From 2969baa2be5015507f84ace7095decee99467c88 Mon Sep 17 00:00:00 2001
From: Jong Kim <jong.kim@noaa.gov>
Date: Mon, 17 Apr 2023 14:18:59 +0000
Subject: [PATCH 01/19] add ufswm build option as external

---
 CMakeLists.txt                 | 18 +++++++++++
 modulefiles/ufs_common.lua     | 59 ++++++++++++++++++++++++++++++++++
 modulefiles/ufs_hera.intel.lua | 33 +++++++++++++++++++
 3 files changed, 110 insertions(+)
 create mode 100644 modulefiles/ufs_common.lua
 create mode 100644 modulefiles/ufs_hera.intel.lua

diff --git a/CMakeLists.txt b/CMakeLists.txt
index dc2bdbb9..affc3a9e 100755
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -21,6 +21,14 @@ enable_testing()
 include( ecbuild_system NO_POLICY_SCOPE )
 ecbuild_declare_project()
 
+# Inlcude externalproject
+# -----------------------
+include(ExternalProject)
+
+# Initialize bundle
+# -----------------
+ecbuild_bundle_initialize()
+
 list( APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 include( landda_compiler_flags )
 
@@ -36,6 +44,16 @@ include_directories( ${NETCDF_INCLUDE_DIRS} )
 ################################################################################
 set( LANDDA_LINKER_LANGUAGE CXX)
 
+ExternalProject_Add(ufs-weather-model
+  PREFIX ${CMAKE_CURRENT_BINARY_DIR}/ufs-weather-model
+  GIT_REPOSITORY https://github.com/ufs-community/ufs-weather-model
+  GIT_SUBMODULES_RECURSE TRUE
+  GIT_TAG develop
+  SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/ufs-weather-model
+  CMAKE_ARGS ${SOURCE_DIR} -DAPP=LND -DMPI=ON -DCMAKE_BUILD_TYPE=Release
+  INSTALL_COMMAND cmake
+  )
+
 add_subdirectory( vector2tile )
 add_subdirectory( ufs-land-driver )
 add_subdirectory( DA_update/add_jedi_incr )
diff --git a/modulefiles/ufs_common.lua b/modulefiles/ufs_common.lua
new file mode 100644
index 00000000..22109f8d
--- /dev/null
+++ b/modulefiles/ufs_common.lua
@@ -0,0 +1,59 @@
+help([[
+loads UFS Model common libraries
+]])
+
+jasper_ver=os.getenv("jasper_ver") or "2.0.32"
+load(pathJoin("jasper", jasper_ver))
+
+zlib_ver=os.getenv("zlib_ver") or "1.2.13"
+load(pathJoin("zlib", zlib_ver))
+
+libpng_ver=os.getenv("libpng_ver") or "1.6.37"
+load(pathJoin("libpng", libpng_ver))
+
+hdf5_ver=os.getenv("hdf5_ver") or "1.14.0"
+load(pathJoin("hdf5", hdf5_ver))
+
+netcdf_c_ver=os.getenv("netcdf_ver") or "4.9.0"
+load(pathJoin("netcdf-c", netcdf_c_ver))
+
+netcdf_fortran_ver=os.getenv("netcdf_fortran_ver") or "4.6.0"
+load(pathJoin("netcdf-fortran", netcdf_fortran_ver))
+
+pio_ver=os.getenv("pio_ver") or "2.5.9"
+load(pathJoin("parallelio", pio_ver))
+
+esmf_ver=os.getenv("esmf_ver") or "8.3.0b09"
+load(pathJoin("esmf", esmf_ver))
+
+fms_ver=os.getenv("fms_ver") or "2022.04"
+load(pathJoin("fms",fms_ver))
+
+bacio_ver=os.getenv("bacio_ver") or "2.4.1"
+load(pathJoin("bacio", bacio_ver))
+
+crtm_ver=os.getenv("crtm_ver") or "2.4.0"
+load(pathJoin("crtm", crtm_ver))
+
+g2_ver=os.getenv("g2_ver") or "3.4.5"
+load(pathJoin("g2", g2_ver))
+
+g2tmpl_ver=os.getenv("g2tmpl_ver") or "1.10.2"
+load(pathJoin("g2tmpl", g2tmpl_ver))
+
+ip_ver=os.getenv("ip_ver") or "3.3.3"
+load(pathJoin("ip", ip_ver))
+
+sp_ver=os.getenv("sp_ver") or "2.3.3"
+load(pathJoin("sp", sp_ver))
+
+w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
+load(pathJoin("w3emc", w3emc_ver))
+
+gftl_shared_ver=os.getenv("gftl_shared_ver") or "v1.5.0"
+load(pathJoin("gftl-shared", gftl_shared_ver))
+
+mapl_ver=os.getenv("mapl_ver") or "2.22.0-esmf-8.3.0b09"
+load(pathJoin("mapl", mapl_ver))
+
+whatis("Description: UFS build environment common libraries")
diff --git a/modulefiles/ufs_hera.intel.lua b/modulefiles/ufs_hera.intel.lua
new file mode 100644
index 00000000..3accf3f8
--- /dev/null
+++ b/modulefiles/ufs_hera.intel.lua
@@ -0,0 +1,33 @@
+help([[
+loads UFS Model prerequisites for Hera/Intel
+]])
+
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.3.0/envs/unified-env/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/jcsda/jedipara/spack-stack/modulefiles")
+
+stack_intel_ver=os.getenv("stack_intel_ver") or "2021.5.0"
+load(pathJoin("stack-intel", stack_intel_ver))
+
+stack_impi_ver=os.getenv("stack_impi_ver") or "2021.5.1"
+load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
+
+stack_python_ver=os.getenv("stack_python_ver") or "3.9.12"
+load(pathJoin("stack-python", stack_python_ver))
+
+cmake_ver=os.getenv("cmake_ver") or "3.23.1"
+load(pathJoin("cmake", cmake_ver))
+
+ecbuild_ver=os.getenv("ecbuild_ver") or "3.6.5"
+load(pathJoin("ecbuild", ecbuild_ver))
+
+load("ufs_common")
+
+setenv("CC", "mpiicc")
+setenv("CXX", "mpiicpc")
+setenv("FC", "mpiifort")
+setenv("CMAKE_Platform", "hera.intel")
+
+setenv("EPICHOME", "/scratch1/NCEPDEV/nems/role.epic")
+setenv("JEDI_INSTALL", pathJoin(os.getenv("EPICHOME"),"contrib"))
+
+whatis("Description: UFS build environment")

From 4ef4afcdbaf0a68ca8aa69706038b0ec169286bc Mon Sep 17 00:00:00 2001
From: Jong Kim <jong.kim@noaa.gov>
Date: Mon, 17 Apr 2023 14:51:47 +0000
Subject: [PATCH 02/19] add orion modulefile

