diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index a61185b98048b83d8595e027611a97970f5f1215..cb688bbd815ec8b44cb3d0852605cb194c223c11 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -134,7 +134,8 @@ deploy-exp-release-dev-cscs:
"argv": ["\$LAB_KERNEL_PATH/bin/env.sh", "{connection_file}", "--profile=default"],
"display_name": "EBRAINS_experimental_release",
"name": "spack_experimental_release",
- "language": "python"
+ "language": "python",
+ "env": { "LAB_KERNEL_INFO": "spack_experimental_release_\$(date +"%d-%m-%y")" }
}
EOF
EOS
@@ -175,7 +176,8 @@ deploy-exp-release-prod-cscs:
"argv": ["\$LAB_KERNEL_PATH/bin/env.sh", "{connection_file}", "--profile=default"],
"display_name": "EBRAINS_experimental_release",
"name": "spack_experimental_release",
- "language": "python"
+ "language": "python",
+ "env": { "LAB_KERNEL_INFO": "spack_experimental_release_\$(date +"%d-%m-%y")" }
}
EOF
EOS
@@ -216,7 +218,8 @@ deploy-exp-release-prod-jsc:
"argv": ["\$LAB_KERNEL_PATH/bin/env.sh", "{connection_file}", "--profile=default"],
"display_name": "EBRAINS_experimental_release",
"name": "spack_experimental_release",
- "language": "python"
+ "language": "python",
+ "env": { "LAB_KERNEL_INFO": "spack_experimental_release_\$(date +"%d-%m-%y")" }
}
EOF
EOS
diff --git a/operations/steps_to_update_experimental_release.txt b/operations/steps_to_update_experimental_release.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ac98315d2fd67e3578a02c37c36667c7fa3b8265
--- /dev/null
+++ b/operations/steps_to_update_experimental_release.txt
@@ -0,0 +1,11 @@
+Steps to update the current experimental release with no major upgrades (i.e. install it in the same Spack instance as before - respective CI/CD env variable is ${site}_INSTALLATION_ROOT_{env})
+
+1) Back up the Lab's experimental kernel configuration in both CSCS and JSC prod
+cp -r /srv/jupyterlab_kernels/prod/experimental /srv/backup/experimental_{date}
+2) Merge the master branch of the ebrains-spack-builds repo to the experimental_rel branch.
+Make sure that the master branch has uncommented in the spack.yaml file only those packages that have been built successfully.
+3) Start the scheduled pipeline with description "deploy experimental release in the dev CSCS cluster"
+4) Check if the pipeline executed successfully
+5) On Friday morning (not every Friday, could be when we have important or numerous changes) run the scheduled pipeline with description "deploy experimental release in prod environments".
+6) Only one job will continue (due to credentials mismatch in the gitlab runner)
+7) Check the result of the job. If it is successful retry the other job that failed previously. If it is not, restore the experimental kernel's configuration from step #1 in its original location.
diff --git a/packages/apbs/package.py b/packages/apbs/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..cf459b4f5c63938609a24771baa61ffadeadab2a
--- /dev/null
+++ b/packages/apbs/package.py
@@ -0,0 +1,46 @@
+# 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 Apbs(CMakePackage):
+ """
+ APBS (Adaptive Poisson-Boltzmann Solver) solves the equations of continuum electrostatics
+ for large biomolecular assemblages. This software was designed “from the ground upâ€
+ using modern design principles to ensure its ability to interface with other computational
+ packages and evolve as methods and applications change over time. The APBS code is
+ accompanied by extensive documentation for both users and programmers and is supported
+ by a variety of utilities for preparing calculations and analyzing results.
+ Finally, the free, open-source APBS license ensures its accessibility to the entire
+ biomedical community.
+ """
+
+ # Homepage and Github URL.
+ homepage = "https://www.poissonboltzmann.org/"
+ url = "https://github.com/Electrostatics/apbs/archive/refs/tags/v3.4.0.tar.gz"
+
+ # List of GitHub accounts to notify when the package is updated.
+ maintainers = ['thielblz', 'richtesn']
+
+ # SHA256 checksum.
+ version('3.4.0', sha256='572ff606974119430020ec948c78e171d8525fb0e67a56dad937a897cac67461')
+
+ # Dependencies.
+ depends_on('cmake@3.19', type='build')
+ depends_on('python@3.9:3.10', type=('build'))
+ depends_on('blas', type='build')
+ depends_on('suite-sparse', type='build')
+ depends_on('maloc', type='build')
+
+ def cmake_args(self):
+ # Min and max Python versions need to be set as variables to pass tests.
