Merge branch 'jonbob/mpas/update-070617' (PR #1630)

Update MPAS components and framework, bring in threading optimizations This PR updates all MPAS submodules and framework, including: * bfb framework threading optimization from Abhinov MPAS#1237; * bfb mpas-o threading optimization from Abhinov MPAS#1235; * update path to new Albany install (cherry-picked from branch agsalin/machines/AlbanyNewInstall); * various framework and component updates. Tested with: * PET_Ln9.T62_oEC60to30v3.GMPAS-NYF.edison_intel * SMS.T62_oEC60to30v3.GMPAS-IAF.edison_intel (bfb with current master) * PET.T62_oEC60to30v3.GMPAS-NYF.titan Note: this commit is answer-changing only for compsets with MPASLI [non-BFB]
E3SM-Project · Aug 7, 2017 · 6725a21 · 6725a21
2 parents 0af35b6 + c9b1e61
commit 6725a21
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diff --git a/cime/config/acme/machines/config_compilers.xml b/cime/config/acme/machines/config_compilers.xml
@@ -648,7 +648,7 @@ for mct, etc.
   <PNETCDF_PATH>$(PNETCDFROOT)</PNETCDF_PATH>
   <ADD_SLIBS> $(shell $(NETCDF_PATH)/bin/nf-config --flibs) -L/usr/lib64 -L/usr/lib64/atlas -lblas -llapack</ADD_SLIBS>
   <CXX_LIBS>-lstdc++ -lmpi_cxx</CXX_LIBS>
-  <ALBANY_PATH>/projects/install/rhel6-x86_64/ACME/AlbanyTrilinos/Albany/build/install</ALBANY_PATH>
+  <ALBANY_PATH>/data/acme/AlbanyTrilinos_06262017/Albany/build/install</ALBANY_PATH>
 </compiler>
 
 <compiler COMPILER="intel" MACH="sandia-srn-sems">
@@ -660,7 +660,7 @@ for mct, etc.
   <ADD_SLIBS> $(shell $(NETCDF_PATH)/bin/nf-config --flibs) -L/usr/lib64 -L/usr/lib64/atlas -lblas -llapack</ADD_SLIBS>
   <ADD_SLIBS> /projects/sems/install/rhel6-x86_64/sems/compiler/intel/15.0.2/base/mkl/lib/mic/libmkl_scalapack_lp64.a -Wl,--start-group /projects/sems/install/rhel6-x86_64/sems/compiler/intel/15.0.2/base/mkl/lib/intel64/libmkl_intel_lp64.a /projects/sems/install/rhel6-x86_64/sems/compiler/intel/15.0.2/base/mkl/lib/intel64/libmkl_core.a /projects/sems/install/rhel6-x86_64/sems/compiler/intel/15.0.2/base/mkl/lib/intel64/libmkl_sequential.a -Wl,--end-group /projects/sems/install/rhel6-x86_64/sems/compiler/intel/15.0.2/base/mkl/lib/mic/libmkl_blacs_intelmpi_lp64.a -lpthread -lm </ADD_SLIBS>
   <CXX_LIBS>-lstdc++ -lmpi_cxx</CXX_LIBS>
-  <ALBANY_PATH>/projects/install/rhel6-x86_64/ACME/AlbanyTrilinos/Albany/build/install</ALBANY_PATH>
+  <ALBANY_PATH>/data/acme/AlbanyTrilinos_06262017/Albany/build/install</ALBANY_PATH>
 </compiler>
 
 <compiler COMPILER="gnu" MACH="anlworkstation">
@@ -684,7 +684,7 @@ for mct, etc.
   <PIO_FILESYSTEM_HINTS>lustre </PIO_FILESYSTEM_HINTS>
   <ADD_SLIBS MPILIB="openmpi"> -mkl=cluster </ADD_SLIBS>
   <ADD_SLIBS MPILIB="mpi-serial"> -mkl </ADD_SLIBS>
-  <ALBANY_PATH>/projects/ccsm/AlbanyTrilinos/Albany/build/install</ALBANY_PATH>
+  <ALBANY_PATH>/projects/ccsm/AlbanyTrilinos_06262017/Albany/build/install</ALBANY_PATH>
 </compiler>
 
