From 944dd5d3e28efbac763495b6001fde985c315b17 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Oriol=20Tint=C3=B3?= <oriol.tinto@lmu.de>
Date: Wed, 22 Mar 2023 16:34:32 +0100
Subject: [PATCH] Adding spack repository with icon templates and modify build
icon to add the repository
---
spack_repo/packages/dwd-icon-tools/package.py | 87 ++++++++
spack_repo/packages/icon-nwp/package.py | 199 ++++++++++++++++++
spack_repo/repo.yaml | 2 +
templates/common/build_icon.sh | 1 +
4 files changed, 289 insertions(+)
create mode 100644 spack_repo/packages/dwd-icon-tools/package.py
create mode 100644 spack_repo/packages/icon-nwp/package.py
create mode 100644 spack_repo/repo.yaml
diff --git a/spack_repo/packages/dwd-icon-tools/package.py b/spack_repo/packages/dwd-icon-tools/package.py
new file mode 100644
index 0000000..7614cd5
--- /dev/null
+++ b/spack_repo/packages/dwd-icon-tools/package.py
@@ -0,0 +1,87 @@
+# 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)
+
+# ----------------------------------------------------------------------------
+# If you submit this package back to Spack as a pull request,
+# please first remove this boilerplate and all FIXME comments.
+#
+# This is a template package file for Spack. We've put "FIXME"
+# next to all the things you'll want to change. Once you've handled
+# them, you can save this file and test your package like this:
+#
+# spack install dwd-icon-tools
+#
+# You can edit this file again by typing:
+#
+# spack edit dwd-icon-tools
+#
+# See the Spack documentation for more information on packaging.
+# ----------------------------------------------------------------------------
+
+from spack.package import *
+from pathlib import Path
+
+
+class DwdIconTools(Package):
+ """DWD Icon Tools"""
+
+ homepage = "https://www.example.com"
+ git = "ssh://git@gitlab.lrz.de/dkrz-mirror/dwd_icon_tools.git"
+
+ version("2.5.2", branch="icontools-2.5.2")
+
+ depends_on("netcdf-c")
+ depends_on("eccodes")
+
+ def patch(self):
+ """
+ Because of the lack of access rights to the original submodule repositories,
+ we patch the gitmodules file to point to a different mirror.
+ """
+ git_submodules_file = Path().cwd() / ".gitmodules"
+ git_mirror = "git@gitlab.lrz.de:dkrz-mirror"
+ git_modules_patch = f"""
+ [submodule "externals/libcdi"]
+ path = externals/libcdi
+ url = {git_mirror}/libcdi.git
+ """
+
+ # Replace the content of the original file with the patch
+ with git_submodules_file.open("w") as out_f:
+ out_f.write(git_modules_patch)
+
+ # Run git submodule update
+ git = which("git")
+ git("submodule", "update", "--init", "--recursive")
+
+
+ def setup_build_environment(self, env):
+ spec = self.spec
+ # Some environment variables to set
+ env_variables_to_set = {
+# "CC": spec["mpi"].mpicc,
+# "FC": spec["mpi"].mpifc,
+# "F77": spec["mpi"].mpif77,
+ "CXXFLAGS": "-O2 -g -fopenmp -Wunused -DNOMPI",
+ "FCFLAGS": "-I/usr/include --std=f2008 -O2 -g -cpp -fopenmp -fbounds-check -Wunused -DNOMPI",
+ "LIBS": "-leccodes -lgfortran -lhdf5 -lxml2",
+ }
+ for variable, value in env_variables_to_set.items():
+ env.set(variable, value)
+
+
+
+ def install(self, spec, prefix):
+ options = [
+ f"--prefix={prefix}",
+ "--enable-grib2",
+ "--enable-iso-c-interface",
+ f"--with-netcdf={spec['netcdf-c'].prefix}"
+ ]
+
+ configure(*options)
+ make()
+ make("install")
+
diff --git a/spack_repo/packages/icon-nwp/package.py b/spack_repo/packages/icon-nwp/package.py
new file mode 100644
index 0000000..72e9a89
--- /dev/null
+++ b/spack_repo/packages/icon-nwp/package.py
@@ -0,0 +1,199 @@
+# 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.package import *
+from pathlib import Path
+
+
+class IconNwp(Package):
+ """
+ Recipe to build ICON-NWP using the LMU gitlab repository.
+ """
+
+ homepage = "https://code.mpimet.mpg.de/projects/iconpublic"
+
+ # Main repository (pointing to LMU's gitlab)
+ git = "ssh://git@gitlab.physik.uni-muenchen.de/w2w/icon.git"
+
+ # Version w2w-B6 points to a different repository and branch)
+ version("w2w-B6", git="ssh://git@gitlab.physik.uni-muenchen.de/w2w/icon-w2w.git", branch="icon-w2w/icon-nwp-B6")
+ # FIXME: The ugly configuration system in older icon versions prevents us from using this package with it.
