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base repository: C2SM/spack-c2sm
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  • 15 commits
  • 55 files changed
  • 7 contributors

Commits on Sep 12, 2024

  1. Updated icon4py and gt4py tags (#999)

    nfarabullini authored Sep 12, 2024

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Commits on Oct 1, 2024

  1. Remove dead tools and add package_overlap.py (#1001)

    dominichofer authored Oct 1, 2024

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Commits on Oct 2, 2024

  1. python: Remove workaround for Tsa (#1004)

    dominichofer authored Oct 2, 2024

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Commits on Oct 3, 2024

  1. Update pull_request.yml (#1005)

    jonasjucker authored Oct 3, 2024

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Commits on Oct 14, 2024

  1. remove libcdi-pio and scalesppm (#1007)

    jonasjucker authored Oct 14, 2024

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Commits on Oct 22, 2024

  1. Test everything always (#1003)

    dominichofer authored Oct 22, 2024

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  2. Update Testing.rst (#1008)

    jonasjucker authored Oct 22, 2024

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Commits on Oct 25, 2024

  1. Clean up (#1009)

    dominichofer authored Oct 25, 2024

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Commits on Nov 5, 2024

  1. Add gridtools_cpp 2.3.6 (#1010)

    * Add gridtools_cpp 2.3.6
    
    * Update package.py
    
    * Remove old versions
    
    * GitHub Action: Apply Pep8-formatting
    
    ---------
    
    Co-authored-by: juckerj <[email protected]>
    Co-authored-by: github-actions <[email protected]>
    3 people authored Nov 5, 2024

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Commits on Nov 11, 2024

  1. add diskcache dependeny to py-gt4py (#1013)

    halungge authored Nov 11, 2024

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  2. Icontools: Remove version restriction of eccodes (#1014)

    dominichofer authored Nov 11, 2024

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Commits on Nov 18, 2024

  1. Update package.py (#1019)

    jonasjucker authored Nov 18, 2024

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Commits on Nov 19, 2024

  1. use libfyaml from upstream (#1030)

    Co-authored-by: Michael Jähn <[email protected]>
    jonasjucker and mjaehn authored Nov 19, 2024

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  2. Fix: Remove serialbox as permanent dep of ICON (#1031)

    * only make serialbox a dep when needed
    
    * GitHub Action: Apply Pep8-formatting
    
    ---------
    
    Co-authored-by: github-actions <[email protected]>
    jonasjucker and github-actions authored Nov 19, 2024

