From a8d082597eb1ea641743272a65983f0999ee538b Mon Sep 17 00:00:00 2001
From: Johannes Hjorth <hjorth@kth.se>
Date: Tue, 18 Mar 2025 11:22:53 +0100
Subject: [PATCH 1/3] feat(py-snudda): update dependency on BluePyOpt 1.14.18
---
packages/py-snudda/package.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/packages/py-snudda/package.py b/packages/py-snudda/package.py
index 97b72292..8d0ca3d8 100644
--- a/packages/py-snudda/package.py
+++ b/packages/py-snudda/package.py
@@ -24,7 +24,7 @@ class PySnudda(PythonPackage):
depends_on("unzip", type=("build"))
depends_on("py-setuptools", type=("build"))
depends_on("py-importlib-metadata", type=("build","run"))
- depends_on("py-bluepyopt@1.14.11:", type=("build","run"))
+ depends_on("py-bluepyopt@1.14.18:", type=("build","run"))
depends_on("py-h5py@3.12.1:", type=("build","run"))
depends_on("py-ipyparallel@8.4.1:", type=("build","run"))
depends_on("py-matplotlib@3.8:", type=("build","run"))
--
GitLab
From b3e0efa7efee5e273047bf5a7016abad2a314a1f Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Tue, 18 Mar 2025 11:41:29 +0000
Subject: [PATCH 2/3] feat(py-bluepyopt): copy package from upstream
---
packages/py-bluepyopt/package.py | 41 ++++++++++++++++++++++++++++
packages/py-bluepyopt/pmi_rank.patch | 17 ++++++++++++
2 files changed, 58 insertions(+)
create mode 100644 packages/py-bluepyopt/package.py
create mode 100644 packages/py-bluepyopt/pmi_rank.patch
diff --git a/packages/py-bluepyopt/package.py b/packages/py-bluepyopt/package.py
new file mode 100644
index 00000000..67cfa6b6
--- /dev/null
+++ b/packages/py-bluepyopt/package.py
@@ -0,0 +1,41 @@
+# 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.package import *
+
+
+class PyBluepyopt(PythonPackage):
+ """Bluebrain Python Optimisation Library"""
+
+ homepage = "https://github.com/BlueBrain/BluePyOpt"
+ pypi = "bluepyopt/bluepyopt-1.9.27.tar.gz"
+
+ license("LGPL-3.0-only")
+
+ # NOTE : while adding new release check pmi_rank.patch compatibility
+ version("1.14.11", sha256="fe2830c36699a93d2ef9ddef316da42f9c57ca6654c92356eab973ee2298ebf7")
+ version("1.14.4", sha256="7567fd736053250ca06030f67ad93c607b100c2b98df8dc588c26b64cb3e171c")
+
+ # patch required to avoid hpe-mpi linked mechanism library
+ patch("pmi_rank.patch")
+
+ variant("scoop", default=False, description="Use BluePyOpt together with py-scoop")
+
+ depends_on("py-setuptools", type="build")
+ depends_on("py-numpy@1.6:", type=("build", "run"))
+ depends_on("py-pandas@0.18:", type=("build", "run"))
+ depends_on("py-deap@1.3.3:", type=("build", "run"))
+ depends_on("py-efel@2.13:", type=("build", "run"))
+ depends_on("py-ipyparallel", type=("build", "run"))
+ depends_on("py-pickleshare@0.7.3:", type=("build", "run"))
+ depends_on("py-jinja2@2.8:", type=("build", "run"))
+ depends_on("py-future", type=("build", "run"))
+ depends_on("py-pebble@4.6:", type=("build", "run"))
+ depends_on("py-scoop@0.7:", type=("build", "run"), when="+scoop")
+ depends_on("neuron@7.4:", type=("build", "run"), when="@:1.14.4")
+ depends_on("neuron@7.8:", type=("build", "run"), when="@1.14.11:")
+
+ def setup_run_environment(self, env):
+ env.unset("PMI_RANK")
+ env.set("NEURON_INIT_MPI", "0")
diff --git a/packages/py-bluepyopt/pmi_rank.patch b/packages/py-bluepyopt/pmi_rank.patch
new file mode 100644
index 00000000..21a73849
--- /dev/null
+++ b/packages/py-bluepyopt/pmi_rank.patch
@@ -0,0 +1,17 @@
+diff --git a/bluepyopt/ephys/simulators.py b/bluepyopt/ephys/simulators.py
+index e71ad8b..3c93237 100644
+--- a/bluepyopt/ephys/simulators.py
++++ b/bluepyopt/ephys/simulators.py
+@@ -89,6 +89,12 @@ class NrnSimulator(object):
+ NrnSimulator._nrn_disable_banner()
+ self.banner_disabled = True
+
++ # certain mpi libraries (hpe-mpt) use PMI_RANK env variable to initialize
++ # MPI before calling MPI_Init (which is undesirable). Unset this variable
++ # if exist to avoid issue with loading neuron and mechanism library.
++ if 'PMI_RANK' in os.environ:
++ os.environ.pop("PMI_RANK")
++
+ import neuron # NOQA
+
+ return neuron
--
GitLab
From 3a218965d70438e710232b3bf25f8c737fbc3ea0 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Tue, 18 Mar 2025 11:42:42 +0000
Subject: [PATCH 3/3] feat(py-bluepyopt): add version 1.14.18
---
packages/py-bluepyopt/package.py | 1 +
spack.yaml | 2 +-
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/packages/py-bluepyopt/package.py b/packages/py-bluepyopt/package.py
index 67cfa6b6..aa4e5254 100644
--- a/packages/py-bluepyopt/package.py
+++ b/packages/py-bluepyopt/package.py
@@ -14,6 +14,7 @@ class PyBluepyopt(PythonPackage):
license("LGPL-3.0-only")
# NOTE : while adding new release check pmi_rank.patch compatibility
+ version("1.14.18", sha256="23d6239294d944c8f9d4ea298091bcf243d236735844e1bcba60535a0f520ca8")
version("1.14.11", sha256="fe2830c36699a93d2ef9ddef316da42f9c57ca6654c92356eab973ee2298ebf7")
version("1.14.4", sha256="7567fd736053250ca06030f67ad93c607b100c2b98df8dc588c26b64cb3e171c")
diff --git a/spack.yaml b/spack.yaml
index b99a8270..809334f9 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -18,7 +18,7 @@ spack:
- jaxsnn@10.0-a1
- py-bluepyefe@2.3.6
- py-bluepymm@0.8.7
- - py-bluepyopt@1.14.11
+ - py-bluepyopt@1.14.18
- py-bsb-core@5.0.2
- py-bsb-hdf5@5.0.2
- py-bsb-yaml@4.2.2
--
GitLab