changes to defaults. Including atm fixes

abishekg7 · Oct 10, 2020 · 3afa98f · 3afa98f
1 parent 7fa4141
commit 3afa98f
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Showing 15 changed files with 107 additions and 57 deletions.
diff --git a/Config/config_postprocess.xml b/Config/config_postprocess.xml
@@ -30,7 +30,7 @@
       <entry id="CASE"
 	     type="string"
 	     valid_values=""  
-	     value="inherit"
+	     value="b.e13.B1950C5.ne30_g16.ihesp24_1950cntl.002"
 	     group="case_info"
 	     desc="case name"
 	     ></entry> 
@@ -54,63 +54,63 @@
       <entry id="DOUT_S_ROOT"
 	     type="string"
 	     valid_values=""  
-	     value="inherit"
+	     value="/scratch/training/CESM_post/datasets/b.e13.B1950C5.ne30_g16.ihesp24_1950cntl.002"
 	     group="case_info"
 	     desc="Fully qualified path to the location of the short term archive output, DOUT_S_ROOT, on local disk where case history files reside. Assumes the adherence to the CESM file naming conventions."
 	     ></entry> 
 
       <entry id="ATM_GRID"
 	     type="string"
 	     valid_values="0.9x1.25"  
-	     value="inherit"
+	     value="ne30"
 	     group="case_info"
 	     desc="Atmosphere model grid"
 	     ></entry> 
 
       <entry id="ICE_GRID"
 	     type="string"
 	     valid_values="gx1v6" 
-	     value="inherit"
+	     value="gx1v6"
 	     group="case_info"
 	     desc="Sea-Ice model grid"
 	     ></entry> 
 
       <entry id="ICE_NX"
 	     type="string"
 	     valid_values="320"  
-	     value="inherit"
+	     value="320"
 	     group="case_info"
 	     desc="Sea-Ice model grid NX - default 320 for 1-degree ocean grid"
 	     ></entry> 
 
       <entry id="ICE_NY"
 	     type="string"
 	     valid_values="384"
-	     value="inherit"
+	     value="384"
 	     group="case_info"
 	     desc="Sea-Ice model grid NY - default 384 for 1-degree ocean grid"
 	     ></entry> 
 
       <entry id="LND_GRID"
 	     type="string"
 	     valid_values="0.9x1.25"
-	     value="inherit"
+	     value="ne30"
 	     group="case_info"
 	     desc="Land model grid"
 	     ></entry> 
 
       <entry id="OCN_GRID"
 	     type="string"
 	     valid_values="gx1v6"   
-	     value="inherit"
+	     value="gx1v6"
 	     group="case_info"
 	     desc="Ocean model grid"
 	     ></entry> 
 
       <entry id="CESM_TAG"
 	     type="string"
 	     valid_values="cesm2_0"  
-	     value="inherit"
+	     value="ihesp24"
 	     group="case_info"
 	     desc="CESM tag used to create this case"
 	     ></entry> 

diff --git a/Machines/machine_postprocess.xml b/Machines/machine_postprocess.xml
@@ -336,14 +336,14 @@
     </modules>
     <components>
       <component name="atm">
-	<averages_pes queue="mn_small" nodes="1" pes_per_node="3" wallclock="6:00" memory="18000">3</averages_pes>
-	<diagnostics_pes queue="mn_small" nodes="1" pes_per_node="3" wallclock="6:00" memory="18000">3</diagnostics_pes>
+	<averages_pes queue="mn_small" nodes="1" pes_per_node="3" wallclock="6:00" memory="2000">3</averages_pes>
+	<diagnostics_pes queue="mn_small" nodes="1" pes_per_node="3" wallclock="6:00" memory="2000">3</diagnostics_pes>
 	<regrid_pes queue="mn_small" nodes="1" pes_per_node="3" wallclock="6:00" memory="18000">3</regrid_pes>
 	<obs_root>/scratch/training/CESM_post/obs_root/amwg/amwg_data</obs_root> <!-- TODO: update this and other obs_roots -->
       </component>
       <component name="ice">
-	<averages_pes queue="mn_small"  nodes="1" pes_per_node="3" wallclock="6:00" memory="18000">3</averages_pes>
-	<diagnostics_pes queue="mn_small"  nodes="1" pes_per_node="3" wallclock="6:00" memory="18000">3</diagnostics_pes>
+	<averages_pes queue="mn_small"  nodes="1" pes_per_node="4" wallclock="1:00" memory="2000">4</averages_pes>
+	<diagnostics_pes queue="mn_small"  nodes="1" pes_per_node="4" wallclock="1:00" memory="2000">4</diagnostics_pes>
 	<obs_root>/scratch/training/CESM_post/obs_root/pcwg/ice/data</obs_root>
       </component>
       <component name="lnd">
@@ -353,8 +353,8 @@
 	<obs_root>/glade/p/cesm/lmwg/diag/lnd_diag_data</obs_root>
       </component>
       <component name="ocn">
-	<averages_pes queue="mn_small"  nodes="1" pes_per_node="3" wallclock="6:00" memory="18000">3</averages_pes>
-	<diagnostics_pes queue="mn_small"  nodes="1" pes_per_node="3" wallclock="6:00" memory="18000">3</diagnostics_pes>
+	<averages_pes queue="mn_small"  nodes="1" pes_per_node="4" wallclock="1:00" memory="2000">4</averages_pes>
+	<diagnostics_pes queue="mn_small"  nodes="1" pes_per_node="4" wallclock="1:00" memory="2000">4</diagnostics_pes>
 	<obs_root>/scratch/training/CESM_post/obs_root</obs_root> <!-- TODO: move to a permanent dir -->
       </component>
       <component name="ilamb">