 <compiler COMPILER="intel" MACH="chama">
@@ -699,7 +699,7 @@ for mct, etc.
   <PIO_FILESYSTEM_HINTS>lustre </PIO_FILESYSTEM_HINTS>
   <ADD_SLIBS MPILIB="openmpi"> -mkl=cluster </ADD_SLIBS>
   <ADD_SLIBS MPILIB="mpi-serial"> -mkl </ADD_SLIBS>
-  <ALBANY_PATH>/projects/ccsm/AlbanyTrilinos/Albany/build/install</ALBANY_PATH>
+  <ALBANY_PATH>/projects/ccsm/AlbanyTrilinos_06262017/Albany/build/install</ALBANY_PATH>
 </compiler>
 
 <compiler COMPILER="intel" MACH="redsky">

diff --git a/cime/config/acme/machines/config_machines.xml b/cime/config/acme/machines/config_machines.xml
@@ -607,6 +607,7 @@
         <command name="load">sems-openmpi/1.8.7</command>
         <command name="load">sems-cmake/2.8.12</command>
         <command name="load">sems-netcdf/4.4.1/exo_parallel</command>
+        <command name="load">sems-boost/1.58.0/base</command>
       </modules>
     </module_system>
     <environment_variables>

diff --git a/components/mpas-cice/bld/build-namelist b/components/mpas-cice/bld/build-namelist
@@ -438,6 +438,7 @@ add_default($nl, 'config_pio_stride');
 add_default($nl, 'config_write_output_on_startup');
 add_default($nl, 'config_test_case_diag');
 add_default($nl, 'config_test_case_diag_type');
+add_default($nl, 'config_full_abort_write');
 
 #################################
 # Namelist group: decomposition #
@@ -526,6 +527,7 @@ add_default($nl, 'config_perform_unit_test');
 add_default($nl, 'config_unit_test_type');
 add_default($nl, 'config_unit_test_subtype');
 add_default($nl, 'config_use_test_ice_shelf');
+add_default($nl, 'config_testing_system_test');
 
 ###################################
 # Namelist group: velocity_solver #

diff --git a/components/mpas-cice/bld/build-namelist-section b/components/mpas-cice/bld/build-namelist-section
@@ -22,6 +22,7 @@ add_default($nl, 'config_pio_stride');
 add_default($nl, 'config_write_output_on_startup');
 add_default($nl, 'config_test_case_diag');
 add_default($nl, 'config_test_case_diag_type');
+add_default($nl, 'config_full_abort_write');
 
 #################################
 # Namelist group: decomposition #
@@ -106,6 +107,7 @@ add_default($nl, 'config_perform_unit_test');
 add_default($nl, 'config_unit_test_type');
 add_default($nl, 'config_unit_test_subtype');
 add_default($nl, 'config_use_test_ice_shelf');
+add_default($nl, 'config_testing_system_test');
 
 ###################################
 # Namelist group: velocity_solver #

diff --git a/components/mpas-cice/bld/namelist_files/namelist_defaults_mpas-cice.xml b/components/mpas-cice/bld/namelist_files/namelist_defaults_mpas-cice.xml
@@ -30,6 +30,7 @@
 <config_write_output_on_startup>false</config_write_output_on_startup>
 <config_test_case_diag>false</config_test_case_diag>
 <config_test_case_diag_type>'none'</config_test_case_diag_type>
+<config_full_abort_write>true</config_full_abort_write>
 
 <!-- decomposition -->
 <config_block_decomp_file_prefix>'graph.info.part.'</config_block_decomp_file_prefix>
@@ -83,6 +84,7 @@
 <config_unit_test_type>''</config_unit_test_type>
 <config_unit_test_subtype>''</config_unit_test_subtype>
 <config_use_test_ice_shelf>false</config_use_test_ice_shelf>
+<config_testing_system_test>false</config_testing_system_test>
 
 <!-- velocity_solver -->
 <config_dynamics_subcycle_number>1</config_dynamics_subcycle_number>

diff --git a/components/mpas-cice/bld/namelist_files/namelist_definition_mpas-cice.xml b/components/mpas-cice/bld/namelist_files/namelist_definition_mpas-cice.xml
@@ -143,6 +143,14 @@ Valid values: MISSING POSSIBLE VALUES
 Default: Defined in namelist_defaults.xml
 </entry>
 
+<entry id="config_full_abort_write" type="logical"
+	category="io" group="io">
+MISSING DESCRIPTION
+
+Valid values: MISSING POSSIBLE VALUES
+Default: Defined in namelist_defaults.xml
+</entry>
+
 
