From 3fbf807e856a90001af271664441708f231cc52e Mon Sep 17 00:00:00 2001
From: Dennis Terhorst <d.terhorst@fz-juelich.de>
Date: Mon, 25 Mar 2024 21:23:54 +0100
Subject: [PATCH 01/10] feat(nest): bump version to 3.7_rc1
---
packages/nest/package.py | 1 +
spack.yaml | 2 +-
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/packages/nest/package.py b/packages/nest/package.py
index f88e8f3e..df1f76ed 100644
--- a/packages/nest/package.py
+++ b/packages/nest/package.py
@@ -28,6 +28,7 @@ class Nest(CMakePackage):
maintainers = ['terhorst']
version('master', branch='master')
+ version('3.7_rc1', sha256='6f5948ac717d4b66c84ed53ba5c9b0e44e4e9cc3c1f3d15d8d8f21024313061e')
version('3.6', sha256='68d6b11791e1284dc94fef35d84c08dd7a11322c0f1e1fc9b39c5e6882284922')
patch('nest-simulator-3.6-p1-CxxRealPath.patch', when='@3.6')
version('3.5', sha256='3cdf5720854a4d8a7d359f9de9d2fb3619a0be2e36932028d6940360741547bd')
diff --git a/spack.yaml b/spack.yaml
index 726a38bc..9fce7ff1 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -13,7 +13,7 @@ spack:
- biobb-structure-checking@3.12.1
- biobb-structure-utils@4.0.0
- hxtorch@8.0-a3
- - nest@3.6 +sonata
+ - nest@3.7_rc1 +sonata
- neuron@8.2.3 +mpi
- py-bluepyefe@2.2.18
- py-bluepymm@0.7.65
--
GitLab
From f7c366b8ce1acb9ecc453a4e8c991c54928f16e3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Mon, 18 Mar 2024 10:59:45 +0100
Subject: [PATCH 02/10] feat(jax): add new versions
---
packages/py-chex/package.py | 36 +++++++++++
packages/py-jax/package.py | 72 ++++++++++++++++++++++
packages/py-jaxlib/package.py | 109 ++++++++++++++++++++++++++++++++++
3 files changed, 217 insertions(+)
create mode 100644 packages/py-chex/package.py
create mode 100644 packages/py-jax/package.py
create mode 100644 packages/py-jaxlib/package.py
diff --git a/packages/py-chex/package.py b/packages/py-chex/package.py
new file mode 100644
index 00000000..7e41890f
--- /dev/null
+++ b/packages/py-chex/package.py
@@ -0,0 +1,36 @@
+# 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 *
+
+
+# EBRAINS: based on spack/0.21.2
+class PyChex(PythonPackage):
+ """Chex is a library of utilities for helping to write reliable JAX code."""
+
+ homepage = "https://github.com/deepmind/chex"
+ pypi = "chex/chex-0.1.0.tar.gz"
+
+ # begin EBRAINS (added): bring upstream
+ version("0.1.7", sha256="74ed49799ac4d229881456d468136f1b19a9f9839e3de72b058824e2a4f4dedd")
+ version("0.1.5", sha256="686858320f8f220c82a6c7eeb54dcdcaa4f3d7f66690dacd13a24baa1ee8299e")
+ # end EBRAINS
+ version("0.1.0", sha256="9e032058f5fed2fc1d5e9bf8e12ece5910cf6a478c12d402b6d30984695f2161")
+
+ depends_on("python@3.7:", type=("build", "run"))
+ depends_on("py-setuptools", type="build")
+ depends_on("py-absl-py@0.9.0:", type=("build", "run"))
+ # begin EBRAINS (added): bring upstream
+ depends_on("py-typing-extensions@4.2.0:", when="@0.1.6: ^python@:3.10", type=("build", "run"))
+ # end EBRAINS
+ depends_on("py-dm-tree@0.1.5:", type=("build", "run"))
+ depends_on("py-jax@0.1.55:", type=("build", "run"))
+ # begin EBRAINS (added): bring upstream
+ depends_on("py-jax@0.4.6:", when="@0.1.7:", type=("build", "run"))
+ # end EBRAINS
+ depends_on("py-jaxlib@0.1.37:", type=("build", "run"))
+ depends_on("py-numpy@1.18.0:", type=("build", "run"))
+ depends_on("py-toolz@0.9.0:", type=("build", "run"))
diff --git a/packages/py-jax/package.py b/packages/py-jax/package.py
new file mode 100644
index 00000000..233de5b5
--- /dev/null
+++ b/packages/py-jax/package.py
@@ -0,0 +1,72 @@
+# 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 *
+
+
+# EBRAINS: based on spack/0.21.2
+class PyJax(PythonPackage):
+ """JAX is Autograd and XLA, brought together for high-performance
+ machine learning research. With its updated version of Autograd,
+ JAX can automatically differentiate native Python and NumPy
+ functions. It can differentiate through loops, branches,
+ recursion, and closures, and it can take derivatives of
+ derivatives of derivatives. It supports reverse-mode
+ differentiation (a.k.a. backpropagation) via grad as well as
+ forward-mode differentiation, and the two can be composed
+ arbitrarily to any order."""
