Spackify JEDI components for NEPTUNE-JEDI

.github/workflows/ubuntu-ci-x86_64-gnu.yaml

@@ -82,9 +82,10 @@ jobs:
             spack stack create env --site linux.default --template ${TEMPLATE} --name ${ENVNAME} --compiler gcc
             spack env activate ${ENVDIR}
 
-            # Turn off variant "adp" for neptune-dev (NRL internal only)
+            # Turn off variants "adp" and "jedi" for neptune-dev (NRL internal only)
             if [[ "${TEMPLATE}" == *"neptune-dev"* ]]; then
               sed -i 's/+adp/~adp/g' ${ENVDIR}/spack.yaml
+              sed -i 's/+jedi/~jedi/g' ${ENVDIR}/spack.yaml
             fi
 
             unset SPACK_DISABLE_LOCAL_CONFIG

.github/workflows/ubuntu-ci-x86_64-oneapi-ifx.yaml

@@ -82,9 +82,10 @@ jobs:
             spack stack create env --site linux.default --template ${TEMPLATE} --name ${ENVNAME} --compiler oneapi
             spack env activate ${ENVDIR}
 
-            # Turn off variant "adp" for neptune-dev (NRL internal only)
+            # Turn off variants "adp" and "jedi" for neptune-dev (NRL internal only)
             if [[ "${TEMPLATE}" == *"neptune-dev"* ]]; then
               sed -i 's/+adp/~adp/g' ${ENVDIR}/spack.yaml
+              sed -i 's/+jedi/~jedi/g' ${ENVDIR}/spack.yaml
             fi
 
             unset SPACK_DISABLE_LOCAL_CONFIG

.github/workflows/ubuntu-ci-x86_64-oneapi.yaml

@@ -82,9 +82,10 @@ jobs:
             spack stack create env --site linux.default --template ${TEMPLATE} --name ${ENVNAME} --compiler oneapi
             spack env activate ${ENVDIR}
 
-            # Turn off variant "adp" for neptune-dev (NRL internal only)
+            # Turn off variants "adp" and "jedi" for neptune-dev (NRL internal only)
             if [[ "${TEMPLATE}" == *"neptune-dev"* ]]; then
               sed -i 's/+adp/~adp/g' ${ENVDIR}/spack.yaml
+              sed -i 's/+jedi/~jedi/g' ${ENVDIR}/spack.yaml
             fi
 
             unset SPACK_DISABLE_LOCAL_CONFIG

configs/common/packages_gcc.yaml

@@ -20,3 +20,6 @@ packages:
     ectrans:
       require:
       - +fftw
+    oops:
+      require:
+      - ~mkl

configs/common/packages_oneapi.yaml

@@ -19,40 +19,43 @@ packages:
     # Individual package settings
     antlr:
       require:
-      - '%gcc'
+      - '%c,cxx=gcc'
     bison:
       require:
-      - '%gcc'
+      - '%c,cxx=gcc'
     cmake:
       require:
-      - '%gcc'
+      - '%c,cxx=gcc'
     ectrans:
       require:
       - +mkl ~fftw
     gmake:
       require:
-      - '%gcc'
+      - '%c=gcc'
     libbsd:
       require:
-      - '%gcc'
+      - '%c=gcc'
     libmd:
       require:
-      - '%gcc'
+      - '%c=gcc'
     met:
       require:
       - +shared-intel
     nco:
       require:
-      - '%gcc'
+      - '%c,cxx=gcc'
+    oops:
+      require:
+      - +mkl
     parallel-netcdf:
       require:
       - +shared-intel
     py-maturin:
       require:
-      - '%gcc'
+      - '%c=gcc'
     py-scipy:
       require:
       - 'cxxflags="-O1"'
     qt:
       require:
-      - '%gcc'
+      - '%c,cxx=gcc'