diff --git a/Templates/batch_ada.tmpl b/Templates/batch_ada.tmpl
@@ -9,7 +9,6 @@
 #BSUB -R "span[ptile={{ ppn }}]"
 #BSUB -J {{ processName }}
 #BSUB -W {{ wallclock }}
-#BSUB -P {{ project }} 
 #BSUB -L /bin/bash           #Uses the bash login shell to initialize the job's execution environment.
 #BSUB -R "rusage[mem={{memory}}]"  #Request 25000MB per process (CPU) for the job
 

diff --git a/Templates/postprocess.tmpl b/Templates/postprocess.tmpl
@@ -56,8 +56,8 @@ log_filename={{ caseRoot }}/logs/{{ processName }}.log.$today
 {{ imb_env_vars }}
 {{ mpirun }} {{ imb_run }} {{ imb_options }} >> ${log_filename} 2>&1
 {% elif standalone %}
-{{ mpirun }} ./{{ postProcessCmd }} {{ debug }} {{ backtrace }} --caseroot {{ caseRoot }} --standalone {{ cmdl_opt }} >> ${log_filename} 2>&1
+{{ mpirun }} {{ postProcessCmd }} {{ debug }} {{ backtrace }} --caseroot {{ caseRoot }} --standalone {{ cmdl_opt }} >> ${log_filename} 2>&1
 {% else %}
-{{ mpirun }} ./{{ postProcessCmd }} {{ debug }} {{ backtrace }} --caseroot {{ caseRoot }} >> ${log_filename} 2>&1
+{{ mpirun }} {{ postProcessCmd }} {{ debug }} {{ backtrace }} --caseroot {{ caseRoot }} >> ${log_filename} 2>&1
 {% endif %}
 
diff --git a/atm_diag/regridclimo.ncl b/atm_diag/regridclimo.ncl
@@ -156,9 +156,9 @@ end if
     print("Regridding: ")
     print("SRC:"+srcFileName)
     print("DST:"+dstFileName)
-    if(isfilepresent(dstFileName)) then
-      system("rm "+dstFileName)
-    end if
+;    if(isfilepresent(dstFileName)) then
+      system("rm -f "+dstFileName)
+;    end if
     src_file=addfile(srcFileName,"r")
     dst_file=addfile(dstFileName,"c")
 
@@ -223,7 +223,7 @@ end if
     var_in_exclude = (/"lat", "lon", "area", "date_written", "time_written"/)  
 
     ;--- Specify a list of variables on the source SE file that should be directly copied 
-    var_in_copy = (/"time_bnds"/)  
+    var_in_copy = (/"time_bnds","cosp_ht_bnds","cosp_sr_bnds","cosp_prs_bnds","cosp_tau_bnds"/)  
 
     ;--- Specify a list of variables to be regridded
     var_out        = "All_Variables"     ; to be regridded
@@ -293,11 +293,34 @@ end if
     ib       = ind(dNames.eq."ilev")
     klev     = dSizes(ia)
     klevi    = dSizes(ib)
-                                       ; standard CAM dimensions
-    dimNames = (/"time",    "lat",    "lon", "lev",  "ilev", "nbnd", "chars"/)  
-    dimSizes = (/ -1   ,    nlat ,    mlon ,  klev,  klevi ,   2   ,    8   /) 
-    dimUnlim = (/ True ,    False,    False, False,  False , False , False  /)   
-    filedimdef(dst_file,dimNames,dimSizes,dimUnlim)
+; cosp dimensions
+    if (any("cosp_scol".eq.dNames))
+       iscol = ind(dNames.eq."cosp_scol")
+       nscol = dSizes(iscol)
+       itau = ind(dNames.eq."cosp_tau")
+       ntau = dSizes(itau)
+       iprs = ind(dNames.eq."cosp_prs")
+       nprs = dSizes(iprs)
+       isr = ind(dNames.eq."cosp_sr")
+       nsr = dSizes(isr)
+       isza = ind(dNames.eq."cosp_sza")
+       nsza = dSizes(isza)
+       iht = ind(dNames.eq."cosp_ht")
+       nht = dSizes(iht)
+; CAM dimensions plus cosp
+       dimNames = (/"time",    "lat",    "lon", "lev",  "ilev", "nbnd", "chars","cosp_scol","cosp_prs","cosp_sr","cosp_tau","cosp_sza","cosp_ht"/)
+       dimSizes = (/ -1   ,    nlat ,    mlon ,  klev,  klevi ,   2   ,    8   ,nscol      ,nprs      ,nsr      ,ntau      ,nsza      ,nht      /)
+       dimUnlim = (/ True ,    False,    False, False,  False , False , False  ,False      ,False     ,False    ,False     ,False    ,False     /)
+       filedimdef(dst_file,dimNames,dimSizes,dimUnlim)
+    else	
+; standard CAM dimensions
+       dimNames = (/"time",    "lat",    "lon", "lev",  "ilev", "nbnd", "chars"/)  
+       dimSizes = (/ -1   ,    nlat ,    mlon ,  klev,  klevi ,   2   ,    8   /) 
+       dimUnlim = (/ True ,    False,    False, False,  False , False , False  /)   
+       filedimdef(dst_file,dimNames,dimSizes,dimUnlim)
+    end if
+
+
 
