Fix macOS build errors; fv3atm: register diagnostics from stochastic …

…physics only if allocated; ccpp-physics: cleanup CCPP cmake flags part 1 (#897)

* Changes from CCPP/physics and fv3atm:
- Fix duplicate symbols and undefined symbols errors on macOS
- Register diagnostics from stochastic physics only if allocated in fv3atm
-Updates the submodule pointer for ccpp-physics for the changes described in Cleanup CCPP cmake flags part 1, remove extra logic that reduces optimization for radiation_aerosols.f, update CODEOWNERS, update README.md NCAR/ccpp-physics#773
- Update top-level README.md in ccpp-physics
* Set ECF_TRIES to 1 on WCOSS systems in ufs-weather-model

cmake/Intel.cmake

@@ -52,3 +52,9 @@ set(CMAKE_Fortran_FLAGS_RELEASE "-O2 -fPIC" CACHE STRING "" FORCE)
 set(CMAKE_C_FLAGS_BITFORBIT       "-O2 -fPIC" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_BITFORBIT     "-O2 -fPIC" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_FLAGS_BITFORBIT "-O2 -fPIC" CACHE STRING "" FORCE)
+
+if(APPLE)
+  # The linker on macOS does not include `common symbols` by default
+  # Passing the -c flag includes them and fixes an error with undefined symbols
+  set(CMAKE_Fortran_ARCHIVE_FINISH "<CMAKE_RANLIB> -c <TARGET>")
+endif()

tests/OpnReqTests_hera.intel.log

@@ -0,0 +1,327 @@
+
+baseline dir = /scratch1/NCEPDEV/stmp4/Dom.Heinzeller/FV3_OPNREQ_TEST/OPNREQ_TEST/control_bit_base
+working dir  = /scratch1/NCEPDEV/stmp2/Dom.Heinzeller/FV3_OPNREQ_TEST/opnReqTest_31847/control_bit_base
+Checking test bit_base control results ....
+Moving baseline bit_base control files ....
+ Moving sfcf000.nc .........OK
+ Moving sfcf021.nc .........OK
+ Moving sfcf024.nc .........OK
+ Moving atmf000.nc .........OK
+ Moving atmf021.nc .........OK
+ Moving atmf024.nc .........OK
+ Moving GFSFLX.GrbF00 .........OK
+ Moving GFSFLX.GrbF21 .........OK
+ Moving GFSFLX.GrbF24 .........OK
+ Moving GFSPRS.GrbF00 .........OK
+ Moving GFSPRS.GrbF21 .........OK
+ Moving GFSPRS.GrbF24 .........OK
+ Moving RESTART/coupler.res .........OK
+ Moving RESTART/fv_core.res.nc .........OK
+ Moving RESTART/fv_core.res.tile1.nc .........OK
+ Moving RESTART/fv_core.res.tile2.nc .........OK
+ Moving RESTART/fv_core.res.tile3.nc .........OK
+ Moving RESTART/fv_core.res.tile4.nc .........OK
+ Moving RESTART/fv_core.res.tile5.nc .........OK
+ Moving RESTART/fv_core.res.tile6.nc .........OK
+ Moving RESTART/fv_srf_wnd.res.tile1.nc .........OK
+ Moving RESTART/fv_srf_wnd.res.tile2.nc .........OK
+ Moving RESTART/fv_srf_wnd.res.tile3.nc .........OK
+ Moving RESTART/fv_srf_wnd.res.tile4.nc .........OK
+ Moving RESTART/fv_srf_wnd.res.tile5.nc .........OK
+ Moving RESTART/fv_srf_wnd.res.tile6.nc .........OK
+ Moving RESTART/fv_tracer.res.tile1.nc .........OK
+ Moving RESTART/fv_tracer.res.tile2.nc .........OK
+ Moving RESTART/fv_tracer.res.tile3.nc .........OK
+ Moving RESTART/fv_tracer.res.tile4.nc .........OK
+ Moving RESTART/fv_tracer.res.tile5.nc .........OK
+ Moving RESTART/fv_tracer.res.tile6.nc .........OK
+ Moving RESTART/phy_data.tile1.nc .........OK
+ Moving RESTART/phy_data.tile2.nc .........OK
+ Moving RESTART/phy_data.tile3.nc .........OK
+ Moving RESTART/phy_data.tile4.nc .........OK
+ Moving RESTART/phy_data.tile5.nc .........OK
+ Moving RESTART/phy_data.tile6.nc .........OK
+ Moving RESTART/sfc_data.tile1.nc .........OK
+ Moving RESTART/sfc_data.tile2.nc .........OK
+ Moving RESTART/sfc_data.tile3.nc .........OK