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Commits on Nov 21, 2024

  1. Fix: Link netcdf-c libs in ICON (#1032)

    jonasjucker authored Nov 21, 2024

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Showing with 228 additions and 1,863 deletions.
  1. +0 −18 .github/workflows/auto_create_PR.yml
  2. +1 −1 .github/workflows/pull_request.yml
  3. +1 −1 .gitignore
  4. +16 −15 Jenkinsfile
  5. +6 −6 README.md
  6. +0 −16 create_new_sysconfig.sh
  7. +7 −15 docs/InstanceManagement.rst
  8. +1 −22 docs/Testing.rst
  9. +0 −29 docs/UpstreamManagement.rst
  10. +0 −1 docs/index.rst
  11. +11 −32 repos/c2sm/packages/icon/package.py
  12. +2 −2 repos/c2sm/packages/icontools/package.py
  13. +0 −192 repos/c2sm/packages/libcdi-pio/librt.patch
  14. +0 −90 repos/c2sm/packages/libcdi-pio/nag.patch
  15. +0 −249 repos/c2sm/packages/libcdi-pio/package.py
  16. +0 −20 repos/c2sm/packages/libfyaml/package.py
  17. +3 −21 repos/c2sm/packages/py-gridtools-cpp/package.py
  18. +3 −2 repos/c2sm/packages/py-gt4py/package.py
  19. +1 −1 repos/c2sm/packages/py-icon4py/package.py
  20. +0 −5 repos/c2sm/packages/python/package.py
  21. +0 −11 repos/c2sm/packages/scales-ppm/mpirun/1.0.6.patch
  22. +0 −87 repos/c2sm/packages/scales-ppm/package.py
  23. +0 −1 requirements.txt
  24. +12 −15 setup-env.sh
  25. +0 −5 src/__init__.py
  26. +0 −34 src/format.py
  27. +0 −87 src/github.py
  28. +0 −18 src/machine.py
  29. +0 −12 src/machine.sh
  30. +0 −90 src/report_tests.py
  31. +0 −34 src/scope.py
  32. +0 −70 src/spack_commands.py
  33. +0 −25 status.sh
  34. +0 −20 sysconfigs/copy_alps_env_files_from.sh
  35. +0 −14 sysconfigs/eiger/compilers.yaml
  36. +0 −2 sysconfigs/eiger/concretizer.yaml
  37. +0 −6 sysconfigs/eiger/config.yaml
  38. +0 −226 sysconfigs/eiger/packages.yaml
  39. +0 −2 sysconfigs/eiger/repos.yaml
  40. +0 −1 sysconfigs/euler/repos.yaml
  41. +0 −2 sysconfigs/uenv/concretizer.yaml
  42. +0 −6 sysconfigs/uenv/config.yaml
  43. +0 −2 sysconfigs/unknown/concretizer.yaml
  44. +0 −4 sysconfigs/unknown/config.yaml
  45. +0 −2 sysconfigs/unknown/repos.yaml
  46. 0 test/__init__.py
  47. +0 −41 test/conftest.py
  48. +20 −39 test/integration_test.py
  49. +94 −0 test/spack_commands.py
  50. +23 −140 test/system_test.py
  51. +4 −129 test/unit_test.py
  52. +7 −0 tools/package_overlap.py
  53. +16 −0 tools/summarize_logs.py
  54. 0 {sysconfigs/euler → user-config}/config.yaml
  55. 0 {sysconfigs/uenv → user-config}/repos.yaml
18 changes: 0 additions & 18 deletions .github/workflows/auto_create_PR.yml

This file was deleted.