configs/templates/neptune-dev/spack.yaml

@@ -12,8 +12,8 @@ spack:
   - neptune-env +debug +openmp +espc +ncview ^esmf@=8.9.1
   - neptune-env ~debug ~openmp +espc +ncview ^esmf@=8.9.1
   - neptune-env +debug ~openmp +espc +ncview ^esmf@=8.9.1
-  - neptune-python-env    ^neptune-env ~debug +openmp +espc +ncview ^esmf@=8.9.1
-  - jedi-neptune-env +adp ^neptune-env ~debug +openmp +espc +ncview ^esmf@=8.9.1
+  - neptune-python-env          ^neptune-env ~debug +openmp +espc +ncview ^esmf@=8.9.1
+  - jedi-neptune-env +adp +jedi ^neptune-env ~debug +openmp +espc +ncview ^esmf@=8.9.1
   - crtm@3.1.2
   - crtm@v2.4.1-jedi.2
 

repos/spack_stack/spack_repo/spack_stack/packages/ioda/ioda_cmake_import.patch

@@ -0,0 +1,18 @@
+--- a/cmake/ioda-import.cmake.in
++++ b/cmake/ioda-import.cmake.in
+@@ -65,6 +65,15 @@
+ if(@odc_FOUND@)
+     find_dependency( odc 1.0.2 REQUIRED )
+ endif()
++
++if(@bufr_FOUND@)
++    find_dependency( bufr 12.0.1 REQUIRED )
++endif()
++
++if(@bufr_query_FOUND@)
++    find_dependency( bufr_query 0.0.4 REQUIRED )
++endif()
++
+ # Header-only. Not exposed.
+ #find_dependency( Boost 1.64.0 )
+

repos/spack_stack/spack_repo/spack_stack/packages/ioda/package.py

@@ -0,0 +1,79 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack_repo.builtin.build_systems.cmake import CMakePackage, generator
+
+from spack.package import *
+
+
+class Ioda(CMakePackage):
+    """Interface for Observation Data Access"""
+
+    homepage = "https://github.com/JCSDA/ioda"
+    git = "https://github.com/JCSDA/ioda.git"
+
+    maintainers("climbfuji")
+
+    version("develop", branch="develop", no_cache=True)
+    version("2.9.0.20250826", commit="6e76616001067384f7d0ca4341ad78e81527af8b")
+
+    patch("ioda_cmake_import.patch", when="@2.9.0.20250826")
+
+    variant("doc", default=False, description="Build IODA documentation")
+    # Let's always assume IODA_BUILD_LANGUAGE_FORTRAN=on.
+    # variant('fortran', default=True, description='Build the ioda Fortran interface')
+    variant("odc", default=True, description="Build ODC bindings")
+    # ioda has no explicit OpenMP calls, but header files from Eigen and oops do use openmp.
+    variant("openmp", default=True, description="Build with OpenMP support")
+    # Let's always BUILD_PYTHON_BINDINGS.
+    # variant('python', default=True, description='Build the ioda Python interface')
+
+    generator("make")
+
+    # Project doesn't list "c" as a dependency in CMakeLists.txt, but cmake step fails w/o it
+    depends_on("c", type=("build"))
+    depends_on("cxx", type=("build"))
+    depends_on("fortran", type=("build"))
+
+    depends_on("boost@1.64.0:")
+    depends_on("bufr")
+    depends_on("bufr@12.0.1:", when="@2.9:")
+    # This is optional, and it needs netcdf-cxx - which versions?
+    depends_on("bufr-query@0.0.4:", when="@2.9:")
+    depends_on("cmake", type=("build"))
+    depends_on("cmake@3.14:", type=("build"), when="@2.9:")
+    depends_on("ecbuild", type=("build"))
+    depends_on("ecbuild@3.3.2:", type=("build"), when="@2.9:")
+    depends_on("eckit")
+    depends_on("eckit@1.23.0:", when="@2.9:")
+    depends_on("eigen")
+    depends_on("fckit")
+    depends_on("fckit@0.10.1:", when="@2.9:")
+    depends_on("gsl-lite")
+    depends_on("hdf5@1.12.0: +mpi")
+    depends_on("hdf5@1.14.0: +mpi", when="@2.9:")
+    depends_on("jedi-cmake", type=("build"))
+    depends_on("llvm-openmp", when="+openmp %apple-clang", type=("build", "link", "run"))
+    depends_on("mpi")
+    depends_on("nccmp")
+    # netcdf-cxx needed for bufr-query, but which version?
+    depends_on("netcdf-cxx", when="@2.9:")
+    depends_on("odc", when="+odc")
+    depends_on("odc@1.4.6:", when="@2.9: +odc")
+    depends_on("oops+openmp", when="+openmp")
+    depends_on("oops~openmp", when="~openmp")
+    depends_on("oops@1.10", when="@2.9:")
+    depends_on("python")
+    depends_on("python@3.9:3.11", when="@2.9:")
+    depends_on("py-pybind11")
+    depends_on("py-pycodestyle")
+    depends_on("udunits")
+    depends_on("udunits@2.2.0:", when="@2.9:")
+
+    def cmake_args(self):
+        res = [
+            self.define_from_variant("ENABLE_IODA_DOC", "doc"),
+        ]
+        return res

