Merge pull request #5 from eclare108213/update_E3SM_3

Update development branch to E3SM master
eclare108213 · Jan 13, 2023 · d913a2b · d913a2b
2 parents dc3b176 + ee53d92
commit d913a2b
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diff --git a/AUTHORS b/AUTHORS
@@ -0,0 +1,20 @@
+# This is the list of E3SM's significant contributing institutions in
+# alphabetical order.
+#
+# This does not list every person who has contributed code,
+# since many employees of one institution may be contributing.
+# To see the full list of contributors, see the revision history in
+# source control. Note that revision history for code imported
+# at the start of the repository was not retained.
+# Code in submodules is also not included.
+
+Argonne National Laboratory
+Brookhaven National Laboratory
+Lawrence Berkeley National Laboratory
+Lawrence Livermore National Laboratory
+Los Alamos National Laboratory
+National Center for Atmospheric Research
+Oak Ridge National Laboratory
+Pacific Northwest National Laboratory
+Sandia National Laboratory
+
diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,15 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: Energy Exascale Earth System Model
+message: '  If you use this software, please cite it using the metadata from this file.'
+type: software
+authors:
+  - given-names: E3SM
+    family-names: Project
+version: 2.1.0
+doi: 10.11578/E3SM/dc.20230110.5
+repository-code: 'https://github.com/E3SM-Project/E3SM'
+url: 'https://e3sm.org'
+license: BSD-3-Clause
diff --git a/LICENSE b/LICENSE
@@ -2,7 +2,7 @@ Except for the separable pieces descibed below, E3SM is released
 under the following 3-Clause BSD Open Source license.
 
 *******************************************************************************
-Copyright ©2021, UChicago Argonne, LLC All Rights Reserved
+Copyright ©2023, UChicago Argonne, LLC All Rights Reserved
 
 Software Name: Energy Exascale Earth System Model (E3SM)
 

diff --git a/README.md b/README.md
@@ -9,7 +9,7 @@ the most challenging and demanding climate-change research problems and
 Department of Energy mission needs while efficiently using DOE Leadership
 Computing Facilities.  
 
-DOI: [10.11578/E3SM/dc.20210927.1](http://dx.doi.org/10.11578/E3SM/dc.20210927.1)
+DOI: [10.11578/E3SM/dc.20230110.5](http://dx.doi.org/10.11578/E3SM/dc.20230110.5)
 
