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Multi-valued variants (#2386)

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Modifications:
- added support for multi-valued variants
- refactored code related to variants into variant.py
- added new generic features to AutotoolsPackage that leverage multi-valued variants
- modified openmpi to use new features
- added unit tests for the new semantics
This commit is contained in:
Massimiliano Culpo
2017-05-01 22:08:47 +02:00
committed by Todd Gamblin
parent 5d0d670b72
commit 9e4b0eb34a
22 changed files with 1959 additions and 436 deletions
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32
var/spack/repos/builtin.mock/packages/a/package.py
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@@ -25,7 +25,7 @@
from spack import *
class A(Package):
class A(AutotoolsPackage):
"""Simple package with no dependencies"""
homepage = "http://www.example.com"
@@ -33,5 +33,35 @@ class A(Package):
version('1.0', '0123456789abcdef0123456789abcdef')
variant(
'foo',
values=('bar', 'baz', 'fee'),
default='bar',
description='',
multi=True
)
variant(
'foobar',
values=('bar', 'baz', 'fee'),
default='bar',
description='',
multi=False
)
def with_or_without_fee(self, activated):
if not activated:
return '--no-fee'
return '--fee-all-the-time'
def autoreconf(self, spec, prefix):
pass
def configure(self, spec, prefix):
pass
def build(self, spec, prefix):
pass
def install(self, spec, prefix):
pass

57
var/spack/repos/builtin.mock/packages/multivalue_variant/package.py Normal file
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@@ -0,0 +1,57 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class MultivalueVariant(Package):
homepage = "http://www.llnl.gov"
url = "http://www.llnl.gov/mpileaks-1.0.tar.gz"
version(1.0, 'foobarbaz')
version(2.1, 'foobarbaz')
version(2.2, 'foobarbaz')
version(2.3, 'foobarbaz')
variant('debug', default=False, description='Debug variant')
variant(
'foo',
description='Multi-valued variant',
values=('bar', 'baz', 'barbaz'),
multi=True
)
variant(
'fee',
description='Single-valued variant',
default='bar',
values=('bar', 'baz', 'barbaz'),
multi=False
)
depends_on('mpi')
depends_on('callpath')
def install(self, spec, prefix):
pass

3
var/spack/repos/builtin/packages/cdo/package.py
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@@ -27,7 +27,8 @@
class Cdo(Package):
"""CDO is a collection of command line Operators to manipulate and analyse
Climate and NWP model Data. """
Climate and NWP model Data.
"""
homepage = "https://code.zmaw.de/projects/cdo"
url = "https://code.zmaw.de/attachments/download/12760/cdo-1.7.2.tar.gz"

274
var/spack/repos/builtin/packages/mvapich2/package.py
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@@ -22,11 +22,20 @@
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import sys
from spack import *
from spack.error import SpackError
class Mvapich2(Package):
def _process_manager_validator(values):
if len(values) > 1 and 'slurm' in values:
raise SpackError(
'slurm cannot be activated along with other process managers'
)
class Mvapich2(AutotoolsPackage):
"""MVAPICH2 is an MPI implementation for Infiniband networks."""
