From 1b3f546ba459735ea91c73494b1fd5a93653917e Mon Sep 17 00:00:00 2001 From: Cyrus Harrison Date: Mon, 28 Oct 2019 15:32:16 -0700 Subject: [PATCH] update conduit for 0.5.0 release (#13455) * add support for static (via ~shared) and use vtk-m 1.2 * updating vtkh package to output cmake configure file and pinning it to vtkm 1.2 * trying a different cmake for vtkh * removing problematic b * making conduit respect ~python * fixing ascent python logic * update ascent package * consistant cmake usage * conditionally add tbb in ascent if vtkh * applying becker fix * adding vtkh tag * fixing vtkh tagged version * updating ascent and conduit for static builds * enabling openmp * reverting files that should not have been changed * ascent updates * more robust handling of variants * fixing ascent package typo * ascent: add optional support for mfem * enable mfem conduit support for ascent * add optional adios dep to conduit * remove ver req from conduit * ascent: remove confusing comment * tweaks to conduit and ascent pkg recipes * fix typo in conduit package * pref conduit master * fixing mfem typo for ascent * reverting files * adding mirror for bzip * changing mfem to depend on conduit@master to get updated relay * restore use of conduit 0.3.1 or greater for mfem * set master as prefered conduit version * allow mfem to use conduit master * adding rover package and editing ascent * updating vtkm cmake dep * updates from axom * guard ascent python support on +shared * removing rover to simply ascent package * add fortran variant to conduit, to allow us to turn off conduit support even when a fortran compiler is specified * fix fortran compiler check so it can work on cray systems * working towards cuda fix for vtkm lagrange filter * update ascent package with more variants, and patch to avoid nvcc issue * hdf5 flags fix for BGQ * flake8 * extra guards for cuda patch * conduit and ascent fortran fix * fix patch for non cuda case * add test variant to conduit, tweak ascent pkg * change min ver of cmake used for ascent * h5z-zfp package: unset FC when ~fortran * conform to expected upstream solution * pinning vtkm * going back to vtkm master * add back vtk-m variant for shared libs * update ascent and vtkh packages * wire up option to run tests during install * add post install test * add testing to ascent * tweak for blueos xl * add ctest output on error for run_tests * enable ctest output on error for run_tests * add testing of the using-with-make example * update using-with-make examples * typo in ascent using-with-cmake test * fix ascent using test exe names * more fixes, less sleep * more fixes, less sleep ... * remove unwired up version * improvments suggested on review * adding new cmake * Update package.py * Update package.py * changes post cori os update * fix cray hack * Update package.py Fixing 'fix'. Inconsistent variable names in conduit package * type in spack recipes * add zfp support to conduit * fix indent error in conduit pkg * move to use build phases, add sphinx rtd as dep, fix ex names in tests * add conduit 0.5.0 release * flake8 * remove old cray hack * incorp feedback from review * fix to use proper build env sig --- .../repos/builtin/packages/ascent/package.py | 25 +++-- .../repos/builtin/packages/conduit/package.py | 92 +++++++++++++++---- 2 files changed, 92 insertions(+), 25 deletions(-) diff --git a/var/spack/repos/builtin/packages/ascent/package.py b/var/spack/repos/builtin/packages/ascent/package.py index d837e51010..8d8210edd1 100644 --- a/var/spack/repos/builtin/packages/ascent/package.py +++ b/var/spack/repos/builtin/packages/ascent/package.py @@ -72,7 +72,7 @@ class Ascent(Package): # package dependencies ########################################################################### - depends_on("cmake@3.9.2:3.9.999", type='build') + depends_on("cmake@3.14:", type='build') depends_on("conduit~python", when="~python") depends_on("conduit+python", when="+python+shared") depends_on("conduit~shared~python", when="~shared") @@ -120,8 +120,8 @@ class Ascent(Package): ####################### depends_on("py-sphinx", when="+python+doc", type='build') - def