2 changes: 1 addition & 1 deletion .github/workflows/pull_request.yml
Original file line number Diff line number Diff line change
@@ -16,7 +16,7 @@ jobs:
docs-folder: "docs/"
# Great extra actions to compose with:
# Create an artifact of the html output.
- uses: actions/upload-artifact@v1
- uses: actions/upload-artifact@v4.4.0
with:
name: DocumentationHTML
path: docs/_build/
2 changes: 1 addition & 1 deletion .gitignore
Original file line number Diff line number Diff line change
@@ -8,5 +8,5 @@ env/
spack-build_stage/
spack-test_stage/
spack-misc_cache/
user-config/
user-config/linux/
user-cache/
31 changes: 16 additions & 15 deletions Jenkinsfile
Original file line number Diff line number Diff line change
@@ -12,13 +12,10 @@ pipeline {
}
post {
always {
archiveArtifacts artifacts: 'log/**/*.log', allowEmptyArchive: true
withCredentials([string(credentialsId: 'd976fe24-cabf-479e-854f-587c152644bc', variable: 'GITHUB_AUTH_TOKEN')]) {
sh """
source env/bin/activate
python3 src/report_tests.py --auth_token ${GITHUB_AUTH_TOKEN} --build_id ${BUILD_ID} --issue_id ${ghprbPullId}
"""
}
sh """
python3 tools/summarize_logs.py || true
"""
archiveArtifacts artifacts: 'log/*', allowEmptyArchive: true
deleteDir()
}
}
@@ -32,36 +29,40 @@ pipeline {
"""
}
}
stage('Unit Tests') {
stage('Bootstrap spack') {
// Bootstrapping spack is a separate stage to avoid problems with concurrently bootstrapping spack in the tests.
steps {
sh """
mkdir -p log/${NODENAME}/unit_test
source env/bin/activate
python3 test/unit_test.py ${NODENAME} > log/${NODENAME}/unit_test/summary.log 2>&1
source ./setup-env.sh
spack spec gnuconfig
"""
}
}
stage('Bootstrap spack') {
stage('Unit Tests') {
steps {
sh """
source env/bin/activate
. ./setup-env.sh
spack spec gnuconfig
python3 test/unit_test.py
"""
}
}
stage('Integration Tests') {
steps {
sh """
source env/bin/activate
pytest -v -n auto --scope \"""" + env.ghprbCommentBody + " \" test/integration_test.py"
source ./setup-env.sh $USER_ENV_ROOT
pytest -v -n auto test/integration_test.py
"""
}
}
stage('System Tests') {
steps {
sh """
source env/bin/activate
pytest -v -n auto --maxprocesses=24 --scope \"""" + env.ghprbCommentBody + " \" test/system_test.py"
source ./setup-env.sh $USER_ENV_ROOT
pytest -v -n auto test/system_test.py
"""
}
}
}
12 changes: 6 additions & 6 deletions README.md
Original file line number Diff line number Diff line change
@@ -66,11 +66,11 @@ After an update we advice to rebuild packages, preferably in a new shell so that
| | Command |
| --- | --- |
| Clone | `git clone --depth 1 --recurse-submodules --shallow-submodules -b <branch/tag> https://github.com/C2SM/spack-c2sm.git` |
| Load | `. spack-c2sm/setup-env.sh` autodetects machine <br>or<br>`. spack-c2sm/setup-env.sh <machine>` forces machine<br>or<br>`. spack-c2sm/setup-env.sh unknown` uses blank config<br>`spack compiler find` [autodetects compilers](https://spack.readthedocs.io/en/v0.18.1/command_index.html?highlight=spack%20load#spack-compiler-find)<br>`spack external find --all` [autodetects externally installed packages](https://spack.readthedocs.io/en/v0.18.1/command_index.html?highlight=spack%20load#spack-external-find)|
| Update | `git pull`<br>`git submodule update --recursive` |
| Clean | `spack uninstall -a` [uninstalls all packages](https://spack.readthedocs.io/en/v0.18.1/command_index.html?highlight=spack%20load#spack-uninstall)<br>`spack clean -a` [cleans all misc caches](https://spack.readthedocs.io/en/v0.18.1/command_index.html?highlight=spack%20load#spack-clean)<br>`rm -rf ~/.spack` removes user scope data |
| Load | `. spack-c2sm/setup-env.sh` to run without an upstream<br>or<br>`. spack-c2sm/setup-env.sh /user-environment` to use `/user-environment` as an upsream<br>`spack compiler find` [autodetects compilers](https://spack.readthedocs.io/en/v0.21.1/command_index.html?highlight=spack%20load#spack-compiler-find)<br>`spack external find --all` [autodetects externally installed packages](https://spack.readthedocs.io/en/v0.21.1/command_index.html?highlight=spack%20load#spack-external-find)|
| Clean | `spack uninstall -a` [uninstalls all packages](https://spack.readthedocs.io/en/v0.21.1/command_index.html?highlight=spack%20load#spack-uninstall)<br>`spack clean -a` [cleans all misc caches](https://spack.readthedocs.io/en/v0.21.1/command_index.html?highlight=spack%20load#spack-clean)|