+ # See tests/CMakeLists.txt lines 6-14.
+ args = [
+ '-DPYTHON_MIN_VERSION=3.9',
+ '-DPYTHON_MAX_VERSION=3.10',
+ ]
+ return args
diff --git a/packages/arbor/package.py b/packages/arbor/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..c9d1e1e1c9d0837ee75afa0d1fcb7268505e8406
--- /dev/null
+++ b/packages/arbor/package.py
@@ -0,0 +1,83 @@
+# 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 Arbor(CMakePackage, CudaPackage):
+ """Arbor is a high-performance library for computational neuroscience
+ simulations."""
+
+ homepage = 'https://arbor-sim.org'
+ git = 'https://github.com/arbor-sim/arbor.git'
+ url = 'https://github.com/arbor-sim/arbor/releases/download/v0.6/arbor-v0.6-full.tar.gz'
+ maintainers = ['bcumming', 'brenthuisman', 'haampie', 'schmitts']
+
+ version('master', branch='master', submodules=True)
+ version('0.6', sha256='4cd333b18effc8833428ddc0b99e7dc976804771bc85da90034c272c7019e1e8', url='https://github.com/arbor-sim/arbor/releases/download/v0.6/arbor-v0.6-full.tar.gz')
+ version('0.5.2', sha256='290e2ad8ca8050db1791cabb6b431e7c0409c305af31b559e397e26b300a115d', url='https://github.com/arbor-sim/arbor/releases/download/v0.5.2/arbor-v0.5.2-full.tar.gz')
+ version('0.5', sha256='d0c8a4c7f97565d7c30493c66249be794d1dc424de266fc79cecbbf0e313df59', url='https://github.com/arbor-sim/arbor/releases/download/v0.5/arbor-v0.5-full.tar.gz')
+
+ variant('assertions', default=False, description='Enable arb_assert() assertions in code.')
+ variant('doc', default=False, description='Build documentation.')
+ variant('mpi', default=False, description='Enable MPI support')
+ variant('neuroml', default=True, description='Build NeuroML support library.')
+ variant('python', default=True, description='Enable Python frontend support')
+ variant('vectorize', default=False, description='Enable vectorization of computational kernels')
+
+ # https://docs.arbor-sim.org/en/latest/install/build_install.html?highlight=requirements#compilers
+ conflicts('%gcc@:8.3')
+ conflicts('%clang@:7')
+ # Cray compiler v9.2 and later is Clang-based.
+ conflicts('%cce@:9.1')
+ conflicts('%intel')
+
+ depends_on('cmake@3.12:', type='build')
+
+ # misc dependencies
+ depends_on('fmt@7.1:', when='@0.5.3:') # required by the modcc compiler
+ depends_on('nlohmann-json')
+ depends_on('cuda@10:', when='+cuda')
+ depends_on('libxml2', when='+neuroml')
+
+ # mpi
+ depends_on('mpi', when='+mpi')
+ depends_on('py-mpi4py', when='+mpi+python', type=('build', 'run'))
+
+ # python (bindings)
+ extends('python', when='+python')
+ depends_on('python@3.6:', when="+python", type=('build', 'run'))
+ depends_on('py-numpy', when='+python', type=('build', 'run'))
+ depends_on('py-pybind11@2.8.1:', when='+python', type=('build', 'run'))
+
+ # sphinx based documentation
+ depends_on('python@3.6:', when="+doc", type='build')
+ depends_on('py-sphinx', when="+doc", type='build')
+ depends_on('py-svgwrite', when='+doc', type='build')
+
+ @property
+ def build_targets(self):
+ return ['all', 'html'] if '+doc' in self.spec else ['all']
+
+ def cmake_args(self):
+ args = [
+ self.define_from_variant('ARB_WITH_ASSERTIONS', 'assertions'),
+ self.define_from_variant('ARB_WITH_MPI', 'mpi'),
+ self.define_from_variant('ARB_WITH_NEUROML', 'neuroml'),
+ self.define_from_variant('ARB_WITH_PYTHON', 'python'),
+ self.define_from_variant('ARB_VECTORIZE', 'vectorize'),
+ ]
+
+ if '+cuda' in self.spec:
+ args.append('-DARB_GPU=cuda')
+
+ # query spack for the architecture-specific compiler flags set by its wrapper
+ args.append('-DARB_ARCH=none')
+ opt_flags = self.spec.target.optimization_flags(
+ self.spec.compiler.name,
+ self.spec.compiler.version)
+ args.append('-DARB_CXX_FLAGS_TARGET=' + opt_flags)
+
+ return args
diff --git a/packages/oppulance/package.py b/packages/oppulance/package.py
index 5934d9093cd5d167b8968bd07e1a5d7ac61d3056..f212ef57431170016b6897ab94fde2cd055163f6 100644
--- a/packages/oppulance/package.py
+++ b/packages/oppulance/package.py
@@ -21,8 +21,8 @@ class Oppulance(Package):
releases = [
{
- 'version': '2.0-rc1',
- 'tag': 'ebrains_release-2-rc1'
+ 'version': '2.0-rc5',
+ 'tag': 'ebrains-2.0-rc5'
},
]
diff --git a/packages/py-pdb2pqr/package.py b/packages/py-pdb2pqr/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..39c2a60bf3a2fd8d4271d6ef1c4ff9fbb6376406
--- /dev/null
+++ b/packages/py-pdb2pqr/package.py
@@ -0,0 +1,27 @@
+# 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 PyPdb2pqr(PythonPackage):
+ """
+ PDB2PQR - determining titration states,
+ adding missing atoms, and assigning
+ charges/radii to biomolecules.