repos/spack_stack/spack_repo/spack_stack/packages/ioda_converters/package.py

@@ -0,0 +1,46 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack_repo.builtin.build_systems.cmake import CMakePackage, generator
+
+from spack.package import *
+
+
+class IodaConverters(CMakePackage):
+    """Interface for Observation Data Access"""
+
+    homepage = "https://github.com/JCSDA/ioda-converters"
+    git = "https://github.com/JCSDA/ioda-converters.git"
+
+    maintainers("climbfuji")
+
+    version("develop", branch="develop", no_cache=True)
+    version("0.0.1.20250830", commit="a91f432d9d50940910605e689cd1cf93a1ce3798")
+
+    generator("make")
+
+    # Project doesn't list "c" as a dependency in CMakeLists.txt, but cmake step fails w/o it
+    depends_on("c", type=("build"))
+    depends_on("cxx", type=("build"))
+    depends_on("fortran", type=("build"))
+
+    extends("python")
+
+    depends_on("ecbuild", type=("build"))
+    depends_on("ecbuild@3.3.2:", type=("build"), when="@0.0.1:")
+
+    depends_on("bufr@12:")
+    depends_on("eccodes")
+    depends_on("eckit")
+    depends_on("eigen@3")
+    depends_on("gsl-lite")
+    depends_on("ioda")
+    depends_on("jedi-cmake", type=("build"))
+    depends_on("mpi")
+    depends_on("netcdf-cxx")
+    depends_on("netcdf-fortran")
+    depends_on("oops")
+    depends_on("py-cartopy")
+    depends_on("py-pybind11")

repos/spack_stack/spack_repo/spack_stack/packages/jedi_neptune_env/package.py

@@ -4,6 +4,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack_repo.builtin.build_systems.bundle import BundlePackage
+
 from spack.package import *
 
 
@@ -20,11 +21,19 @@ class JediNeptuneEnv(BundlePackage):
 
     variant("adp", default=False, description="Build ADP preprocessors")
 
+    variant("jedi", default=False, description="Build JEDI components required for JEDI-NEPTUNE")
+
     depends_on("jedi-base-env", type="run")
     depends_on("neptune-env", type="run")
     depends_on("neptune-python-env", type="run")
 
     with when("+adp"):
         depends_on("adp-preprocessors", type="run")
 
-    # There is no need for install() since there is no code.
+    with when("+jedi"):
+        depends_on("oops@1.10.0.20250827", type="run")
+        depends_on("crtm@v2.4.1-jedi.2", type="run")
+        depends_on("ioda@2.9.0.20250826", type="run")
+        depends_on("ioda-converters@0.0.1.20250830", type="run")
+        depends_on("ropp-ufo@11.0.20251022", type="run")
+        depends_on("ufo@1.10.0.20250821 +crtm-v2 +ropp", type="run")

repos/spack_stack/spack_repo/spack_stack/packages/oops/include_algorithm.patch

@@ -0,0 +1,10 @@
+--- a/src/oops/base/ParameterTraitsObsVariables.h
++++ b/src/oops/base/ParameterTraitsObsVariables.h
+@@ -7,6 +7,7 @@
+
+ #pragma once
+
++#include <algorithm>
+ #include <string>
+ #include <vector>
+

