diff options
| -rw-r--r-- | lib/spack/spack/test/cmd/providers.py | 3 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/charmpp/package.py | 142 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/namd/package.py | 24 |
3 files changed, 125 insertions, 44 deletions
diff --git a/lib/spack/spack/test/cmd/providers.py b/lib/spack/spack/test/cmd/providers.py index 3d537c553f..dd0c8a9eb7 100644 --- a/lib/spack/spack/test/cmd/providers.py +++ b/lib/spack/spack/test/cmd/providers.py @@ -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:', diff --git a/var/spack/repos/builtin/packages/charmpp/package.py b/var/spack/repos/builtin/packages/charmpp/package.py index 158dd59937..e9a133604c 100644 --- a/var/spack/repos/builtin/packages/charmpp/package.py +++ b/var/spack/repos/builtin/packages/charmpp/package.py @@ -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 @@ class Charmpp(Package): 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 @@ class Charmpp(Package): 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 @@ class Charmpp(Package): ("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 @@ class Charmpp(Package): "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 @@ class Charmpp(Package): 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 @@ class Charmpp(Package): '--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 @@ class Charmpp(Package): # 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 @@ class Charmpp(Package): 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 diff --git a/var/spack/repos/builtin/packages/namd/package.py b/var/spack/repos/builtin/packages/namd/package.py index dcd80e94a8..d6f5b11b4a 100644 --- a/var/spack/repos/builtin/packages/namd/package.py +++ b/var/spack/repos/builtin/packages/namd/package.py @@ -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 @@ class Namd(MakefilePackage): 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), |