+ Moving RESTART/sfc_data.tile4.nc .........OK
+ Moving RESTART/sfc_data.tile5.nc .........OK
+ Moving RESTART/sfc_data.tile6.nc .........OK
+
+  0: The total amount of wall time                        = 152.597749
+
+Test bit_base control PASS
+
+
+baseline dir = /scratch1/NCEPDEV/stmp4/Dom.Heinzeller/FV3_OPNREQ_TEST/OPNREQ_TEST/control_dbg_base
+working dir  = /scratch1/NCEPDEV/stmp2/Dom.Heinzeller/FV3_OPNREQ_TEST/opnReqTest_31847/control_dbg_base
+Checking test dbg_base control results ....
+Moving baseline dbg_base control files ....
+ Moving sfcf001.nc .........OK
+ Moving sfcf001.nc .........OK
+
+  0: The total amount of wall time                        = 146.316531
+
+Test dbg_base control PASS
+
+
+baseline dir = /scratch1/NCEPDEV/stmp4/Dom.Heinzeller/FV3_OPNREQ_TEST/OPNREQ_TEST/control_std_base
+working dir  = /scratch1/NCEPDEV/stmp2/Dom.Heinzeller/FV3_OPNREQ_TEST/opnReqTest_31847/control_dcp
+Checking test dcp control results ....
+ Comparing sfcf000.nc .........OK
+ Comparing sfcf021.nc .........OK
+ Comparing sfcf024.nc .........OK
+ Comparing atmf000.nc .........OK
+ Comparing atmf021.nc .........OK
+ Comparing atmf024.nc .........OK
+ Comparing GFSFLX.GrbF00 .........OK
+ Comparing GFSFLX.GrbF21 .........OK
+ Comparing GFSFLX.GrbF24 .........OK
+ Comparing GFSPRS.GrbF00 .........OK
+ Comparing GFSPRS.GrbF21 .........OK
+ Comparing GFSPRS.GrbF24 .........OK
+ Comparing RESTART/coupler.res .........OK
+ Comparing RESTART/fv_core.res.nc .........OK
+ Comparing RESTART/fv_core.res.tile1.nc .........OK
+ Comparing RESTART/fv_core.res.tile2.nc .........OK
+ Comparing RESTART/fv_core.res.tile3.nc .........OK
+ Comparing RESTART/fv_core.res.tile4.nc .........OK
+ Comparing RESTART/fv_core.res.tile5.nc .........OK
+ Comparing RESTART/fv_core.res.tile6.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile1.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile2.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile3.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile4.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile5.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile6.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile1.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile2.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile3.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile4.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile5.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile6.nc .........OK
+ Comparing RESTART/phy_data.tile1.nc .........OK
+ Comparing RESTART/phy_data.tile2.nc .........OK
+ Comparing RESTART/phy_data.tile3.nc .........OK
+ Comparing RESTART/phy_data.tile4.nc .........OK
+ Comparing RESTART/phy_data.tile5.nc .........OK
+ Comparing RESTART/phy_data.tile6.nc .........OK
+ Comparing RESTART/sfc_data.tile1.nc .........OK
+ Comparing RESTART/sfc_data.tile2.nc .........OK
+ Comparing RESTART/sfc_data.tile3.nc .........OK
+ Comparing RESTART/sfc_data.tile4.nc .........OK
+ Comparing RESTART/sfc_data.tile5.nc .........OK
+ Comparing RESTART/sfc_data.tile6.nc .........OK
+
+  0: The total amount of wall time                        = 129.238103
+
+Test dcp control PASS
+
+
+baseline dir = /scratch1/NCEPDEV/stmp4/Dom.Heinzeller/FV3_OPNREQ_TEST/OPNREQ_TEST/control_std_base
+working dir  = /scratch1/NCEPDEV/stmp2/Dom.Heinzeller/FV3_OPNREQ_TEST/opnReqTest_31847/control_mpi
+Checking test mpi control results ....