+
+ homepage = "https://github.com/google/jax"
+ pypi = "jax/jax-0.2.25.tar.gz"
+
+ # begin EBRAINS (added): bring upstream
+ version("0.4.13", sha256="03bfe6749dfe647f16f15f6616638adae6c4a7ca7167c75c21961ecfd3a3baaa")
+ # end EBRAINS
+ version("0.4.3", sha256="d43f08f940aa30eb339965cfb3d6bee2296537b0dc2f0c65ccae3009279529ae")
+ version("0.3.23", sha256="bff436e15552a82c0ebdef32737043b799e1e10124423c57a6ae6118c3a7b6cd")
+ version("0.2.25", sha256="822e8d1e06257eaa0fdc4c0a0686c4556e9f33647fa2a766755f984786ae7446")
+
+ # begin EBRAINS (modified): bring upstream
+ depends_on("python@3.7:", type=("build", "run"))
+ depends_on("python@3.8:", when="@0.4:", type=("build", "run"))
+ depends_on("python@3.9:", when="@0.4.14:", type=("build", "run"))
+ depends_on("py-setuptools", type="build")
+ depends_on("py-numpy@1.22:", when="@0.4.14:", type=("build", "run"))
+ depends_on("py-numpy@1.21:", when="@0.4.9:", type=("build", "run"))
+ depends_on("py-numpy@1.20:", when="@0.3:", type=("build", "run"))
+ depends_on("py-numpy@1.18:", type=("build", "run"))
+ depends_on("py-opt-einsum", type=("build", "run"))
+ depends_on("py-scipy@1.2.1:", type=("build", "run"))
+ depends_on("py-scipy@1.5:", when="@0.3:", type=("build", "run"))
+ depends_on("py-scipy@1.7:", when="@0.4.7:", type=("build", "run"))
+ depends_on("py-ml-dtypes@0.2.0:", when="@0.4.14:", type=("build", "run"))
+ depends_on("py-ml-dtypes@0.1.0:", when="@0.4.9:", type=("build", "run"))
+ depends_on("py-ml-dtypes@0.0.3:", when="@0.4.7:", type=("build", "run"))
+ depends_on("py-importlib-metadata@4.6:", when="@0.4.11: ^python@:3.9", type="run")
+ # end EBRAINS
+
+ # See _minimum_jaxlib_version in jax/version.py
+ # begin EBRAINS (modified): bring upstream
+ jax_to_jaxlib = {
+ "0.4.14": "0.4.14",
+ "0.4.13": "0.4.13",
+ "0.4.3": "0.4.2",
+ "0.3.23": "0.3.15",
+ "0.2.25": "0.1.69",
+ }
+ # end EBRAINS
+
+ for jax, jaxlib in jax_to_jaxlib.items():
+ # begin EBRAINS (modified): bring upstream
+ depends_on(f"py-jaxlib@{jaxlib}", when=f"@{jax}", type=("build", "run"))
+ # end EBRAINS
+
+ # Historical dependencies
+ depends_on("py-absl-py", when="@:0.3", type=("build", "run"))
+ depends_on("py-typing-extensions", when="@:0.3", type=("build", "run"))
+ # begin EBRAINS (deleted):
+ # depends_on("py-etils+epath", when="@0.3", type=("build", "run"))
+ # end EBRAINS
diff --git a/packages/py-jaxlib/package.py b/packages/py-jaxlib/package.py
new file mode 100644
index 00000000..af04f737
--- /dev/null
+++ b/packages/py-jaxlib/package.py
@@ -0,0 +1,109 @@
+# 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)
+
+import tempfile
+
+from spack.package import *
+
+
+# EBRAINS: based on spack/0.21.2
+class PyJaxlib(PythonPackage, CudaPackage):
+ """XLA library for Jax"""
+
+ homepage = "https://github.com/google/jax"
+ url = "https://github.com/google/jax/archive/refs/tags/jaxlib-v0.1.74.tar.gz"
+
+ tmp_path = ""
+ buildtmp = ""
+
+ # begin EBRAINS (added): bring upstream
+ version("0.4.13", sha256="45766238b57b992851763c64bc943858aebafe4cad7b3df6cde844690bc34293")
+ # end EBRAINS
+ version("0.4.3", sha256="2104735dc22be2b105e5517bd5bc6ae97f40e8e9e54928cac1585c6112a3d910")
+ version("0.3.22", sha256="680a6f5265ba26d5515617a95ae47244005366f879a5c321782fde60f34e6d0d")
+ version("0.1.74", sha256="bbc78c7a4927012dcb1b7cd135c7521f782d7dad516a2401b56d3190f81afe35")
+
+ # begin EBRAINS (deleted): Variant with default=False is provided by CudaPackage
+ # variant("cuda", default=True, description="Build with CUDA")
+ # end EBRAINS
+
+ # jaxlib/setup.py
+ # begin EBRAINS (modified): bring upstream
+ depends_on("python@3.9:", when="@0.4.14:", type=("build", "run"))
+ depends_on("python@3.8:", when="@0.4:", type=("build", "run"))
+ depends_on("python@3.7:", type=("build", "run"))
+ depends_on("py-setuptools", type="build")
+ depends_on("py-numpy@1.22:", when="@0.4.14:", type=("build", "run"))
+ depends_on("py-numpy@1.21:", when="@0.4.9:", type=("build", "run"))
+ depends_on("py-numpy@1.20:", when="@0.3:", type=("build", "run"))
+ depends_on("py-numpy@1.18:", type=("build", "run"))
+ depends_on("py-scipy@1.5:", type=("build", "run"))
+ depends_on("py-scipy@1.7:", when="@0.4.7:", type=("build", "run"))
+ depends_on("py-ml-dtypes@0.2.0:", when="@0.4.14:", type=("build", "run"))
+ depends_on("py-ml-dtypes@0.1.0:", when="@0.4.9:", type=("build", "run"))
+ depends_on("py-ml-dtypes@0.0.3:", when="@0.4.7:", type=("build", "run"))
+ # end EBRAINS
+
+ # .bazelversion
+ depends_on("bazel@5.1.1:5.9", when="@0.3:", type="build")
+ # https://github.com/google/jax/issues/8440
+ depends_on("bazel@4.1:4", when="@0.1", type="build")
+
+ # README.md
+ # begin EBRAINS (added): bring upstream
+ depends_on("cuda@11.8:", when="@0.4.8:+cuda")
+ # end EBRAINS
+ depends_on("cuda@11.4:", when="@0.4:+cuda")
+ depends_on("cuda@11.1:", when="@0.3+cuda")
+ # https://github.com/google/jax/issues/12614
+ depends_on("cuda@11.1:11.7.0", when="@0.1+cuda")
+ depends_on("cudnn@8.2:", when="@0.4:+cuda")
+ depends_on("cudnn@8.0.5:", when="+cuda")
+
+ # Historical dependencies
+ depends_on("py-absl-py", when="@:0.3", type=("build", "run"))
+ depends_on("py-flatbuffers@1.12:2", when="@0.1", type=("build", "run"))
+
+ def patch(self):
+ self.tmp_path = tempfile.mkdtemp(prefix="spack")
+ self.buildtmp = tempfile.mkdtemp(prefix="spack")
+ filter_file(
+ 'f"--output_path={output_path}",',
+ 'f"--output_path={output_path}",'
+ f' "--sources_path={self.tmp_path}",'
+ ' "--nohome_rc",'
+ ' "--nosystem_rc",'
+ f' "--jobs={make_jobs}",',
+ "build/build.py",
+ string=True,
+ )
+ filter_file(
+ "args = parser.parse_args()",
+ "args, junk = parser.parse_known_args()",
+ "build/build_wheel.py",
+ string=True,
+ )
+
+ def install(self, spec, prefix):
+ args = []
+ args.append("build/build.py")
+ if "+cuda" in spec:
+ args.append("--enable_cuda")
+ args.append("--cuda_path={0}".format(self.spec["cuda"].prefix))
+ args.append("--cudnn_path={0}".format(self.spec["cudnn"].prefix))
+ capabilities = ",".join(
+ "{0:.1f}".format(float(i) / 10.0) for i in spec.variants["cuda_arch"].value
+ )
+ args.append("--cuda_compute_capabilities={0}".format(capabilities))
+ args.append(
+ "--bazel_startup_options="
+ "--output_user_root={0}".format(self.wrapped_package_object.buildtmp)
+ )
+ python(*args)
+ with working_dir(self.wrapped_package_object.tmp_path):
+ args = std_pip_args + ["--prefix=" + self.prefix, "."]