homepage = "http://mvapich.cse.ohio-state.edu/"
url = "http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.2.tar.gz"
@@ -55,62 +64,39 @@ class Mvapich2(Package):
# serialized - User serializes calls to MPI (MPI_THREAD_SERIALIZED)
# multiple - Fully multi-threaded (MPI_THREAD_MULTIPLE)
# runtime - Alias to "multiple"
variant('threads', default='multiple',
description='Control the level of thread support')
variant(
'threads',
default='multiple',
values=('single', 'funneled', 'serialized', 'multiple'),
multi=False,
description='Control the level of thread support'
)
# 32 is needed when job size exceeds 32768 cores
variant('ch3_rank_bits', default=32,
description='Number of bits allocated to the rank field (16 or 32)'
)
variant(
'ch3_rank_bits',
default='32',
values=('16', '32'),
multi=False,
description='Number of bits allocated to the rank field (16 or 32)'
)
##########
# TODO : Process managers should be grouped into the same variant,
# as soon as variant capabilities will be extended See
# https://groups.google.com/forum/#!topic/spack/F8-f8B4_0so
SLURM = 'slurm'
HYDRA = 'hydra'
GFORKER = 'gforker'
REMSHELL = 'remshell'
SLURM_INCOMPATIBLE_PMS = (HYDRA, GFORKER, REMSHELL)
variant(SLURM, default=False,
description='Set slurm as the only process manager')
variant(HYDRA, default=False,
description='Set hydra as one of the process managers')
variant(GFORKER, default=False,
description='Set gforker as one of the process managers')
variant(REMSHELL, default=False,
description='Set remshell as one of the process managers')
##########
variant(
'process_managers',
description='List of the process managers to activate',
values=('slurm', 'hydra', 'gforker', 'remshell'),
multi=True,
validator=_process_manager_validator
)
##########
# TODO : Network types should be grouped into the same variant, as
# soon as variant capabilities will be extended
PSM = 'psm'
SOCK = 'sock'
NEMESISIBTCP = 'nemesisibtcp'
NEMESISIB = 'nemesisib'
NEMESIS = 'nemesis'
MRAIL = 'mrail'
SUPPORTED_NETWORKS = (PSM, SOCK, NEMESIS, NEMESISIB, NEMESISIBTCP)
variant(
PSM, default=False,
description='Configure for QLogic PSM-CH3')
variant(
SOCK, default=False,
description='Configure for TCP/IP-CH3')
variant(
NEMESISIBTCP, default=False,
description='Configure for both OFA-IB-Nemesis and TCP/IP-Nemesis')
variant(
NEMESISIB, default=False,
description='Configure for OFA-IB-Nemesis')
variant(
NEMESIS, default=False,
description='Configure for TCP/IP-Nemesis')
variant(
MRAIL, default=False,
description='Configure for OFA-IB-CH3')
##########
'fabrics',
description='The fabric enabled for this build',
default='psm',
values=(
'psm', 'sock', 'nemesisib', 'nemesis', 'mrail', 'nemesisibtcp'
)
)
# FIXME : CUDA support is missing
depends_on('bison')
@@ -123,110 +109,52 @@ def url_for_version(self, version):
else:
return "%s/mvapich/mv2/mvapich2-%s.tar.gz" % (base_url, version)
@staticmethod
def enabled(x):
"""Given a variant name returns the string that means the variant is
enabled
@property
def process_manager_options(self):
spec = self.spec
:param x: variant name
:return:
"""
return '+' + x
other_pms = []
for x in ('hydra', 'gforker', 'remshell'):
if 'process_managers={0}'.format(x) in spec:
other_pms.append(x)
opts = ['--with-pm=%s' % ':'.join(other_pms)]
def set_build_type(self, spec, configure_args):
"""Appends to configure_args the flags that depends only on the build
type (i.e. release or debug)
:param spec: spec
:param configure_args: list of current configure arguments
"""
if '+debug' in spec:
build_type_options = [
"--disable-fast",
"--enable-error-checking=runtime",
"--enable-error-messages=all",
# Permits debugging with TotalView
"--enable-g=dbg", "--enable-debuginfo"
]
else:
build_type_options = ["--enable-fast=all"]
configure_args.extend(build_type_options)
