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Charm++: fix build prefix; add ucx/pmi support (#15666)

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* Add pmi support (required by ucx, ofi, and gni backends)
* Add support for ucx backend
* Add dependency on MPI for pmi=simplepmi, slurmpmi, or slurmpmi2
* Remove charmpp as an MPI provider since the changes in this PR can
  add MPI as a dependency (mentioned previously)
* Install into transport_protocol-OS-arch subdirectory to match
  default charmpp installation behavior (which helps dependents find it)
This commit is contained in:
Sajid Ali 2020-05-11 18:27:38 -05:00 committed by GitHub
parent fa702b8311
commit b526a90220
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GPG key ID: 4AEE18F83AFDEB23
3 changed files with 125 additions and 44 deletions
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3
lib/spack/spack/test/cmd/providers.py
View file

@ -22,8 +22,7 @@ def test_it_just_runs(pkg):
@pytest.mark.parametrize('vpkg,provider_list', [
(('mpi',), ['charmpp@6.7.1:',
'intel-mpi',
(('mpi',), ['intel-mpi',
'intel-parallel-studio',
'mpich',
'mpich@1:',

142
var/spack/repos/builtin/packages/charmpp/package.py
View file

@ -58,10 +58,18 @@ class Charmpp(Package):
"backend",
default="netlrts",
values=("mpi", "multicore", "netlrts", "verbs", "gni",
"ofi", "pami", "pamilrts"),
"ucx", "ofi", "pami", "pamilrts"),
description="Set the backend to use"
)
# Process management interface
variant(
"pmi",
default="none",
values=("none", "simplepmi", "slurmpmi", "slurmpmi2", "pmix"),
description="The ucx/ofi/gni backends need PMI to run!"
)
# Other options
variant("papi", default=False, description="Enable PAPI integration")
variant("syncft", default=False, description="Compile with Charm++ fault tolerance support")
@ -78,29 +86,23 @@ class Charmpp(Package):
variant("production", default=True, description="Build charm++ with all optimizations")
variant("tracing", default=False, description="Enable tracing modules")
# FIXME: backend=mpi also provides mpi, but spack does not support
# depends_on("mpi") and provides("mpi") in the same package currently.
for b in ['multicore', 'netlrts', 'verbs', 'gni', 'ofi', 'pami',
'pamilrts']:
provides('mpi@2', when='@6.7.1: build-target=AMPI backend={0}'.format(b))
provides('mpi@2', when='@6.7.1: build-target=LIBS backend={0}'.format(b))
def setup_dependent_build_environment(self, env, dependent_spec):
env.set('MPICC', self.prefix.bin.ampicc)
env.set('MPICXX', self.prefix.bin.ampicxx)
env.set('MPIF77', self.prefix.bin.ampif77)
env.set('MPIF90', self.prefix.bin.ampif90)
def setup_dependent_package(self, module, dependent_spec):
self.spec.mpicc = self.prefix.bin.ampicc
self.spec.mpicxx = self.prefix.bin.ampicxx
self.spec.mpifc = self.prefix.bin.ampif90
self.spec.mpif77 = self.prefix.bin.ampif77
depends_on("mpi", when="backend=mpi")
depends_on("papi", when="+papi")
depends_on("cuda", when="+cuda")
depends_on("ucx", when="backend=ucx")
depends_on("slurm@:17-11-9-2", when="pmi=slurmpmi")
depends_on("slurm@17-11-9-2:", when="pmi=slurmpmi2")
# FIXME : As of now spack's OpenMPI recipe does not have a PMIx variant
# But if users have external installs of OpenMPI with PMIx support, this
# will allow them to build charm++ with it.
depends_on("openmpi", when="pmi=pmix")
depends_on("mpi", when="pmi=simplepmi")
depends_on("mpi", when="pmi=slurmpmi")
depends_on("mpi", when="pmi=slurmpmi2")
# Git versions of Charm++ require automake and autoconf
depends_on("automake", when="@develop")
depends_on("autoconf", when="@develop")
@ -108,11 +110,12 @@ def setup_dependent_package(self, module, dependent_spec):
conflicts("~tracing", "+papi")
conflicts("backend=multicore", "+smp")
conflicts("backend=ucx", when="@:6.9.99")
def install(self, spec, prefix):
target = spec.variants["build-target"].value
@property
def charmarch(self):
plat = sys.platform
if plat.startswith("linux"):
plat = "linux"
elif plat.startswith("win"):
@ -123,12 +126,13 @@ def install(self, spec, prefix):
plat = "cnk"
mach = platform.machine()
if mach.startswith("ppc"):
mach = "ppc"
elif mach.startswith("arm"):
mach = "arm"
comm = spec.variants['backend'].value
comm = self.spec.variants['backend'].value
# Define Charm++ version names for various (plat, mach, comm)
# combinations. Note that not all combinations are supported.
@ -145,6 +149,7 @@ def install(self, spec, prefix):
("linux", "x86_64", "netlrts"): "netlrts-linux-x86_64",
("linux", "x86_64", "verbs"): "verbs-linux-x86_64",
