From 6c0ea1de8c51d726c3b92957d3e56d0bcaf2fff2 Mon Sep 17 00:00:00 2001 From: Denise Worthen Date: Fri, 22 Nov 2019 11:40:08 -0500 Subject: [PATCH 01/12] Update .gitmodules --- .gitmodules | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.gitmodules b/.gitmodules index 269f4f9a..29971fa0 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,22 +1,22 @@ [submodule "FV3"] path = FV3 - url = https://github.com/NOAA-EMC/fv3atm + url = https://github.com/DeniseWorthen/fv3atm branch = develop [submodule "NEMS"] path = NEMS - url = https://github.com/NOAA-EMC/NEMS.git + url = https://github.com/DeniseWorthen/NEMS.git branch = develop [submodule "CICE_SRC"] path = CICE_SRC - url = https://github.com/NOAA-EMC/CICE5.git + url = https://github.com/DeniseWorthen/CICE5.git branch = develop [submodule "FMS"] path = FMS - url = https://github.com/NOAA-EMC/FMS + url = https://github.com/DeniseWorthen/FMS branch = GFS-FMS [submodule "stochastic_physics"] path = stochastic_physics url = https://github.com/noaa-psd/stochastic_physics [submodule "MOM6"] path = MOM6 - url = https://github.com/NOAA-EMC/MOM6-interface + url = https://github.com/DeniseWorthen/MOM6-interface From e72146c632d758842b6e2ba58caa3fc20552f112 Mon Sep 17 00:00:00 2001 From: "denise.worthen" Date: Fri, 22 Nov 2019 16:50:53 +0000 Subject: [PATCH 02/12] update submodules for nems,stochastic_physics --- NEMS | 2 +- stochastic_physics | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/NEMS b/NEMS index 22be22b0..95f9ac34 160000 --- a/NEMS +++ b/NEMS @@ -1 +1 @@ -Subproject commit 22be22b0ad8836a6c8264075f79cbcca64ba74a7 +Subproject commit 95f9ac3441d40c069259199ebd674084ac5a366c diff --git a/stochastic_physics b/stochastic_physics index 25c3321e..231e5b72 160000 --- a/stochastic_physics +++ b/stochastic_physics @@ -1 +1 @@ -Subproject commit 25c3321ec77fe0de50b60399a4eff71363fabd90 +Subproject commit 231e5b7283580662d3ae5fcaef93bb3f43cf42cf From 190d88fdaf67b0a48f12cf9fa0fc13c55880b3c2 Mon Sep 17 00:00:00 2001 From: "denise.worthen" Date: Sat, 23 Nov 2019 18:24:53 +0000 Subject: [PATCH 03/12] update NEMS,stochastic_physics --- NEMS | 2 +- stochastic_physics | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/NEMS b/NEMS index 95f9ac34..22be22b0 160000 --- a/NEMS +++ b/NEMS @@ -1 +1 @@ -Subproject commit 95f9ac3441d40c069259199ebd674084ac5a366c +Subproject commit 22be22b0ad8836a6c8264075f79cbcca64ba74a7 diff --git a/stochastic_physics b/stochastic_physics index 231e5b72..25c3321e 160000 --- a/stochastic_physics +++ b/stochastic_physics @@ -1 +1 @@ -Subproject commit 231e5b7283580662d3ae5fcaef93bb3f43cf42cf +Subproject commit 25c3321ec77fe0de50b60399a4eff71363fabd90 From 0c8cb0b8451a11f7ab897cb4d31fc6233cf96c31 Mon Sep 17 00:00:00 2001 From: "denise.worthen" Date: Mon, 2 Dec 2019 15:21:56 +0000 Subject: [PATCH 04/12] update CICE submode for feature/halfdeg (with build change) and MOM_input template for initial condition files --- CICE_SRC | 2 +- parm/MOM_input_template | 56 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 57 insertions(+), 1 deletion(-) diff --git a/CICE_SRC b/CICE_SRC index a2dc77db..33111b25 160000 --- a/CICE_SRC +++ b/CICE_SRC @@ -1 +1 @@ -Subproject commit a2dc77db2ff6e17aa6659b495e7aa05d31275dcd +Subproject commit 33111b257e9f22b2991333931ed16931d0d45217 diff --git a/parm/MOM_input_template b/parm/MOM_input_template index 00bb2c9f..afc5e9ec 100644 --- a/parm/MOM_input_template +++ b/parm/MOM_input_template @@ -151,6 +151,62 @@ MINIMUM_DEPTH = 9.5 ! [m] default = 0.0 ! MINIMUM_DEPTH is assumed to be land and all fluxes are masked out. ! If MASKING_DEPTH is specified, then all depths shallower than ! MINIMUM_DEPTH but