---
 modulefiles/ufs_orion.intel.lua | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 modulefiles/ufs_orion.intel.lua

diff --git a/modulefiles/ufs_orion.intel.lua b/modulefiles/ufs_orion.intel.lua
new file mode 100644
index 00000000..406dc4ee
--- /dev/null
+++ b/modulefiles/ufs_orion.intel.lua
@@ -0,0 +1,30 @@
+help([[
+loads UFS Model prerequisites for Orion/Intel
+]])
+
+prepend_path("MODULEPATH", "/work/noaa/epic-ps/role-epic-ps/spack-stack/spack-stack-1.3.0/envs/unified-env/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/work/noaa/da/role-da/spack-stack/modulefiles")
+
+stack_intel_ver=os.getenv("stack_intel_ver") or "2022.0.2"
+load(pathJoin("stack-intel", stack_intel_ver))
+
+stack_impi_ver=os.getenv("stack_impi_ver") or "2021.5.1"
+load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
+
+stack_python_ver=os.getenv("stack_python_ver") or "3.9.7"
+load(pathJoin("stack-python", stack_python_ver))
+
+cmake_ver=os.getenv("cmake_ver") or "3.22.1"
+load(pathJoin("cmake", cmake_ver))
+
+ecbuild_ver=os.getenv("ecbuild_ver") or "3.6.5"
+load(pathJoin("ecbuild", ecbuild_ver))
+
+load("ufs_common")
+
+setenv("CC", "mpiicc")
+setenv("CXX", "mpiicpc")
+setenv("FC", "mpiifort")
+setenv("CMAKE_Platform", "orion.intel")
+
+whatis("Description: UFS build environment")

From 8241ddec8717f486f1fd659e70d5665bd641585d Mon Sep 17 00:00:00 2001
From: jkbk2004 <jong.kim@noaa.gov>
Date: Mon, 17 Apr 2023 10:26:18 -0500
Subject: [PATCH 03/19] add JEDIINSTALL to orion module

---
 modulefiles/ufs_orion.intel.lua | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/modulefiles/ufs_orion.intel.lua b/modulefiles/ufs_orion.intel.lua
index 406dc4ee..6ba1dc40 100644
--- a/modulefiles/ufs_orion.intel.lua
+++ b/modulefiles/ufs_orion.intel.lua
@@ -27,4 +27,7 @@ setenv("CXX", "mpiicpc")
 setenv("FC", "mpiifort")
 setenv("CMAKE_Platform", "orion.intel")
 
+setenv("EPICHOME", "/work/noaa/epic-ps/role-epic-ps")
+setenv("JEDI_INSTALL", pathJoin(os.getenv("EPICHOME"),"contrib"))
+
 whatis("Description: UFS build environment")

From 66c4bfaeff88e8974b2daebc4208cc21b19a6596 Mon Sep 17 00:00:00 2001
From: JONG KIM <jong.kim@noaa.gov>
Date: Thu, 20 Apr 2023 17:57:46 -0400
Subject: [PATCH 04/19] combining lua files

---
 modulefiles/ufs_hera.intel.lua | 54 +++++++++++++++++++++++++++++++++-
 1 file changed, 53 insertions(+), 1 deletion(-)

diff --git a/modulefiles/ufs_hera.intel.lua b/modulefiles/ufs_hera.intel.lua
index 3accf3f8..00e5e9dc 100644
--- a/modulefiles/ufs_hera.intel.lua
+++ b/modulefiles/ufs_hera.intel.lua
@@ -20,7 +20,59 @@ load(pathJoin("cmake", cmake_ver))
 ecbuild_ver=os.getenv("ecbuild_ver") or "3.6.5"
 load(pathJoin("ecbuild", ecbuild_ver))
 
-load("ufs_common")
+jasper_ver=os.getenv("jasper_ver") or "2.0.32"
+load(pathJoin("jasper", jasper_ver))
+
+zlib_ver=os.getenv("zlib_ver") or "1.2.13"
+load(pathJoin("zlib", zlib_ver))
+
+libpng_ver=os.getenv("libpng_ver") or "1.6.37"
+load(pathJoin("libpng", libpng_ver))
+
+hdf5_ver=os.getenv("hdf5_ver") or "1.14.0"
+load(pathJoin("hdf5", hdf5_ver))
+
+netcdf_c_ver=os.getenv("netcdf_ver") or "4.9.0"
+load(pathJoin("netcdf-c", netcdf_c_ver))
+
+netcdf_fortran_ver=os.getenv("netcdf_fortran_ver") or "4.6.0"
+load(pathJoin("netcdf-fortran", netcdf_fortran_ver))
+
+pio_ver=os.getenv("pio_ver") or "2.5.9"
+load(pathJoin("parallelio", pio_ver))
+
+esmf_ver=os.getenv("esmf_ver") or "8.3.0b09"
+load(pathJoin("esmf", esmf_ver))
+
+fms_ver=os.getenv("fms_ver") or "2022.04"
+load(pathJoin("fms",fms_ver))
+
+bacio_ver=os.getenv("bacio_ver") or "2.4.1"
+load(pathJoin("bacio", bacio_ver))
+
+crtm_ver=os.getenv("crtm_ver") or "2.4.0"
+load(pathJoin("crtm", crtm_ver))
+
+g2_ver=os.getenv("g2_ver") or "3.4.5"
+load(pathJoin("g2", g2_ver))
+
+g2tmpl_ver=os.getenv("g2tmpl_ver") or "1.10.2"
+load(pathJoin("g2tmpl", g2tmpl_ver))
+
+ip_ver=os.getenv("ip_ver") or "3.3.3"
+load(pathJoin("ip", ip_ver))
+
+sp_ver=os.getenv("sp_ver") or "2.3.3"
+load(pathJoin("sp", sp_ver))
+
+w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
+load(pathJoin("w3emc", w3emc_ver))
+
+gftl_shared_ver=os.getenv("gftl_shared_ver") or "v1.5.0"
+load(pathJoin("gftl-shared", gftl_shared_ver))
+
+mapl_ver=os.getenv("mapl_ver") or "2.22.0-esmf-8.3.0b09"
+load(pathJoin("mapl", mapl_ver))
 
 setenv("CC", "mpiicc")
 setenv("CXX", "mpiicpc")

From 5d44a4114eaa50b4837447a14a185d931d03e610 Mon Sep 17 00:00:00 2001
From: JONG KIM <jong.kim@noaa.gov>
Date: Thu, 20 Apr 2023 17:58:55 -0400
Subject: [PATCH 05/19] Update landda_hera.intel.lua

---
 modulefiles/landda_hera.intel.lua | 85 ++++++++++++++++++++++++++-----
 1 file changed, 72 insertions(+), 13 deletions(-)

diff --git a/modulefiles/landda_hera.intel.lua b/modulefiles/landda_hera.intel.lua
index 55b5af4e..00e5e9dc 100644
--- a/modulefiles/landda_hera.intel.lua
+++ b/modulefiles/landda_hera.intel.lua
@@ -1,26 +1,85 @@
 help([[
-loads Land DA prerequisites for Hera/Intel
+loads UFS Model prerequisites for Hera/Intel
 ]])
 