+ Comparing sfcf000.nc .........OK
+ Comparing sfcf021.nc .........OK
+ Comparing sfcf024.nc .........OK
+ Comparing atmf000.nc .........OK
+ Comparing atmf021.nc .........OK
+ Comparing atmf024.nc .........OK
+ Comparing GFSFLX.GrbF00 .........OK
+ Comparing GFSFLX.GrbF21 .........OK
+ Comparing GFSFLX.GrbF24 .........OK
+ Comparing GFSPRS.GrbF00 .........OK
+ Comparing GFSPRS.GrbF21 .........OK
+ Comparing GFSPRS.GrbF24 .........OK
+ Comparing RESTART/coupler.res .........OK
+ Comparing RESTART/fv_core.res.nc .........OK
+ Comparing RESTART/fv_core.res.tile1.nc .........OK
+ Comparing RESTART/fv_core.res.tile2.nc .........OK
+ Comparing RESTART/fv_core.res.tile3.nc .........OK
+ Comparing RESTART/fv_core.res.tile4.nc .........OK
+ Comparing RESTART/fv_core.res.tile5.nc .........OK
+ Comparing RESTART/fv_core.res.tile6.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile1.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile2.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile3.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile4.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile5.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile6.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile1.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile2.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile3.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile4.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile5.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile6.nc .........OK
+ Comparing RESTART/phy_data.tile1.nc .........OK
+ Comparing RESTART/phy_data.tile2.nc .........OK
+ Comparing RESTART/phy_data.tile3.nc .........OK
+ Comparing RESTART/phy_data.tile4.nc .........OK
+ Comparing RESTART/phy_data.tile5.nc .........OK
+ Comparing RESTART/phy_data.tile6.nc .........OK
+ Comparing RESTART/sfc_data.tile1.nc .........OK
+ Comparing RESTART/sfc_data.tile2.nc .........OK
+ Comparing RESTART/sfc_data.tile3.nc .........OK
+ Comparing RESTART/sfc_data.tile4.nc .........OK
+ Comparing RESTART/sfc_data.tile5.nc .........OK
+ Comparing RESTART/sfc_data.tile6.nc .........OK
+
+ 0: The total amount of wall time                        = 199.088882
+
+Test mpi control PASS
+
+
+baseline dir = /scratch1/NCEPDEV/stmp4/Dom.Heinzeller/FV3_OPNREQ_TEST/OPNREQ_TEST/control_std_base
+working dir  = /scratch1/NCEPDEV/stmp2/Dom.Heinzeller/FV3_OPNREQ_TEST/opnReqTest_31847/control_rst
+Checking test rst control results ....