def set_process_manager(self, spec, configure_args):
"""Appends to configure_args the flags that will enable the
appropriate process managers
:param spec: spec
:param configure_args: list of current configure arguments
"""
# Check that slurm variant is not activated together with
# other pm variants
has_slurm_incompatible_variants = \
any(self.enabled(x) in spec
for x in Mvapich2.SLURM_INCOMPATIBLE_PMS)
if self.enabled(Mvapich2.SLURM) in spec and \
has_slurm_incompatible_variants:
raise RuntimeError(" %s : 'slurm' cannot be activated \
together with other process managers" % self.name)
process_manager_options = []
# See: http://slurm.schedmd.com/mpi_guide.html#mvapich2
if self.enabled(Mvapich2.SLURM) in spec:
if 'process_managers=slurm' in spec:
if self.version > Version('2.0'):
process_manager_options = [
"--with-pmi=pmi2",
"--with-pm=slurm"
opts = [
'--with-pmi=pmi2',
'--with-pm=slurm'
]
else:
process_manager_options = [
"--with-pmi=slurm",
"--with-pm=no"
opts = [
'--with-pmi=slurm',
'--with-pm=no'
]
elif has_slurm_incompatible_variants:
pms = []
# The variant name is equal to the process manager name in
# the configuration options
for x in Mvapich2.SLURM_INCOMPATIBLE_PMS:
if self.enabled(x) in spec:
pms.append(x)
process_manager_options = [
"--with-pm=%s" % ':'.join(pms)
]
configure_args.extend(process_manager_options)
return opts
def set_network_type(self, spec, configure_args):
# Check that at most one variant has been activated
count = 0
for x in Mvapich2.SUPPORTED_NETWORKS:
if self.enabled(x) in spec:
count += 1
if count > 1:
raise RuntimeError('network variants are mutually exclusive \
(only one can be selected at a time)')
network_options = []
@property
def network_options(self):
opts = []
# From here on I can suppose that only one variant has been selected
if self.enabled(Mvapich2.PSM) in spec:
network_options = ["--with-device=ch3:psm"]
elif self.enabled(Mvapich2.SOCK) in spec:
network_options = ["--with-device=ch3:sock"]
elif self.enabled(Mvapich2.NEMESISIBTCP) in spec:
network_options = ["--with-device=ch3:nemesis:ib,tcp"]
elif self.enabled(Mvapich2.NEMESISIB) in spec:
network_options = ["--with-device=ch3:nemesis:ib"]
elif self.enabled(Mvapich2.NEMESIS) in spec:
network_options = ["--with-device=ch3:nemesis"]
elif self.enabled(Mvapich2.MRAIL) in spec:
network_options = ["--with-device=ch3:mrail", "--with-rdma=gen2"]
configure_args.extend(network_options)
if 'fabrics=psm' in self.spec:
opts = ["--with-device=ch3:psm"]
elif 'fabrics=sock' in self.spec:
opts = ["--with-device=ch3:sock"]
elif 'fabrics=nemesisibtcp' in self.spec:
opts = ["--with-device=ch3:nemesis:ib,tcp"]
elif 'fabrics=nemesisib' in self.spec:
opts = ["--with-device=ch3:nemesis:ib"]
elif 'fabrics=nemesis' in self.spec:
opts = ["--with-device=ch3:nemesis"]
elif 'fabrics=mrail' in self.spec:
opts = ["--with-device=ch3:mrail", "--with-rdma=gen2"]
return opts
def setup_environment(self, spack_env, run_env):
if self.enabled(Mvapich2.SLURM) in self.spec and \
self.version > Version('2.0'):
spec = self.spec
if 'process_managers=slurm' in spec and spec.satisfies('@2.0:'):
run_env.set('SLURM_MPI_TYPE', 'pmi2')
def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
@@ -251,48 +179,44 @@ def setup_dependent_package(self, module, dependent_spec):
join_path(self.prefix.lib, 'libmpi.{0}'.format(dso_suffix))
]
def install(self, spec, prefix):
@run_before('configure')
def die_without_fortran(self):
# Until we can pass variants such as +fortran through virtual
# dependencies depends_on('mpi'), require Fortran compiler to
# avoid delayed build errors in dependents.
if (self.compiler.f77 is None) or (self.compiler.fc is None):
raise InstallError('Mvapich2 requires both C and Fortran ',
'compilers!')
raise InstallError(
'Mvapich2 requires both C and Fortran compilers!'