-setenv("EPICHOME", "/scratch1/NCEPDEV/nems/role.epic")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.3.0/envs/unified-env/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/jcsda/jedipara/spack-stack/modulefiles")
+
+stack_intel_ver=os.getenv("stack_intel_ver") or "2021.5.0"
+load(pathJoin("stack-intel", stack_intel_ver))
+
+stack_impi_ver=os.getenv("stack_impi_ver") or "2021.5.1"
+load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
+
+stack_python_ver=os.getenv("stack_python_ver") or "3.9.12"
+load(pathJoin("stack-python", stack_python_ver))
+
+cmake_ver=os.getenv("cmake_ver") or "3.23.1"
+load(pathJoin("cmake", cmake_ver))
+
+ecbuild_ver=os.getenv("ecbuild_ver") or "3.6.5"
+load(pathJoin("ecbuild", ecbuild_ver))
+
+jasper_ver=os.getenv("jasper_ver") or "2.0.32"
+load(pathJoin("jasper", jasper_ver))
+
+zlib_ver=os.getenv("zlib_ver") or "1.2.13"
+load(pathJoin("zlib", zlib_ver))
+
+libpng_ver=os.getenv("libpng_ver") or "1.6.37"
+load(pathJoin("libpng", libpng_ver))
+
+hdf5_ver=os.getenv("hdf5_ver") or "1.14.0"
+load(pathJoin("hdf5", hdf5_ver))
+
+netcdf_c_ver=os.getenv("netcdf_ver") or "4.9.0"
+load(pathJoin("netcdf-c", netcdf_c_ver))
 
-prepend_path("MODULEPATH", pathJoin(os.getenv("EPICHOME"),"miniconda3/modulefiles"))
+netcdf_fortran_ver=os.getenv("netcdf_fortran_ver") or "4.6.0"
+load(pathJoin("netcdf-fortran", netcdf_fortran_ver))
 
-load("miniconda3/4.12.0")
+pio_ver=os.getenv("pio_ver") or "2.5.9"
+load(pathJoin("parallelio", pio_ver))
 
-prepend_path("MODULEPATH", pathJoin(os.getenv("EPICHOME"),"spack-stack/envs/landda-release-1.0-intel/install/modulefiles/Core"))
+esmf_ver=os.getenv("esmf_ver") or "8.3.0b09"
+load(pathJoin("esmf", esmf_ver))
 
-load("stack-intel")
-load("stack-intel-oneapi-mpi")
-load("netcdf-c")
-load("netcdf-fortran")
-load("cmake")
-load("ecbuild")
-load("stack-python")
+fms_ver=os.getenv("fms_ver") or "2022.04"
+load(pathJoin("fms",fms_ver))
+
+bacio_ver=os.getenv("bacio_ver") or "2.4.1"
+load(pathJoin("bacio", bacio_ver))
+
+crtm_ver=os.getenv("crtm_ver") or "2.4.0"
+load(pathJoin("crtm", crtm_ver))
+
+g2_ver=os.getenv("g2_ver") or "3.4.5"
+load(pathJoin("g2", g2_ver))
+
+g2tmpl_ver=os.getenv("g2tmpl_ver") or "1.10.2"
+load(pathJoin("g2tmpl", g2tmpl_ver))
+
+ip_ver=os.getenv("ip_ver") or "3.3.3"
+load(pathJoin("ip", ip_ver))
+
+sp_ver=os.getenv("sp_ver") or "2.3.3"
+load(pathJoin("sp", sp_ver))
+
+w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
+load(pathJoin("w3emc", w3emc_ver))
+
+gftl_shared_ver=os.getenv("gftl_shared_ver") or "v1.5.0"
+load(pathJoin("gftl-shared", gftl_shared_ver))
+
+mapl_ver=os.getenv("mapl_ver") or "2.22.0-esmf-8.3.0b09"
+load(pathJoin("mapl", mapl_ver))
 
 setenv("CC", "mpiicc")
 setenv("CXX", "mpiicpc")
 setenv("FC", "mpiifort")
+setenv("CMAKE_Platform", "hera.intel")
+
+setenv("EPICHOME", "/scratch1/NCEPDEV/nems/role.epic")
 setenv("JEDI_INSTALL", pathJoin(os.getenv("EPICHOME"),"contrib"))
 
-whatis("Description: Land DA build environment")
+whatis("Description: UFS build environment")

From 8f638f938f652d65ada4858b3ba3dd0cc8c2d33e Mon Sep 17 00:00:00 2001
From: Jong Kim <jong.kim@noaa.gov>
Date: Fri, 21 Apr 2023 18:31:58 +0000
Subject: [PATCH 06/19] update hera modulefile

---
 modulefiles/landda_hera.intel.lua | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/modulefiles/landda_hera.intel.lua b/modulefiles/landda_hera.intel.lua
index 00e5e9dc..97473220 100644
--- a/modulefiles/landda_hera.intel.lua
+++ b/modulefiles/landda_hera.intel.lua
@@ -74,12 +74,15 @@ load(pathJoin("gftl-shared", gftl_shared_ver))
 mapl_ver=os.getenv("mapl_ver") or "2.22.0-esmf-8.3.0b09"
 load(pathJoin("mapl", mapl_ver))
 
+load("ufs-pyenv")
+load("atlas")
+
 setenv("CC", "mpiicc")
 setenv("CXX", "mpiicpc")
 setenv("FC", "mpiifort")
 setenv("CMAKE_Platform", "hera.intel")
 
 setenv("EPICHOME", "/scratch1/NCEPDEV/nems/role.epic")
-setenv("JEDI_INSTALL", pathJoin(os.getenv("EPICHOME"),"contrib"))
+setenv("JEDI_INSTALL", pathJoin(os.getenv("EPICHOME"),"contrib/v1.1"))
 
 whatis("Description: UFS build environment")

From 93a52cfe7b26e2d47f8d099db321e6b46362dc16 Mon Sep 17 00:00:00 2001
From: jkbk2004 <jkbk2004@gmail.com>
Date: Sat, 22 Apr 2023 10:56:27 -0400
Subject: [PATCH 07/19] update singularity moduelfile

---
 modulefiles/landda_singularity.intel.lua | 97 ++++++++++++++++++++----
 1 file changed, 84 insertions(+), 13 deletions(-)

diff --git a/modulefiles/landda_singularity.intel.lua b/modulefiles/landda_singularity.intel.lua
index 49a9a32e..a8a9d61e 100644
--- a/modulefiles/landda_singularity.intel.lua
+++ b/modulefiles/landda_singularity.intel.lua
@@ -1,26 +1,97 @@
 help([[
-loads Land DA prerequisites for Singularity/Intel
+loads UFS Model prerequisites for Hera/Intel
 ]])
 
 setenv("EPICHOME", "/opt")
 
---prepend_path("MODULEPATH", pathJoin(os.getenv("EPICHOME"),"miniconda3/modulefiles"))
---miniconda3_ver=os.getenv("miniconda3_ver") or "4.12.0"
---load(pathJoin("miniconda3", miniconda3_ver))
+prepend_path("MODULEPATH", pathJoin(os.getenv("EPICHOME"),"spack-stack/spack-stack-1.3.0/envs/unified-dev/install/modulefiles/Core"))
 
