H}/g&quot; \

</font>
</pre>