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Commit a351b56c authored by Eleni Mathioulaki's avatar Eleni Mathioulaki
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Merge branch 'master' into 'experimental_rel' 

create new experimental release

See merge request technical-coordination/project-internal/devops/platform/ebrains-spack-builds!119
parents 044bec6d 73de9809
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packages/hxtorch/package.py 0 → 100644
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− 0
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# 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 import *
class Hxtorch(WafPackage):
"""hxtorch --- a PyTorch-based toplevel for the BrainScaleS-2 neuromorphic hardware systems"""
homepage = "https://github.com/electronicvisions/hxtorch"
# This repo provides a waf binary used for the build below
git = "https://github.com/electronicvisions/pynn-brainscales.git"
version('2.0-rc6', branch='waf')
# PPU compiler dependencies
depends_on('oppulance@2.0:')
# host software dependencies
depends_on('bitsery', type=('build', 'link', 'run'))
depends_on('binutils+gold+ld+plugins', type=('build', 'link', 'run')) # specialize
depends_on('boost@1.69.0: +graph+icu+mpi+python+numpy+coroutine+context cxxstd=17', type=('build', 'link', 'run')) # specialize boost (non-clingo, type=('build', 'link', 'run'))
depends_on('cereal', type=('build', 'link', 'run'))
depends_on('cppcheck', type=('build', 'link', 'run'))
depends_on('doxygen+graphviz', type=('build', 'link', 'run'))
depends_on('genpybind@ebrains', type=('build', 'link', 'run'))
depends_on('gflags', type=('build', 'link', 'run'))
depends_on('googletest@1.11.0: +gmock', type=('build', 'link', 'run')) # variadic templates needed
depends_on('intel-tbb', type=('build', 'link', 'run')) # ppu gdbserver
depends_on('libelf', type=('build', 'link', 'run'))
depends_on('liblockfile', type=('build', 'link', 'run'))
depends_on('llvm', type=('build', 'link', 'run'))
depends_on('log4cxx', type=('build', 'link', 'run'))
depends_on('pkg-config', type=('build', 'link', 'run'))
depends_on('python@3.7.0:', type=('build', 'link', 'run')) # BrainScaleS(-2, type=('build', 'link', 'run')) only supports Python >= 3.7
depends_on('py-h5py', type=('build', 'link', 'run')) # PyNN tests need it
depends_on('py-matplotlib', type=('build', 'link', 'run'))
depends_on('py-nose', type=('build', 'link', 'run'))
depends_on('py-numpy', type=('build', 'link', 'run'))
depends_on('py-pybind11', type=('build', 'link', 'run'))
depends_on('py-pybind11-stubgen', type=('build', 'link', 'run'))
depends_on('py-pycodestyle', type=('build', 'link', 'run'))
depends_on('py-pyelftools', type=('build', 'link', 'run'))
depends_on('py-pylint', type=('build', 'link', 'run'))
depends_on('py-torch', type=('build', 'link', 'run'))
depends_on('py-pyyaml', type=('build', 'link', 'run'))
depends_on('py-scipy', type=('build', 'link', 'run'))
depends_on('py-sqlalchemy', type=('build', 'link', 'run'))
depends_on('util-linux', type=('build', 'link', 'run'))
depends_on('yaml-cpp+shared', type=('build', 'link', 'run'))
extends('python')
def setup_build_environment(self, env):
"""waf needs to find headers and libraries by itself (mostly `boost`
tool, but also `gtest`); it also needs to run executables during
configuration."""