+ # version("2.5.0-nwp3", branch="icon-nwp/op-release-2.5.0-nwp3")
+ version("2.6.4-nwp3", branch="icon-nwp/op-release-2.6.4-nwp3")
+ version("2.6.5-nwp0", branch="icon-nwp/op-release-2.6.5-nwp0")
+ version("master", branch="master")
+ version("psp", branch="icon-nwp/icon-nwp-psp")
+
+
+ # Dependencies
+ depends_on("mpi")
+ depends_on("netcdf-c")
+ depends_on("netcdf-fortran")
+ depends_on("eccodes")
+ depends_on("libxml2")
+
+ # Extra dependencies for B6, including yaml, and the hdf5 filters for compression.
+ depends_on("libyaml", when="@w2w-B6")
+ depends_on("hdf5-blosc", when="@w2w-B6")
+ depends_on("h5z-zfp", when="@w2w-B6")
+ depends_on("sz~hdf5", when="@w2w-B6")
+ depends_on("sz3~hdf5", when="@w2w-B6")
+
+ phases = ["configure", "build", "install"]
+
+ def patch(self):
+ """
+ Because of the lack of access rights to the original submodule repositories,
+ we patch the gitmodules file to point to a different mirror.
+ """
+ git_submodules_file = Path().cwd() / ".gitmodules"
+
+ git_mirror = "git@gitlab.lrz.de:dkrz-mirror"
+
+ git_modules_patch = f"""
+ [submodule "externals/mtime"]
+ path = externals/mtime
+ url = {git_mirror}/libmtime.git
+ [submodule "externals/jsbach"]
+ path = externals/jsbach
+ url = {git_mirror}/jsbach.git
+ [submodule "externals/yac"]
+ path = externals/yac
+ url = {git_mirror}/YAC.git
+ [submodule "externals/self"]
+ path = externals/self
+ url = {git_mirror}/libself.git
+ [submodule "externals/tixi"]
+ path = externals/tixi
+ url = {git_mirror}/libtixi.git
+ [submodule "externals/yaxt"]
+ path = externals/yaxt
+ url = {git_mirror}/yaxt.git
+ [submodule "externals/rte-rrtmgp"]
+ path = externals/rte-rrtmgp
+ url = https://github.com/earth-system-radiation/rte-rrtmgp.git
+ [submodule "externals/cub"]
+ path = externals/cub
+ url = https://github.com/NVlabs/cub.git
+ [submodule "externals/omni-xmod-pool"]
+ path = externals/omni-xmod-pool
+ url = https://github.com/claw-project/omni-xmod-pool.git
+ [submodule "externals/cdi"]
+ path = externals/cdi
+ url = {git_mirror}/libcdi.git
+ [submodule "externals/sct"]
+ path = externals/sct
+ url = {git_mirror}/sct.git
+ [submodule "externals/ecrad"]
+ path = externals/ecrad
+ url = {git_mirror}/libecrad.git
+ [submodule "externals/dace_icon"]
+ path = externals/dace_icon
+ url = {git_mirror}/dace-icon-interface.git
+ [submodule "externals/emvorado"]
+ path = externals/emvorado
+ url = {git_mirror}/emvorado-for-icon.git
+ [submodule "utils/mkexp"]
+ path = utils/mkexp
+ url = https://git.mpimet.mpg.de/public/mkexp
+ [submodule "externals/art"]
+ path = externals/art
+ url = {git_mirror}/art.git
+ [submodule "externals/ppm"]
+ path = externals/ppm
+ url = https://gitlab.dkrz.de/jahns/ppm.git
+ [submodule "externals/probtest"]
+ path = externals/probtest
+ url = {git_mirror}/cscs-sw_probtest.git
+ """
+
+ # Replace the content of the original file with the patch
+ with git_submodules_file.open("w") as out_f:
+ out_f.write(git_modules_patch)
+
+ # Run git submodule update
+ git = which("git")
+ git("submodule", "update", "--init", "--recursive")
+
+ def setup_build_environment(self, env):
+
+ spec = self.spec
+
+ # Some environment variables to set
+ env_variables_to_set = {
+ "CC": spec["mpi"].mpicc,
+ "FC": spec["mpi"].mpifc,
+ "F77": spec["mpi"].mpif77,
+ }
+ for variable, value in env_variables_to_set.items():