deeper than MASKING_DEPTH are rounded to MINIMUM_DEPTH. +THICKNESS_CONFIG = "file" ! + ! A string that determines how the initial layer + ! thicknesses are specified for a new run: + ! file - read interface heights from the file specified + ! thickness_file - read thicknesses from the file specified + ! by (THICKNESS_FILE). + ! coord - determined by ALE coordinate. + ! uniform - uniform thickness layers evenly distributed + ! between the surface and MAXIMUM_DEPTH. + ! DOME - use a slope and channel configuration for the + ! DOME sill-overflow test case. + ! benchmark - use the benchmark test case thicknesses. + ! search - search a density profile for the interface + ! densities. This is not yet implemented. + ! circle_obcs - the circle_obcs test case is used. + ! DOME2D - 2D version of DOME initialization. + ! adjustment2d - TBD AJA. + ! sloshing - TBD AJA. + ! seamount - TBD AJA. + ! rossby_front - a mixed layer front in thermal wind balance. + ! USER - call a user modified routine. +THICKNESS_FILE = "MOM6.mx050.res.nc" ! + ! The name of the thickness file. +TS_CONFIG = "file" ! + ! A string that determines how the initial tempertures + ! and salinities are specified for a new run: + ! file - read velocities from the file specified + ! by (TS_FILE). + ! fit - find the temperatures that are consistent with + ! the layer densities and salinity S_REF. + ! TS_profile - use temperature and salinity profiles + ! (read from TS_FILE) to set layer densities. + ! benchmark - use the benchmark test case T & S. + ! linear - linear in logical layer space. + ! DOME2D - 2D DOME initialization. + ! adjustment2d - TBD AJA. + ! sloshing - TBD AJA. + ! seamount - TBD AJA. + ! rossby_front - a mixed layer front in thermal wind balance. + ! SCM_ideal_hurr - used in the SCM idealized hurricane test. + ! USER - call a user modified routine. +TS_FILE = "MOM6.mx050.res.nc" ! + ! The initial condition file for temperature. +VELOCITY_CONFIG = "file" ! + ! A string that determines how the initial velocities + ! are specified for a new run: + ! file - read velocities from the file specified + ! by (VELOCITY_FILE). + ! zero - the fluid is initially at rest. + ! uniform - the flow is uniform (determined by + ! parameters INITIAL_U_CONST and INITIAL_V_CONST). + ! rossby_front - a mixed layer front in thermal wind balance. + ! soliton - Equatorial Rossby soliton. + ! USER - call a user modified routine.", default="zero" +VELOCITY_FILE = "MOM6.mx050.res.nc" ! + ! The initial condition file for velocities. GRID_ROTATION_ANGLE_BUGS = False ! [Boolean] default = True ! If true, use an older algorithm to calculate the sine and ! cosines needed rotate between grid-oriented directions and From 040d0275510fcdd6cdbb424a0b3eb46641da5b0b Mon Sep 17 00:00:00 2001 From: "denise.worthen" Date: Fri, 6 Dec 2019 13:58:28 +0000 Subject: [PATCH 05/12] Revert "update CICE submode for feature/halfdeg (with build change) and" This reverts commit 0c8cb0b8451a11f7ab897cb4d31fc6233cf96c31. --- CICE_SRC | 2 +- parm/MOM_input_template | 56 ----------------------------------------- 2 files changed, 1 insertion(+), 57 deletions(-) diff --git a/CICE_SRC b/CICE_SRC index 33111b25..a2dc77db 160000 --- a/CICE_SRC +++ b/CICE_SRC @@ -1 +1 @@ -Subproject commit 33111b257e9f22b2991333931ed16931d0d45217 +Subproject commit a2dc77db2ff6e17aa6659b495e7aa05d31275dcd diff --git a/parm/MOM_input_template b/parm/MOM_input_template index afc5e9ec..00bb2c9f 100644 --- a/parm/MOM_input_template +++ b/parm/MOM_input_template @@ -151,62 +151,6 @@ MINIMUM_DEPTH = 9.5 ! [m] default = 0.0 ! MINIMUM_DEPTH is assumed to be land and all fluxes are masked out. ! If MASKING_DEPTH is