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Commit c44f1599 authored by Takumi.Matsunobu's avatar Takumi.Matsunobu
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Merge remote-tracking branch 'origin/build_only' into D2_takumi

parents c6aa171e ecfcc413
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conf/build_only/jobs.yml 0 → 100644
+ 12
− 0
View file @ c44f1599
JOBS:
TRANSFER_PROJECT:
FILE: templates/common/transfer_project.sh
PLATFORM: LOCAL
BUILD_ICON:
FILE: templates/common/build_icon.sh
DEPENDENCIES: TRANSFER_PROJECT
WALLCLOCK: 04:00
PROCESSORS: 16
RETRIALS: 2 # retry because spack downloads sometimes timeout
NODES: 1
\ No newline at end of file
conf/common/jobs.yml → conf/common/jobs.generic
+ 3
− 0
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## This file contains the template of the generic workflow
## It can be used as a reference to create a custom workflow.
JOBS:
TRANSFER_PROJECT:
FILE: templates/common/transfer_project.sh
......
conf/real-from-dwd-ana/jobs.yml
+ 64
− 1
View file @ c44f1599
JOBS:
TRANSFER_PROJECT:
FILE: templates/common/transfer_project.sh
PLATFORM: LOCAL
BUILD_ICON:
FILE: templates/common/build_icon.sh
DEPENDENCIES: TRANSFER_PROJECT
WALLCLOCK: 04:00
PROCESSORS: 16
RETRIALS: 2 # retry because spack downloads sometimes timeout
NODES: 1
BUILD_PYTHON_ENVIRONMENT:
FILE: templates/common/build_python_environment.sh
# Right now we rely on spack for building icon and having a python interpreter, so we need this dependency:
DEPENDENCIES: BUILD_ICON
WALLCLOCK: 01:00
PROCESSORS: 16
NODES: 1
PREPARE_EXPERIMENT:
FILE: templates/real-from-dwd-ana/prepare_experiment.sh
DEPENDENCIES: BUILD_ICON
RUNNING: once
WALLCLOCK: 01:00
PREPARE_DATE_LOCAL:
FILE: templates/real-from-dwd-ana/prepare_date_local.sh
......@@ -16,6 +39,46 @@ JOBS:
PREPARE_MEMBER:
FILE: templates/real-from-dwd-ana/prepare_member.sh
DEPENDENCIES: PREPARE_EXPERIMENT PREPARE_DATE_REMOTE PREPARE_DATE_LOCAL
RUNNING: member
WALLCLOCK: 01:00
PREPARE_NAMELIST:
FILE: templates/real-from-dwd-ana/prepare_namelist.py
\ No newline at end of file
FILE: templates/real-from-dwd-ana/prepare_namelist.py
DEPENDENCIES: TRANSFER_PROJECT BUILD_PYTHON_ENVIRONMENT PREPARE_MEMBER RUN_ICON-1
WALLCLOCK: 00:05
RUNNING: chunk
TYPE: python
EXECUTABLE: "%HPCROOTDIR%/%python_environment.folder_name%/bin/python3"
RUN_ICON:
FILE: templates/common/run_icon.sh
DEPENDENCIES: PREPARE_NAMELIST
WALLCLOCK: 04:00
RUNNING: chunk
PROCESSORS: 64
MEMORY: 81920
CUSTOM_DIRECTIVES: [ "#SBATCH --exclusive" ]
COMPRESS:
FILE: templates/common/compress.py
DEPENDENCIES: RUN_ICON BUILD_PYTHON_ENVIRONMENT COMPRESS-1
RUNNING: chunk
TYPE: python
EXECUTABLE: "%HPCROOTDIR%/%python_environment.folder_name%/bin/python3"
PROCESSORS: 16
MEMORY: 16384
WALLCLOCK: 01:00
TRANSFER:
FILE: templates/common/transfer.sh
DEPENDENCIES: COMPRESS
# Since this is running locally, can simply leave a long wallclock.
WALLCLOCK: 24:00
RUNNING: member
PLATFORM: LOCAL
CLEAN:
FILE: templates/common/clean.sh
DEPENDENCIES: TRANSFER
WALLCLOCK: 00:10
RUNNING: member
conf/real-from-ideal/jobs.yml
+ 63
− 0
View file @ c44f1599
JOBS:
TRANSFER_PROJECT:
FILE: templates/common/transfer_project.sh
PLATFORM: LOCAL
BUILD_ICON:
FILE: templates/common/build_icon.sh
DEPENDENCIES: TRANSFER_PROJECT
WALLCLOCK: 04:00
PROCESSORS: 16
RETRIALS: 2 # retry because spack downloads sometimes timeout
NODES: 1
BUILD_PYTHON_ENVIRONMENT:
FILE: templates/common/build_python_environment.sh
# Right now we rely on spack for building icon and having a python interpreter, so we need this dependency:
DEPENDENCIES: BUILD_ICON
WALLCLOCK: 01:00
PROCESSORS: 16
NODES: 1
PREPARE_EXPERIMENT:
FILE: templates/real-from-ideal/prepare_experiment.sh
DEPENDENCIES: BUILD_ICON
RUNNING: once
WALLCLOCK: 01:00
PREPARE_IDEAL_DIRECTORY:
FILE: templates/real-from-ideal/prepare_ideal_directory.sh
......@@ -41,6 +64,46 @@ JOBS:
PREPARE_MEMBER:
FILE: templates/real-from-ideal/prepare_member.sh
DEPENDENCIES: FG_ANA_FROM_IDEALIZED EXTPAR_FROM_IDEALIZED
RUNNING: member
WALLCLOCK: 01:00
PREPARE_NAMELIST:
FILE: templates/real-from-ideal/prepare_namelist.py
DEPENDENCIES: TRANSFER_PROJECT BUILD_PYTHON_ENVIRONMENT PREPARE_MEMBER RUN_ICON-1
WALLCLOCK: 00:05
RUNNING: chunk
TYPE: python
EXECUTABLE: "%HPCROOTDIR%/%python_environment.folder_name%/bin/python3"
RUN_ICON:
FILE: templates/common/run_icon.sh
DEPENDENCIES: PREPARE_NAMELIST
WALLCLOCK: 04:00
RUNNING: chunk
PROCESSORS: 64
MEMORY: 81920
CUSTOM_DIRECTIVES: [ "#SBATCH --exclusive" ]
COMPRESS:
FILE: templates/common/compress.py
DEPENDENCIES: RUN_ICON BUILD_PYTHON_ENVIRONMENT COMPRESS-1
RUNNING: chunk
TYPE: python
EXECUTABLE: "%HPCROOTDIR%/%python_environment.folder_name%/bin/python3"
PROCESSORS: 16
MEMORY: 16384
WALLCLOCK: 01:00
TRANSFER:
FILE: templates/common/transfer.sh
DEPENDENCIES: COMPRESS
# Since this is running locally, can simply leave a long wallclock.
WALLCLOCK: 24:00
RUNNING: member
PLATFORM: LOCAL
CLEAN:
FILE: templates/common/clean.sh
DEPENDENCIES: TRANSFER
WALLCLOCK: 00:10
RUNNING: member
examples/example_utils.sh
+ 3
− 3
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......@@ -68,7 +68,7 @@ function configure_and_install_autosubmit() {
function setup_project() {
local EXPID=$1
PROJECT_ORIGIN="https://gitlab.physik.uni-muenchen.de/w2w/autoicon.git"
PROJECT_BRANCH="master"
: ${PROJECT_BRANCH:="master"}
# If experiment directory doesn't exist, create it and set up the experiment
if [ ! -e autosubmit/$EXPID/ ]; then
......@@ -108,7 +108,7 @@ GIT:
EOF
# Create and write the additional config file
cat >autosubmit/${EXPID}/conf/myconf.yml <<EOF
cat >autosubmit/${EXPID}/conf/01_myconf.yml <<EOF
spack:
init: "" # command to load spack environment, e.g. module load spack, use spack/setup-env.sh if empty
url: https://github.com/spack/spack.git # url to download spack if necessary
......@@ -140,7 +140,7 @@ EOF
# If EXTRA_NAMELIST is provided, create and write the extra namelist file
if [ ! -z "$EXTRA_CONFIGURATION" ]; then
cat >autosubmit/${EXPID}/conf/extra_conf.yml <<EOF
cat >autosubmit/${EXPID}/conf/00_extra_conf.yml <<EOF
$EXTRA_CONFIGURATION
EOF
fi
......