+ pip(*args)
+ remove_linked_tree(self.wrapped_package_object.tmp_path)
+ remove_linked_tree(self.wrapped_package_object.buildtmp)
--
GitLab
From 5e3eb8056ebe3656fb28ace503e46d5adce13279 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Tue, 19 Mar 2024 13:27:49 +0100
Subject: [PATCH 03/10] feat: add py-optax
---
packages/py-optax/package.py | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)
create mode 100644 packages/py-optax/package.py
diff --git a/packages/py-optax/package.py b/packages/py-optax/package.py
new file mode 100644
index 00000000..c5cf8840
--- /dev/null
+++ b/packages/py-optax/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2024 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 import *
+
+
+class PyOptax(PythonPackage):
+ """A gradient processing and optimization library in JAX."""
+
+ homepage = "https://github.com/deepmind/optax"
+ pypi = "optax/optax-0.1.4.tar.gz"
+
+ version("0.1.4", sha256="fb7a0550d57a6636164a3de25986a8a19be8ff6431fcdf1225b4e05175810f22")
+
+ depends_on("python@3.8:", type=("build", "run"))
+ depends_on("py-setuptools", type="build")
+
+ depends_on("py-absl-py@0.7.1:", type=("build", "run"))
+ depends_on("py-chex@0.1.5:", type=("build", "run"))
+ depends_on("py-jax@0.1.55:", type=("build", "run"))
+ depends_on("py-jaxlib@0.1.37:", type=("build", "run"))
+ depends_on("py-numpy@1.18:", type=("build", "run"))
--
GitLab
From 923deb59241db8bdb47acddf9eb49c50fb0eb5e0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Mon, 18 Mar 2024 10:22:39 +0100
Subject: [PATCH 04/10] feat(BSS2): add jaxsnn (event-based ML)
---
packages/jaxsnn/package.py | 157 +++++++++++++++++++++++++++++++++++++
1 file changed, 157 insertions(+)
create mode 100644 packages/jaxsnn/package.py
diff --git a/packages/jaxsnn/package.py b/packages/jaxsnn/package.py
new file mode 100644
index 00000000..d1d7f5eb
--- /dev/null
+++ b/packages/jaxsnn/package.py
@@ -0,0 +1,157 @@
+# 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)
+import os
+import unittest.mock
+import xml.etree.ElementTree as ET
+
+from spack import *
+from spack.util.environment import EnvironmentModifications
+import spack.build_environment
+
+
+class Jaxsnn(WafPackage):
+ """jaxsnn is an event-based approach to machine-learning-inspired training
+ and simulation of SNNs, including support for the BrainScaleS-2
+ neuromorphic backend."""
+
+ homepage = "https://github.com/electronicvisions/jaxsnn"
+ # This repo provides a custom waf binary used for the build below
+ git = "https://github.com/electronicvisions/pynn-brainscales.git"
+
+ maintainers = ['emuller']
+
+ version('8.0-a3', tag='jaxsnn-8.0-a3')
+ version('8.0-a2', tag='jaxsnn-8.0-a2')
+ version('8.0-a1', tag='jaxsnn-8.0-a1')
+
+ # for now, this is still "on top" of hxtorch…
+ depends_on('hxtorch@8.0-a3', when='@8.0-a3', type=('build', 'link', 'run', 'test'))
+ depends_on('hxtorch@8.0-a2', when='@8.0-a2', type=('build', 'link', 'run', 'test'))
+ depends_on('hxtorch@8.0-a1', when='@8.0-a1', type=('build', 'link', 'run', 'test'))
+
+ # main dependencies w/o hxtorch.core dependencies (those come via hxtorch above)
+ depends_on('py-jax@0.4.13:', type=('build', 'link', 'run'))
+ depends_on('py-matplotlib', type=('build', 'link', 'run'))
+ depends_on('py-optax', type=('build', 'link', 'run'))
+ depends_on('py-tree-math', type=('build', 'link', 'run'))
+ extends('python')
+
+ def do_fetch(self, mirror_only=False):
+ """Setup the project."""
+
+ self.stage.create()
+ self.stage.fetch(mirror_only)
+
+ # if fetcher didn't do anything, it's cached already
+ if not os.path.exists(self.stage.source_path):
+ return
+
+ with working_dir(self.stage.source_path):
+ python = which('python3')
+ python('./waf', 'setup', '--repo-db-url=https://github.com/electronicvisions/projects',
+ '--clone-depth=2',
+ '--without-munge',
+ '--without-hxcomm-hostarq',
+ '--project=jaxsnn',
+ '--release-branch=ebrains-' + str(self.spec.version)
+ )
+
+ # in the configure step, we need access to all archived .git folders
+ def custom_archive(self, destination):
+ super(spack.fetch_strategy.GitFetchStrategy, self).archive(destination)
+ with unittest.mock.patch('spack.fetch_strategy.GitFetchStrategy.archive', new=custom_archive):
+ self.stage.cache_local()
+
+ def _setup_common_env(self, env):
+ # grenade needs to find some libraries for the JIT-compilation of
+ # programs for BrainScaleS-2's embedded processor.