specified, then all depths shallower than ! MINIMUM_DEPTH but deeper than MASKING_DEPTH are rounded to MINIMUM_DEPTH. -THICKNESS_CONFIG = "file" ! - ! A string that determines how the initial layer - ! thicknesses are specified for a new run: - ! file - read interface heights from the file specified - ! thickness_file - read thicknesses from the file specified - ! by (THICKNESS_FILE). - ! coord - determined by ALE coordinate. - ! uniform - uniform thickness layers evenly distributed - ! between the surface and MAXIMUM_DEPTH. - ! DOME - use a slope and channel configuration for the - ! DOME sill-overflow test case. - ! benchmark - use the benchmark test case thicknesses. - ! search - search a density profile for the interface - ! densities. This is not yet implemented. - ! circle_obcs - the circle_obcs test case is used. - ! DOME2D - 2D version of DOME initialization. - ! adjustment2d - TBD AJA. - ! sloshing - TBD AJA. - ! seamount - TBD AJA. - ! rossby_front - a mixed layer front in thermal wind balance. - ! USER - call a user modified routine. -THICKNESS_FILE = "MOM6.mx050.res.nc" ! - ! The name of the thickness file. -TS_CONFIG = "file" ! - ! A string that determines how the initial tempertures - ! and salinities are specified for a new run: - ! file - read velocities from the file specified - ! by (TS_FILE). - ! fit - find the temperatures that are consistent with - ! the layer densities and salinity S_REF. - ! TS_profile - use temperature and salinity profiles - ! (read from TS_FILE) to set layer densities. - ! benchmark - use the benchmark test case T & S. - ! linear - linear in logical layer space. - ! DOME2D - 2D DOME initialization. - ! adjustment2d - TBD AJA. - ! sloshing - TBD AJA. - ! seamount - TBD AJA. - ! rossby_front - a mixed layer front in thermal wind balance. - ! SCM_ideal_hurr - used in the SCM idealized hurricane test. - ! USER - call a user modified routine. -TS_FILE = "MOM6.mx050.res.nc" ! - ! The initial condition file for temperature. -VELOCITY_CONFIG = "file" ! - ! A string that determines how the initial velocities - ! are specified for a new run: - ! file - read velocities from the file specified - ! by (VELOCITY_FILE). - ! zero - the fluid is initially at rest. - ! uniform - the flow is uniform (determined by - ! parameters INITIAL_U_CONST and INITIAL_V_CONST). - ! rossby_front - a mixed layer front in thermal wind balance. - ! soliton - Equatorial Rossby soliton. - ! USER - call a user modified routine.", default="zero" -VELOCITY_FILE = "MOM6.mx050.res.nc" ! - ! The initial condition file for velocities. GRID_ROTATION_ANGLE_BUGS = False ! [Boolean] default = True ! If true, use an older algorithm to calculate the sine and ! cosines needed rotate between grid-oriented directions and From 6d15ca750634fcbe25b438eaf3cbc63e3ec26e2a Mon Sep 17 00:00:00 2001 From: "denise.worthen" Date: Fri, 6 Dec 2019 14:00:01 +0000 Subject: [PATCH 06/12] update CICE submodule --- CICE_SRC | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CICE_SRC b/CICE_SRC index a2dc77db..f18f8398 160000 --- a/CICE_SRC +++ b/CICE_SRC @@ -1 +1 @@ -Subproject commit a2dc77db2ff6e17aa6659b495e7aa05d31275dcd +Subproject commit f18f8398abc6e4111bbf7c046d24d4be6c37065a From 7bf2632a1282ecbea7883cd1af9433fa0c9dd770 Mon Sep 17 00:00:00 2001 From: "denise.worthen" Date: Thu, 12 Dec 2019 07:51:47 -0500 Subject: [PATCH 07/12] update develop branch in my fork to use NOAA-EMC develop branches --- .gitmodules | 10 +++++----- CICE_SRC | 2 +- MOM6 | 2 +- stochastic_physics | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.gitmodules b/.gitmodules index 29971fa0..269f4f9a 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,22 +1,22 @@ [submodule "FV3"] path = FV3 - url = https://github.com/DeniseWorthen/fv3atm + url = https://github.com/NOAA-EMC/fv3atm branch = develop [submodule "NEMS"] path = NEMS - url = https://github.com/DeniseWorthen/NEMS.git + url = https://github.com/NOAA-EMC/NEMS.git branch = develop [submodule "CICE_SRC"] path = CICE_SRC - url = https://github.com/DeniseWorthen/CICE5.git + url = https://github.com/NOAA-EMC/CICE5.git branch = develop [submodule "FMS"] path = FMS - url = https://github.com/DeniseWorthen/FMS + url = https://github.com/NOAA-EMC/FMS branch = GFS-FMS [submodule "stochastic_physics"] path = stochastic_physics url = https://github.com/noaa-psd/stochastic_physics [submodule "MOM6"] path = MOM6 - url = https://github.com/DeniseWorthen/MOM6-interface + url = https://github.com/NOAA-EMC/MOM6-interface diff --git a/CICE_SRC b/CICE_SRC index f18f8398..8a922615 160000 --- a/CICE_SRC +++ b/CICE_SRC @@ -1 +1 @@ -Subproject commit f18f8398abc6e4111bbf7c046d24d4be6c37065a +Subproject commit 8a92261596c017796a92d36c8d48bd6869b4a34a diff --git a/MOM6 b/MOM6 index 5821b916..12db82d2 160000 --- a/MOM6 +++ b/MOM6 @@ -1 +1 @@ -Subproject commit 5821b916405bae73e3f1c0f54ec496dd21ab232e +Subproject commit 12db82d276da212448403da5265f6720f40a7cfb diff --git a/stochastic_physics b/stochastic_physics index 25c3321e..231e5b72 160000 --- a/stochastic_physics +++ b/stochastic_physics @@ -1 +1 @@ -Subproject commit 25c3321ec77fe0de50b60399a4eff71363fabd90 +Subproject commit 231e5b7283580662d3ae5fcaef93bb3f43cf42cf From bf4bbcecb4400f25cf78f18ecc08619ddff76b77 Mon Sep 17 00:00:00 2001 From: Denise Worthen Date: Mon, 20 Jan 2020 15:08:20 -0500 Subject: [PATCH 08/12] Update configure.fv3_coupled.hera.intel --- conf/configure.fv3_coupled.hera.intel | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/configure.fv3_coupled.hera.intel b/conf/configure.fv3_coupled.hera.intel index 82339766..ea3dc985 100644 --- a/conf/configure.fv3_coupled.hera.intel +++ b/conf/configure.fv3_coupled.hera.intel @@ -108,7 +108,7 @@ endif FFLAGS_OPT = -O2 -debug minimal -fp-model source -qoverride-limits -qopt-prefetch=3 FFLAGS_REPRO = -O2 -debug minimal -fp-model consistent -qoverride-limits -g -traceback -FFLAGS_DEBUG = -g -O0 -check all -check noarg_temp_created -check nopointer -warn -warn noerrors -fp-stack-check -fstack-protector-all -fpe0 -debug -traceback -ftrapuv +FFLAGS_DEBUG = -g -O0 -check all -check noarg_temp_created -check nopointer -warn -warn noerrors -fp-stack-check -fstack-protector-all -fpe0 -debug -traceback -ftrapuv -link_mpi=dbg TRANSCENDENTALS := -fast-transcendentals FFLAGS_OPENMP = -qopenmp From 78096965583cdc8eab7a2a92e3a27d66a3b3a8f2 Mon Sep 17 00:00:00 2001 From: Denise Worthen Date: Mon, 20 Jan 2020 15:09:19 -0500 Subject: [PATCH 09/12] Update configure.fv3_coupled.cheyenne.intel --- conf/configure.fv3_coupled.cheyenne.intel | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/configure.fv3_coupled.cheyenne.intel b/conf/configure.fv3_coupled.cheyenne.intel index ff489f28..5b305910 100644 --- a/conf/configure.fv3_coupled.cheyenne.intel +++ b/conf/configure.fv3_coupled.cheyenne.intel @@ -130,7 +130,7 @@ endif FFLAGS_OPT = -O2 -debug minimal -fp-model source -qoverride-limits -qopt-prefetch=3 FFLAGS_REPRO = -O2 -debug minimal -fp-model consistent -qoverride-limits -g -traceback -FFLAGS_DEBUG = -g -O0 -check all -check noarg_temp_created -check nopointer -warn -warn noerrors -fp-stack-check -fstack-protector-all -fpe0 -debug -traceback -ftrapuv +FFLAGS_DEBUG = -g -O0 -check all -check noarg_temp_created -check nopointer -warn -warn noerrors -fp-stack-check -fstack-protector-all -fpe0 -debug -traceback -ftrapuv -link_mpi=dbg TRANSCENDENTALS := -fast-transcendentals FFLAGS_OPENMP = -qopenmp From 57236a665d1efcbac28a53826daaa7a0385746eb Mon Sep 17 00:00:00 2001 From: "denise.worthen" Date: Fri, 24 Jan 2020 17:43:29 +0000 Subject: [PATCH 10/12] update gitmodules, FV3 for gfsv16 incomming commit, NEMS for nomerg2atm, new MOM6 dev/emc --- .gitmodules | 4 ++-- FV3 | 2 +- MOM6 | 2 +- NEMS | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.gitmodules b/.gitmodules index 269f4f9a..088a0e24 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,10 +1,10 @@ [submodule "FV3"] path = FV3 - url = https://github.com/NOAA-EMC/fv3atm + url = https://github.com/DusanJovic-NOAA/fv3atm branch = develop [submodule "NEMS"] path = NEMS - url = https://github.com/NOAA-EMC/NEMS.git + url = https://github.com/DeniseWorthen/NEMS.git branch = develop [submodule "CICE_SRC"] path = CICE_SRC diff --git a/FV3 b/FV3 index b1ddd67b..89f06ff8 160000 --- a/FV3 +++ b/FV3 @@ -1 +1 @@ -Subproject commit b1ddd67b83bd170160c1ebcca7010172335f120b +Subproject commit 89f06ff8d789749642756009ed7dcfb8c3ee9eed diff --git a/MOM6 b/MOM6 index 575f570b..1fd34930 160000 --- a/MOM6 +++ b/MOM6 @@ -1 +1 @@ -Subproject commit 575f570b53c376747630621a60a4a10cf659a264 +Subproject commit 1fd3493066a84c43a77303f255df721fdb33e0a8 diff --git a/NEMS b/NEMS index daae3883..a50e0d9f 160000 --- a/NEMS +++ b/NEMS @@ -1 +1 @@ -Subproject commit daae3883eb5e70b007f20388d2e949aed3be6b79 +Subproject commit a50e0d9f43c030337c6cf83c068ad6a6fc1e6431 From 2ac97e1e1b528da74049141525c19e5ede46c5db Mon Sep 17 00:00:00 2001 From: "denise.worthen" Date: Fri, 24 Jan 2020 21:05:45 +0000 Subject: [PATCH 11/12] Revert changes that were meant for a branch, not develop This reverts commit 57236a665d1efcbac28a53826daaa7a0385746eb. --- .gitmodules | 4 ++-- FV3 | 2 +- MOM6 | 2 +- NEMS | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.gitmodules b/.gitmodules index 088a0e24..269f4f9a 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,10 +1,10 @@ [submodule "FV3"] path = FV3 - url = https://github.com/DusanJovic-NOAA/fv3atm + url = https://github.com/NOAA-EMC/fv3atm branch = develop [submodule "NEMS"] path = NEMS - url = https://github.com/DeniseWorthen/NEMS.git + url = https://github.com/NOAA-EMC/NEMS.git branch = develop [submodule "CICE_SRC"] path = CICE_SRC diff --git a/FV3 b/FV3 index 89f06ff8..b1ddd67b 160000 --- a/FV3 +++ b/FV3 @@ -1 +1 @@ -Subproject commit 89f06ff8d789749642756009ed7dcfb8c3ee9eed +Subproject commit b1ddd67b83bd170160c1ebcca7010172335f120b diff --git a/MOM6 b/MOM6 index 1fd34930..575f570b 160000 --- a/MOM6 +++ b/MOM6 @@ -1 +1 @@ -Subproject commit 1fd3493066a84c43a77303f255df721fdb33e0a8 +Subproject commit 575f570b53c376747630621a60a4a10cf659a264 diff --git a/NEMS b/NEMS index a50e0d9f..daae3883 160000 --- a/NEMS +++ b/NEMS @@ -1 +1 @@ -Subproject commit a50e0d9f43c030337c6cf83c068ad6a6fc1e6431 +Subproject commit daae3883eb5e70b007f20388d2e949aed3be6b79 From 7d96f6f34e397ec495f4aba34b3f7a3ec96de0f1 Mon Sep 17 00:00:00 2001 From: "denise.worthen" Date: Mon, 4 May 2020 13:23:04 +0000 Subject: [PATCH 12/12] update MOM6 and CICE5 submodules for porting to orion --- CICE_SRC | 2 +- MOM6 | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CICE_SRC b/CICE_SRC index 27e5e3fa..468841ab 160000 --- a/CICE_SRC +++ b/CICE_SRC @@ -1 +1 @@ -Subproject commit 27e5e3fa9d4b6045aa4a5b607344f8a19f67306e +Subproject commit 468841abc0c24735b47d7ea94bafd6e5620e2536 diff --git a/MOM6 b/MOM6 index 1fd34930..fd705338 160000 --- a/MOM6 +++ b/MOM6 @@ -1 +1 @@ -Subproject commit 1fd3493066a84c43a77303f255df721fdb33e0a8 +Subproject commit fd70533890d8adb51a9e8e85fc4adeef2e5f4fc5