-prepend_path("MODULEPATH", pathJoin(os.getenv("EPICHOME"),"spack-stack/envs/landda-release-1.0-intel/install/modulefiles/Core"))
+stack_intel_ver=os.getenv("stack_intel_ver") or "2021.8.0"
+load(pathJoin("stack-intel", stack_intel_ver))
 
-load("stack-intel")
-load("stack-intel-oneapi-mpi")
-load("netcdf-c")
-load("netcdf-fortran")
-load("cmake")
-load("ecbuild")
-load("stack-python")
+load("intel-oneapi-mpi/2021.8.0")
+stack_impi_ver=os.getenv("stack_impi_ver") or "2021.8.0"
+load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
+
+stack_python_ver=os.getenv("stack_python_ver") or "3.8.10"
+load(pathJoin("stack-python", stack_python_ver))
+
+cmake_ver=os.getenv("cmake_ver") or "3.23.1"
+load(pathJoin("cmake", cmake_ver))
+
+ecbuild_ver=os.getenv("ecbuild_ver") or "3.6.5"
+load(pathJoin("ecbuild", ecbuild_ver))
+
+jasper_ver=os.getenv("jasper_ver") or "2.0.32"
+load(pathJoin("jasper", jasper_ver))
+
+zlib_ver=os.getenv("zlib_ver") or "1.2.13"
+load(pathJoin("zlib", zlib_ver))
+
+libpng_ver=os.getenv("libpng_ver") or "1.6.37"
+load(pathJoin("libpng", libpng_ver))
+
+hdf5_ver=os.getenv("hdf5_ver") or "1.14.0"
+load(pathJoin("hdf5", hdf5_ver))
+
+netcdf_c_ver=os.getenv("netcdf_ver") or "4.9.2"
+load(pathJoin("netcdf-c", netcdf_c_ver))
+
+netcdf_fortran_ver=os.getenv("netcdf_fortran_ver") or "4.6.0"
+load(pathJoin("netcdf-fortran", netcdf_fortran_ver))
+
+pio_ver=os.getenv("pio_ver") or "2.5.9"
+load(pathJoin("parallelio", pio_ver))
+
+esmf_ver=os.getenv("esmf_ver") or "8.3.0b09"
+load(pathJoin("esmf", esmf_ver))
+
+fms_ver=os.getenv("fms_ver") or "2022.04"
+load(pathJoin("fms",fms_ver))
+
+bacio_ver=os.getenv("bacio_ver") or "2.4.1"
+load(pathJoin("bacio", bacio_ver))
+
+crtm_ver=os.getenv("crtm_ver") or "2.4.0"
+load(pathJoin("crtm", crtm_ver))
+
+g2_ver=os.getenv("g2_ver") or "3.4.5"
+load(pathJoin("g2", g2_ver))
+
+g2tmpl_ver=os.getenv("g2tmpl_ver") or "1.10.2"
+load(pathJoin("g2tmpl", g2tmpl_ver))
+
+ip_ver=os.getenv("ip_ver") or "3.3.3"
+load(pathJoin("ip", ip_ver))
+
+sp_ver=os.getenv("sp_ver") or "2.3.3"
+load(pathJoin("sp", sp_ver))
+
+w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
+load(pathJoin("w3emc", w3emc_ver))
+
+gftl_shared_ver=os.getenv("gftl_shared_ver") or "1.5.0"
+load(pathJoin("gftl-shared", gftl_shared_ver))
+
+mapl_ver=os.getenv("mapl_ver") or "2.22.0-esmf-8.3.0b09"
+load(pathJoin("mapl", mapl_ver))
+
+load("py-cftime/1.0.3.4")
+load("py-cython/0.29.32")
+load("py-f90nml/1.4.3")
+load("py-jinja2/3.1.2")
+load("py-netcdf4/1.5.3")
+load("py-numpy/1.22.3")
+load("py-pandas/1.4.0")
+load("py-python-dateutil/2.8.2")
+load("py-pyyaml/6.0")
+
+load("atlas")
 
 setenv("CC", "mpiicc")
 setenv("CXX", "mpiicpc")
 setenv("FC", "mpiifort")
+
 setenv("JEDI_INSTALL", pathJoin(os.getenv("EPICHOME"),""))
 
-whatis("Description: Land DA build environment")
+whatis("Description: UFS build environment")

From e506511f018557982b845ad0b8f3f2078736acad Mon Sep 17 00:00:00 2001
From: jkbk2004 <jkbk2004@gmail.com>
Date: Sat, 22 Apr 2023 11:10:48 -0400
Subject: [PATCH 08/19] update singularity modulefile: compiler

---
 modulefiles/landda_singularity.intel.lua | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modulefiles/landda_singularity.intel.lua b/modulefiles/landda_singularity.intel.lua
index a8a9d61e..de27a367 100644
--- a/modulefiles/landda_singularity.intel.lua
+++ b/modulefiles/landda_singularity.intel.lua
@@ -9,8 +9,8 @@ prepend_path("MODULEPATH", pathJoin(os.getenv("EPICHOME"),"spack-stack/spack-sta
 stack_intel_ver=os.getenv("stack_intel_ver") or "2021.8.0"
 load(pathJoin("stack-intel", stack_intel_ver))
 
-load("intel-oneapi-mpi/2021.8.0")
-stack_impi_ver=os.getenv("stack_impi_ver") or "2021.8.0"
+load("intel-oneapi-mpi/2023.0.0")
+stack_impi_ver=os.getenv("stack_impi_ver") or "2023.0.0"
 load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
 
 stack_python_ver=os.getenv("stack_python_ver") or "3.8.10"

From a9255ead58da6e1f7edbeee61c6dda04f8ce424b Mon Sep 17 00:00:00 2001
From: JONG KIM <jong.kim@noaa.gov>
Date: Sat, 22 Apr 2023 14:36:06 -0400
Subject: [PATCH 09/19] Update landda_singularity.intel.lua

---
 modulefiles/landda_singularity.intel.lua | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modulefiles/landda_singularity.intel.lua b/modulefiles/landda_singularity.intel.lua
index de27a367..a8a9d61e 100644
--- a/modulefiles/landda_singularity.intel.lua
+++ b/modulefiles/landda_singularity.intel.lua
@@ -9,8 +9,8 @@ prepend_path("MODULEPATH", pathJoin(os.getenv("EPICHOME"),"spack-stack/spack-sta
 stack_intel_ver=os.getenv("stack_intel_ver") or "2021.8.0"
 load(pathJoin("stack-intel", stack_intel_ver))
 
-load("intel-oneapi-mpi/2023.0.0")
-stack_impi_ver=os.getenv("stack_impi_ver") or "2023.0.0"
+load("intel-oneapi-mpi/2021.8.0")
+stack_impi_ver=os.getenv("stack_impi_ver") or "2021.8.0"
 load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
 
 stack_python_ver=os.getenv("stack_python_ver") or "3.8.10"