spack_repo/packages/dwd-icon-tools/package.py
+ 23
− 6
View file @ c44f1599
......@@ -56,13 +56,28 @@ class DwdIconTools(Package):
git("submodule", "update", "--init", "--recursive")
def setup_build_environment(self, env):
spec = self.spec
# Some environment variables to set
env_variables_to_set = {
"CXXFLAGS": "-O2 -g -fopenmp -Wunused -DNOMPI",
"FCFLAGS": "-I/usr/include --std=f2008 -O2 -g -cpp -fopenmp -fbounds-check -Wunused -DNOMPI",
"LIBS": f"-leccodes -lgfortran -lhdf5 -lxml2",
}
if self.spec.satisfies("%gcc"):
env_variables_to_set = {
"CXXFLAGS": "-O2 -g -fopenmp -Wunused -DNOMPI",
"FCFLAGS": "-I/usr/include --std=f2008 -O2 -g -cpp -fopenmp -fbounds-check -Wunused -DNOMPI",
"LIBS": f"-leccodes -lgfortran -lhdf5 -lxml2",
}
elif self.spec.satisfies("%intel"):
# Intel
env_variables_to_set = {
"CXXFLAGS": "-O2 -g -qopenmp -Wunused -DNOMPI",
"FCFLAGS": "-I/usr/include -stand f08 -O2 -g -fpp -qopenmp -check bounds -Wunused -DNOMPI",
"CFLAGS": "-std=gnu99 -O3 -DHAVE_LIBNETCDF -DHAVE_NETCDF4 -DHAVE_CF_INTERFACE -DHAVE_LIBGRIB "
"-DHAVE_LIBGRIB_API -DpgiFortran -D__ICON__ -DHAVE_CONFIG_H -traceback",
"LIBS": f"-leccodes -lgfortran -lhdf5 -lxml2",
"V": "1",
"VERBOSE": "1",
"LDFLAGS": "-Wl,--copy-dt-needed-entries",
}
else:
raise AssertionError("Compiler does not match gcc nor intel")
for variable, value in env_variables_to_set.items():
env.set(variable, value)
......@@ -72,6 +87,8 @@ class DwdIconTools(Package):
"--with-eccodes=yes",
"--enable-grib2",
"--enable-iso-c-interface",
"--enable-static",
"--disable-shared",
f"--with-netcdf={spec['netcdf-c'].prefix}"
]
......
spack_repo/packages/icon-nwp/package.py
+ 17
− 90
View file @ c44f1599
......@@ -19,8 +19,7 @@ class IconNwp(Package):
homepage = "https://code.mpimet.mpg.de/projects/iconpublic"
# maintainers("oriol.tinto")
# 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")
version("w2w-B6", branch="w2w/B6_MCRPH")
# 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")
......@@ -70,13 +69,6 @@ class IconNwp(Package):
depends_on("openblas", when="%gcc")
depends_on("intel-mkl", when="%intel")
# 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 do_fetch(self, mirror_only=False):
......@@ -99,80 +91,8 @@ class IconNwp(Package):
def patch(self):
# Run git submodule update
git = which("git")
if self.spec.variants['source'].value == 'lmu':
self.patch_submodules()
git("submodule", "update", "--init", "--recursive")
def patch_submodules(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)
def setup_build_environment(self, env):
spec = self.spec
......@@ -187,7 +107,7 @@ class IconNwp(Package):
def configure(self, spec, prefix):
spec = self.spec
print(spec["mpi"].mpifc)
INCLUDES = [f"-I{spec['libxml2'].prefix}/include/libxml2", ]
libs = [
f"-L{spec['netcdf-c'].prefix.lib} -lnetcdf ", # netcdf-c libs
......@@ -201,11 +121,7 @@ class IconNwp(Package):
elif self.spec.satisfies("%intel"):
libs.append("-qmkl=sequential")
if self.spec.version == Version("w2w-B6"):
libs.append("-lyaml")
mtune = "generic"
INCLUDES = [f"-I{spec['libxml2'].prefix}/include/libxml2", ]