 Please visit the [project website](https://e3sm.org) or our [Confluence site](https://acme-climate.atlassian.net/wiki/spaces/DOC/overview)
 for further details.
@@ -64,11 +64,11 @@ the following BibTeX entry is provided.
 	author = {{E3SM Project}},
 	abstractNote = {{E3SM} is a state-of-the-art fully coupled model of the {E}arth's 
 		climate including important biogeochemical and cryospheric processes.},
-	howpublished = {[Computer Software] \url{https://dx.doi.org/10.11578/E3SM/dc.20210927.1}},
-	url = {https://dx.doi.org/10.11578/E3SM/dc.20210927.1},
-	doi = {10.11578/E3SM/dc.20210927.1},
-	year = 2021,
-	month = sep,
+	howpublished = {[Computer Software] \url{https://dx.doi.org/10.11578/E3SM/dc.20230110.5}},
+	url = {https://dx.doi.org/10.11578/E3SM/dc.20230110.5},
+	doi = {10.11578/E3SM/dc.20230110.5},
+	year = 2023,
+	month = jan,
 }
 ```
 

diff --git a/cime_config/allactive/config_pesall.xml b/cime_config/allactive/config_pesall.xml
@@ -781,6 +781,46 @@
     </mach>
   </grid>
   <grid name="a%ne120np4">
+    <mach name="pm-cpu|alvarez">
+      <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SWAV.*" pesize="any">
+        <comment>ne120-wcycl on 42 nodes 128x1c8 ~0.7 sypd</comment>
+        <MAX_MPITASKS_PER_NODE>128</MAX_MPITASKS_PER_NODE>
+        <MAX_TASKS_PER_NODE>256</MAX_TASKS_PER_NODE>
+        <ntasks>
+          <ntasks_atm>3072</ntasks_atm>
+          <ntasks_cpl>384</ntasks_cpl>
+          <ntasks_ice>3072</ntasks_ice>
+          <ntasks_lnd>2560</ntasks_lnd>
+          <ntasks_rof>512</ntasks_rof>
+          <ntasks_ocn>2304</ntasks_ocn>
+          <ntasks_glc>1</ntasks_glc>
+          <ntasks_wav>1</ntasks_wav>
+        </ntasks>
+        <nthrds>
+          <nthrds_atm>1</nthrds_atm>
+          <nthrds_cpl>1</nthrds_cpl>
+          <nthrds_ice>1</nthrds_ice>
+          <nthrds_lnd>1</nthrds_lnd>
+          <nthrds_rof>1</nthrds_rof>
+          <nthrds_ocn>1</nthrds_ocn>
+          <nthrds_glc>1</nthrds_glc>
+          <nthrds_wav>1</nthrds_wav>
+        </nthrds>
+        <rootpe>
+          <rootpe_atm>0</rootpe_atm>
+          <rootpe_cpl>0</rootpe_cpl>
+          <rootpe_ice>0</rootpe_ice>
+          <rootpe_lnd>0</rootpe_lnd>
+          <rootpe_rof>2560</rootpe_rof>
+          <rootpe_ocn>3072</rootpe_ocn>
+          <rootpe_glc>0</rootpe_glc>
+          <rootpe_wav>0</rootpe_wav>
+        </rootpe>
+        <pstrid>
+          <pstrid_cpl>8</pstrid_cpl>
+        </pstrid>
+      </pes>
+    </mach>
     <mach name="theta">
       <pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SWAV.*" pesize="any">
         <comment>ne120-wcycl on 145 nodes, MPI-only</comment>

diff --git a/cime_config/machines/cmake_macros/gnu_alvarez.cmake b/cime_config/machines/cmake_macros/gnu_alvarez.cmake
@@ -2,7 +2,7 @@ string(APPEND CONFIG_ARGS " --host=cray")
 if (COMP_NAME STREQUAL gptl)
   string(APPEND CPPDEFS " -DHAVE_NANOTIME -DBIT64 -DHAVE_SLASHPROC -DHAVE_GETTIMEOFDAY")
 endif()
-string(APPEND SLIBS " -L$ENV{CRAY_HDF5_PARALLEL_PREFIX}/lib -lhdf5_hl -lhdf5 -L$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX} -L$ENV{CRAY_PARALLEL_NETCDF_PREFIX}/lib -lpnetcdf -lnetcdf -lnetcdff")
+string(APPEND SLIBS " -L$ENV{CRAY_HDF5_PARALLEL_PREFIX}/lib -lhdf5_hl -lhdf5 -L$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}/lib -L$ENV{CRAY_PARALLEL_NETCDF_PREFIX}/lib -lpnetcdf -lnetcdf -lnetcdff")
 string(APPEND SLIBS " -lblas -llapack")
 set(CXX_LINKER "FORTRAN")
 set(NETCDF_PATH "$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}")

diff --git a/cime_config/machines/cmake_macros/gnu_pm-cpu.cmake b/cime_config/machines/cmake_macros/gnu_pm-cpu.cmake
@@ -2,7 +2,7 @@ string(APPEND CONFIG_ARGS " --host=cray")
 if (COMP_NAME STREQUAL gptl)
   string(APPEND CPPDEFS " -DHAVE_NANOTIME -DBIT64 -DHAVE_SLASHPROC -DHAVE_GETTIMEOFDAY")
 endif()
-string(APPEND SLIBS " -L$ENV{CRAY_HDF5_PARALLEL_PREFIX}/lib -lhdf5_hl -lhdf5 -L$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX} -L$ENV{CRAY_PARALLEL_NETCDF_PREFIX}/lib -lpnetcdf -lnetcdf -lnetcdff")
+string(APPEND SLIBS " -L$ENV{CRAY_HDF5_PARALLEL_PREFIX}/lib -lhdf5_hl -lhdf5 -L$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}/lib -L$ENV{CRAY_PARALLEL_NETCDF_PREFIX}/lib -lpnetcdf -lnetcdf -lnetcdff")
 string(APPEND SLIBS " -lblas -llapack")
 set(CXX_LINKER "FORTRAN")
 set(NETCDF_PATH "$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}")

diff --git a/cime_config/machines/cmake_macros/gnu_pm-gpu.cmake b/cime_config/machines/cmake_macros/gnu_pm-gpu.cmake
@@ -2,7 +2,7 @@ string(APPEND CONFIG_ARGS " --host=cray")
 if (COMP_NAME STREQUAL gptl)