include = []
for dep in self.spec.traverse(deptype='build'):
query = self.spec[dep.name]
try:
include.extend(query.headers.directories)
print('headers:', query.headers.directories, "\n")
except:
pass
library = []
for dep in self.spec.traverse(deptype=('link', 'run')):
query = self.spec[dep.name]
try:
library.extend(query.libs.directories)
print('libs:', query.libs.directories, "\n")
except:
pass
path = []
for dep in self.spec.traverse(deptype=('build', 'link', 'run')):
query = self.spec[dep.name]
try:
path.append(query.prefix.bin)
print('bin:', query.prefix.bin, "\n")
except:
pass
# llvm might be built with ~shared_libs but still builds shared libs
if not any('llvm' in lib for lib in library):
library.append(self.spec['llvm'].prefix.lib)
env.set('CPATH', ':'.join(include))
env.set('C_INCLUDE_PATH', ':'.join(include))
env.set('CPLUS_INCLUDE_PATH', ':'.join(include))
env.set('LIBRARY_PATH', ':'.join(library))
env.set('LD_LIBRARY_PATH', ':'.join(library))
env.prepend_path('PATH', ':'.join(path))
def setup_run_environment(self, env):
env.prepend_path('PYTHONPATH', self.prefix.lib)
# override configure step as we perform a project setup first
def configure(self, spec, prefix):
"""Setup and configure the project."""
self.waf('setup', '--repo-db-url=https://github.com/electronicvisions/projects', '--without-munge',
'--project=hxtorch@ebrains-' + str(spec.version),
'--project=haldls@ebrains-' + str(spec.version),
'--project=grenade@ebrains-' + str(spec.version),
'--project=code-format@ebrains-' + str(spec.version),
'--project=logger@ebrains-' + str(spec.version),
'--project=halco@ebrains-' + str(spec.version),
'--project=hate@ebrains-' + str(spec.version),
'--project=fisch@ebrains-' + str(spec.version),
'--project=ztl@ebrains-' + str(spec.version),
'--project=hxcomm@ebrains-' + str(spec.version),
'--project=rant@ebrains-' + str(spec.version),
'--project=pywrap@ebrains-' + str(spec.version),
'--project=lib-boost-patches@ebrains-' + str(spec.version),
'--project=sctrltp@ebrains-' + str(spec.version),
'--project=hwdb@ebrains-' + str(spec.version),
'--project=visions-slurm@ebrains-' + str(spec.version),
'--project=flange@ebrains-' + str(spec.version),
'--project=lib-rcf@ebrains-' + str(spec.version),
'--project=bss-hw-params@ebrains-' + str(spec.version),
'--project=libnux@ebrains-' + str(spec.version)
)
args = ['--prefix={0}'.format(self.prefix)]
args += self.configure_args()
self.waf('configure', *args)
def build_args(self):
args = ['--keep', '--test-execnone', '-v']
return args
packages/py-bluepyopt/package.py 0 → 100644
+ 45
− 0
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##############################################################################
# Copyright 2013-2020 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 PyBluepyopt(PythonPackage):
"""Bluebrain Python Optimisation Library"""
homepage = "https://github.com/BlueBrain/BluePyOpt"
pypi = "bluepyopt/bluepyopt-1.9.27.tar.gz"
# NOTE : while adding new release check pmi_rank.patch compatibility
version('1.10.38', sha256='fb1411c6a8fbfac52d36b837225bae882fd6524acfb4d0580189312ef3c1cfcc')
version('1.9.37', sha256='4399af71de48b288832e92f0de73c431bf88d6e76e2c4ea250c3b38fb38a45a8')
version('1.9.27', sha256='4cce15b92b32311c808cae5e005b664deb6e8dc5df4ca13ea7b59252ae346522')