CPPFLAGS = []
if "+plexrt" in self.spec:
......@@ -218,22 +134,33 @@ class IconNwp(Package):
INCLUDES.append(f"-I{spec['petsc'].prefix}/include")
libs.append(f"-L{spec['petsc'].prefix.lib} -lpetsc")
if self.spec.satisfies("%gcc"):
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"
ARCH_FLAG = f"-mtune={mtune}"
ICON_FCFLAGS = "-std=f2008 -fallow-argument-mismatch -fmodule-private -fimplicit-none -Wall"
elif self.spec.satisfies("%intel"):
FCFLAGS = "-stand none -implicitnone -warn all -warn unused -fall-intrinsics -g -w"
ARCH_FLAG = f"-xHost"
ICON_FCFLAGS = "-stand f08 -implicitnone -warn all"
else:
raise AssertionError
options = [
f"CC={spec['mpi'].mpicc}",
f"FC={spec['mpi'].mpifc}",
f"CFLAGS=-g -mpc64 {' '.join(INCLUDES)}",
f"ICON_CFLAGS=-O3 -g -mtune={mtune}",
f"ICON_CFLAGS=-O3 -g {ARCH_FLAG}",
f"ICON_BUNDLED_CFLAGS=-O3 -mtune={mtune}",
f"CPPFLAGS={' '.join(CPPFLAGS)}",
"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",
f"ICON_OCEAN_FCFLAGS=-O3 -mtune={mtune}",
f"FCFLAGS={FCFLAGS}",
f"ICON_OCEAN_FCFLAGS=-O3 {ARCH_FLAG}",
f"LDFLAGS={' '.join(libs)}",
f"LIBS={' '.join(libs)}",
f"--prefix={prefix}",
]
ICON_FCFLAGS="-std=f2008 -fallow-argument-mismatch -fmodule-private -fimplicit-none -Wall"
if "+debug" in self.spec:
options.append(f"ICON_FCFLAGS={ICON_FCFLAGS} -fbacktrace -fbounds-check -fstack-protector-all -finit-real=nan -finit-integer=-2147483648 -finit-character=127 -w -O2")
else:
......
spack_repo/packages/sz3/package.py deleted 100644 → 0
+ 0
− 53
View file @ c6aa171e
# Copyright 2013-2023 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 *
class Sz3(CMakePackage):
"""SZ3 is the next generation of the SZ compressor framework"""
homepage = "https://github.com/szcompressor/SZ3"
git = "https://github.com/szcompressor/SZ3"
# maintainers("disheng222")
tags = ["e4s"]
version("master")
version("3.1.7", commit="c49fd17f2d908835c41000c1286c510046c0480e")
version("3.1.5.4", commit="4c6ddf628f27d36b28d1bbda02174359cd05573d")
version("3.1.5.1", commit="5736a63b917e439dd62248b4ff6234e96726af5d")
version("3.1.3.1", commit="323cb17b412d657c4be681b52c34beaf933fe7af")
version("3.1.3", commit="695dff8dc326f3b165f6676d810f46add088a585")
variant("hdf5", default=False, description="enable hdf5 filter support")
variant("mdz", default=True, description="build mdz executable")
depends_on("zstd")
depends_on("gsl")
depends_on("pkgconfig")
depends_on("hdf5", when="+hdf5")
def setup_run_environment(self, env):
if "+hdf5" in self.spec:
env.prepend_path("HDF5_PLUGIN_PATH", self.prefix.lib64)
def cmake_args(self):
return [
"-DSZ3_USE_BUNDLED_ZSTD=OFF",
"-DSZ3_DEBUG_TIMINGS=OFF",
self.define_from_variant("BUILD_MDZ", "mdz"),
self.define_from_variant("BUILD_H5Z_FILTER", "hdf5"),
]
def test(self):
if self.spec.satisfies("@:3.1.6"):
print("smoke tests are only supported on 3.1.7 and later, skipping")
return
self.run_test(self.prefix.bin.sz3_smoke_test, purpose="sz3 works")
if "+mdz" in self.spec:
self.run_test(self.prefix.bin.mdz_smoke_test, purpose="mdz works")
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