)
# we'll set different configure flags depending on our
# environment
configure_args = [
"--prefix=%s" % prefix,
"--enable-shared",
"--enable-romio",
"--disable-silent-rules",
def configure_args(self):
args = [
'--enable-shared',
'--enable-romio',
'-disable-silent-rules',
'--enable-fortran=all',
"--enable-threads={0}".format(spec.variants['threads'].value),
"--with-ch3-rank-bits={0}".format(
spec.variants['ch3_rank_bits'].value),
]
if self.compiler.f77 and self.compiler.fc:
configure_args.append("--enable-fortran=all")
elif self.compiler.f77:
configure_args.append("--enable-fortran=f77")
elif self.compiler.fc:
configure_args.append("--enable-fortran=fc")
if '+debug' in self.spec:
args.extend([
'--disable-fast',
'--enable-error-checking=runtime',
'--enable-error-messages=all',
# Permits debugging with TotalView
'--enable-g=dbg',
'--enable-debuginfo'
])
else:
configure_args.append("--enable-fortran=none")
args.append('--enable-fast=all')
# Set the type of the build (debug, release)
self.set_build_type(spec, configure_args)
# Set the process manager
self.set_process_manager(spec, configure_args)
# Determine network type by variant
self.set_network_type(spec, configure_args)
configure(*configure_args)
make()
make("install")
self.filter_compilers()
args.extend(self.process_manager_options)
args.extend(self.network_options)
return args
@run_after('install')
def filter_compilers(self):
"""Run after install to make the MPI compilers use the
compilers that Spack built the package with.
@@ -302,7 +226,7 @@ def filter_compilers(self):
be bound to whatever compiler they were built with.
"""
bin = self.prefix.bin
mpicc = join_path(bin, 'mpicc')
mpicc = join_path(bin, 'mpicc')
mpicxx = join_path(bin, 'mpicxx')
mpif77 = join_path(bin, 'mpif77')
mpif90 = join_path(bin, 'mpif90')

26
var/spack/repos/builtin/packages/netcdf/package.py
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@@ -24,6 +24,16 @@
##############################################################################
from spack import *
import numbers
def is_integral(x):
"""Any integer value"""
try:
return isinstance(int(x), numbers.Integral) and not isinstance(x, bool)
except ValueError:
return False
class Netcdf(AutotoolsPackage):
"""NetCDF is a set of software libraries and self-describing,
@@ -52,10 +62,18 @@ class Netcdf(AutotoolsPackage):
# These variants control the number of dimensions (i.e. coordinates and
# attributes) and variables (e.g. time, entity ID, number of coordinates)
# that can be used in any particular NetCDF file.
variant('maxdims', default=1024,
description='Defines the maximum dimensions of NetCDF files.')
variant('maxvars', default=8192,
description='Defines the maximum variables of NetCDF files.')
variant(
'maxdims',
default=1024,
description='Defines the maximum dimensions of NetCDF files.',
values=is_integral
)
variant(
'maxvars',
default=8192,
description='Defines the maximum variables of NetCDF files.',
values=is_integral
)
depends_on("m4", type='build')
depends_on("hdf", when='+hdf4')

111
var/spack/repos/builtin/packages/openmpi/package.py
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@@ -22,13 +22,16 @@
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import os
from spack import *
def _verbs_dir():
"""Try to find the directory where the OpenFabrics verbs package is
installed. Return None if not found."""
installed. Return None if not found.