 <!-- decomposition -->
 
@@ -476,6 +484,14 @@ Valid values: MISSING POSSIBLE VALUES
 Default: Defined in namelist_defaults.xml
 </entry>
 
+<entry id="config_testing_system_test" type="logical"
+	category="unit_test" group="unit_test">
+MISSING DESCRIPTION
+
+Valid values: MISSING POSSIBLE VALUES
+Default: Defined in namelist_defaults.xml
+</entry>
+
 
 <!-- velocity_solver -->
 

diff --git a/components/mpas-cice/driver/ice_comp_mct.F b/components/mpas-cice/driver/ice_comp_mct.F
@@ -826,7 +826,7 @@ subroutine ice_run_mct( EClock, cdata_i, x2i_i, i2x_i)!{{{
 
         if (debugOn) call mpas_log_write('   Starting forward update', masterOnly=.true.)
         call mpas_timer_start("time integration", .false.)
-        call cice_timestep(domain, domain % clock, itimestep)
+        call cice_timestep(domain, domain % clock, itimestep, ierr)
         call mpas_timer_stop("time integration")
         if (debugOn) call mpas_log_write('   Finished forward update', masterOnly=.true.)
 

diff --git a/components/mpas-cice/model b/components/mpas-cice/model
diff --git a/components/mpas-o/bld/build-namelist b/components/mpas-o/bld/build-namelist
@@ -1403,6 +1403,8 @@ add_default($nl, 'config_AM_waterMassCensus_minTemperature');
 add_default($nl, 'config_AM_waterMassCensus_maxTemperature');
 add_default($nl, 'config_AM_waterMassCensus_minSalinity');
 add_default($nl, 'config_AM_waterMassCensus_maxSalinity');
+add_default($nl, 'config_AM_waterMassCensus_compute_predefined_regions');
+add_default($nl, 'config_AM_waterMassCensus_region_group');
 
 #################################################
 # Namelist group: AM_layerVolumeWeightedAverage #

diff --git a/components/mpas-o/bld/build-namelist-section b/components/mpas-o/bld/build-namelist-section
@@ -977,6 +977,8 @@ add_default($nl, 'config_AM_waterMassCensus_minTemperature');
 add_default($nl, 'config_AM_waterMassCensus_maxTemperature');
 add_default($nl, 'config_AM_waterMassCensus_minSalinity');
 add_default($nl, 'config_AM_waterMassCensus_maxSalinity');
+add_default($nl, 'config_AM_waterMassCensus_compute_predefined_regions');
+add_default($nl, 'config_AM_waterMassCensus_region_group');
 
 #################################################
 # Namelist group: AM_layerVolumeWeightedAverage #

diff --git a/components/mpas-o/bld/namelist_files/namelist_defaults_mpas-o.xml b/components/mpas-o/bld/namelist_files/namelist_defaults_mpas-o.xml
@@ -16,7 +16,7 @@
 <config_calendar_type>'gregorian'</config_calendar_type>
 
 <!-- io -->
-<config_write_output_on_startup>.true.</config_write_output_on_startup>
+<config_write_output_on_startup>.false.</config_write_output_on_startup>
 <config_pio_num_iotasks>0</config_pio_num_iotasks>
 <config_pio_stride>1</config_pio_stride>
 
@@ -851,6 +851,8 @@
 <config_AM_waterMassCensus_maxTemperature>30.0</config_AM_waterMassCensus_maxTemperature>
 <config_AM_waterMassCensus_minSalinity>32.0</config_AM_waterMassCensus_minSalinity>
 <config_AM_waterMassCensus_maxSalinity>37.0</config_AM_waterMassCensus_maxSalinity>
+<config_AM_waterMassCensus_compute_predefined_regions>.true.</config_AM_waterMassCensus_compute_predefined_regions>
+<config_AM_waterMassCensus_region_group>''</config_AM_waterMassCensus_region_group>
 
 <!-- AM_layerVolumeWeightedAverage -->
 <config_AM_layerVolumeWeightedAverage_enable>.true.</config_AM_layerVolumeWeightedAverage_enable>

diff --git a/components/mpas-o/bld/namelist_files/namelist_definition_mpas-o.xml b/components/mpas-o/bld/namelist_files/namelist_definition_mpas-o.xml
@@ -5547,6 +5547,22 @@ Valid values: any real number greater than config_AM_waterMassCensus_minSalinity
 Default: Defined in namelist_defaults.xml
 </entry>
 
