FATES Performance Optimizations and Patch(PFT) level Shared Memory Paralellism

cime_config/machines/cmake_macros/gnu_eddi.cmake

@@ -1,12 +1,12 @@
+string(APPEND CMAKE_CXX_FLAGS " -fpermissive")
 if (COMP_NAME STREQUAL gptl)
-  string(APPEND CPPDEFS " -DHAVE_VPRINTF -DHAVE_GETTIMEOFDAY -DHAVE_BACKTRACE")
+  string(APPEND CPPDEFS " -DHAVE_VPRINTF -DHAVE_TIMES -DHAVE_GETTIMEOFDAY -DHAVE_BACKTRACE")
 endif()
 string(APPEND CMAKE_Fortran_FLAGS_RELEASE " -fno-unsafe-math-optimizations ")
-string(APPEND CMAKE_Fortran_FLAGS_DEBUG " -g -fbacktrace -fbounds-check -ffpe-trap=invalid,zero,overflow -Wall")
+string(APPEND CMAKE_Fortran_FLAGS_DEBUG " -g -fbacktrace -fbounds-check -ffpe-trap=invalid,zero,overflow -Wsurprising -finit-real=snan") #-fsanitize=thread")
 string(APPEND CMAKE_EXE_LINKER_FLAGS " -lcurl")
 if (MPILIB STREQUAL mpi-serial)
   set(SCC "gcc")
-endif()
-if (MPILIB STREQUAL mpi-serial)
   set(SFC "gfortran")
 endif()
+

cime_config/machines/config_machines.xml

@@ -4939,15 +4939,16 @@
 
   <machine MACH="eddi">
     <DESC>small developer workhorse at lbl climate sciences</DESC>
+    <NODENAME_REGEX>eddi</NODENAME_REGEX>
     <OS>LINUX</OS>
     <COMPILERS>gnu</COMPILERS>
     <MPILIBS>openmpi</MPILIBS>
     <PROJECT>ngeet</PROJECT>
-    <CIME_OUTPUT_ROOT>/raid1/lbleco/e3sm/</CIME_OUTPUT_ROOT>
-    <DIN_LOC_ROOT>/home/rgknox/Models/InputDatasets/cesm_input_data/</DIN_LOC_ROOT>
-    <DIN_LOC_ROOT_CLMFORC>/home/rgknox/Models/InputDatasets/cesm_input_data/atm/datm7/</DIN_LOC_ROOT_CLMFORC>
-    <DOUT_S_ROOT>/home/rgknox/Models//cesm_archive/$CASE</DOUT_S_ROOT>
-    <BASELINE_ROOT>/home/rgknox/Models//cesm_baselines/$COMPILER</BASELINE_ROOT>
+    <CIME_OUTPUT_ROOT>/home/rgknox/Models/cime_output</CIME_OUTPUT_ROOT>
+    <DIN_LOC_ROOT>/home/rgknox/Models/InputDatasets/e3sm_input_datasets/</DIN_LOC_ROOT>
+    <DIN_LOC_ROOT_CLMFORC>/home/rgknox/Models/InputDatasets/e3sm_input_datasets/atm/datm7/</DIN_LOC_ROOT_CLMFORC>
+    <DOUT_S_ROOT>/home/rgknox/LandRuns/E3SM/e3sm_archive/$CASE</DOUT_S_ROOT>
+    <BASELINE_ROOT>/home/rgknox/LandRuns/E3SM/e3sm_baselines/$COMPILER</BASELINE_ROOT>
     <CCSM_CPRNC>/raid1/lbleco/cesm/cesm_tools/cprnc/cprnc</CCSM_CPRNC>
     <GMAKE_J>1</GMAKE_J>
     <BATCH_SYSTEM>none</BATCH_SYSTEM>
@@ -4961,14 +4962,14 @@
     <mpirun mpilib="openmpi">
       <executable>mpirun</executable>
       <arguments>
-        <arg name="num_tasks">-np {{ total_tasks }}</arg>
-        <arg name="tasks_per_node"> -npernode $MAX_MPITASKS_PER_NODE</arg>
+        <arg name="num_tasks"> -np {{ total_tasks }}</arg>
+        <arg name="tasks_per_node"> --map-by ppr:{{ tasks_per_node }}:socket:PE=$ENV{OMP_NUM_THREADS} --bind-to core</arg>
       </arguments>
     </mpirun>
     <module_system type="none"/>
     <environment_variables compiler="gnu" >
-      <env name="CMAKE_ROOT">/usr/local/share/cmake-3.21/</env>
-      <env name="NETCDF_PATH">$ENV{NETCDF_HOME}</env>
+      <env name="NETCDF_C_PATH">$SHELL{nc-config --prefix}</env>
+      <env name="NETCDF_FORTRAN_PATH">$SHELL{nf-config --prefix}</env>
     </environment_variables>
   </machine>
 