+ Comparing atmf024.nc .........OK
+ Comparing GFSFLX.GrbF24 .........OK
+ Comparing GFSPRS.GrbF24 .........OK
+ Comparing RESTART/coupler.res .........OK
+ Comparing RESTART/fv_core.res.nc .........OK
+ Comparing RESTART/fv_core.res.tile1.nc .........OK
+ Comparing RESTART/fv_core.res.tile2.nc .........OK
+ Comparing RESTART/fv_core.res.tile3.nc .........OK
+ Comparing RESTART/fv_core.res.tile4.nc .........OK
+ Comparing RESTART/fv_core.res.tile5.nc .........OK
+ Comparing RESTART/fv_core.res.tile6.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile1.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile2.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile3.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile4.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile5.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile6.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile1.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile2.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile3.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile4.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile5.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile6.nc .........OK
+ Comparing RESTART/phy_data.tile1.nc .........OK
+ Comparing RESTART/phy_data.tile2.nc .........OK
+ Comparing RESTART/phy_data.tile3.nc .........OK
+ Comparing RESTART/phy_data.tile4.nc .........OK
+ Comparing RESTART/phy_data.tile5.nc .........OK
+ Comparing RESTART/phy_data.tile6.nc .........OK
+ Comparing RESTART/sfc_data.tile1.nc .........OK
+ Comparing RESTART/sfc_data.tile2.nc .........OK
+ Comparing RESTART/sfc_data.tile3.nc .........OK
+ Comparing RESTART/sfc_data.tile4.nc .........OK
+ Comparing RESTART/sfc_data.tile5.nc .........OK
+ Comparing RESTART/sfc_data.tile6.nc .........OK
+ Comparing sfcf024.nc .........OK
+
+  0: The total amount of wall time                        = 62.455018
+
+Test rst control PASS
+
+
+baseline dir = /scratch1/NCEPDEV/stmp4/Dom.Heinzeller/FV3_OPNREQ_TEST/OPNREQ_TEST/control_std_base
+working dir  = /scratch1/NCEPDEV/stmp2/Dom.Heinzeller/FV3_OPNREQ_TEST/opnReqTest_31847/control_std_base
+Checking test std_base control results ....
+Moving baseline std_base control files ....
+ Moving sfcf000.nc .........OK
+ Moving sfcf021.nc .........OK
+ Moving sfcf024.nc .........OK
+ Moving atmf000.nc .........OK
+ Moving atmf021.nc .........OK
+ Moving atmf024.nc .........OK
+ Moving GFSFLX.GrbF00 .........OK
+ Moving GFSFLX.GrbF21 .........OK
+ Moving GFSFLX.GrbF24 .........OK
+ Moving GFSPRS.GrbF00 .........OK
+ Moving GFSPRS.GrbF21 .........OK
+ Moving GFSPRS.GrbF24 .........OK
+ Moving RESTART/coupler.res .........OK
+ Moving RESTART/fv_core.res.nc .........OK
+ Moving RESTART/fv_core.res.tile1.nc .........OK
+ Moving RESTART/fv_core.res.tile2.nc .........OK
+ Moving RESTART/fv_core.res.tile3.nc .........OK
+ Moving RESTART/fv_core.res.tile4.nc .........OK
+ Moving RESTART/fv_core.res.tile5.nc .........OK
+ Moving RESTART/fv_core.res.tile6.nc .........OK
+ Moving RESTART/fv_srf_wnd.res.tile1.nc .........OK
+ Moving RESTART/fv_srf_wnd.res.tile2.nc .........OK
+ Moving RESTART/fv_srf_wnd.res.tile3.nc .........OK
+ Moving RESTART/fv_srf_wnd.res.tile4.nc .........OK
+ Moving RESTART/fv_srf_wnd.res.tile5.nc .........OK
+ Moving RESTART/fv_srf_wnd.res.tile6.nc .........OK
+ Moving RESTART/fv_tracer.res.tile1.nc .........OK
+ Moving RESTART/fv_tracer.res.tile2.nc .........OK