   string(APPEND CPPDEFS " -DHAVE_NANOTIME -DBIT64 -DHAVE_SLASHPROC -DHAVE_GETTIMEOFDAY")
 endif()
-string(APPEND SLIBS " -L$ENV{CRAY_HDF5_PARALLEL_PREFIX}/lib -lhdf5_hl -lhdf5 -L$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX} -L$ENV{CRAY_PARALLEL_NETCDF_PREFIX}/lib -lpnetcdf -lnetcdf -lnetcdff")
+string(APPEND SLIBS " -L$ENV{CRAY_HDF5_PARALLEL_PREFIX}/lib -lhdf5_hl -lhdf5 -L$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}/lib -L$ENV{CRAY_PARALLEL_NETCDF_PREFIX}/lib -lpnetcdf -lnetcdf -lnetcdff")
 string(APPEND SLIBS " -lblas -llapack")
 set(CXX_LINKER "FORTRAN")
 set(NETCDF_PATH "$ENV{CRAY_NETCDF_HDF5PARALLEL_PREFIX}")

diff --git a/cime_config/machines/config_machines.xml b/cime_config/machines/config_machines.xml
@@ -237,10 +237,10 @@
         <command name="load">craype-accel-host</command>
         <command name="load">cray-libsci</command>
         <command name="load">craype</command>
-        <command name="load">cray-mpich/8.1.17</command>
-        <command name="load">cray-hdf5-parallel/1.12.1.5</command>
-        <command name="load">cray-netcdf-hdf5parallel/4.8.1.5</command>
-        <command name="load">cray-parallel-netcdf/1.12.2.5</command>
+        <command name="load">cray-mpich/8.1.22</command>
+        <command name="load">cray-hdf5-parallel/1.12.2.1</command>
+        <command name="load">cray-netcdf-hdf5parallel/4.9.0.1</command>
+        <command name="load">cray-parallel-netcdf/1.12.3.1</command>
         <command name="load">cmake/3.22.0</command>
       </modules>
     </module_system>
@@ -359,10 +359,10 @@
       <modules>
         <command name="load">cray-libsci</command>
         <command name="load">craype</command>
-        <command name="load">cray-mpich/8.1.17</command>
-        <command name="load">cray-hdf5-parallel/1.12.1.5</command>
-        <command name="load">cray-netcdf-hdf5parallel/4.8.1.5</command>
-        <command name="load">cray-parallel-netcdf/1.12.2.5</command>
+        <command name="load">cray-mpich/8.1.22</command>
+        <command name="load">cray-hdf5-parallel/1.12.2.1</command>
+        <command name="load">cray-netcdf-hdf5parallel/4.9.0.1</command>
+        <command name="load">cray-parallel-netcdf/1.12.3.1</command>
         <command name="load">cmake/3.22.0</command>
       </modules>
     </module_system>

diff --git a/cime_config/tests.py b/cime_config/tests.py
@@ -91,7 +91,7 @@
             "SMS_R_Ld5.ne4_ne4.FSCM-ARM97.eam-scm",
             "SMS_D_Ln5.ne4_oQU240.F2010",
             "SMS_Ln5.ne4pg2_oQU480.F2010",
-            "ERS.ne4_oQU240.F2010.eam-hommexx"
+            "ERS_D.ne4_oQU240.F2010.eam-hommexx"
             )
         },
 

diff --git a/codemeta.json b/codemeta.json
@@ -7,11 +7,11 @@
       "name": "E3SM Project",
     }
   ],
-  "identifier": "http://dx.doi.org/10.11578/E3SM/dc.20180418.36",
+  "identifier": "http://dx.doi.org/10.11578/E3SM/dc.20230110.5",
   "codeRepository": "https://github.com/E3SM-Project/E3SM",
-  "datePublished": "2018-04-20",
+  "datePublished": "2023-01-11",
   "keywords": "climate modeling",
   "license": "BSD",
   "title": "Energy Exascale Earth System Model",
-  "version": "v1.0.0"
+  "version": "v2.1.0"
 }
diff --git a/components/eam/cime_config/config_pes.xml b/components/eam/cime_config/config_pes.xml
@@ -1663,6 +1663,36 @@
     </mach>
   </grid>
   <grid name="a%ne120np4">
+    <mach name="pm-cpu|alvarez">
+      <pes compset=".*EAM.+ELM.+MPASSI.+DOCN.+SGLC.+SWAV.*" pesize="any">
+        <comment>pm-cpu ne120pg2 F-compset with MPASSI on 43 nodes 128x1c8 0.6 sypd</comment>
+        <MAX_MPITASKS_PER_NODE>128</MAX_MPITASKS_PER_NODE>
+        <MAX_TASKS_PER_NODE>256</MAX_TASKS_PER_NODE>
+        <ntasks>
+          <ntasks_atm>5504</ntasks_atm>
+          <ntasks_lnd>5504</ntasks_lnd>
+          <ntasks_rof>5504</ntasks_rof>
+          <ntasks_ice>5200</ntasks_ice>
+          <ntasks_ocn>5200</ntasks_ocn>
+          <ntasks_glc>64</ntasks_glc>
+          <ntasks_wav>64</ntasks_wav>
+          <ntasks_cpl>688</ntasks_cpl>
+        </ntasks>
+        <nthrds>
+          <nthrds_atm>1</nthrds_atm>
+          <nthrds_lnd>1</nthrds_lnd>
+          <nthrds_rof>1</nthrds_rof>
+          <nthrds_ice>1</nthrds_ice>
+          <nthrds_ocn>1</nthrds_ocn>
+          <nthrds_glc>1</nthrds_glc>
+          <nthrds_wav>1</nthrds_wav>
+          <nthrds_cpl>1</nthrds_cpl>
+        </nthrds>
+        <pstrid>
+          <pstrid_cpl>8</pstrid_cpl>
+        </pstrid>
+      </pes>
+    </mach>
     <mach name="theta">
       <pes compset=".*EAM.+ELM.+DOCN.+SGLC.+SWAV.*" pesize="any">
         <comment>ne120 F-compset on 128 nodes 0.524sypd</comment>