("linux", "x86_64", "ofi"): "ofi-linux-x86_64",
("linux", "x86_64", "ucx"): "ucx-linux-x86_64",
("linux", "x86_64", "uth"): "uth-linux-x86_64",
("linux", "ppc", "mpi"): "mpi-linux-ppc",
("linux", "ppc", "multicore"): "multicore-linux-ppc",
@ -167,7 +172,47 @@ def install(self, spec, prefix):
"The communication mechanism %s is not supported "
"on a %s platform with a %s CPU" %
(comm, plat, mach))
version = versions[(plat, mach, comm)]
return versions[(plat, mach, comm)]
# FIXME: backend=mpi also provides mpi, but spack does not support
# depends_on("mpi") and provides("mpi") in the same package currently.
# for b in ['multicore', 'netlrts', 'verbs', 'gni', 'ofi', 'pami',
# 'pamilrts']:
# provides('mpi@2', when='@6.7.1:
# build-target=AMPI backend={0}'.format(b))
# provides('mpi@2', when='@6.7.1:
# build-target=LIBS backend={0}'.format(b))
def install(self, spec, prefix):
if not("backend=mpi" in self.spec) or \
not("backend=netlrts" in self.spec):
if ("+pthreads" in self.spec):
raise InstallError("The pthreads option is only\
available on the Netlrts and MPI \
network layers.")
if ("backend=ucx" in self.spec) or \
("backend=ofi" in self.spec) or \
("backend=gni" in self.spec):
if ("pmi=none" in self.spec):
raise InstallError("The UCX/OFI/GNI backends need \
PMI to run. Please add pmi=... \
Note that PMIx is the preferred \
option.")
if ("pmi=simplepmi" in self.spec) or \
("pmi=slurmpmi" in self.spec) or \
("pmi=slurmpmi2" in self.spec):
if ("^openmpi" in self.spec):
raise InstallError("To use any process management \
interface other than PMIx, \
a non OpenMPI based MPI must be \
present on the system")
target = spec.variants["build-target"].value
builddir = prefix + "/" + str(self.charmarch)
# We assume that Spack's compiler wrappers make this work. If
# not, then we need to query the compiler vendor from Spack
@ -176,9 +221,17 @@ def install(self, spec, prefix):
os.path.basename(self.compiler.cc),
os.path.basename(self.compiler.fc),
"-j%d" % make_jobs,
"--destination=%s" % prefix,
"--destination=%s" % builddir,
]
if "pmi=slurmpmi" in spec:
options.append("slurmpmi")
if "pmi=slurmpmi2" in spec:
options.append("slurmpmi2")
if "pmi=pmix" in spec:
options.append("ompipmix")
options.extend(["--basedir=%s" % spec["openmpi"].prefix])
if 'backend=mpi' in spec:
# in intelmpi <prefix>/include and <prefix>/lib fails so --basedir
# cannot be used
@ -190,6 +243,9 @@ def install(self, spec, prefix):
'--libdir={0}'.format(libdir)
for libdir in spec["mpi"].libs.directories
])
if "backend=ucx" in spec:
options.extend(["--basedir=%s" % spec["ucx"].prefix])
if "+papi" in spec:
options.extend(["papi", "--basedir=%s" % spec["papi"].prefix])
if "+smp" in spec:
@ -223,11 +279,11 @@ def install(self, spec, prefix):
# could dissect the build script; the build instructions say
# this wouldn't be difficult.
build = Executable(join_path(".", "build"))
build(target, version, *options)
build(target, self.charmarch, *options)
# Charm++'s install script does not copy files, it only creates
# symbolic links. Fix this.
for dirpath, dirnames, filenames in os.walk(prefix):
for dirpath, dirnames, filenames in os.walk(builddir):
for filename in filenames:
filepath = join_path(dirpath, filename)
if os.path.islink(filepath):
@ -239,18 +295,32 @@ def install(self, spec, prefix):
os.rename(tmppath, filepath)
except (IOError, OSError):
pass
shutil.rmtree(join_path(prefix, "tmp"))
shutil.rmtree(join_path(builddir, "tmp"))
# A broken 'doc' link in the prefix can break the build.
# Remove it and replace it if it is broken.
try:
os.stat(prefix.doc)
except OSError:
os.remove(prefix.doc)
mkdirp(prefix.doc)
if self.spec.satisfies('@6.9.99'):
# A broken 'doc' link in the prefix can break the build.
# Remove it and replace it if it is broken.
try:
os.stat(prefix.doc)
except OSError:
os.remove(prefix.doc)
mkdirp(prefix.doc)
@run_after('install')
@on_package_attributes(run_tests=True)
def check_build(self):
make('-C', join_path(self.stage.source_path, 'charm/tests'),
'test', parallel=False)
def setup_dependent_build_environment(self, env, dependent_spec):
env.set('MPICC', self.prefix.bin.ampicc)
env.set('MPICXX', self.prefix.bin.ampicxx)
env.set('MPIF77', self.prefix.bin.ampif77)
env.set('MPIF90', self.prefix.bin.ampif90)
def setup_dependent_package(self, module, dependent_spec):
self.spec.mpicc = self.prefix.bin.ampicc
self.spec.mpicxx = self.prefix.bin.ampicxx
self.spec.mpifc = self.prefix.bin.ampif90
self.spec.mpif77 = self.prefix.bin.ampif77
self.spec.charmarch = self.charmarch