From ba63a49a2a806355cf20ad8741b1ccc069815d40 Mon Sep 17 00:00:00 2001
From: JONG KIM <jong.kim@noaa.gov>
Date: Sat, 22 Apr 2023 20:49:56 -0400
Subject: [PATCH 10/19] Delete ufs_hera.intel.lua

---
 modulefiles/ufs_hera.intel.lua | 85 ----------------------------------
 1 file changed, 85 deletions(-)
 delete mode 100644 modulefiles/ufs_hera.intel.lua

diff --git a/modulefiles/ufs_hera.intel.lua b/modulefiles/ufs_hera.intel.lua
deleted file mode 100644
index 00e5e9dc..00000000
--- a/modulefiles/ufs_hera.intel.lua
+++ /dev/null
@@ -1,85 +0,0 @@
-help([[
-loads UFS Model prerequisites for Hera/Intel
-]])
-
-prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.3.0/envs/unified-env/install/modulefiles/Core")
-prepend_path("MODULEPATH", "/scratch1/NCEPDEV/jcsda/jedipara/spack-stack/modulefiles")
-
-stack_intel_ver=os.getenv("stack_intel_ver") or "2021.5.0"
-load(pathJoin("stack-intel", stack_intel_ver))
-
-stack_impi_ver=os.getenv("stack_impi_ver") or "2021.5.1"
-load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
-
-stack_python_ver=os.getenv("stack_python_ver") or "3.9.12"
-load(pathJoin("stack-python", stack_python_ver))
-
-cmake_ver=os.getenv("cmake_ver") or "3.23.1"
-load(pathJoin("cmake", cmake_ver))
-
-ecbuild_ver=os.getenv("ecbuild_ver") or "3.6.5"
-load(pathJoin("ecbuild", ecbuild_ver))
-
-jasper_ver=os.getenv("jasper_ver") or "2.0.32"
-load(pathJoin("jasper", jasper_ver))
-
-zlib_ver=os.getenv("zlib_ver") or "1.2.13"
-load(pathJoin("zlib", zlib_ver))
-
-libpng_ver=os.getenv("libpng_ver") or "1.6.37"
-load(pathJoin("libpng", libpng_ver))
-
-hdf5_ver=os.getenv("hdf5_ver") or "1.14.0"
-load(pathJoin("hdf5", hdf5_ver))
-
-netcdf_c_ver=os.getenv("netcdf_ver") or "4.9.0"
-load(pathJoin("netcdf-c", netcdf_c_ver))
-
-netcdf_fortran_ver=os.getenv("netcdf_fortran_ver") or "4.6.0"
-load(pathJoin("netcdf-fortran", netcdf_fortran_ver))
-
-pio_ver=os.getenv("pio_ver") or "2.5.9"
-load(pathJoin("parallelio", pio_ver))
-
-esmf_ver=os.getenv("esmf_ver") or "8.3.0b09"
-load(pathJoin("esmf", esmf_ver))
-
-fms_ver=os.getenv("fms_ver") or "2022.04"
-load(pathJoin("fms",fms_ver))
-
-bacio_ver=os.getenv("bacio_ver") or "2.4.1"
-load(pathJoin("bacio", bacio_ver))
-
-crtm_ver=os.getenv("crtm_ver") or "2.4.0"
-load(pathJoin("crtm", crtm_ver))
-
-g2_ver=os.getenv("g2_ver") or "3.4.5"
-load(pathJoin("g2", g2_ver))
-
-g2tmpl_ver=os.getenv("g2tmpl_ver") or "1.10.2"
-load(pathJoin("g2tmpl", g2tmpl_ver))
-
-ip_ver=os.getenv("ip_ver") or "3.3.3"
-load(pathJoin("ip", ip_ver))
-
-sp_ver=os.getenv("sp_ver") or "2.3.3"
-load(pathJoin("sp", sp_ver))
-
-w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
-load(pathJoin("w3emc", w3emc_ver))
-
-gftl_shared_ver=os.getenv("gftl_shared_ver") or "v1.5.0"
-load(pathJoin("gftl-shared", gftl_shared_ver))
-
-mapl_ver=os.getenv("mapl_ver") or "2.22.0-esmf-8.3.0b09"
-load(pathJoin("mapl", mapl_ver))
-
-setenv("CC", "mpiicc")
-setenv("CXX", "mpiicpc")
-setenv("FC", "mpiifort")
-setenv("CMAKE_Platform", "hera.intel")
-
-setenv("EPICHOME", "/scratch1/NCEPDEV/nems/role.epic")
-setenv("JEDI_INSTALL", pathJoin(os.getenv("EPICHOME"),"contrib"))
-
-whatis("Description: UFS build environment")

From cf8a10ea9a8c4054968eb07e5d8da81395a90e48 Mon Sep 17 00:00:00 2001
From: JONG KIM <jong.kim@noaa.gov>
Date: Sat, 22 Apr 2023 20:50:06 -0400
Subject: [PATCH 11/19] Delete ufs_orion.intel.lua

---
 modulefiles/ufs_orion.intel.lua | 33 ---------------------------------
 1 file changed, 33 deletions(-)
 delete mode 100644 modulefiles/ufs_orion.intel.lua

diff --git a/modulefiles/ufs_orion.intel.lua b/modulefiles/ufs_orion.intel.lua
deleted file mode 100644
index 6ba1dc40..00000000
--- a/modulefiles/ufs_orion.intel.lua
+++ /dev/null
@@ -1,33 +0,0 @@
-help([[
-loads UFS Model prerequisites for Orion/Intel
-]])
-
-prepend_path("MODULEPATH", "/work/noaa/epic-ps/role-epic-ps/spack-stack/spack-stack-1.3.0/envs/unified-env/install/modulefiles/Core")
-prepend_path("MODULEPATH", "/work/noaa/da/role-da/spack-stack/modulefiles")
-
-stack_intel_ver=os.getenv("stack_intel_ver") or "2022.0.2"
-load(pathJoin("stack-intel", stack_intel_ver))
-
-stack_impi_ver=os.getenv("stack_impi_ver") or "2021.5.1"
-load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
-
-stack_python_ver=os.getenv("stack_python_ver") or "3.9.7"
-load(pathJoin("stack-python", stack_python_ver))
-
-cmake_ver=os.getenv("cmake_ver") or "3.22.1"
-load(pathJoin("cmake", cmake_ver))
-
-ecbuild_ver=os.getenv("ecbuild_ver") or "3.6.5"
-load(pathJoin("ecbuild", ecbuild_ver))
-
-load("ufs_common")
-
-setenv("CC", "mpiicc")
-setenv("CXX", "mpiicpc")
-setenv("FC", "mpiifort")
-setenv("CMAKE_Platform", "orion.intel")
-
-setenv("EPICHOME", "/work/noaa/epic-ps/role-epic-ps")
-setenv("JEDI_INSTALL", pathJoin(os.getenv("EPICHOME"),"contrib"))
-
-whatis("Description: UFS build environment")