+ ppu_include_dirs = []
+ ppu_dep_names = ['bitsery', 'boost', 'cereal']
+ for ppu_dep_name in ppu_dep_names:
+ dep = self.spec[ppu_dep_name]
+ dep_include_dirs = set(dep.headers.directories)
+ ppu_include_dirs.extend(list(dep_include_dirs))
+ for dir in reversed(ppu_include_dirs):
+ env.prepend_path("C_INCLUDE_PATH", dir)
+ env.prepend_path("CPLUS_INCLUDE_PATH", dir)
+
+ def setup_build_environment(self, env):
+ my_envmod = EnvironmentModifications(env)
+ spack.build_environment.set_wrapper_variables(self, my_envmod)
+ my_env = {}
+ my_envmod.apply_modifications(my_env)
+
+ def get_path(env, name):
+ path = env.get(name, "").strip()
+ if path:
+ return path.split(os.pathsep)
+ return []
+
+ # spack tries to find headers and libraries by itself (i.e. it's not
+ # relying on the compiler to find it); we explicitly expose the
+ # spack-provided env vars that contain include and library paths
+ if 'SPACK_INCLUDE_DIRS' in my_env:
+ for dir in reversed(get_path(my_env, "SPACK_INCLUDE_DIRS")):
+ env.prepend_path("C_INCLUDE_PATH", dir)
+ env.prepend_path("CPLUS_INCLUDE_PATH", dir)
+ if 'SPACK_LINK_DIRS' in my_env:
+ for dir in reversed(get_path(my_env, "SPACK_LINK_DIRS")):
+ env.prepend_path("LIBRARY_PATH", dir)
+ env.prepend_path("LD_LIBRARY_PATH", dir)
+ for dir in reversed(self.compiler.implicit_rpaths()):
+ env.prepend_path("LIBRARY_PATH", dir)
+ # technically this is probably not needed for the non-configure steps
+ env.prepend_path("LD_LIBRARY_PATH", dir)
+
+ def setup_dependent_build_environment(self, env, dependent_spec):
+ self._setup_common_env(env)
+
+ def setup_run_environment(self, env):
+ self._setup_common_env(env)
+
+ def setup_dependent_run_environment(self, env, dependent_spec):
+ self._setup_common_env(env)
+
+ # override configure step as we perform a project setup first
+ def configure(self, spec, prefix):
+ """Configure the project."""
+
+ args = ['--prefix={0}'.format(self.prefix)]
+ args += self.configure_args()
+ self.waf('configure', '--build-profile=release', '--disable-doxygen', *args)
+
+ def build_args(self):
+ args = ['--keep', '--test-execnone', '-v']
+ return args
+
+ def build_test(self):
+ self.builder.waf('build', '--test-execall')
+ copy_tree('build/test_results', join_path(self.prefix, '.build'))
+ copy_tree('build/test_results', join_path(self.stage.path, ".install_time_tests"))
+ # propagate failures from junit output to spack
+ tree = ET.parse('build/test_results/summary.xml')
+ for testsuite in tree.getroot():
+ for testcase in testsuite:
+ if (testcase.get('name').startswith("pycodestyle") or
+ testcase.get('name').startswith("pylint")):
+ continue
+ for elem in testcase:
+ if (elem.tag == 'failure') and not (
+ elem.get('message').startswith("pylint:") or
+ elem.get('message').startswith("pycodestyle:") or
+ ("OK" in elem.get('message') and "Segmentation fault" in elem.get('message'))):
+ raise RuntimeError("Failed test found: {}".format(testcase.get('name')))
+
+ def install_args(self):
+ args = ['--test-execnone']
+ return args
+
+ def install_test(self):
+ with working_dir('spack-test', create=True):
+ old_pythonpath = os.environ.get('PYTHONPATH', '')
+ os.environ['PYTHONPATH'] = ':'.join([str(self.prefix.lib), old_pythonpath])
+ bash = which("bash")
+ # ignore segfaults for now (exit code 139)
+ bash('-c', '(python -c "import jaxsnn; print(jaxsnn.__file__)" || ( test $? -eq 139 && echo "segfault")) || exit $?')
--
GitLab
From 156f31d46a2328444f1a056e6807f60bd9b7f993 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Mon, 18 Mar 2024 10:22:52 +0100
Subject: [PATCH 05/10] feat(BSS2): enable jaxsnn
---
spack.yaml | 1 +
1 file changed, 1 insertion(+)
diff --git a/spack.yaml b/spack.yaml
index 9fce7ff1..9fc9e2c3 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -15,6 +15,7 @@ spack:
- hxtorch@8.0-a3
- nest@3.7_rc1 +sonata
- neuron@8.2.3 +mpi
+ - jaxsnn@8.0-a3
- py-bluepyefe@2.2.18
- py-bluepymm@0.7.65
- py-bluepyopt@1.13.86
--
GitLab
From 9c517f6c6876dc61414d00f0d7cf7ace35fad411 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Thu, 21 Mar 2024 12:35:56 +0100
Subject: [PATCH 06/10] chore(bss2): reduce build/test system-specific
duplication
---
packages/build-brainscales/package.py | 136 ++++++++++++++++++++++++++
packages/hxtorch/package.py | 125 +----------------------
packages/jaxsnn/package.py | 117 +---------------------
packages/pynn-brainscales/package.py | 126 +-----------------------
4 files changed, 151 insertions(+), 353 deletions(-)
create mode 100644 packages/build-brainscales/package.py
diff --git a/packages/build-brainscales/package.py b/packages/build-brainscales/package.py
new file mode 100644
index 00000000..a162821d
--- /dev/null
+++ b/packages/build-brainscales/package.py
@@ -0,0 +1,136 @@
+# Copyright 2013-2024 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)
+import os
+import unittest.mock
+import xml.etree.ElementTree as ET
+
+from spack import *
+from spack.util.environment import EnvironmentModifications
+import spack.build_environment
+
+
+class BuildBrainscales(WafPackage):
+ """Common stuff for BrainScaleS packages..."""
+
+ def do_fetch(self, mirror_only=False):
+ """Setup the project."""
+
+ self.stage.create()
+ self.stage.fetch(mirror_only)
+
+ # if fetcher didn't do anything, it's cached already
+ if not os.path.exists(self.stage.source_path):
+ return
+
+ with working_dir(self.stage.source_path):
+ python = which('python3')
+ if self.spec.satisfies('@:7'):
+ python('./waf', 'setup', '--repo-db-url=https://github.com/electronicvisions/projects',
+ '--clone-depth=2',
+ '--without-munge',
+ '--without-hxcomm-hostarq',
+ '--without-hxcomm-extoll',
+ '--project=' + str(self.spec.name),
+ '--release-branch=ebrains-' + str(self.spec.version)
+ )
+ else:
+ python('./waf', 'setup', '--repo-db-url=https://github.com/electronicvisions/projects',
+ '--clone-depth=2',
+ '--without-munge',
+ '--without-hxcomm-hostarq',
+ '--project=' + str(self.spec.name),
+ '--release-branch=ebrains-' + str(self.spec.version)
+ )
+
+
+ # in the configure step, we need access to all archived .git folders
+ def custom_archive(self, destination):
+ super(spack.fetch_strategy.GitFetchStrategy, self).archive(destination)
+ with unittest.mock.patch('spack.fetch_strategy.GitFetchStrategy.archive', new=custom_archive):
+ self.stage.cache_local()
+
+ def _setup_common_env(self, env):
+ # grenade needs to find some libraries for the JIT-compilation of
+ # programs for BrainScaleS-2's embedded processor.