 ;--- The following are explicitly added because they are 'special'
 
@@ -332,6 +355,13 @@ end if
                vdims = getfilevardims(src_file, var_in(nv))
                filevardef(dst_file, var_in(nv), getfilevartypes(src_file,var_in(nv)) \
                                              , (/ "time", vdims(1),  "lat", "lon" /)        )
+               delete(vdims)
+           end if
+           if (rank_in .eq.4.and.var_in(nv).eq."FISCCP1_COSP") then
+               vdims = getfilevardims(src_file, var_in(nv))
+               filevardef(dst_file, var_in(nv), getfilevartypes(src_file,var_in(nv)) \
+                                             , (/ "time", "cosp_prs", "cosp_tau","lat", "lon" /)        )
+               delete(vdims)
            end if
 
            dumAtts = new( 1, getfilevartypes(src_file,var_in(nv)))
@@ -374,13 +404,13 @@ end if
            any(var_in(nv).eq.var_in_copy)       ) then
 
            rank_in = dimsizes(getfilevardimsizes(src_file, var_in(nv)))
-
            if (rank_in .eq.1 .or. any(var_in(nv).eq.var_in_copy) ) then
                dst_file->$var_in(nv)$ = (/ src_file->$var_in(nv)$ /)
            end if
            if (rank_in .ge.2 .and. .not.any(var_in(nv).eq.var_in_copy)) then
                dst_file->$var_in(nv)$ = (/ ESMF_regrid_with_weights(src_file->$var_in(nv)$,wgtFileName,Opt_RGRD) /)
            end if
+	   delete(rank_in)
         end if
        end if
     end do       ; nv

diff --git a/create_python_env b/create_python_env
@@ -143,8 +143,10 @@ if [ -d $env ]; then
     info="$progname - ${pp_dir}/cesm-env2 virtual environment already exists. Skipping conda create"
     print_result "$info"
 else
-   export CONDA_ENVS_PATH=${pp_dir}
-   export CONDA_PKGS_DIRS=${pp_dir}/conda_pkgs
+   #export CONDA_ENVS_PATH=${pp_dir}
+   export CONDA_ENVS_PATH=${env}
+   #export CONDA_PKGS_DIRS=${pp_dir}/conda_pkgs
+   export CONDA_PKGS_DIRS=${env}/conda_pkgs
    conda create python=2.7 -n cesm-env2
    #virtualenv --system-site-packages -p python2 cesm-env2
 fi

diff --git a/diagnostics/diagnostics/atm/Config/config_diags_atm.xml b/diagnostics/diagnostics/atm/Config/config_diags_atm.xml
@@ -228,15 +228,15 @@
       <entry id="ATMDIAG_test_first_yr"
              type="integer"
              valid_values=""
-             value=""
+             value="36"
              group="date_params"
              desc="Start year for test case for diagnostics."
              ></entry>
 
       <entry id="ATMDIAG_test_nyrs"
              type="integer"
              valid_values=""
-             value=""
+             value="9"
              group="date_params"
              desc="The number of years of test data to be used for the diagnostics."
              ></entry>

diff --git a/diagnostics/diagnostics/ice/Config/config_diags_ice.xml b/diagnostics/diagnostics/ice/Config/config_diags_ice.xml
@@ -346,15 +346,15 @@ Applies to both model and control cases."
   <entry id="ICEDIAG_GRIDFILECONT"
          type="char"
          valid_values=""
-         value="/glade/p/cesm/omwg/grids/($ICEDIAG_GRID_CONT)_grid.nc"
+         value="$OCNDIAG_OBSROOTPATH/grids/($ICEDIAG_GRID_CONT)_grid.nc"
          group="input_path"
          desc="Grid file for control case. Note - this is an ocean grid file."
          ></entry>
 
   <entry id="ICEDIAG_GRIDFILEDIFF"
          type="char"
          valid_values=""
-         value="/glade/p/cesm/omwg/grids/($ICEDIAG_GRID_DIFF)_grid.nc"
+         value="$OCNDIAG_OBSROOTPATH/grids/($ICEDIAG_GRID_DIFF)_grid.nc"
          group="input_path"
          desc="Grid file for diff case. Note - this is an ocean grid file."
          ></entry>