setup_environment(self, spack_env, run_env): - spack_env.set('CTEST_OUTPUT_ON_FAILURE', '1') + def setup_build_environment(self, env): + env.set('CTEST_OUTPUT_ON_FAILURE', '1') def install(self, spec, prefix): """ @@ -353,12 +353,21 @@ def create_host_config(self, spec, prefix, py_site_pkgs_dir=None): cfg.write("# MPI Support\n") if "+mpi" in spec: + mpicc_path = spec['mpi'].mpicc + mpicxx_path = spec['mpi'].mpicxx + mpifc_path = spec['mpi'].mpifc + # if we are using compiler wrappers on cray systems + # use those for mpi wrappers, b/c spec['mpi'].mpicxx + # etc make return the spack compiler wrappers + # which can trip up mpi detection in CMake 3.14 + if cpp_compiler == "CC": + mpicc_path = "cc" + mpicxx_path = "CC" + mpifc_path = "ftn" cfg.write(cmake_cache_entry("ENABLE_MPI", "ON")) - cfg.write(cmake_cache_entry("MPI_C_COMPILER", spec['mpi'].mpicc)) - cfg.write(cmake_cache_entry("MPI_CXX_COMPILER", - spec['mpi'].mpicxx)) - cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER", - spec['mpi'].mpifc)) + cfg.write(cmake_cache_entry("MPI_C_COMPILER", mpicc_path)) + cfg.write(cmake_cache_entry("MPI_CXX_COMPILER", mpicxx_path)) + cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER", mpifc_path)) mpiexe_bin = join_path(spec['mpi'].prefix.bin, 'mpiexec') if os.path.isfile(mpiexe_bin): # starting with cmake 3.10, FindMPI expects MPIEXEC_EXECUTABLE diff --git a/var/spack/repos/builtin/packages/conduit/package.py b/var/spack/repos/builtin/packages/conduit/package.py index af1cc70c85..acc1498b70 100644 --- a/var/spack/repos/builtin/packages/conduit/package.py +++ b/var/spack/repos/builtin/packages/conduit/package.py @@ -38,6 +38,7 @@ class Conduit(Package): git = "https://github.com/LLNL/conduit.git" version('master', branch='master', submodules=True, preferred=True) + version('0.5.0', sha256='7efac668763d02bd0a2c0c1b134d9f5ee27e99008183905bb0512e5502b8b4fe') version('0.4.0', sha256='c228e6f0ce5a9c0ffb98e0b3d886f2758ace1a4b40d00f3f118542c0747c1f52') version('0.3.1', sha256='7b358ca03bb179876291d4a55d6a1c944b7407a80a588795b9e47940b1990521') version('0.3.0', sha256='52e9cf5720560e5f7492876c39ef2ea20ae73187338361d2744bdf67567da155') @@ -66,6 +67,9 @@ class Conduit(Package): variant("silo", default=False, description="Build Conduit Silo support") variant("adios", default=False, description="Build Conduit ADIOS support") + # zfp compression + variant("zfp", default=True, description="Build Conduit ZFP support") + # variants for dev-tools (docs, etc) variant("doc", default=False, description="Build Conduit's documentation") # doxygen support is wip, since doxygen has several dependencies @@ -94,6 +98,10 @@ class Conduit(Package): ####################### # I/O Packages ####################### + + ############### + # HDF5 + ############### # TODO: cxx variant is disabled due to build issue Cyrus # experienced on BGQ. When on, the static build tries # to link against shared libs. @@ -105,15 +113,26 @@ class Conduit(Package): depends_on("hdf5~cxx~mpi~fortran", when="+hdf5~hdf5_compat+shared") depends_on("hdf5~shared~cxx~mpi~fortran", when="+hdf5~hdf5_compat~shared") + ############### + # Silo + ############### # we are not using silo's fortran features depends_on("silo~fortran", when="+silo+shared") depends_on("silo~shared~fortran", when="+silo~shared") + ############### + # ADIOS + ############### depends_on("adios+mpi~hdf5+shared", when="+adios+mpi+shared") depends_on("adios+mpi~hdf5~shared~blosc", when="+adios+mpi~shared") depends_on("adios~mpi~hdf5+shared", when="+adios~mpi+shared") depends_on("adios~mpi~hdf5~shared~blosc", when="+adios~mpi~shared") + ####################### + # ZFP + ####################### + depends_on("zfp", when="+zfp") + ####################### # MPI ####################### @@ -123,10 +142,14 @@ class Conduit(Package): # Documentation related ####################### depends_on("py-sphinx", when="+python+doc", type='build') + depends_on("py-sphinx-rtd-theme", when="+python+doc", type='build') depends_on("doxygen", when="+doc+doxygen") - def setup_environment(self, spack_env, run_env): - spack_env.set('CTEST_OUTPUT_ON_FAILURE', '1') + # build phases used by this package + phases = ["configure", "build", "install"] + + def setup_build_environment(self, env): + env.set('CTEST_OUTPUT_ON_FAILURE', '1') def url_for_version(self, version): """ @@ -145,9 +168,9 @@ def url_for_version(self, version): return "https://github.com/LLNL/conduit/releases/download/v{0}/conduit-v{1}-src-with-blt.tar.gz".format(v, v) return url - def install(self, spec, prefix): + def configure(self, spec, prefix): """ - Build and install Conduit. + Configure Conduit. """ with working_dir('spack-build', create=True): py_site_pkgs_dir = None @@ -157,6 +180,9 @@ def install(self, spec, prefix): host_cfg_fname = self.create_host_config(spec, prefix, py_site_pkgs_dir) + # save this filename for + # other package recipe steps to access + self.host_cfg_fname = host_cfg_fname cmake_args = [] # if we have a static build, we need to avoid any of # spack's default cmake settings related to rpaths @@ -170,17 +196,31 @@ def install(self, spec, prefix): cmake_args.extend(["-C", host_cfg_fname, "../src"]) print("Configuring Conduit...") cmake(*cmake_args) + + def build(self, spec, prefix): + """ + Build Conduit. + """ + with working_dir('spack-build'): print("Building Conduit...") make() - # run unit tests if requested - if "+test" in spec and self.run_tests: - print("Running Conduit Unit Tests...") - make("test") - print("Installing Conduit...") + + @run_after('build') + @on_package_attributes(run_tests=True) + def test(self): + with working_dir('spack-build'): + print("Running Conduit Unit Tests...") + make("test") + + def install(self, spec, prefix): + """ + Install Conduit. + """ + with working_dir('spack-build'): make("install") # install copy of host config for provenance print("Installing Conduit CMake Host Config File...") - install(host_cfg_fname, prefix) + install(self.host_cfg_fname, prefix) @run_after('install') @on_package_attributes(run_tests=True) @@ -203,7 +243,7 @@ def check_install(self): example_src_dir] cmake(*cmake_args) make() - example = Executable('./example') + example = Executable('./conduit_example') example() print("Checking using-with-make example...") example_src_dir = join_path(install_prefix, @@ -216,7 +256,7 @@ def check_install(self): for example_file in example_files: shutil.copy(example_file, ".") make("CONDUIT_DIR={0}".format(install_prefix)) - example = Executable('./example') + example = Executable('./conduit_example') example() def create_host_config(self, spec, prefix, py_site_pkgs_dir=None): @@ -366,12 +406,21 @@ def create_host_config(self, spec, prefix, py_site_pkgs_dir=None): cfg.write("# MPI Support\n") if "+mpi" in spec: + mpicc_path = spec['mpi'].mpicc + mpicxx_path = spec['mpi'].mpicxx + mpifc_path = spec['mpi'].mpifc + # if we are using compiler wrappers on cray systems + # use those for mpi wrappers, b/c spec['mpi'].mpicxx + # etc make return the spack compiler wrappers + # which can trip up mpi detection in CMake 3.14 + if cpp_compiler == "CC": + mpicc_path = "cc" + mpicxx_path = "CC" + mpifc_path = "ftn" cfg.write(cmake_cache_entry("ENABLE_MPI", "ON")) - cfg.write(cmake_cache_entry("MPI_C_COMPILER", spec['mpi'].mpicc)) - cfg.write(cmake_cache_entry("MPI_CXX_COMPILER", - spec['mpi'].mpicxx)) - cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER", - spec['mpi'].mpifc)) + cfg.write(cmake_cache_entry("MPI_C_COMPILER", mpicc_path)) + cfg.write(cmake_cache_entry("MPI_CXX_COMPILER", mpicxx_path)) + cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER", mpifc_path)) mpiexe_bin = join_path(spec['mpi'].prefix.bin, 'mpiexec') if os.path.isfile(mpiexe_bin): # starting with cmake 3.10, FindMPI expects MPIEXEC_EXECUTABLE @@ -385,6 +434,15 @@ def create_host_config(self, spec, prefix, py_site_pkgs_dir=None): else: cfg.write(cmake_cache_entry("ENABLE_MPI", "OFF")) + ####################### + # ZFP + ####################### + cfg.write("# zfp from spack \n") + if "+zfp" in spec: + cfg.write(cmake_cache_entry("ZFP_DIR", spec['zfp'].prefix)) + else: + cfg.write("# zfp not built by spack \n") + ####################################################################### # I/O Packages #######################################################################