repos/spack_stack/spack_repo/spack_stack/packages/oops/package.py

@@ -0,0 +1,70 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack_repo.builtin.build_systems.cmake import CMakePackage, generator
+
+from spack.package import *
+
+
+class Oops(CMakePackage):
+    """Object Oriented Prediction System"""
+
+    homepage = "https://github.com/JCSDA/oops"
+    git = "https://github.com/JCSDA/oops.git"
+
+    maintainers("climbfuji")
+
+    version("develop", branch="develop", no_cache=True)
+    # This commit plus the patch below accounts for commit
+    # 2340e9b664f82de9fa01c136c3a31d87e4a0bec9 in NRL GitHub
+    version("1.10.0.20250827", commit="91889ad09d3789f14a1184701dd80a4913d3ce3e")
+
+    patch("include_algorithm.patch", when="@1.10.0.20250827")
+
+    variant("l95", default=True, description="Build LORENZ95 toy model")
+    variant("mkl", default=False, description="Use MKL for LAPACK implementation (if available)")
+    variant("openmp", default=True, description="Build oops with OpenMP support")
+    variant("qg", default=True, description="Build QG toy model")
+    variant('gptl', default=False, description='Use GPTL profiling library (if available)')
+
+    generator("make")
+
+    # Project doesn't list "c" as a dependency in CMakeLists.txt, but cmake step fails w/o it
+    depends_on("c", type="build")
+    depends_on("cxx", type="build")
+    depends_on("fortran", type="build")
+
+    depends_on("boost@1.64:")
+    depends_on("cmake", type=("build"))
+    depends_on("cmake@3.12:", type=("build"), when="@1.10:")
+    depends_on("ecbuild", type=("build"))
+    depends_on("ecbuild@3.3.2:", type=("build"), when="@1.10:")
+    depends_on("eckit")
+    depends_on("eckit@1.24.4:", when="@1.10:")
+    depends_on("ecmwf-atlas")
+    depends_on("ecmwf-atlas@0.35.0:", when="@1.10:")
+    depends_on("eigen")
+    depends_on("fckit")
+    depends_on("fckit@0.11.0:", when="@1.10:")
+    depends_on('gptl', when='+gptl')
+    depends_on("jedi-cmake", type=("build"))
+    depends_on("lapack", when="~mkl")
+    depends_on("mkl", when="+mkl")
+    depends_on("llvm-openmp", when="+openmp %apple-clang", type=("build", "link", "run"))
+    depends_on("mpi")
+    depends_on("netcdf-c+mpi")
+    depends_on("netcdf-fortran")
+    depends_on("nlohmann-json")
+    depends_on("nlohmann-json-schema-validator")
+
+    def cmake_args(self):
+        res = [
+            self.define_from_variant("ENABLE_LORENZ95_MODEL", "l95"),
+            self.define_from_variant("ENABLE_QG_MODEL", "qg"),
+            self.define_from_variant("ENABLE_MKL", "mkl"),
+            self.define_from_variant("OPENMP", "openmp"),
+            self.define_from_variant("ENABLE_GPTL", "gptl"),
+        ]
+        return res

repos/spack_stack/spack_repo/spack_stack/packages/ropp_ufo/package.py

@@ -0,0 +1,34 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack_repo.builtin.build_systems.cmake import CMakePackage, generator
+
+from spack.package import *
+
+
+class RoppUfo(CMakePackage):
+    """Unified Forward Operator Interface for Radio Occultation Pre-processing package (ROPP)"""
+
+    # DH* TODO CHANGE BACK TO JCSDA-INTERNAL ONCE THE NRL VERSION WAS MERGED BACK
+    homepage = "https://github.nrlmry.navy.mil/jcsda/ropp-ufo"
+    git = "https://github.nrlmry.navy.mil/jcsda/ropp-ufo.git"
+
+    maintainers("climbfuji")
+
+    version("develop", branch="develop", no_cache=True)
+    # this is the ropp-submodule branch ... update once merged
+    version("11.0.20251022", commit="02e21ef0696e67675184797427af265c06973ecf", submodules=True)
+
+    # Project doesn't list "c" as a dependency in CMakeLists.txt, but cmake step fails w/o it
+    depends_on("c", type=("build"))
+    depends_on("fortran", type=("build"))
+
+    depends_on("cmake", type=("build"))
+    depends_on("cmake@3.12:", type=("build"), when="@11:")
+    depends_on("ecbuild", type=("build"))
+    depends_on("ecbuild@3.3.2:", type=("build"), when="@11:")
+    depends_on("jedi-cmake", type=("build"))
+    depends_on("netcdf-c")
+    depends_on("netcdf-fortran")