From dccf7d23e28c66bc3bf212abd9c84d893c2bc120 Mon Sep 17 00:00:00 2001
From: JONG KIM <jong.kim@noaa.gov>
Date: Sat, 22 Apr 2023 20:50:17 -0400
Subject: [PATCH 12/19] Delete ufs_common.lua

---
 modulefiles/ufs_common.lua | 59 --------------------------------------
 1 file changed, 59 deletions(-)
 delete mode 100644 modulefiles/ufs_common.lua

diff --git a/modulefiles/ufs_common.lua b/modulefiles/ufs_common.lua
deleted file mode 100644
index 22109f8d..00000000
--- a/modulefiles/ufs_common.lua
+++ /dev/null
@@ -1,59 +0,0 @@
-help([[
-loads UFS Model common libraries
-]])
-
-jasper_ver=os.getenv("jasper_ver") or "2.0.32"
-load(pathJoin("jasper", jasper_ver))
-
-zlib_ver=os.getenv("zlib_ver") or "1.2.13"
-load(pathJoin("zlib", zlib_ver))
-
-libpng_ver=os.getenv("libpng_ver") or "1.6.37"
-load(pathJoin("libpng", libpng_ver))
-
-hdf5_ver=os.getenv("hdf5_ver") or "1.14.0"
-load(pathJoin("hdf5", hdf5_ver))
-
-netcdf_c_ver=os.getenv("netcdf_ver") or "4.9.0"
-load(pathJoin("netcdf-c", netcdf_c_ver))
-
-netcdf_fortran_ver=os.getenv("netcdf_fortran_ver") or "4.6.0"
-load(pathJoin("netcdf-fortran", netcdf_fortran_ver))
-
-pio_ver=os.getenv("pio_ver") or "2.5.9"
-load(pathJoin("parallelio", pio_ver))
-
-esmf_ver=os.getenv("esmf_ver") or "8.3.0b09"
-load(pathJoin("esmf", esmf_ver))
-
-fms_ver=os.getenv("fms_ver") or "2022.04"
-load(pathJoin("fms",fms_ver))
-
-bacio_ver=os.getenv("bacio_ver") or "2.4.1"
-load(pathJoin("bacio", bacio_ver))
-
-crtm_ver=os.getenv("crtm_ver") or "2.4.0"
-load(pathJoin("crtm", crtm_ver))
-
-g2_ver=os.getenv("g2_ver") or "3.4.5"
-load(pathJoin("g2", g2_ver))
-
-g2tmpl_ver=os.getenv("g2tmpl_ver") or "1.10.2"
-load(pathJoin("g2tmpl", g2tmpl_ver))
-
-ip_ver=os.getenv("ip_ver") or "3.3.3"
-load(pathJoin("ip", ip_ver))
-
-sp_ver=os.getenv("sp_ver") or "2.3.3"
-load(pathJoin("sp", sp_ver))
-
-w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
-load(pathJoin("w3emc", w3emc_ver))
-
-gftl_shared_ver=os.getenv("gftl_shared_ver") or "v1.5.0"
-load(pathJoin("gftl-shared", gftl_shared_ver))
-
-mapl_ver=os.getenv("mapl_ver") or "2.22.0-esmf-8.3.0b09"
-load(pathJoin("mapl", mapl_ver))
-
-whatis("Description: UFS build environment common libraries")

From 0cce6ed18a63dd5babf64aa260e45a8acc822c6d Mon Sep 17 00:00:00 2001
From: ulmononian <cameron_book@alumni.brown.edu>
Date: Thu, 27 Apr 2023 23:28:44 -0500
Subject: [PATCH 13/19] Restore orion modulefile (with slight update) and add
 landda_container.intel modulefile.

---
 modulefiles/landda_container.intel.lua | 75 +++++++++++++++++++++
 modulefiles/landda_orion.intel.lua     | 90 ++++++++++++++++++++++----
 2 files changed, 151 insertions(+), 14 deletions(-)
 create mode 100644 modulefiles/landda_container.intel.lua

diff --git a/modulefiles/landda_container.intel.lua b/modulefiles/landda_container.intel.lua
new file mode 100644
index 00000000..f7c0036d
--- /dev/null
+++ b/modulefiles/landda_container.intel.lua
@@ -0,0 +1,75 @@
+help([[
+loads Land DA prerequisites for Singularity/Intel
+]])
+
+setenv("EPICHOME", "/opt")
+
+prepend_path("MODULEPATH", pathJoin(os.getenv("EPICHOME"),"spack-stack/spack-stack-1.3.0/envs/unified-dev/install/modulefiles/Core"))
+
+load("stack-intel/2021.8.0")
+load("stack-intel-oneapi-mpi/2021.8.0")
+load("stack-python/3.8.10")
+load("cmake/3.23.1")
+load("ecbuild/3.6.5")
+load("libjpeg/2.1.0")
+load("jasper/2.0.32")
+load("zlib/1.2.13")
+load("libpng/1.6.37")
+load("pkg-config/0.29.2")
+load("hdf5/1.14.0")
+load("curl/7.68.0")
+load("zstd/1.5.2")
+load("netcdf-c/4.9.2")
+load("netcdf-fortran/4.6.0")
+load("parallel-netcdf/1.12.2")
+load("parallelio/2.5.9")
+load("esmf/8.3.0b09")
+load("fms/2022.04")
+load("bacio/2.4.1")
+load("crtm-fix/2.4.0_emc")
+load("git-lfs/2.9.2")
+load("crtm/2.4.0")
+load("g2/3.4.5")
+load("g2tmpl/1.10.2")
+load("ip/3.3.3")
+load("sp/2.3.3")
+load("w3emc/2.9.2")
+load("gftl/1.8.1")
+load("gftl-shared/1.5.0")
+load("yafyaml/0.5.1")
+load("mapl/2.22.0-esmf-8.3.0b09")
+load("openblas/0.3.19")
+load("py-setuptools/59.4.0")
+load("py-numpy/1.22.3")
+load("py-cftime/1.0.3.4")
+load("py-cython/0.29.32")
+load("py-f90nml/1.4.3")
+load("py-markupsafe/2.1.1")
+load("py-jinja2/3.1.2")
+load("py-netcdf4/1.5.3")
+load("py-bottleneck/1.3.5")
+load("py-pyparsing/3.0.9")
+load("py-packaging/21.3")
+load("py-numexpr/2.8.3")
+load("py-six/1.16.0")
+load("py-python-dateutil/2.8.2")
+load("py-pytz/2022.2.1")
+load("py-pandas/1.4.0")
+load("py-pyyaml/6.0")
+--modules below this line used for jedi builds
+load("udunits/2.2.28")
+load("boost/1.78.0")
+load("eigen/3.4.0")
+load("eckit/1.20.2")
+load("fftw/3.3.10")
+load("fckit/0.10.0")
+load("fiat/1.1.0")
+load("ectrans/1.2.0")
+load("atlas/0.32.1")
+
+setenv("CC", "mpiicc")
+setenv("CXX", "mpiicpc")
+setenv("FC", "mpiifort")
+
+setenv("JEDI_INSTALL", pathJoin(os.getenv("EPICHOME"),""))
+
diff --git a/modulefiles/landda_orion.intel.lua b/modulefiles/landda_orion.intel.lua
index 212e03cf..2fb76f77 100644
--- a/modulefiles/landda_orion.intel.lua
+++ b/modulefiles/landda_orion.intel.lua
@@ -1,26 +1,88 @@
 help([[
-loads Land DA prerequisites for Orion/Intel
+loads UFS Model prerequisites for Orion/Intel
 ]])
 