"""
try:
# Try to locate Verbs by looking for a utility in the path
ibv_devices = which("ibv_devices")
@@ -43,7 +46,7 @@ def _verbs_dir():
if path == "/":
path = "/usr"
return path
except:
except TypeError:
return None
@@ -82,22 +85,20 @@ class Openmpi(AutotoolsPackage):
patch('configure.patch', when="@1.10.0:1.10.1")
patch('fix_multidef_pmi_class.patch', when="@2.0.0:2.0.1")
# Fabrics
variant('psm', default=False, description='Build support for the PSM library')
variant('psm2', default=False,
description='Build support for the Intel PSM2 library')
variant('pmi', default=False,
description='Build support for PMI-based launchers')
variant('verbs', default=_verbs_dir() is not None,
description='Build support for OpenFabrics verbs')
variant('mxm', default=False, description='Build Mellanox Messaging support')
variant(
'fabrics',
default=None if _verbs_dir() is None else 'verbs',
description='List of fabrics that are enabled',
values=('psm', 'psm2', 'pmi', 'verbs', 'mxm'),
multi=True
)
# Schedulers
# TODO: support for alps and loadleveler is missing
variant('tm', default=False,
description='Build TM (Torque, PBSPro, and compatible) support')
variant('slurm', default=False,
description='Build SLURM scheduler component')
variant(
'schedulers',
description='List of schedulers for which support is enabled',
values=('alps', 'lsf', 'tm', 'slurm', 'sge', 'loadleveler'),
multi=True
)
# Additional support options
variant('java', default=False, description='Build Java support')
@@ -114,7 +115,7 @@ class Openmpi(AutotoolsPackage):
depends_on('hwloc')
depends_on('hwloc +cuda', when='+cuda')
depends_on('jdk', when='+java')
depends_on('sqlite', when='+sqlite3')
depends_on('sqlite', when='+sqlite3@:1.11')
def url_for_version(self, version):
return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (
@@ -153,15 +154,22 @@ def setup_dependent_package(self, module, dependent_spec):
join_path(self.prefix.lib, 'libmpi.{0}'.format(dso_suffix))
]
@property
def verbs(self):
def with_or_without_verbs(self, activated):
# Up through version 1.6, this option was previously named
# --with-openib
if self.spec.satisfies('@:1.6'):
return 'openib'
opt = 'openib'
# In version 1.7, it was renamed to be --with-verbs
elif self.spec.satisfies('@1.7:'):
return 'verbs'
if self.spec.satisfies('@1.7:'):
opt = 'verbs'
# If the option has not been activated return
# --without-openib or --without-verbs
if not activated:
return '--without-{0}'.format(opt)
line = '--with-{0}'.format(opt)
path = _verbs_dir()
if (path is not None) and (path not in ('/usr', '/usr/local')):
line += '={0}'.format(path)
return line
@run_before('autoreconf')
def die_without_fortran(self):
@@ -175,48 +183,17 @@ def die_without_fortran(self):
def configure_args(self):
spec = self.spec
config_args = [
'--enable-shared',
'--enable-static',
'--enable-mpi-cxx',
# Schedulers
'--with-tm' if '+tm' in spec else '--without-tm',
'--with-slurm' if '+slurm' in spec else '--without-slurm',
# Fabrics
'--with-psm' if '+psm' in spec else '--without-psm',
'--enable-static'
]
if self.spec.satisfies('@2.0:'):
# for Open-MPI 2.0:, C++ bindings are disabled by default.
config_args.extend(['--enable-mpi-cxx'])
# Intel PSM2 support
if spec.satisfies('@1.10:'):
if '+psm2' in spec:
config_args.append('--with-psm2')
else:
config_args.append('--without-psm2')
# PMI support
if spec.satisfies('@1.5.5:'):
if '+pmi' in spec:
config_args.append('--with-pmi')
else:
config_args.append('--without-pmi')
# Mellanox Messaging support
if spec.satisfies('@1.5.4:'):
if '+mxm' in spec:
config_args.append('--with-mxm')
else:
config_args.append('--without-mxm')
# OpenFabrics verbs support
if '+verbs' in spec:
path = _verbs_dir()
if path is not None and path not in ('/usr', '/usr/local'):
config_args.append('--with-{0}={1}'.format(self.verbs, path))
else:
config_args.append('--with-{0}'.format(self.verbs))
else:
config_args.append('--without-{0}'.format(self.verbs))
# Fabrics and schedulers
config_args.extend(self.with_or_without('fabrics'))
config_args.extend(self.with_or_without('schedulers'))
# Hwloc support
if spec.satisfies('@1.5.2:'):
@@ -270,11 +247,11 @@ def configure_args(self):
@run_after('install')
def filter_compilers(self):
"""Run after install to make the MPI compilers use the
compilers that Spack built the package with.
compilers that Spack built the package with.
If this isn't done, they'll have CC, CXX and FC set
to Spack's generic cc, c++ and f90. We want them to
be bound to whatever compiler they were built with.
If this isn't done, they'll have CC, CXX and FC set
to Spack's generic cc, c++ and f90. We want them to
be bound to whatever compiler they were built with.
"""
kwargs = {'ignore_absent': True, 'backup': False, 'string': False}
wrapper_basepath = join_path(self.prefix, 'share', 'openmpi')