+<entry id="config_AM_waterMassCensus_compute_predefined_regions" type="logical"
+	category="AM_waterMassCensus" group="AM_waterMassCensus">
+Computes predefined regions. (Does not require a region mask file.)
+
+Valid values: .true. or .false.
+Default: Defined in namelist_defaults.xml
+</entry>
+
+<entry id="config_AM_waterMassCensus_region_group" type="char*1024"
+	category="AM_waterMassCensus" group="AM_waterMassCensus">
+The name of the region group, for which the WMC should be computed in addition to the existing WMC.
+
+Valid values: 'all', '', or the name of a region group.
+Default: Defined in namelist_defaults.xml
+</entry>
+
 
 <!-- AM_layerVolumeWeightedAverage -->
 

diff --git a/components/mpas-o/model b/components/mpas-o/model
diff --git a/components/mpasli/bld/build-namelist b/components/mpasli/bld/build-namelist
@@ -416,6 +416,7 @@ add_default($nl, 'config_sia_tangent_slope_calculation');
 add_default($nl, 'config_flowParamA_calculation');
 add_default($nl, 'config_do_velocity_reconstruction_for_external_dycore');
 add_default($nl, 'config_simple_velocity_type');
+add_default($nl, 'config_use_glp');
 
 #############################
 # Namelist group: advection #
@@ -545,6 +546,14 @@ add_default($nl, 'config_SGH_bed_roughness_max');
 add_default($nl, 'config_SGH_creep_coefficient');
 add_default($nl, 'config_SGH_englacial_porosity');
 add_default($nl, 'config_SGH_till_max');
+add_default($nl, 'config_SGH_chnl_active');
+add_default($nl, 'config_SGH_chnl_alpha');
+add_default($nl, 'config_SGH_chnl_beta');
+add_default($nl, 'config_SGH_chnl_conduc_coeff');
+add_default($nl, 'config_SGH_chnl_creep_coefficient');
+add_default($nl, 'config_SGH_incipient_channel_width');
+add_default($nl, 'config_SGH_include_pressure_melt');
+add_default($nl, 'config_SGH_shmip_forcing');
 
 ##################################
 # Namelist group: AM_globalStats #

diff --git a/components/mpasli/bld/build-namelist-section b/components/mpasli/bld/build-namelist-section
@@ -10,6 +10,7 @@ add_default($nl, 'config_sia_tangent_slope_calculation');
 add_default($nl, 'config_flowParamA_calculation');
 add_default($nl, 'config_do_velocity_reconstruction_for_external_dycore');
 add_default($nl, 'config_simple_velocity_type');
+add_default($nl, 'config_use_glp');
 
 #############################
 # Namelist group: advection #
@@ -139,6 +140,14 @@ add_default($nl, 'config_SGH_bed_roughness_max');
 add_default($nl, 'config_SGH_creep_coefficient');
 add_default($nl, 'config_SGH_englacial_porosity');
 add_default($nl, 'config_SGH_till_max');
+add_default($nl, 'config_SGH_chnl_active');
+add_default($nl, 'config_SGH_chnl_alpha');
+add_default($nl, 'config_SGH_chnl_beta');
+add_default($nl, 'config_SGH_chnl_conduc_coeff');
+add_default($nl, 'config_SGH_chnl_creep_coefficient');
+add_default($nl, 'config_SGH_incipient_channel_width');
+add_default($nl, 'config_SGH_include_pressure_melt');
+add_default($nl, 'config_SGH_shmip_forcing');
 
 ##################################
 # Namelist group: AM_globalStats #

diff --git a/components/mpasli/bld/namelist_files/namelist_defaults_mpasli.xml b/components/mpasli/bld/namelist_files/namelist_defaults_mpasli.xml
@@ -10,6 +10,7 @@
 <config_flowParamA_calculation>'constant'</config_flowParamA_calculation>
 <config_do_velocity_reconstruction_for_external_dycore>.false.</config_do_velocity_reconstruction_for_external_dycore>
 <config_simple_velocity_type>'uniform'</config_simple_velocity_type>
+<config_use_glp>.false.</config_use_glp>
 
 <!-- advection -->
 <config_thickness_advection>'fo'</config_thickness_advection>
@@ -84,7 +85,7 @@
 <config_print_thickness_advection_info>.false.</config_print_thickness_advection_info>
 <config_print_calving_info>.false.</config_print_calving_info>
 <config_print_thermal_info>.false.</config_print_thermal_info>
-<config_always_compute_fem_grid>.false.</config_always_compute_fem_grid>
+<config_always_compute_fem_grid>.true.</config_always_compute_fem_grid>
 <config_print_velocity_cleanup_details>.false.</config_print_velocity_cleanup_details>
 