-setenv("EPICHOME", "/work/noaa/epic-ps/role-epic-ps")
+prepend_path("MODULEPATH", "/work/noaa/epic-ps/role-epic-ps/spack-stack/spack-stack-1.3.0/envs/unified-env/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/work/noaa/da/role-da/spack-stack/modulefiles")
+
+stack_intel_ver=os.getenv("stack_intel_ver") or "2022.0.2"
+load(pathJoin("stack-intel", stack_intel_ver))
+
+stack_impi_ver=os.getenv("stack_impi_ver") or "2021.5.1"
+load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
+
+stack_python_ver=os.getenv("stack_python_ver") or "3.9.7"
+load(pathJoin("stack-python", stack_python_ver))
+
+cmake_ver=os.getenv("cmake_ver") or "3.22.1"
+load(pathJoin("cmake", cmake_ver))
+
+ecbuild_ver=os.getenv("ecbuild_ver") or "3.6.5"
+load(pathJoin("ecbuild", ecbuild_ver))
+
+jasper_ver=os.getenv("jasper_ver") or "2.0.32"
+load(pathJoin("jasper", jasper_ver))
+
+zlib_ver=os.getenv("zlib_ver") or "1.2.13"
+load(pathJoin("zlib", zlib_ver))
+
+libpng_ver=os.getenv("libpng_ver") or "1.6.37"
+load(pathJoin("libpng", libpng_ver))
+
+hdf5_ver=os.getenv("hdf5_ver") or "1.14.0"
+load(pathJoin("hdf5", hdf5_ver))
+
+netcdf_c_ver=os.getenv("netcdf_ver") or "4.9.0"
+load(pathJoin("netcdf-c", netcdf_c_ver))
+
+netcdf_fortran_ver=os.getenv("netcdf_fortran_ver") or "4.6.0"
+load(pathJoin("netcdf-fortran", netcdf_fortran_ver))
 
-prepend_path("MODULEPATH", pathJoin(os.getenv("EPICHOME"),"miniconda3/modulefiles"))
+pio_ver=os.getenv("pio_ver") or "2.5.9"
+load(pathJoin("parallelio", pio_ver))
 
-load("miniconda3/4.12.0")
+esmf_ver=os.getenv("esmf_ver") or "8.3.0b09"
+load(pathJoin("esmf", esmf_ver))
 
-prepend_path("MODULEPATH", pathJoin(os.getenv("EPICHOME"),"spack-stack/envs/landda-release-1.0-intel/install/modulefiles/Core"))
+fms_ver=os.getenv("fms_ver") or "2022.04"
+load(pathJoin("fms",fms_ver))
 
-load("stack-intel")
-load("stack-intel-oneapi-mpi")
-load("netcdf-c")
-load("netcdf-fortran")
-load("cmake")
-load("ecbuild")
-load("stack-python")
+bacio_ver=os.getenv("bacio_ver") or "2.4.1"
+load(pathJoin("bacio", bacio_ver))
+
+crtm_ver=os.getenv("crtm_ver") or "2.4.0"
+load(pathJoin("crtm", crtm_ver))
+
+g2_ver=os.getenv("g2_ver") or "3.4.5"
+load(pathJoin("g2", g2_ver))
+
+g2tmpl_ver=os.getenv("g2tmpl_ver") or "1.10.2"
+load(pathJoin("g2tmpl", g2tmpl_ver))
+
+ip_ver=os.getenv("ip_ver") or "3.3.3"
+load(pathJoin("ip", ip_ver))
+
+sp_ver=os.getenv("sp_ver") or "2.3.3"
+load(pathJoin("sp", sp_ver))
+
+w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
+load(pathJoin("w3emc", w3emc_ver))
+
+gftl_shared_ver=os.getenv("gftl_shared_ver") or "v1.5.0"
+load(pathJoin("gftl-shared", gftl_shared_ver))
+
+mapl_ver=os.getenv("mapl_ver") or "2.22.0-esmf-8.3.0b09"
+load(pathJoin("mapl", mapl_ver))
+
+load("ufs-pyenv")
 
 setenv("CC", "mpiicc")
 setenv("CXX", "mpiicpc")
 setenv("FC", "mpiifort")
-setenv("JEDI_INSTALL", pathJoin(os.getenv("EPICHOME"),"contrib"))
+setenv("CMAKE_Platform", "orion.intel")
+
+setenv("EPICHOME", "/work/noaa/epic-ps/role-epic-ps")
+setenv("JEDI_INSTALL", pathJoin(os.getenv("EPICHOME"),"contrib/v1.1"))
+
+whatis("Description: UFS build environment")
 
-whatis("Description: Land DA build environment")

From 641eb6f6b0357856785f63d622572045c4f36c66 Mon Sep 17 00:00:00 2001
From: JONG KIM <jong.kim@noaa.gov>
Date: Fri, 28 Apr 2023 08:44:39 -0400
Subject: [PATCH 14/19] Update CMakeLists.txt

---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index affc3a9e..84a7f032 100755
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -12,7 +12,7 @@ cmake_minimum_required( VERSION 3.12 )
 project( LandDA VERSION 0.0.0 LANGUAGES C CXX Fortran)
 
 if(DEFINED ENV{JEDI_INSTALL})
-  set( JEDI_INSTALL  $ENV{JEDI_INSTALL}/fv3-bundle)
+  set( JEDI_INSTALL  $ENV{JEDI_INSTALL}/jedi-bundle)
 else()
   message(FATAL_ERROR "Define the environment variable 'JEDI_INSTALL' to point to the parent directory of fv3-bundle on your system")
 endif()

From 4213c5c7c1a79d491fbb5c0e1fa29a9b17f90780 Mon Sep 17 00:00:00 2001
From: JONG KIM <jong.kim@noaa.gov>
Date: Fri, 28 Apr 2023 08:47:04 -0400
Subject: [PATCH 15/19] Update release.environment

---
 release.environment | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/release.environment b/release.environment
index 443fb9f8..ff178c02 100644
--- a/release.environment
+++ b/release.environment
@@ -36,6 +36,6 @@ export OUTDIR=${LANDDA_EXPTS}/${exp_name}
 export TEST_BASEDIR=${TEST_BASEDIR:-${EPICHOME}/landda/cycle_land/DA_GHCN_test/mem000/restarts/vector}
 