+ env.set(variable, value)
+
+ def configure(self, spec, prefix):
+ spec = self.spec
+ print(spec['mpi'].mpifc)
+
+ libs = [
+ f"-L{spec['netcdf-c'].prefix.lib} -lnetcdf ", # netcdf-c libs
+ f"-L{spec['netcdf-fortran'].prefix.lib} -lnetcdff", # netcdf-fortran libs
+ "-lopenblas", # OpenBlas
+ f"-L{spec['eccodes'].prefix.lib} -leccodes_f90 -leccodes",
+ f"-L{spec['libxml2'].prefix.lib} -lxml2", # XML2 libs
+ ]
+
+ if self.spec.version == Version("w2w-B6"):
+ libs.append("-lyaml")
+
+ mtune = "generic"
+ INCLUDES = f"-I{spec['libxml2'].prefix}/include/libxml2"
+ options = [
+ f"CC={spec['mpi'].mpicc}",
+ f"FC={spec['mpi'].mpifc}",
+ f"CFLAGS=-g -mpc64 {INCLUDES}",
+ f"ICON_CFLAGS=-O3 -g -mtune={mtune}",
+ f"ICON_BUNDLED_CFLAGS=-O3 -mtune={mtune}",
+ "FCFLAGS=-std=legacy -fmodule-private -fimplicit-none -fmax-identifier-length=63 -Wall -Wcharacter-truncation -Wconversion -Wunderflow -Wunused-parameter -Wno-surprising -fall-intrinsics -g -mpc64 -w",
+ "ICON_FCFLAGS=-fbacktrace -fbounds-check -fstack-protector-all -finit-real=nan -finit-integer=-2147483648 -finit-character=127 -w -O2",
+ f"ICON_OCEAN_FCFLAGS=-O3 -mtune={mtune}",
+ f"LDFLAGS={' '.join(libs)}",
+ f"LIBS={' '.join(libs)}",
+ f"--prefix={prefix}",
+ f"--enable-grib2",
+ ]
+
+ # For some reason there's a problem with OpenMPI with gcc@11.3.0 which makes the configuration fail.
+ if self.spec.compiler.name == "gcc" and self.spec.compiler.version == Version("11.3.0"):
+ options.append("--enable-mpi-checks=no")
+ configure(*options)
+
+ def build(self, spec, prefix):
+ make()
+
+ def install(self, spec, prefix):
+ make("install")
+
+ # Create extra folders with the data and the docs
+ self.make_extra_folders(prefix)
+
+ def setup_run_environment(self, env):
+ env.set("ICON_BASE_PATH", self.spec.prefix)
+ env.set("ICON_DATA_PATH", self.spec.prefix.join("data"))
+ env.set("ICON_DOCS_PATH", self.spec.prefix.join("doc"))
+
+
+ def make_extra_folders(self, prefix):
+ mkdir = which("mkdir")
+ rsync = which("rsync")
+ curl = which("curl")
+
+ # copy executables and documentation
+ mkdir("-p", f"{prefix}/data")
+ mkdir("-p", f"{prefix}/doc")
+ mkdir("-p", f"{prefix}/run")
+ rsync("-av", "data/", f"{prefix}/data")
+ rsync("-av", "run/", f"{prefix}/run")
+ rsync("-av", "--include='*.pdf'", "--exclude='*.*'", "doc/", f"{prefix}/doc/")
+ curl("https://code.mpimet.mpg.de/attachments/download/19568/ICON_tutorial_2019.pdf", "--output", f"{prefix}/doc/ICON_tutorial_2019.pdf")
+ curl("http://www.cosmo-model.org/content/model/documentation/core/emvorado_userguide.pdf", "--output", f"{prefix}/doc/emvorado_userguide.pdf")
+
diff --git a/spack_repo/repo.yaml b/spack_repo/repo.yaml
new file mode 100644
index 0000000..332f5cb
--- /dev/null
+++ b/spack_repo/repo.yaml
@@ -0,0 +1,2 @@
+repo:
+ namespace: 'autosubmit-icon-repository'
diff --git a/templates/common/build_icon.sh b/templates/common/build_icon.sh
index 65b6386..75789e7 100644
--- a/templates/common/build_icon.sh
+++ b/templates/common/build_icon.sh
@@ -18,6 +18,7 @@ SPACK_BUILD_ICON=%icon.spack_cmd%
if [ ! -z $SPACK_BUILD_ICON ]; then
echo "Installing ICON with spack!"
echo "cmd=$SPACK_BUILD_ICON"
+ spack repo add ${WORKDIR}/proj/spack_repo
spack install $SPACK_BUILD_ICON
spack load $SPACK_BUILD_ICON
fi
--
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