+ """
+
+ # Url for the package's homepage.
+ homepage = "http://www.poissonboltzmann.org/"
+ pypi = "pdb2pqr/pdb2pqr-3.5.2.tar.gz"
+
+ # List of GitHub accounts to
+ # notify when the package is updated.
+ maintainers = ['richtesn', 'thielblz']
+
+ version('3.5.2', sha256='9d145ff3797a563ce818f9d2488413ac339f66c58230670c2455b2572cccd957')
+
+ depends_on('python@3.8:', type=('build','run'))
diff --git a/packages/py-pynn/package.py b/packages/py-pynn/package.py
index 9726f1c6a8b8f3d080eeecf40ee9d498440d8c22..3f14ed7b1ddce44f5cdb96d52149ff1a5de81705 100644
--- a/packages/py-pynn/package.py
+++ b/packages/py-pynn/package.py
@@ -23,6 +23,8 @@ class PyPynn(PythonPackage):
version('0.8.1', sha256='ce94246284588414d1570c1d5d697805f781384e771816727c830b01ee30fe39')
version('0.7.5', sha256='15f75f422f3b71c6129ecef23f29d8baeb3ed6502e7a321b8a2596c78ef7e03c')
+ variant('mpi', default=False, description='Enable MPI support')
+
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'))
@@ -34,6 +36,9 @@ class PyPynn(PythonPackage):
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('mpi', when='+mpi')
+ depends_on('py-mpi4py', type=('build', 'run'), when='+mpi')
+
depends_on('py-mock@1.0:', type='test')
patch('pynn-0.9.6-python3.patch', when='@0.9.6 ^python@3:')
diff --git a/packages/pynn-brainscales/package.py b/packages/pynn-brainscales/package.py
index 68dbdeff7dcf1f2d5ed17cc6a4c8e091c8bdbb71..0cb2c05025977d0eeef82dc787ae42e196fafb32 100644
--- a/packages/pynn-brainscales/package.py
+++ b/packages/pynn-brainscales/package.py
@@ -9,20 +9,12 @@ class PynnBrainscales(WafPackage):
"""PyNN toplevel for the BrainScaleS-2 neuromorphic hardware systems"""
homepage = "https://github.com/electronicvisions/pynn-brainscales"
- #url = "https://github.com/electronicvisions/pynn-brainscales/archive/v0.1.0.tar.gz"
git = "https://github.com/electronicvisions/pynn-brainscales.git"
- version('2.0-rc1', branch='waf')
+ version('2.0-rc5', branch='waf')
# PPU compiler dependencies
- depends_on('gettext')
- depends_on('zlib')
- depends_on('bison')
- depends_on('flex')
- depends_on('m4')
- depends_on('texinfo')
- depends_on('wget')
- conflicts('flex', when='@2.6.3', msg='Binutils 2.25 for Nux doesn\'t build with flex 2.6.3.')
+ depends_on('oppulance@2.0:')
# host software dependencies
depends_on('bitsery', type=('build', 'link', 'run'))
@@ -108,29 +100,35 @@ class PynnBrainscales(WafPackage):
def configure(self, spec, prefix):
"""Setup and configure the project."""