 # JEDI directories
-export JEDI_EXECDIR=${JEDI_EXECDIR:-"${JEDI_INSTALL}/fv3-bundle/build/bin"}
-export IODA_BUILD_DIR=${JEDI_INSTALL}/ioda-bundle/build
-export JEDI_STATICDIR=${JEDI_INSTALL}/fv3-bundle/fv3-jedi/test/Data
+export JEDI_EXECDIR=${JEDI_EXECDIR:-"${JEDI_INSTALL}/jedi-bundle/build/bin"}
+export IODA_BUILD_DIR=${JEDI_INSTALL}/jedi-bundle/build
+export JEDI_STATICDIR=${JEDI_INSTALL}/jedi-bundle/fv3-jedi/test/Data

From e274fdfd2e7ccff1e8a3132db788c8551a4d5e0b Mon Sep 17 00:00:00 2001
From: Jong Kim <jong.kim@noaa.gov>
Date: Fri, 28 Apr 2023 13:11:41 +0000
Subject: [PATCH 16/19] turn of ci/cd yaml

---
 .github/workflows/{landda_ci_cd.yml => landda_ci_cd._yml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename .github/workflows/{landda_ci_cd.yml => landda_ci_cd._yml} (100%)

diff --git a/.github/workflows/landda_ci_cd.yml b/.github/workflows/landda_ci_cd._yml
similarity index 100%
rename from .github/workflows/landda_ci_cd.yml
rename to .github/workflows/landda_ci_cd._yml

From faa341ef1e92c64a3cbcd4d5f478705b0dd2c6d8 Mon Sep 17 00:00:00 2001
From: Jong Kim <jong.kim@noaa.gov>
Date: Fri, 28 Apr 2023 13:22:52 +0000
Subject: [PATCH 17/19] add run_container script

---
 run_container_executable.sh | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100755 run_container_executable.sh

diff --git a/run_container_executable.sh b/run_container_executable.sh
new file mode 100755
index 00000000..152b3de6
--- /dev/null
+++ b/run_container_executable.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+export SINGULARITYENV_FI_PROVIDER=tcp
+export SINGULARITY_SHELL=/bin/bash
+BINDDIR="/"`pwd | awk -F"/" '{print $2}'`
+CONTAINERLOC=${EPICCONTAINERS:-${HOME}}
+img=${img:-${CONTAINERLOC}/ubuntu20.04-intel-ue-landda.img}
+CONTAINERBASE="/"`echo $img | xargs realpath | awk -F"/" '{print $2}'`
+cmd=$(basename "$0")
+arg="$@"
+if [ ! -z "$LANDDA_INPUTS" ]; then
+  INPUTBASE="/"`echo $LANDDA_INPUTS | xargs realpath | awk -F"/" '{print $2}'`
+  INPUTBIND="-B $INPUTBASE:$INPUTBASE"
+else
+  INPUTBIND=""
+fi
+echo running: ${SINGULARITYBIN} exec $img $cmd $arg
+${SINGULARITYBIN} exec -B $BINDDIR:$BINDDIR -B $CONTAINERBASE:$CONTAINERBASE $INPUTBIND $img $cmd $arg
+

From 5765e8925e13c5ce3ffc13cebf30d83f08c88807 Mon Sep 17 00:00:00 2001
From: Jong Kim <jong.kim@noaa.gov>
Date: Fri, 28 Apr 2023 13:51:41 +0000
Subject: [PATCH 18/19] update runtime_vars with jedi-bundle

---
 test/runtime_vars.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/runtime_vars.sh b/test/runtime_vars.sh
index 2e1a5b65..19d3b07e 100755
--- a/test/runtime_vars.sh
+++ b/test/runtime_vars.sh
@@ -36,12 +36,12 @@ export EXECDIR=${EXECDIR:-$project_binary_dir/bin}
 export LANDDA_INPUTS=${LANDDA_INPUTS:-"`dirname $project_source_dir`/inputs"}
 
 # set IODA path
-export IODA_BUILD_DIR=${IODA_BUILD_DIR:-"${JEDI_INSTALL}/ioda-bundle/build"}
+export IODA_BUILD_DIR=${IODA_BUILD_DIR:-"${JEDI_INSTALL}/jedi-bundle/build"}
 export PYTHON_VERSION=`python -c 'import sys; version=sys.version_info[:3]; print("{0}.{1}".format(*version))'`
 export PYTHONPATH=$PYTHONPATH:${IODA_BUILD_DIR}/lib/python${PYTHON_VERSION}/pyioda:${IODA_BUILD_DIR}/lib/pyiodaconv
 
 # JEDI directories
-export JEDI_EXECDIR=${JEDI_EXECDIR:-"${JEDI_INSTALL}/fv3-bundle/build/bin"}
+export JEDI_EXECDIR=${JEDI_EXECDIR:-"${JEDI_INSTALL}/jedi-bundle/build/bin"}
 export JEDI_STATICDIR=${JEDI_STATICDIR:-"${JEDI_EXECDIR}/../fv3-jedi/test/Data"}
 
 # set executables

From 61c37de3d1155dc17fd95b753658c47a26e00a22 Mon Sep 17 00:00:00 2001
From: Jong Kim <jong.kim@noaa.gov>
Date: Mon, 1 May 2023 12:54:30 +0000
Subject: [PATCH 19/19] update release.environment

---
 release.environment | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/release.environment b/release.environment
index ff178c02..0a6b9c25 100644
--- a/release.environment
+++ b/release.environment
@@ -6,7 +6,7 @@ export LANDDA_INPUTS=${LANDDA_INPUTS:-${LANDDAROOT}/inputs}
 export CYCLEDIR=$(pwd) 
 export LANDDA_EXPTS=${LANDDA_EXPTS:-${LANDDAROOT}/landda_expts}
 if [[ ! $BASELINE =~ 'hera.internal' ]]; then
-  export PYTHON=`which python`
+  export PYTHON=`/usr/bin/which python`
 fi
 export BUILDDIR=${BUILDDIR:-${CYCLEDIR}/build}
 
@@ -14,15 +14,15 @@ export BUILDDIR=${BUILDDIR:-${CYCLEDIR}/build}
 if [[ ${USE_SINGULARITY} =~ yes ]]; then
   EPICHOME=/opt
   #use the python that is built into the container. It has all the pythonpaths set and can run the ioda converters
-  export PYTHON=$PWD/singularity/bin/python
+  export PYTHON=$PWD/build/bin/python
   #JEDI is installed under /opt in the container
   export JEDI_INSTALL=/opt
   #Scripts that launch containerized versions of the executables are in $PWD/singularity/bin They should be called
   #from the host system to be run (e.g. mpiexec -n 6 $BUILDDIR/bin/fv3jedi_letkf.x )
-  export BUILDDIR=$PWD/singularity
-  export JEDI_EXECDIR=${CYCLEDIR}/singularity/bin
+  export BUILDDIR=$PWD/build
+  export JEDI_EXECDIR=${CYCLEDIR}/build/bin
   module try-load singularity
-  export SINGULARITYBIN=`which singularity`
+  export SINGULARITYBIN=`/usr/bin/which singularity`
   sed -i 's/singularity exec/${SINGULARITYBIN} exec/g' run_container_executable.sh
 fi