24
var/spack/repos/builtin/packages/namd/package.py
View file

@ -15,8 +15,11 @@ class Namd(MakefilePackage):
homepage = "http://www.ks.uiuc.edu/Research/namd/"
url = "file://{0}/NAMD_2.12_Source.tar.gz".format(os.getcwd())
git = "https://charm.cs.illinois.edu/gerrit/namd.git"
manual_download = True
version("develop", branch="master")
version('2.14b1', sha256='9407e54f5271b3d3039a5a9d2eae63c7e108ce31b7481e2197c19e1125b43919')
version('2.13', '9e3323ed856e36e34d5c17a7b0341e38')
version('2.12', '2a1191909b1ab03bf0205971ad4d8ee9')
@ -26,7 +29,9 @@ class Namd(MakefilePackage):
variant('interface', default='none', values=('none', 'tcl', 'python'),
description='Enables TCL and/or python interface')
depends_on('charmpp')
depends_on('charmpp@6.10.1:', when="@2.14b1:")
depends_on('charmpp@6.8.2', when="@2.13")
depends_on('charmpp@6.7.1', when="@2.12")
depends_on('fftw@:2.99', when="fftw=2")
depends_on('fftw@3:', when="fftw=3")
@ -73,17 +78,24 @@ def edit(self, spec, prefix):
with open('{0}.arch'.format(self.build_directory), 'w') as fh:
# this options are take from the default provided
# configuration files
optims_opts = {
'gcc': '-m64 -O3 -fexpensive-optimizations -ffast-math',
'intel': '-O2 -ip'
}
# https://github.com/UIUC-PPL/charm/pull/2778
if self.spec.satisfies('^charmpp@:6.10.1'):
optims_opts = {
'gcc': '-m64 -O3 -fexpensive-optimizations \
-ffast-math -lpthread',
'intel': '-O2 -ip'}
else:
optims_opts = {
'gcc': '-m64 -O3 -fexpensive-optimizations \
-ffast-math',
'intel': '-O2 -ip'}
optim_opts = optims_opts[self.compiler.name] \
if self.compiler.name in optims_opts else ''
fh.write('\n'.join([
'NAMD_ARCH = {0}'.format(self.arch),
'CHARMARCH = ',
'CHARMARCH = {0}'.format(self.spec['charmpp'].charmarch),
'CXX = {0.cxx} {0.cxx11_flag}'.format(
self.compiler),
'CXXOPTS = {0}'.format(optim_opts),