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Cherry-pick upstream commits for parallelio , py-pyyaml and roms #11

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Merged
harshula merged 5 commits into from
Sep 29, 2026
Merged

Cherry-pick upstream commits for parallelio , py-pyyaml and roms #11

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553284e
parallelio: add patch for LibFind.cmake (Upstream PR 3840)
danrosen25 Aug 18, 2026
8557415
parallelio: skip RPATHs with NAG (Upstream PR 6064)
mathomp4 Aug 18, 2026
3e8c76e
parallelio: add pkgconfig build dependency (Upstream PR 6289)
mathomp4 Sep 1, 2026
482f5af
py-pyyaml: +libyaml requires c (Upstream PR 6630)
harshula Sep 27, 2026
e084054
roms: Add all test cases and custom application support (Upstream PR …
rsoutelino Jul 11, 2026
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40 changes: 40 additions & 0 deletions repos/spack_repo/builtin/packages/parallelio/cmake-libfind-arch.patch
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Original file line number Diff line number Diff line change
@@ -0,0 +1,40 @@
--- a/cmake/LibFind.cmake
+++ b/cmake/LibFind.cmake
@@ -254,7 +254,7 @@ function (find_package_component PKG)
find_library (${PKGCOMP}_LIBRARY
NAMES ${${PKGCOMP}_LIBRARY_NAMES}
PATHS ${${PKGCOMP}_PREFIX}
- PATH_SUFFIXES lib
+ PATH_SUFFIXES lib lib/${CMAKE_LIBRARY_ARCHITECTURE}
NO_DEFAULT_PATH)

# If found, check if library is static or dynamic
@@ -266,7 +266,7 @@ function (find_package_component PKG)
find_shared_library (${PKGCOMP}_SHARED_LIBRARY
NAMES ${${PKGCOMP}_LIBRARY_NAMES}
PATHS ${${PKGCOMP}_PREFIX}
- PATH_SUFFIXES lib
+ PATH_SUFFIXES lib lib/${CMAKE_LIBRARY_ARCHITECTURE}
NO_DEFAULT_PATH)
if (${PKGCOMP}_SHARED_LIBRARY)
set (${PKGCOMP}_LIBRARY ${${PKGCOMP}_SHARED_LIBRARY})
@@ -278,7 +278,7 @@ function (find_package_component PKG)
find_static_library (${PKGCOMP}_STATIC_LIBRARY
NAMES ${${PKGCOMP}_LIBRARY_NAMES}
PATHS ${${PKGCOMP}_PREFIX}
- PATH_SUFFIXES lib
+ PATH_SUFFIXES lib lib/${CMAKE_LIBRARY_ARCHITECTURE}
NO_DEFAULT_PATH)
if (${PKGCOMP}_STATIC_LIBRARY)
set (${PKGCOMP}_LIBRARY ${${PKGCOMP}_STATIC_LIBRARY})
@@ -307,7 +307,9 @@ function (find_package_component PKG)
mark_as_advanced (${PKGCOMP}_INCLUDE_DIR ${PKGCOMP}_LIBRARY)

# HACK For bug in CMake v3.0:
- set (${PKGCOMP}_FOUND ${${PKGCOMPUP}_FOUND})
+ if (NOT DEFINED ${PKGCOMP}_FOUND AND DEFINED ${PKGCOMPUP}_FOUND)
+ set (${PKGCOMP}_FOUND ${${PKGCOMPUP}_FOUND})
+ endif ()

# Set return variables
if (${PKGCOMP}_FOUND)
17 changes: 17 additions & 0 deletions repos/spack_repo/builtin/packages/parallelio/package.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,10 @@ class Parallelio(CMakePackage):

license("Apache-2.0")

version("2.6.10", sha256="a65bd3c75f5ee6e8c4c5b922b9c6fa2598af9586468d8dbf51caf010261b4128")
version("2.6.9", sha256="22f34258f0e8b9e8271383bc7c6c657f4bbee560d33f87e3c0db53e0da8c8f3b")
version("2.6.8", sha256="ed6c92129b8a5e2d77587fd9656abc0aa7cf82a26a5ad21f8c6a9a79afa2c301")
version("2.6.7", sha256="b346592cb24bf5f98583574c0679020ef3026005cd8f3efa87545d0982581037")
version("2.6.6", sha256="e32e018a521d38c9424940c7cfa7e9b1931b605f3511ee7ab3a718b69faeeb04")
version("2.6.5", sha256="6ae51aa3f76e597a3a840a292ae14eca21359b1a4ea75e476a93aa2088c0677a")
version("2.6.4", sha256="cba53e4ca62ff76195b6f76374fbd1530fba18649c975ae2628ddec7fe55fb31")
Expand Down Expand Up @@ -54,11 +57,16 @@ class Parallelio(CMakePackage):
# netcdf4 filters are only available with the parallel build of netcdf.
patch("pio_260.patch", when="@2.6.0")