+ ppu_include_dirs = []
+ ppu_dep_names = ['bitsery', 'boost', 'cereal']
+ for ppu_dep_name in ppu_dep_names:
+ dep = self.spec[ppu_dep_name]
+ dep_include_dirs = set(dep.headers.directories)
+ ppu_include_dirs.extend(list(dep_include_dirs))
+ for dir in reversed(ppu_include_dirs):
+ env.prepend_path("C_INCLUDE_PATH", dir)
+ env.prepend_path("CPLUS_INCLUDE_PATH", dir)
+
+ def setup_build_environment(self, env):
+ my_envmod = EnvironmentModifications(env)
+ spack.build_environment.set_wrapper_variables(self, my_envmod)
+ my_env = {}
+ my_envmod.apply_modifications(my_env)
+
+ def get_path(env, name):
+ path = env.get(name, "").strip()
+ if path:
+ return path.split(os.pathsep)
+ return []
+
+ # spack tries to find headers and libraries by itself (i.e. it's not
+ # relying on the compiler to find it); we explicitly expose the
+ # spack-provided env vars that contain include and library paths
+ if 'SPACK_INCLUDE_DIRS' in my_env:
+ for dir in reversed(get_path(my_env, "SPACK_INCLUDE_DIRS")):
+ env.prepend_path("C_INCLUDE_PATH", dir)
+ env.prepend_path("CPLUS_INCLUDE_PATH", dir)
+ if 'SPACK_LINK_DIRS' in my_env:
+ for dir in reversed(get_path(my_env, "SPACK_LINK_DIRS")):
+ env.prepend_path("LIBRARY_PATH", dir)
+ env.prepend_path("LD_LIBRARY_PATH", dir)
+ for dir in reversed(self.compiler.implicit_rpaths()):
+ env.prepend_path("LIBRARY_PATH", dir)
+ # technically this is probably not needed for the non-configure steps
+ env.prepend_path("LD_LIBRARY_PATH", dir)
+
+ def setup_dependent_build_environment(self, env, dependent_spec):
+ self._setup_common_env(env)
+
+ def setup_run_environment(self, env):
+ self._setup_common_env(env)
+
+ def setup_dependent_run_environment(self, env, dependent_spec):
+ self._setup_common_env(env)
+
+ # override configure step as we perform a project setup first
+ def configure(self, spec, prefix):
+ """Configure the project."""
+
+ args = ['--prefix={0}'.format(self.prefix)]
+ args += self.configure_args()
+ self.waf('configure', '--build-profile=release', '--disable-doxygen', *args)
+
+ def build_args(self):
+ args = ['--keep', '--test-execnone', '-v']
+ return args
+
+ def build_test(self):
+ self.builder.waf('build', '--test-execall')
+ copy_tree('build/test_results', join_path(self.prefix, '.build'))
+ copy_tree('build/test_results', join_path(self.stage.path, ".install_time_tests"))
+ # propagate failures from junit output to spack
+ tree = ET.parse('build/test_results/summary.xml')
+ for testsuite in tree.getroot():
+ for testcase in testsuite:
+ if (testcase.get('name').startswith("pycodestyle") or
+ testcase.get('name').startswith("pylint")):
+ continue
+ for elem in testcase:
+ if (elem.tag == 'failure') and not (
+ elem.get('message').startswith("pylint:") or
+ elem.get('message').startswith("pycodestyle:") or
+ ("OK" in elem.get('message') and "Segmentation fault" in elem.get('message'))):
+ raise RuntimeError("Failed test found: {}".format(testcase.get('name')))
+
+ def install_args(self):
+ args = ['--test-execnone']
+ return args
diff --git a/packages/hxtorch/package.py b/packages/hxtorch/package.py
index bff7e733..f9751d98 100644
--- a/packages/hxtorch/package.py
+++ b/packages/hxtorch/package.py
@@ -1,18 +1,20 @@
-# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Copyright 2013-2024 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)
import os
import unittest.mock
-import sys
import xml.etree.ElementTree as ET
from spack import *
from spack.util.environment import EnvironmentModifications
import spack.build_environment
+import importlib
+build_brainscales = importlib.import_module("spack.pkg.ebrains-spack-builds.build_brainscales")
-class Hxtorch(WafPackage):
+
+class Hxtorch(build_brainscales.BuildBrainscales):
"""hxtorch --- a PyTorch-based toplevel for the BrainScaleS-2 neuromorphic hardware systems"""
homepage = "https://github.com/electronicvisions/hxtorch"
@@ -77,123 +79,6 @@ class Hxtorch(WafPackage):
depends_on('yaml-cpp+shared', type=('build', 'link', 'run'))
extends('python')
- def do_fetch(self, mirror_only=False):
- """Setup the project."""
-
- self.stage.create()
- self.stage.fetch(mirror_only)
-
- # if fetcher didn't do anything, it's cached already
- if not os.path.exists(self.stage.source_path):
- return
-
- with working_dir(self.stage.source_path):
- python = which('python3')
- if self.spec.satisfies('@:7'):
- python('./waf', 'setup', '--repo-db-url=https://github.com/electronicvisions/projects',
- '--clone-depth=2',
- '--without-munge',
- '--without-hxcomm-hostarq',
- '--without-hxcomm-extoll',
- '--project=hxtorch',
- '--release-branch=ebrains-' + str(self.spec.version)
- )
- else:
- python('./waf', 'setup', '--repo-db-url=https://github.com/electronicvisions/projects',
- '--clone-depth=2',
- '--without-munge',
- '--without-hxcomm-hostarq',
- '--project=hxtorch',
- '--release-branch=ebrains-' + str(self.spec.version)
- )
-
- # in the configure step, we need access to all archived .git folders
- def custom_archive(self, destination):
- super(spack.fetch_strategy.GitFetchStrategy, self).archive(destination)
- with unittest.mock.patch('spack.fetch_strategy.GitFetchStrategy.archive', new=custom_archive):
- self.stage.cache_local()
-
- def _setup_common_env(self, env):
- # grenade needs to find some libraries for the JIT-compilation of
- # programs for BrainScaleS-2's embedded processor.