[**Spec syntax**](https://spack.readthedocs.io/en/v0.18.1/basic_usage.html#specs-dependencies): `<package>`[`@<version>`](https://spack.readthedocs.io/en/v0.18.1/basic_usage.html#version-specifier)[`%<compiler>`](https://spack.readthedocs.io/en/v0.18.1/basic_usage.html#compiler-specifier)[`+<variant> ~<variant>`](https://spack.readthedocs.io/en/v0.18.1/basic_usage.html#variants)[`^<sub-package> +<sub-package-variant>`](https://spack.readthedocs.io/en/v0.18.1/basic_usage.html#specs-dependencies)[`<compiler flags>`](https://spack.readthedocs.io/en/v0.18.1/basic_usage.html#compiler-flags)
[**Spec syntax**](https://spack.readthedocs.io/en/v0.21.1/basic_usage.html#specs-dependencies): `<package>`[`@<version>`](https://spack.readthedocs.io/en/v0.21.1/basic_usage.html#version-specifier)[`%<compiler>`](https://spack.readthedocs.io/en/v0.21.1/basic_usage.html#compiler-specifier)[`+<variant> ~<variant>`](https://spack.readthedocs.io/en/v0.21.1/basic_usage.html#variants)[`^<sub-package> +<sub-package-variant>`](https://spack.readthedocs.io/en/v0.21.1/basic_usage.html#specs-dependencies)[`<compiler flags>`](https://spack.readthedocs.io/en/v0.21.1/basic_usage.html#compiler-flags)

| | Command |
| --- | --- |
@@ -79,7 +79,7 @@ After an update we advice to rebuild packages, preferably in a new shell so that
| Spec | `spack spec <spec>` concretizes abstract spec (unspecfied variant = **any**)<br>*Spack is not required to use the default of an unspecified variant. The default value is only a tiebreaker for the concretizer.* |
| Install | `spack install <spec>` |
| Locate | `spack location --install-dir <spec>` prints location of **all** installs that satisfy the spec |
| [Load env](https://spack.readthedocs.io/en/v0.18.1/command_index.html?highlight=spack%20load#spack-load) | `spack load <spec>` loads run environment |
| [Activate env](https://spack.readthedocs.io/en/v0.18.1/environments.html) | `spack env activate <env_name>` |
| [Deactivate env](https://spack.readthedocs.io/en/v0.18.1/environments.html) | `spack deactivate` |
| [Load env](https://spack.readthedocs.io/en/v0.21.1/command_index.html?highlight=spack%20load#spack-load) | `spack load <spec>` loads run environment |
| [Activate env](https://spack.readthedocs.io/en/v0.21.1/environments.html) | `spack env activate <env_name>` |
| [Deactivate env](https://spack.readthedocs.io/en/v0.21.1/environments.html) | `spack deactivate` |

16 changes: 0 additions & 16 deletions create_new_sysconfig.sh

This file was deleted.

22 changes: 7 additions & 15 deletions docs/InstanceManagement.rst
Original file line number Diff line number Diff line change
@@ -17,7 +17,7 @@ Versions

Generally, we recommend to host a released version of spack-c2sm and upgrade to newer versions when you see fit.
But if you fancy the latest developments before they are released, you may follow the branch ``main``.
For automated systems that regularly set up a new Spack instance, using a fixed version and updating on demand, is more robust and limits the dependencies of your project. Following ``main`` on the other hand automatically updates to the newest features but breaks upon API chaning commits in spack-c2sm.
For automated systems that regularly set up a new Spack instance, using a fixed version and updating on demand, is more robust and limits the dependencies of your project. Following ``main`` on the other hand automatically updates to the newest features but breaks upon API changing commits in spack-c2sm.

Create a new Spack instance
---------------------------
@@ -29,20 +29,13 @@ To get an instance, clone spack-c2sm and its submodule spack.
$ git clone --depth 1 --recurse-submodules --shallow-submodules -b <branch/tag> https://github.com/C2SM/spack-c2sm.git
The arguments ``--depth 1`` and ``--shallow-submodules`` are optional, but they reduce the amount of downloaded data.
It is recommended to clone ``spack-c2sm`` in a location that does **not** undergo a
regular cleanup.
It is recommended to clone ``spack-c2sm`` in a location that does **not** undergo a regular cleanup.

Setup Spack environment
-----------------------

``setup-env.sh`` automatically detects the machine it is running on, or falls back to a generic configuration called 'unknown'.
``setup-env.sh <machine>`` forces a machine. This also works with 'unknown' as a machine, which is useful in a container.
It prints which machine it detected.
You may simply execute

.. code-block:: console
$ . spack-c2sm/setup-env.sh
``setup-env.sh <upstream>`` loads spack with the provided upstream to look for preinstalled software and configurations.
``setup-env.sh`` loads spack without an upstream.