# This patch enhances searchability for dependencies installed externally, such as
# libraries installed via apt in usr/lib/<arch>.
patch("cmake-libfind-arch.patch", when="@2.6.0:2.6.9")

depends_on("c", type="build") # generated
depends_on("cxx", type="build") # generated
depends_on("fortran", type="build") # generated

depends_on("cmake@3.7:", type="build")
depends_on("pkgconfig", type="build", when="@2.6.9:")
depends_on("mpi", when="+mpi")
depends_on("mpi-serial", when="~mpi")
depends_on("netcdf-c +mpi", type="link", when="+mpi")
Expand All @@ -67,6 +75,12 @@ class Parallelio(CMakePackage):
depends_on("parallel-netcdf", type="link", when="+pnetcdf")
depends_on("netcdf-c ~parallel-netcdf", type="link", when="~pnetcdf")

conflicts(
"^netcdf-c@4.9.3:",
when="@:2.6.4",
msg="netcdf-c@4.9.3+ is incompatible with parallelio versions prior to 2.6.5",
)

resource(
name="genf90",
git="https://github.com/PARALLELIO/genf90.git",
Expand Down Expand Up @@ -105,6 +119,9 @@ def cmake_args(self):
define("PIO_ENABLE_EXAMPLES", False),
define_from_variant("WITH_PNETCDF", "pnetcdf"),
]
if spec.satisfies("%nag"):
# NAG cannot pass Spack's padded build rpath through its linker.
args.append(define("CMAKE_SKIP_RPATH", True))
if spec.satisfies("+ncint"):
args.extend([define("PIO_ENABLE_NETCDF_INTEGRATION", True)])
if spec.satisfies("+pnetcdf"):
Expand Down
7 changes: 5 additions & 2 deletions repos/spack_repo/builtin/packages/py_pyyaml/package.py
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Expand Up @@ -38,14 +38,17 @@ class PyPyyaml(PythonPackage):

variant("libyaml", default=True, description="Use libYAML bindings")

with when("+libyaml"):
depends_on("c", type="build")
depends_on("libyaml", type="link")
depends_on("py-cython", when="@6:", type="build")

depends_on("python@2.7,3.5:", type=("build", "link", "run"))
depends_on("python@3.6:", when="@6:", type=("build", "link", "run"))
depends_on("libyaml", when="+libyaml", type="link")
# setuptools versions are not documented upstream, the when= constraint
# should probably be set to a lower version.
depends_on("py-setuptools@62:", type="build", when="@6.0.3:")
depends_on("py-setuptools", type="build")
depends_on("py-cython", when="@6:+libyaml", type="build")

# Includes "longintrepr.h" instead of Python.h
conflicts("^python@3.11:", when="@:5.3")
Expand Down
75 changes: 73 additions & 2 deletions repos/spack_repo/builtin/packages/roms/package.py
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Expand Up @@ -34,9 +34,51 @@ class Roms(MakefilePackage):
"roms_application",
default="benchmark",
description="Makefile to include its associated header file",
values=("upwelling", "benchmark"),
values=(
"basin",
"benchmark",
"bio_toy",
"bl_test",
"canyon",
"channel",
"channel_neck",
"coupling_test",
"damee_4",
"dogbone",
"double_gyre",
"estuary_test",
"flt_test",
"grav_adj",
"inlet_test",
"kelvin",
"lab_canyon",
"lake_jersey",
"lake_signell",
"lmd_test",
"mixed_layer",
"overflow",
"riverplume1",
"riverplume2",
"seamount",
"sed_test1",
"sed_toy",
"shoreface",
"soliton",
"test_chan",
"test_head",
"upwelling",
"wc13",
"weddell",
"windbasin",
"none",
),
multi=False,
)
variant(
"custom_application",
default="none",
description="Path to custom application header file (use roms_application=none with this)",
)
variant(
"debug",
default=False,
Expand All @@ -57,6 +99,23 @@ class Roms(MakefilePackage):
# Note: you cannot set USE_OpenMP and USE_MPI at the same time
conflicts("+mpi+openmp")

@run_before("edit")
def validate_application_config(self):
"""Validate application configuration before starting build"""
custom_app = self.spec.variants["custom_application"].value
roms_app = self.spec.variants["roms_application"].value

# Validate that custom_application and roms_application are not both set
if custom_app != "none" and roms_app != "none":
raise InstallError(
"Cannot specify both custom_application and a built-in roms_application. "
"Set roms_application=none when using custom_application."
)

# Validate the custom header file exists
if custom_app != "none" and not os.path.isfile(custom_app):
raise InstallError("Custom application header file not found: {0}".format(custom_app))

def _copy_arch_file(self, lib):
"""AOCC compiler takes gfortran's makefile as reference"""
copy(
Expand Down Expand Up @@ -112,7 +171,19 @@ def edit(self, spec, prefix):

makefile = FileFilter("makefile")

app_type = self.selected_roms_application
# Handle custom application header file
custom_app = self.spec.variants["custom_application"].value

if custom_app != "none":
# Extract application name from filename (remove .h extension)
custom_app_name = os.path.splitext(os.path.basename(custom_app))[0]

# Copy custom header to ROMS/Include directory
copy(custom_app, join_path("ROMS", "Include", "{0}.h".format(custom_app_name)))

@aidanheerdegen aidanheerdegen Sep 28, 2026

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My concern is that this an arbitrary path that is not under source control or under the provenance umbrella of spack.

@harshula harshula Sep 29, 2026

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Hi @aidanheerdegen , I suspect this discussion should be elsewhere? Perhaps in https://github.com/ACCESS-NRI/CoastRI-ROMS ?


app_type = custom_app_name
else:
app_type = self.selected_roms_application

makefile.filter(
r"ROMS_APPLICATION.*?=.*", "ROMS_APPLICATION = {0}".format(app_type.upper())
Expand Down
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