- ppu_include_dirs = []
- ppu_dep_names = ['bitsery', 'boost', 'cereal']
- for ppu_dep_name in ppu_dep_names:
- dep = self.spec[ppu_dep_name]
- dep_include_dirs = set(dep.headers.directories)
- ppu_include_dirs.extend(list(dep_include_dirs))
- for dir in reversed(ppu_include_dirs):
- env.prepend_path("C_INCLUDE_PATH", dir)
- env.prepend_path("CPLUS_INCLUDE_PATH", dir)
-
- def setup_build_environment(self, env):
- my_envmod = EnvironmentModifications(env)
- spack.build_environment.set_wrapper_variables(self, my_envmod)
- my_env = {}
- my_envmod.apply_modifications(my_env)
-
- def get_path(env, name):
- path = env.get(name, "").strip()
- if path:
- return path.split(os.pathsep)
- return []
-
- # spack tries to find headers and libraries by itself (i.e. it's not
- # relying on the compiler to find it); we explicitly expose the
- # spack-provided env vars that contain include and library paths
- if 'SPACK_INCLUDE_DIRS' in my_env:
- for dir in reversed(get_path(my_env, "SPACK_INCLUDE_DIRS")):
- env.prepend_path("C_INCLUDE_PATH", dir)
- env.prepend_path("CPLUS_INCLUDE_PATH", dir)
- if 'SPACK_LINK_DIRS' in my_env:
- for dir in reversed(get_path(my_env, "SPACK_LINK_DIRS")):
- env.prepend_path("LIBRARY_PATH", dir)
- env.prepend_path("LD_LIBRARY_PATH", dir)
- for dir in reversed(self.compiler.implicit_rpaths()):
- env.prepend_path("LIBRARY_PATH", dir)
- # technically this is probably not needed for the non-configure steps
- env.prepend_path("LD_LIBRARY_PATH", dir)
-
- def setup_dependent_build_environment(self, env, dependent_spec):
- self._setup_common_env(env)
-
- def setup_run_environment(self, env):
- self._setup_common_env(env)
-
- def setup_dependent_run_environment(self, env, dependent_spec):
- self._setup_common_env(env)
-
- # override configure step as we perform a project setup first
- def configure(self, spec, prefix):
- """Configure the project."""
-
- args = ['--prefix={0}'.format(self.prefix)]
- args += self.configure_args()
- self.waf('configure', '--build-profile=release', '--disable-doxygen', *args)
-
- def build_args(self):
- args = ['--keep', '--test-execnone', '-v']
- return args
-
- def build_test(self):
- self.builder.waf('build', '--test-execall')
- copy_tree('build/test_results', join_path(self.prefix, ".build"))
- copy_tree('build/test_results', join_path(self.stage.path, ".install_time_tests"))
- # propagate failures from junit output to spack
- tree = ET.parse('build/test_results/summary.xml')
- for testsuite in tree.getroot():
- for testcase in testsuite:
- for elem in testcase:
- if (elem.tag == 'failure') and not (
- elem.get('message').startswith("pylint:") or
- elem.get('message').startswith("pycodestyle:") or
- ("OK" in elem.get('message') and "Segmentation fault" in elem.get('message'))):
- raise RuntimeError("Failed test found: {}".format(testcase.get('name')))
-
- def install_args(self):
- args = ['--test-execnone']
- return args
-
def install_test(self):
with working_dir('spack-test', create=True):
old_pythonpath = os.environ.get('PYTHONPATH', '')
diff --git a/packages/jaxsnn/package.py b/packages/jaxsnn/package.py
index d1d7f5eb..cd66a377 100644
--- a/packages/jaxsnn/package.py
+++ b/packages/jaxsnn/package.py
@@ -1,4 +1,4 @@
-# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Copyright 2013-2024 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)
@@ -10,8 +10,11 @@ from spack import *
from spack.util.environment import EnvironmentModifications
import spack.build_environment
+import importlib
+build_brainscales = importlib.import_module("spack.pkg.ebrains-spack-builds.build_brainscales")
-class Jaxsnn(WafPackage):
+
+class Jaxsnn(build_brainscales.BuildBrainscales):
"""jaxsnn is an event-based approach to machine-learning-inspired training
and simulation of SNNs, including support for the BrainScaleS-2
neuromorphic backend."""
@@ -38,116 +41,6 @@ class Jaxsnn(WafPackage):
depends_on('py-tree-math', type=('build', 'link', 'run'))
extends('python')
- def do_fetch(self, mirror_only=False):
- """Setup the project."""
-
- self.stage.create()
- self.stage.fetch(mirror_only)
-
- # if fetcher didn't do anything, it's cached already
- if not os.path.exists(self.stage.source_path):
- return
-
- with working_dir(self.stage.source_path):
- python = which('python3')
- python('./waf', 'setup', '--repo-db-url=https://github.com/electronicvisions/projects',
- '--clone-depth=2',
- '--without-munge',
- '--without-hxcomm-hostarq',
- '--project=jaxsnn',
- '--release-branch=ebrains-' + str(self.spec.version)
- )
-
- # in the configure step, we need access to all archived .git folders
- def custom_archive(self, destination):
- super(spack.fetch_strategy.GitFetchStrategy, self).archive(destination)
- with unittest.mock.patch('spack.fetch_strategy.GitFetchStrategy.archive', new=custom_archive):
- self.stage.cache_local()
-
- def _setup_common_env(self, env):
- # grenade needs to find some libraries for the JIT-compilation of
- # programs for BrainScaleS-2's embedded processor.
- ppu_include_dirs = []
- ppu_dep_names = ['bitsery', 'boost', 'cereal']
- for ppu_dep_name in ppu_dep_names:
- dep = self.spec[ppu_dep_name]
- dep_include_dirs = set(dep.headers.directories)
- ppu_include_dirs.extend(list(dep_include_dirs))
- for dir in reversed(ppu_include_dirs):
- env.prepend_path("C_INCLUDE_PATH", dir)
- env.prepend_path("CPLUS_INCLUDE_PATH", dir)
-
- def setup_build_environment(self, env):
- my_envmod = EnvironmentModifications(env)
- spack.build_environment.set_wrapper_variables(self, my_envmod)
- my_env = {}
- my_envmod.apply_modifications(my_env)
-
- def get_path(env, name):
- path = env.get(name, "").strip()
- if path:
- return path.split(os.pathsep)
- return []
-
- # spack tries to find headers and libraries by itself (i.e. it's not
- # relying on the compiler to find it); we explicitly expose the
- # spack-provided env vars that contain include and library paths
- if 'SPACK_INCLUDE_DIRS' in my_env:
- for dir in reversed(get_path(my_env, "SPACK_INCLUDE_DIRS")):
- env.prepend_path("C_INCLUDE_PATH", dir)
- env.prepend_path("CPLUS_INCLUDE_PATH", dir)
- if 'SPACK_LINK_DIRS' in my_env:
- for dir in reversed(get_path(my_env, "SPACK_LINK_DIRS")):
- env.prepend_path("LIBRARY_PATH", dir)
- env.prepend_path("LD_LIBRARY_PATH", dir)
- for dir in reversed(self.compiler.implicit_rpaths()):
- env.prepend_path("LIBRARY_PATH", dir)
- # technically this is probably not needed for the non-configure steps
- env.prepend_path("LD_LIBRARY_PATH", dir)
-
- def setup_dependent_build_environment(self, env, dependent_spec):
- self._setup_common_env(env)
-
- def setup_run_environment(self, env):
- self._setup_common_env(env)
-
- def setup_dependent_run_environment(self, env, dependent_spec):
- self._setup_common_env(env)
-
- # override configure step as we perform a project setup first
- def configure(self, spec, prefix):
- """Configure the project."""