Update Spack instance
@@ -61,10 +54,9 @@ This is required after upgrades at CSCS or if you need new features of a package
Clean Spack instance
--------------------

To clean a Spack instance, empty the caches, uninstall everything and remove misc caches:
To clean a Spack instance, empty the caches and uninstall everything:

.. code-block:: console
$ spack clean -a #[cleans all misc caches](https://spack.readthedocs.io/en/v0.18.1/command_index.html?highlight=spack%20load#spack-clean)
$ spack uninstall -a #[uninstalls all packages](https://spack.readthedocs.io/en/v0.18.1/command_index.html?highlight=spack%20load#spack-uninstall)
$ rm -rf ~/.spack #removes user scope data
$ spack clean -a #[cleans all misc caches](https://spack.readthedocs.io/en/v0.21.1/command_index.html?highlight=spack%20load#spack-clean)
$ spack uninstall -a #[uninstalls all packages](https://spack.readthedocs.io/en/v0.21.1/command_index.html?highlight=spack%20load#spack-uninstall)
23 changes: 1 addition & 22 deletions docs/Testing.rst
Original file line number Diff line number Diff line change
@@ -24,28 +24,7 @@ This is a common way to do it.
Pull Request Testing for spack-c2sm on GitHub
---------------------------------------------

To test a PR, create a comment ``launch jenkins [<packages>] [<machines>]``.

It will test the listed packages on the listed machines.
No package means all packages. No machine means all machines.
The order is irrelevant.

Examples
^^^^^^^^

* ``launch jenkins int2lm balfrin`` tests int2lm on balfrin.
* ``launch jenkins cosmo int2lm balfrin`` tests

* cosmo on balfrin
* int2lm on balfrin

* ``launch jenkins cosmo icon`` tests cosmo and icon on all machines.
* ``launch jenkins balfrin`` tests all packages on balfrin.
* ``launch jenkins`` tests all packages on all machines.
* ``launch jenkins all`` tests all packages on all machines.


Supported packages: all folder names in folder `packages <https://github.com/C2SM/spack-c2sm/tree/main/packages>`__.
To test a PR, create a comment ``launch jenkins``.

Supported machines:

29 changes: 0 additions & 29 deletions docs/UpstreamManagement.rst

This file was deleted.

1 change: 0 additions & 1 deletion docs/index.rst
Original file line number Diff line number Diff line change
@@ -20,7 +20,6 @@ and deploy our software on supercomputers, mostly at the
InstanceManagement
SpackCommands
Testing
UpstreamManagement
CodeDevelopment
SpackChoice

43 changes: 11 additions & 32 deletions repos/c2sm/packages/icon/package.py
Original file line number Diff line number Diff line change
@@ -138,9 +138,6 @@ class Icon(AutotoolsPackage, CudaPackage):
variant('parallel-netcdf',
default=False,
description='Enable usage of the parallel features of NetCDF')
variant('cdi-pio',
default=False,
description='Enable usage of the parallel features of CDI')
variant('sct', default=False, description='Enable the SCT timer')
variant('yaxt', default=False, description='Enable the YAXT data exchange')

@@ -229,29 +226,25 @@ class Icon(AutotoolsPackage, CudaPackage):
depends_on('libxml2', when='+art')

for x in serialization_values:
depends_on('serialbox+fortran', when='serialization={0}'.format(x))
# WORKAROUND: A build and link dependency should imply that the same compiler is used. This enforces it.
depends_on('serialbox %nvhpc', when='%nvhpc')
depends_on('serialbox %gcc', when='%gcc')

depends_on('libcdi-pio+fortran+netcdf', when='+cdi-pio')
depends_on('libcdi-pio grib2=eccodes', when='+cdi-pio+grib2')
depends_on('libcdi-pio+mpi', when='+cdi-pio+mpi')
# WORKAROUND: A build and link dependency should imply that the same compiler is used. This enforces it.
depends_on('serialbox+fortran %nvhpc',
when='serialization={0} %nvhpc'.format(x))
depends_on('serialbox+fortran %gcc',
when='serialization={0} %gcc'.format(x))