version('1.8.68', sha256='b9d432840aab89d4863c935d3dc604816441eba02d731422b92056cee751ca9c')
version('1.6.56', sha256='1c57c91465ca4b947fe157692e7004a3e6df02e4151e3dc77a8831382a8f1ab9')
version('1.8.68', sha256='b9d432840aab89d4863c935d3dc604816441eba02d731422b92056cee751ca9c')
version('1.9.12', sha256='7b623ab9168f460a85d952719ca5249248fc95e6f7a02658b0673b2baa0a8fc6')
# patch required to avoid hpe-mpi linked mechanism library
patch("pmi_rank.patch", when="@1.9.27:")
variant('neuron', default=True, description="Use BluePyOpt together with NEURON")
depends_on('py-setuptools', type='build')
depends_on('py-pandas', type='run')
depends_on('py-numpy', type='run')
depends_on('py-efel', type='run')
depends_on('py-deap', type='run')
depends_on('py-scoop@0.7:', type='run', when='@:1.9.37')
depends_on('py-ipyparallel', type='run')
depends_on('py-pickleshare', type='run')
depends_on('py-future', type='run')
depends_on('py-jinja2', type='run')
depends_on('py-pebble@4.3.10:', type='run')
depends_on('neuron', type='run', when='+neuron')
def setup_run_environment(self, env):
env.unset('PMI_RANK')
env.set('NEURON_INIT_MPI', "0")
env.prepend_path('PATH', self.spec['py-ipyparallel'].prefix.bin)
packages/py-bluepyopt/pmi_rank.patch 0 → 100644
+ 17
− 0
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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
packages/py-libsonata/package.py 0 → 100644
+ 35
− 0
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# Copyright 2013-2018 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 PyLibsonata(PythonPackage):
"""SONATA files reader"""
homepage = "https://github.com/BlueBrain/libsonata"
git = "https://github.com/BlueBrain/libsonata.git"
version('develop', branch='master', submodules=True, get_full_repo=True)
version('0.1.12', tag='v0.1.12', submodules=True, get_full_repo=True)
version('0.1.11', tag='v0.1.11', submodules=True, get_full_repo=True)
version('0.1.10', tag='v0.1.10', submodules=True, get_full_repo=True)
# Important: v0.1.9 is not Spack-compatible (use v0.1.10: instead)
# version('0.1.9', tag='v0.1.9', submodules=True, get_full_repo=True)
version('0.1.8', tag='v0.1.8', submodules=True, get_full_repo=True)
version('0.1.6', tag='v0.1.6', submodules=True, get_full_repo=True)
version('0.1.5', tag='v0.1.5', submodules=True, get_full_repo=True)
version('0.1.4', tag='v0.1.4', submodules=True, get_full_repo=True)
version('0.1.3', tag='v0.1.3', submodules=True, get_full_repo=True)
version('0.1.0', tag='v0.1.0', submodules=True, get_full_repo=True)
version('0.0.3', tag='v0.0.3', submodules=True)
depends_on('cmake@3.3:', type='build')
depends_on('hdf5')
depends_on('py-pybind11')
depends_on('py-numpy@1.12:', type=('build', 'run'))
depends_on('py-setuptools', type='build', when='@0.1:')
depends_on('py-setuptools-scm', type='build', when='@0.1:')
packages/py-pebble/package.py 0 → 100644
+ 21
− 0
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# Copyright 2013-2020 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 PyPebble(PythonPackage):
"""Python API to manage threads and processes within an application."""
homepage = "https://github.com/noxdafox/pebble"
pypi = "pebble/Pebble-4.5.0.tar.gz"
git = "https://github.com/noxdafox/pebble.git"