-
- args = ['--prefix={0}'.format(self.prefix)]
- args += self.configure_args()
- self.waf('configure', '--build-profile=release', '--disable-doxygen', *args)
-
- def build_args(self):
- args = ['--keep', '--test-execnone', '-v']
- return args
-
- def build_test(self):
- self.builder.waf('build', '--test-execall')
- copy_tree('build/test_results', join_path(self.prefix, '.build'))
- copy_tree('build/test_results', join_path(self.stage.path, ".install_time_tests"))
- # propagate failures from junit output to spack
- tree = ET.parse('build/test_results/summary.xml')
- for testsuite in tree.getroot():
- for testcase in testsuite:
- if (testcase.get('name').startswith("pycodestyle") or
- testcase.get('name').startswith("pylint")):
- continue
- for elem in testcase:
- if (elem.tag == 'failure') and not (
- elem.get('message').startswith("pylint:") or
- elem.get('message').startswith("pycodestyle:") or
- ("OK" in elem.get('message') and "Segmentation fault" in elem.get('message'))):
- raise RuntimeError("Failed test found: {}".format(testcase.get('name')))
-
- def install_args(self):
- args = ['--test-execnone']
- return args
-
def install_test(self):
with working_dir('spack-test', create=True):
old_pythonpath = os.environ.get('PYTHONPATH', '')
diff --git a/packages/pynn-brainscales/package.py b/packages/pynn-brainscales/package.py
index e61b7b61..39f07d81 100644
--- a/packages/pynn-brainscales/package.py
+++ b/packages/pynn-brainscales/package.py
@@ -1,18 +1,20 @@
-# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Copyright 2013-2024 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)
import os
import unittest.mock
-import sys
import xml.etree.ElementTree as ET
from spack import *
from spack.util.environment import EnvironmentModifications
import spack.build_environment
+import importlib
+build_brainscales = importlib.import_module("spack.pkg.ebrains-spack-builds.build_brainscales")
-class PynnBrainscales(WafPackage):
+
+class PynnBrainscales(build_brainscales.BuildBrainscales):
"""PyNN toplevel for the BrainScaleS-2 neuromorphic hardware systems"""
homepage = "https://github.com/electronicvisions/pynn-brainscales"
@@ -74,124 +76,6 @@ class PynnBrainscales(WafPackage):
depends_on('yaml-cpp+shared', type=('build', 'link', 'run'))
extends('python')
- def do_fetch(self, mirror_only=False):
- """Setup the project."""
-
- self.stage.create()
- self.stage.fetch(mirror_only)
-
- # if fetcher didn't do anything, it's cached already
- if not os.path.exists(self.stage.source_path):
- return
-
- with working_dir(self.stage.source_path):
- python = which('python3')
- if self.spec.satisfies('@:7'):
- python('./waf', 'setup', '--repo-db-url=https://github.com/electronicvisions/projects',
- '--clone-depth=2',
- '--without-munge',
- '--without-hxcomm-hostarq',
- '--without-hxcomm-extoll',
- '--project=pynn-brainscales',
- '--release-branch=ebrains-' + str(self.spec.version)
- )
- else:
- python('./waf', 'setup', '--repo-db-url=https://github.com/electronicvisions/projects',
- '--clone-depth=2',
- '--without-munge',
- '--without-hxcomm-hostarq',
- '--project=pynn-brainscales',
- '--release-branch=ebrains-' + str(self.spec.version)
- )
-
-
- # in the configure step, we need access to all archived .git folders
- def custom_archive(self, destination):
- super(spack.fetch_strategy.GitFetchStrategy, self).archive(destination)
- with unittest.mock.patch('spack.fetch_strategy.GitFetchStrategy.archive', new=custom_archive):
- self.stage.cache_local()
-
- def _setup_common_env(self, env):
- # grenade needs to find some libraries for the JIT-compilation of
- # programs for BrainScaleS-2's embedded processor.
- ppu_include_dirs = []
- ppu_dep_names = ['bitsery', 'boost', 'cereal']
- for ppu_dep_name in ppu_dep_names:
- dep = self.spec[ppu_dep_name]
- dep_include_dirs = set(dep.headers.directories)
- ppu_include_dirs.extend(list(dep_include_dirs))
- for dir in reversed(ppu_include_dirs):
- env.prepend_path("C_INCLUDE_PATH", dir)
- env.prepend_path("CPLUS_INCLUDE_PATH", dir)
-
- def setup_build_environment(self, env):
- my_envmod = EnvironmentModifications(env)
- spack.build_environment.set_wrapper_variables(self, my_envmod)
- my_env = {}
- my_envmod.apply_modifications(my_env)
-
- def get_path(env, name):
- path = env.get(name, "").strip()
- if path:
- return path.split(os.pathsep)
- return []
-
- # spack tries to find headers and libraries by itself (i.e. it's not
- # relying on the compiler to find it); we explicitly expose the
- # spack-provided env vars that contain include and library paths
- if 'SPACK_INCLUDE_DIRS' in my_env:
- for dir in reversed(get_path(my_env, "SPACK_INCLUDE_DIRS")):
- env.prepend_path("C_INCLUDE_PATH", dir)
- env.prepend_path("CPLUS_INCLUDE_PATH", dir)
- if 'SPACK_LINK_DIRS' in my_env:
- for dir in reversed(get_path(my_env, "SPACK_LINK_DIRS")):
- env.prepend_path("LIBRARY_PATH", dir)
- env.prepend_path("LD_LIBRARY_PATH", dir)
- for dir in reversed(self.compiler.implicit_rpaths()):
- env.prepend_path("LIBRARY_PATH", dir)
- # technically this is probably not needed for the non-configure steps
- env.prepend_path("LD_LIBRARY_PATH", dir)
-
- def setup_dependent_build_environment(self, env, dependent_spec):
- self._setup_common_env(env)
-
- def setup_run_environment(self, env):
- self._setup_common_env(env)
-
- def setup_dependent_run_environment(self, env, dependent_spec):
- self._setup_common_env(env)
-
- # override configure step as we perform a project setup first
- def configure(self, spec, prefix):
- """Configure the project."""