depends_on('eccodes +fortran', when='+emvorado')
depends_on('eccodes', when='+grib2 ~cdi-pio')
depends_on('eccodes', when='+grib2')
depends_on('cosmo-eccodes-definitions',
type=('build', 'run'),
when='+eccodes-definitions')

depends_on('yaxt+fortran', when='+cdi-pio')
depends_on('lapack')
depends_on('blas')
depends_on('netcdf-fortran')

depends_on('netcdf-c', when='~cdi-pio')
depends_on('netcdf-c', when='+coupling')
depends_on('netcdf-c+mpi', when='+parallel-netcdf~cdi-pio')
depends_on('netcdf-c')
depends_on('netcdf-c+mpi', when='+parallel-netcdf')

depends_on('hdf5 +szip +hl +fortran', when='+emvorado')
depends_on('hdf5 +szip', when='+sct')
@@ -343,12 +336,6 @@ def configure_args(self):
]:
args += self.enable_or_disable(x)

if '+cdi-pio' in self.spec:
args.extend([
'--enable-cdi-pio', '--with-external-cdi',
'--with-external-yaxt'
])

if self.compiler.name == 'gcc':
flags['CFLAGS'].append('-g')
flags['ICON_CFLAGS'].append('-O3')
@@ -450,7 +437,7 @@ def configure_args(self):
elif self.compiler.name == 'aocc':
flags['CFLAGS'].extend(['-g', '-O2'])
flags['FCFLAGS'].extend(['-g', '-O2'])
if self.spec.satisfies('~cdi-pio+yaxt'):
if self.spec.satisfies('+yaxt'):
# Enable the PGI/Cray (NO_2D_PARAM) workaround for the test
# suite of the bundled YAXT (apply also when not self.run_tests
# to make sure we get identical installations):
@@ -487,24 +474,16 @@ def configure_args(self):
])
libs += self.spec['serialbox:fortran'].libs

if '+cdi-pio' in self.spec:
libs += self.spec['libcdi-pio:fortran'].libs

if '+emvorado' in self.spec:
libs += self.spec['eccodes:fortran'].libs

if '+grib2~cdi-pio' in self.spec:
if '+grib2' in self.spec:
libs += self.spec['eccodes:c'].libs

if '+cdi-pio' in self.spec:
libs += self.spec['yaxt:fortran'].libs

libs += self.spec['lapack:fortran'].libs
libs += self.spec['blas:fortran'].libs
libs += self.spec['netcdf-fortran'].libs

if '+coupling' in self.spec or '~cdi-pio' in self.spec:
libs += self.spec['netcdf-c'].libs
libs += self.spec['netcdf-c'].libs

if '+emvorado' in self.spec:
libs += self.spec['hdf5:fortran,hl'].libs
4 changes: 2 additions & 2 deletions repos/c2sm/packages/icontools/package.py
Original file line number Diff line number Diff line change
@@ -24,7 +24,7 @@ class Icontools(AutotoolsPackage):
(for example the boundary condition, initial condition file,...) for ICON.
"""

homepage = 'https://c2sm.github.io/tools/icontools.html'
homepage = 'https://c2sm.github.io/tools/icontools/'
c2sm = 'git@github.com:C2SM/icontools.git'
dkrz = 'git@gitlab.dkrz.de:dwd-sw/dwd_icon_tools.git'

@@ -46,7 +46,7 @@ class Icontools(AutotoolsPackage):
'mpi',
type=('build', 'link', 'run'),
)
depends_on('eccodes@2.19.0 +fortran ~aec', type=('build', 'link', 'run'))
depends_on('eccodes +fortran ~aec', type=('build', 'link', 'run'))
depends_on('jasper@1.900.1', type=('build', 'link'))

variant(
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