- self.waf('setup', '--repo-db-url=https://github.com/electronicvisions/projects', '--without-grenade-ppu-support', '--without-munge',
- '--project=pynn-brainscales@ebrains_release-2-rc1',
- '--project=haldls@ebrains_release-2-rc1',
- '--project=grenade@ebrains_release-2-rc1',
- '--project=code-format@ebrains_release-2-rc1',
- '--project=logger@ebrains_release-2-rc1',
- '--project=halco@ebrains_release-2-rc1',
- '--project=hate@ebrains_release-2-rc1',
- '--project=fisch@ebrains_release-2-rc1',
- '--project=ztl@ebrains_release-2-rc1',
- '--project=hxcomm@ebrains_release-2-rc1',
- '--project=rant@ebrains_release-2-rc1',
- '--project=pywrap@ebrains_release-2-rc1',
- '--project=lib-boost-patches@ebrains_release-2-rc1',
- '--project=sctrltp@ebrains_release-2-rc1',
- '--project=hwdb@ebrains_release-2-rc1',
- '--project=visions-slurm@ebrains_release-2-rc1',
- '--project=flange@ebrains_release-2-rc1',
- '--project=lib-rcf@ebrains_release-2-rc1',
- '--project=bss-hw-params@ebrains_release-2-rc1'
+ self.waf('setup', '--repo-db-url=https://github.com/electronicvisions/projects', '--without-munge',
+ '--project=pynn-brainscales@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
diff --git a/packages/sda/package.py b/packages/sda/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..3bb82653351034172b449626bbfad54f5fe9ef5e
--- /dev/null
+++ b/packages/sda/package.py
@@ -0,0 +1,50 @@
+# 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 Sda(MakefilePackage):
+ """
+ SDA 7 can be used to carry out Brownian dynamics simulations of the diffusional association
+ in a continuum aqueous solvent of two solute molecules, e.g. proteins, or of a solute
+ molecule to an inorganic surface. SDA 7 can also be used to simulate the diffusion of
+ multiple proteins, in dilute or concentrated solutions, e.g., to study the effects of
+ macromolecular crowding.
+ """
+
+ # Url for the package's homepage.
+ homepage = "https://mcm.h-its.org/sda/doc/doc_sda7/doc/doc_sda7/index.html"
+ url = "https://mcm.h-its.org/wiki/lib/exe/fetch.php?media=googlecolab:sda-7.3.3d.tgz"
+
+ # A list of GitHub accounts to notify when the package is updated.
+ maintainers = ['richtesn', 'thielblz']
+
+ # Versions and checksums.
+ version('7.3.3d', sha256='295ca0142532759a43375422a4ebc050e15b1c248e45493f5864765a9fe8076f')
+
+ # Dependencies.
+ depends_on('gcc@9.4.0:')
+ depends_on('python@3.8:', type=('build','run'))
+ conflicts('%intel')
+
+ build_directory = 'src'
+ build_jobs = 1
+
+ def edit(self, spec, prefix):
+ makefile = FileFilter('src/Makefile')
+ makefile.filter(r'gfortran', spack_fc)
+ makefile.filter(r'^\s*FC\s*=.*', 'FC = ' + spack_fc)
+ makefile.filter(r'^\s*CC_plus\s*=.*', 'CXX = ' + spack_cxx)
+ makefile.filter(r'\${CC_plus}', '${CXX}')
+ makefile.filter(r'^\s*CC_moins\s*=.*', 'CC = ' + spack_cc)
+ makefile.filter(r'\${CC_moins}', '${CC}')
+
+ @property
+ def install_targets(self):
+ build_directory = 'sda_flex-7.3.3d/src/'
+ targets = ['init libsda sda_flex tools auxi clust test_module']
+ return ['prefix={0}'.format(self.prefix), 'install']
diff --git a/spack.yaml b/spack.yaml
index dd0c326ca4884f3d778b3d39d8ea8251d99e9f06..60a65fdba64664f1a61367033aa31318d999fee5 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -28,9 +28,8 @@ spack:
- py-pyaescrypt
- py-formencode
- tvb-framework ^binutils+ld+gold
- - pynn-brainscales@2.0-rc1 ^log4cxx@0.10.0 ^googletest@1.11.0:+gmock
+ - pynn-brainscales@2.0-rc5 ^log4cxx@0.10.0 ^googletest@1.11.0:+gmock
- py-neo
- #- oppulance@2.0-rc1
#- py-cerebstats
#- py-cerebunit
- py-cerebrus
@@ -53,6 +52,9 @@ spack:
- py-frites
#- biobb-common
#- biobb-md
+ #- apbs
+ - py-pdb2pqr
+ #- sda
# demo for codejam12
#- funniest1022
concretization: together