 <!-- subglacial_hydro -->
@@ -104,6 +105,14 @@
 <config_SGH_creep_coefficient>0.04</config_SGH_creep_coefficient>
 <config_SGH_englacial_porosity>0.01</config_SGH_englacial_porosity>
 <config_SGH_till_max>2.0</config_SGH_till_max>
+<config_SGH_chnl_active>.false.</config_SGH_chnl_active>
+<config_SGH_chnl_alpha>1.25</config_SGH_chnl_alpha>
+<config_SGH_chnl_beta>1.5</config_SGH_chnl_beta>
+<config_SGH_chnl_conduc_coeff>0.1</config_SGH_chnl_conduc_coeff>
+<config_SGH_chnl_creep_coefficient>0.04</config_SGH_chnl_creep_coefficient>
+<config_SGH_incipient_channel_width>2.0</config_SGH_incipient_channel_width>
+<config_SGH_include_pressure_melt>.true.</config_SGH_include_pressure_melt>
+<config_SGH_shmip_forcing>'none'</config_SGH_shmip_forcing>
 
 <!-- AM_globalStats -->
 <config_AM_globalStats_enable>.true.</config_AM_globalStats_enable>

diff --git a/components/mpasli/bld/namelist_files/namelist_definition_mpasli.xml b/components/mpasli/bld/namelist_files/namelist_definition_mpasli.xml
@@ -92,6 +92,14 @@ Valid values: 'uniform', 'radial'
 Default: Defined in namelist_defaults.xml
 </entry>
 
+<entry id="config_use_glp" type="logical"
+	category="velocity_solver" group="velocity_solver">
+If true, then apply Albany's grounding line parameterization
+
+Valid values: .true. or .false.
+Default: Defined in namelist_defaults.xml
+</entry>
+
 
 <!-- advection -->
 
@@ -706,6 +714,70 @@ Valid values: positive real number
 Default: Defined in namelist_defaults.xml
 </entry>
 
+<entry id="config_SGH_chnl_active" type="logical"
+	category="subglacial_hydro" group="subglacial_hydro">
+activate channels in subglacial hydrology model
+
+Valid values: .true. or .false.
+Default: Defined in namelist_defaults.xml
+</entry>
+
+<entry id="config_SGH_chnl_alpha" type="real"
+	category="subglacial_hydro" group="subglacial_hydro">
+power in flux formula
+
+Valid values: positive real number
+Default: Defined in namelist_defaults.xml
+</entry>
+
+<entry id="config_SGH_chnl_beta" type="real"
+	category="subglacial_hydro" group="subglacial_hydro">
+power in flux formula
+
+Valid values: positive real number
+Default: Defined in namelist_defaults.xml
+</entry>
+
+<entry id="config_SGH_chnl_conduc_coeff" type="real"
+	category="subglacial_hydro" group="subglacial_hydro">
+conductivity coefficient
+
+Valid values: positive real number
+Default: Defined in namelist_defaults.xml
+</entry>
+
+<entry id="config_SGH_chnl_creep_coefficient" type="real"
+	category="subglacial_hydro" group="subglacial_hydro">
+creep closure coefficient
+
+Valid values: positive real number
+Default: Defined in namelist_defaults.xml
+</entry>
+
+<entry id="config_SGH_incipient_channel_width" type="real"
+	category="subglacial_hydro" group="subglacial_hydro">
+width of sheet beneath/around channel that contributes to melt within the channel
+
+Valid values: positive real number
+Default: Defined in namelist_defaults.xml
+</entry>
+
+<entry id="config_SGH_include_pressure_melt" type="logical"
+	category="subglacial_hydro" group="subglacial_hydro">
+whether to include the pressure melt term in the channel opening
+
+Valid values: .true. or .false.
+Default: Defined in namelist_defaults.xml
+</entry>
+
+<entry id="config_SGH_shmip_forcing" type="char*1024"
+	category="subglacial_hydro" group="subglacial_hydro">
+calculate time-varying forcing specified by SHMIP experiments C or D
+
+Valid values: 'none', 'C1'-'C4', 'D1'-'D5'
+Default: Defined in namelist_defaults.xml
+</entry>
+
 
 <!-- AM_globalStats -->
 

diff --git a/components/mpasli/model b/components/mpasli/model