cime_config/machines/config_pio.xml

@@ -61,7 +61,7 @@
       <value mach="oic5">netcdf</value>
       <value mach="lawrencium-lr3">netcdf</value>
       <value mach="lawrencium-lr6">netcdf</value>
-	  <value mach="eddi">netcdf</value>
+      <value mach="eddi">netcdf</value>
       <value mach="cades">netcdf</value>
       <value mach="cades-baseline">netcdf</value>
       <value mach="chicoma-cpu">netcdf</value>

components/data_comps/datm/src/datm_comp_mod.F90

@@ -1081,8 +1081,11 @@ subroutine datm_comp_run(EClock, x2a, a2x, &
              rtmp = maxval(avstrm%rAttr(stdew,:))
              call shr_mpi_max(rtmp,tdewmax,mpicom,'datm_tdew',all=.true.)
           endif
-          if (my_task == master_task) &
-               write(logunit,*) trim(subname),' max values = ',tbotmax,tdewmax,anidrmax
+          if (my_task == master_task) then
+             write(logunit,*) trim(subname),' tbotmax: ',tbotmax
+             !write(logunit,*) trim(subname), 'tdewmax: ',tdewmax,stdew
+             write(logunit,*) trim(subname), 'anidrmax: ',anidrmax
+          end if
        endif
        lsize = mct_avect_lsize(a2x)
        do n = 1,lsize

components/elm/bld/ELMBuildNamelist.pm

@@ -3764,20 +3764,26 @@ sub add_default {
 
     # query the definition to find out if the variable is an input pathname
     my $is_input_pathname = $definition->is_input_pathname($var);
+
 
-    # The default values for input pathnames are relative.  If the namelist
-    # variable is defined to be an absolute pathname, then prepend
-    # the E3SM inputdata root directory.
-    if (not defined $settings{'no_abspath'}) {
-      if (defined $settings{'set_abspath'}) {
-        $val = set_abs_filepath($val, $settings{'set_abspath'});
-      } else {
-        if ($is_input_pathname eq 'abs') {
-          $val = set_abs_filepath($val, $inputdata_rootdir);
-        }
-      }
+    if ($is_input_pathname eq 'landroot') {
+	my $landroot = abs_path("$ProgDir/..");
+	$val = set_abs_filepath($val,$landroot);
+    } else {
+	# The default values for input pathnames are relative.  If the namelist
+	# variable is defined to be an absolute pathname, then prepend
+	# the E3SM inputdata root directory.
+	if (not defined $settings{'no_abspath'}) {
+	    if (defined $settings{'set_abspath'}) {
+		$val = set_abs_filepath($val, $settings{'set_abspath'});
+	    } else {
+		if ($is_input_pathname eq 'abs') {
+		    $val = set_abs_filepath($val, $inputdata_rootdir);
+		}
+	    }
+	}
     }
-
+    
     # query the definition to find out if the variable takes a string value.
     # The returned string length will be >0 if $var is a string, and 0 if not.
     my $str_len = $definition->get_str_len($var);

components/elm/bld/namelist_files/namelist_defaults.xml

@@ -131,10 +131,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <paramfile nu_com="RD" use_crop=".false." >lnd/clm2/paramdata/clm_params_c180524_phs.nc</paramfile>
 
 
-<!-- ================================================================== -->
-<!-- FATES default parameter file                                       -->
-<!-- ================================================================== -->
-<fates_paramfile >lnd/clm2/paramdata/fates_params_api.41.0.0_14pft_c250813.nc</fates_paramfile>
+<!-- ======================================================================== -->
+<!-- FATES default parameter file (path relative to E3SM/components/elm/)     -->
+<!-- ======================================================================== -->
+<fates_paramfile >src/external_models/fates/parameter_files/fates_params_default.json</fates_paramfile>
 
 <!-- soil order related parameters (relative to {csmdata}) -->
 <fsoilordercon             >lnd/clm2/paramdata/CNP_parameters_c131108.nc</fsoilordercon>

components/elm/bld/namelist_files/namelist_definition.xml

@@ -531,7 +531,7 @@ constants for biogeochem modules
 </entry>
 
 <entry id="fates_paramfile" type="char*256" category="datasets"
-       input_pathname="abs" group="elm_inparm" valid_values="" >
+       input_pathname="landroot" group="elm_inparm" valid_values="" >
 Full pathname datafile with fates parameters
 </entry>