version('4.5.0', sha256='2de3cd11aa068e0c4a4abbaf8d4ecfdac409d8bfb78a4c211a01f6a4fb17a35f')
version('4.4.1', sha256='7c4d68a3479140cba74d7454d8190e2cb1a93213b44b5befe3c53c201beb8317')
version('4.3.10', sha256='c39a7bf99af6525fcf0783a8859fb10a4f20f4f988ddb66fd6fa7588f9c91731')
depends_on('py-setuptools', type=('build', 'run'))
depends_on('py-futures', type='run', when='^python@:2.9.9')
packages/py-pynn/package.py
+ 22
− 15
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......@@ -12,32 +12,39 @@ class PyPynn(PythonPackage):
"""
homepage = "http://neuralensemble.org/PyNN/"
pypi = "PyNN/PyNN-0.8.3.tar.gz"
git = "https://github.com/NeuralEnsemble/PyNN.git"
pypi = "PyNN/PyNN-0.10.0.tar.gz"
git = "https://github.com/NeuralEnsemble/PyNN.git"
version('0.10.0', sha256='04120fe0e03260d664b337e0ac29d985c3fb3684ef35b1add93a66739891c98f')
version('0.9.6', sha256='d85226800e30bc1692d3f84485c3fa20b921c2ab55f1201d0a3bf23432e16cd2')
version('0.9.5', sha256='91af2126b639a6a795bfc2709ac49423278c4794b6d0da143908b9afcb415f80')
version('0.9.1', sha256='bbc60fea3235427191feb2daa0e2fa07eb1c3946104c068ac8a2a0501263b0b1')
version('0.8.3', sha256='9d59e6cffa4714f0c892ec6b32d1f5f8f75ba3a20d8635bac50c047aa6f2537e')
version('0.8beta', commit='ffb0cb1661f2b0f2778db8f71865978fe7a7a6a4')
version('0.8.1', sha256='ce94246284588414d1570c1d5d697805f781384e771816727c830b01ee30fe39')
version('0.7.5', sha256='15f75f422f3b71c6129ecef23f29d8baeb3ed6502e7a321b8a2596c78ef7e03c')
variant('mpi', default=False, description='Enable MPI support')
depends_on('python@2.7:2.8,3.3:', when="@0.9.5")
depends_on('python@2.7:2.8,3.6:', when="@0.9.6")
depends_on('python@3.7:', when="@0.10.0:")
depends_on('python@2.6:2.8,3.3:')
depends_on('py-jinja2@2.7:', type=('build', 'run'))
depends_on('py-docutils@0.10:', type=('build', 'run'))
depends_on('py-numpy@1.5:', type=('build', 'run'))
depends_on('py-quantities@0.10:', type=('build', 'run'))
depends_on('py-lazyarray@0.2.9:', type=('build', 'run'))
depends_on('py-neo@0.3:0.4.1', type=('build', 'run'), when="@:0.8.3")
depends_on('py-neo@0.5.0:', type=('build', 'run'), when="@0.9.0:")
depends_on('py-lazyarray', type=('build', 'run'), when="@0.9.0:")
depends_on('py-numpy@1.8.2:', type=('build', 'run'), when="@0.9.5")
depends_on('py-numpy@1.13.0:', type=('build', 'run'), when="@0.9.6")
depends_on('py-numpy@1.16.1:', type=('build', 'run'), when="@0.10.0:")
depends_on('mpi', when='+mpi')
depends_on('py-mpi4py', type=('build', 'run'), when='+mpi')
depends_on('py-quantities@0.12.1:', type=('build', 'run'), when="@0.9.5:")
depends_on('py-lazyarray@0.3.2:', type=('build', 'run'), when="@0.9.5")
depends_on('py-lazyarray@0.3.4:', type=('build', 'run'), when="@0.9.6")
depends_on('py-lazyarray@0.5.0:', type=('build', 'run'), when="@0.10.0:")
depends_on('py-neo@0.5.2:', type=('build', 'run'), when="@0.9.5")
depends_on('py-neo@0.8.0', type=('build', 'run'), when="@0.9.6")
depends_on('py-neo@0.10.0:', type=('build', 'run'), when="@0.10.0:")
depends_on('py-lazyarray@0.3.2:', type=('build', 'run'), when="@0.9.5")
depends_on('py-lazyarray@0.3.4:', type=('build', 'run'), when="@0.9.6")
depends_on('py-lazyarray@0.5.0:', type=('build', 'run'), when="@0.10.0:")
depends_on('py-mock@1.0:', type='test')
......