+ Moving RESTART/fv_tracer.res.tile3.nc .........OK
+ Moving RESTART/fv_tracer.res.tile4.nc .........OK
+ Moving RESTART/fv_tracer.res.tile5.nc .........OK
+ Moving RESTART/fv_tracer.res.tile6.nc .........OK
+ Moving RESTART/phy_data.tile1.nc .........OK
+ Moving RESTART/phy_data.tile2.nc .........OK
+ Moving RESTART/phy_data.tile3.nc .........OK
+ Moving RESTART/phy_data.tile4.nc .........OK
+ Moving RESTART/phy_data.tile5.nc .........OK
+ Moving RESTART/phy_data.tile6.nc .........OK
+ Moving RESTART/sfc_data.tile1.nc .........OK
+ Moving RESTART/sfc_data.tile2.nc .........OK
+ Moving RESTART/sfc_data.tile3.nc .........OK
+ Moving RESTART/sfc_data.tile4.nc .........OK
+ Moving RESTART/sfc_data.tile5.nc .........OK
+ Moving RESTART/sfc_data.tile6.nc .........OK
+
+  0: The total amount of wall time                        = 122.209656
+
+Test std_base control PASS
+
+
+baseline dir = /scratch1/NCEPDEV/stmp4/Dom.Heinzeller/FV3_OPNREQ_TEST/OPNREQ_TEST/control_std_base
+working dir  = /scratch1/NCEPDEV/stmp2/Dom.Heinzeller/FV3_OPNREQ_TEST/opnReqTest_31847/control_thr
+Checking test thr control results ....
+ Comparing sfcf000.nc .........OK
+ Comparing sfcf021.nc .........OK
+ Comparing sfcf024.nc .........OK
+ Comparing atmf000.nc .........OK
+ Comparing atmf021.nc .........OK
+ Comparing atmf024.nc .........OK
+ Comparing GFSFLX.GrbF00 .........OK
+ Comparing GFSFLX.GrbF21 .........OK
+ Comparing GFSFLX.GrbF24 .........OK
+ Comparing GFSPRS.GrbF00 .........OK
+ Comparing GFSPRS.GrbF21 .........OK
+ Comparing GFSPRS.GrbF24 .........OK
+ Comparing RESTART/coupler.res .........OK
+ Comparing RESTART/fv_core.res.nc .........OK
+ Comparing RESTART/fv_core.res.tile1.nc .........OK
+ Comparing RESTART/fv_core.res.tile2.nc .........OK
+ Comparing RESTART/fv_core.res.tile3.nc .........OK
+ Comparing RESTART/fv_core.res.tile4.nc .........OK
+ Comparing RESTART/fv_core.res.tile5.nc .........OK
+ Comparing RESTART/fv_core.res.tile6.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile1.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile2.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile3.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile4.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile5.nc .........OK
+ Comparing RESTART/fv_srf_wnd.res.tile6.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile1.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile2.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile3.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile4.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile5.nc .........OK
+ Comparing RESTART/fv_tracer.res.tile6.nc .........OK
+ Comparing RESTART/phy_data.tile1.nc .........OK
+ Comparing RESTART/phy_data.tile2.nc .........OK
+ Comparing RESTART/phy_data.tile3.nc .........OK
+ Comparing RESTART/phy_data.tile4.nc .........OK
+ Comparing RESTART/phy_data.tile5.nc .........OK
+ Comparing RESTART/phy_data.tile6.nc .........OK
+ Comparing RESTART/sfc_data.tile1.nc .........OK
+ Comparing RESTART/sfc_data.tile2.nc .........OK
+ Comparing RESTART/sfc_data.tile3.nc .........OK
+ Comparing RESTART/sfc_data.tile4.nc .........OK
+ Comparing RESTART/sfc_data.tile5.nc .........OK
+ Comparing RESTART/sfc_data.tile6.nc .........OK
+
+ 0: The total amount of wall time                        = 152.937629
+
+Test thr control PASS
+
+OPERATION REQUIREMENT TEST WAS SUCCESSFUL
+Wed Nov 10 22:02:36 UTC 2021
+Elapsed time: 00h:51m:21s. Have a nice day!