-
- args = ['--prefix={0}'.format(self.prefix)]
- args += self.configure_args()
- self.waf('configure', '--build-profile=release', '--disable-doxygen', *args)
-
- def build_args(self):
- args = ['--keep', '--test-execnone', '-v']
- return args
-
- def build_test(self):
- self.builder.waf('build', '--test-execall')
- copy_tree('build/test_results', join_path(self.prefix, ".build"))
- copy_tree('build/test_results', join_path(self.stage.path, ".install_time_tests"))
- # propagate failures from junit output to spack
- tree = ET.parse('build/test_results/summary.xml')
- for testsuite in tree.getroot():
- for testcase in testsuite:
- for elem in testcase:
- if (elem.tag == 'failure') and not (
- elem.get('message').startswith("pylint:") or
- elem.get('message').startswith("pycodestyle:") or
- ("OK" in elem.get('message') and "Segmentation fault" in elem.get('message'))):
- raise RuntimeError("Failed test found: {}".format(testcase.get('name')))
-
- def install_args(self):
- args = ['--test-execnone']
- return args
-
def install_test(self):
with working_dir('spack-test', create=True):
old_pythonpath = os.environ.get('PYTHONPATH', '')
--
GitLab
From ccfa196bae2a02179d75923b52043258f7c5eee6 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Wed, 27 Mar 2024 16:39:58 +0100
Subject: [PATCH 07/10] fix: don't set env vars for view when installing env
---
install_spack_env.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/install_spack_env.sh b/install_spack_env.sh
index 536696f8..86e62145 100644
--- a/install_spack_env.sh
+++ b/install_spack_env.sh
@@ -76,7 +76,7 @@ cp /tmp/spack.yaml $SPACK_ROOT/var/spack/environments/$EBRAINS_SPACK_ENV/
rm $SPACK_ROOT/var/spack/environments/$EBRAINS_SPACK_ENV/spack.lock || echo "No spack.lock file"
# activate environment
-spack env activate $EBRAINS_SPACK_ENV
+spack env activate --without-view $EBRAINS_SPACK_ENV
# fetch all sources
spack concretize --fresh --test root
--
GitLab
From a2e582c082799abc876575f853777dfef5f9aa13 Mon Sep 17 00:00:00 2001
From: Didi Hou <didi.hou@rwth-aachen.de>
Date: Thu, 28 Mar 2024 09:17:58 +0100
Subject: [PATCH 08/10] feat(wf-multi-area-model): add py-python-louvain
dependency
---
packages/wf-multi-area-model/package.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/packages/wf-multi-area-model/package.py b/packages/wf-multi-area-model/package.py
index 76db0cf2..bdfc5a54 100644
--- a/packages/wf-multi-area-model/package.py
+++ b/packages/wf-multi-area-model/package.py
@@ -28,6 +28,7 @@ class WfMultiAreaModel(Package):
depends_on("py-elephant", type=("run", "test"))
depends_on("r-aod", type=("run", "test"))
depends_on("py-notebook", type=("run", "test"))
+ depends_on("py-python-louvain", type=("run", "test"))
def install(self, spec, prefix):
install_tree(".", join_path(prefix, "notebooks"))
--
GitLab
From 51bdc61237e8a6ed230a48370eb9a005756e0d93 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Wed, 13 Mar 2024 09:57:21 +0100
Subject: [PATCH 09/10] fix(nest): Align MPI variant for hdf5 dependency
---
packages/nest/package.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/packages/nest/package.py b/packages/nest/package.py
index df1f76ed..bc24c386 100644
--- a/packages/nest/package.py
+++ b/packages/nest/package.py
@@ -94,7 +94,8 @@ class Nest(CMakePackage):
depends_on('boost', when="@2.16:+boost", type='build')
depends_on('py-setuptools@:44.99.99', when='@:2.15.99+python', type='build')
depends_on('py-h5py', when='@3.4.99:+sonata', type=('test', 'build', 'run'))
- depends_on('hdf5+cxx', when='@3.4.99:+sonata', type=('build', 'link', 'run'))
+ depends_on('hdf5+cxx+mpi', when='@3.4.99:+sonata+mpi', type=('build', 'link', 'run'))
+ depends_on('hdf5+cxx~mpi', when='@3.4.99:+sonata~mpi', type=('build', 'link', 'run'))
depends_on('py-pandas', when='@3.4.99:+sonata', type=('build', 'run'))
depends_on('py-nose', when='@:2.99.99+python+testsuite', type='test')
--
GitLab
From 69e33d9b78fc54b90c31071dc9d6be651ff2ceb1 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Thu, 28 Mar 2024 13:31:08 +0200
Subject: [PATCH 10/10] fix(nest): remove link dependency on hdf5
the link dependency was added as a workaround to fix building nest~mpi, not needed after aligning the MPI variant for hdf5 dependency
---
packages/nest/package.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/packages/nest/package.py b/packages/nest/package.py
index bc24c386..e1593d4b 100644
--- a/packages/nest/package.py
+++ b/packages/nest/package.py
@@ -94,8 +94,8 @@ class Nest(CMakePackage):
depends_on('boost', when="@2.16:+boost", type='build')
depends_on('py-setuptools@:44.99.99', when='@:2.15.99+python', type='build')
depends_on('py-h5py', when='@3.4.99:+sonata', type=('test', 'build', 'run'))
- depends_on('hdf5+cxx+mpi', when='@3.4.99:+sonata+mpi', type=('build', 'link', 'run'))
- depends_on('hdf5+cxx~mpi', when='@3.4.99:+sonata~mpi', type=('build', 'link', 'run'))
+ depends_on('hdf5+cxx+mpi', when='@3.4.99:+sonata+mpi', type=('build', 'run'))
+ depends_on('hdf5+cxx~mpi', when='@3.4.99:+sonata~mpi', type=('build', 'run'))
depends_on('py-pandas', when='@3.4.99:+sonata', type=('build', 'run'))
depends_on('py-nose', when='@:2.99.99+python+testsuite', type='test')
--
GitLab