packages/py-pyswarms/package.py 0 → 100644
+ 17
− 0
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from spack import *
class PyPyswarms(PythonPackage):
homepage = "https://github.com/ljvmiranda921/pyswarms"
pypi = "pyswarms/pyswarms-1.3.0.tar.gz"
version('1.3.0', sha256='1204aa9c332c662113e3c37d1b109906f4a0859b29ded80c1582dc66387ce34b')
depends_on('py-scipy', type=('build', 'run'))
depends_on('py-numpy', type=('build', 'run'))
depends_on('py-matplotlib@1.3.1:', type=('build', 'run'))
depends_on('py-attrs', type=('build', 'run'))
depends_on('py-tqdm', type=('build', 'run'))
depends_on('py-future', type=('build', 'run'))
depends_on('py-pyyaml', type=('build', 'run'))
packages/snudda/package.py → packages/py-snudda/package.py
+ 6
− 7
View file @ a351b56c
from spack import *
class Snudda(Package):
class PySnudda(Package):
homepage = 'https://pypi.org/project/snudda/'
url = 'https://pypi.org/packages/source/s/snudda/snudda-1.2.9-py3-none-any.whl'
url = 'https://files.pythonhosted.org/packages/py3/s/snudda/snudda-1.2.9-py3-none-any.whl'
list_url = 'https://pypi.org/simple/snudda/'
maintainers = ['hjorth','akarmas']
......@@ -12,20 +12,19 @@ class Snudda(Package):
depends_on('python@3.8:', type=('build','run'))
depends_on('py-pip', type='build')
depends_on('unzip', type='build')
#depends_on('py-bluepyopt', type=('build','run')) must get this from BlueBrainProject https://github.com/BlueBrain/spack/tree/develop/var/spack/repos/builtin/packages/py-bluepyopt
depends_on('py-bluepyopt', type=('build','run')) # got this from BlueBrainProject https://github.com/BlueBrain/spack/tree/develop/var/spack/repos/builtin/packages/py-bluepyopt
depends_on('py-h5py', type=('build','run'))
depends_on('py-ipyparallel', type=('build','run'))
depends_on('py-matplotlib', type=('build','run'))
depends_on('py-mpi4py', type=('build','run'))
depends_on('py-numpy', type=('build','run'))
depends_on('py-scipy', type=('build','run'))
#depends_on('py-libsonata', type=('build','run')) - get it from https://github.com/BlueBrain/spack/tree/develop/var/spack/repos/builtin/packages/py-libsonata
depends_on('py-libsonata', type=('build','run')) # got it from https://github.com/BlueBrain/spack/tree/develop/var/spack/repos/builtin/packages/py-libsonata
depends_on('py-pyzmq', type=('build','run'))
depends_on('py-numexpr', type=('build','run'))
depends_on('py-argparse', type=('build','run'))
depends_on('neuron', type=('build','run'))
#depends_on('pyswarms', type=('build','run')) - must package this
depends_on('py-setuptools', type=('build','run'))
depends_on('py-pyswarms', type=('build','run'))
depends_on('py-setuptools', type=('build'))
depends_on('py-psutil', type=('build','run'))
depends_on('py-cython', type=('build','run'))
depends_on('py-numba', type=('build','run'))
......
packages/pynn-brainscales/package.py
+ 1
− 1
View file @ a351b56c
......@@ -11,7 +11,7 @@ class PynnBrainscales(WafPackage):
homepage = "https://github.com/electronicvisions/pynn-brainscales"
git = "https://github.com/electronicvisions/pynn-brainscales.git"
version('2.0-rc5', branch='waf')
version('2.0-rc6', branch='waf')
# PPU compiler dependencies
depends_on('oppulance@2.0:')
......
spack.yaml
+ 6
− 3
View file @ a351b56c
......@@ -21,14 +21,16 @@ spack:
- nest@3.3 +python +gsl +mpi
- arbor +python +mpi ^python@3:3.9
- neuron +mpi
- py-pynn@0.9.6
# - py-pynn@0.9.6
- py-pynn@0.10.0 +mpi
- tvb-data
- tvb-library ^py-numba@0.54.0 ^binutils+ld+gold
- tvb-storage ^binutils+ld+gold
- py-pyaescrypt
- py-formencode
- tvb-framework ^binutils+ld+gold
- pynn-brainscales@2.0-rc5 ^log4cxx@0.10.0 ^googletest@1.11.0:+gmock
- pynn-brainscales@2.0-rc6 ^log4cxx@0.10.0 ^googletest@1.11.0:+gmock
#- hxtorch@2.0-rc6 ^log4cxx@0.10.0 ^googletest@1.11.0:+gmock
- py-neo
#- py-cerebstats
#- py-cerebunit
......@@ -50,10 +52,11 @@ spack:
- py-lfpy@2.2.6
- py-elephant
- py-frites
#- py-snudda
#- biobb-common
#- biobb-md
#- apbs
- py-pdb2pqr
#- py-pdb2pqr
#- sda
# demo for codejam12
#- funniest1022
......
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