From 7610926e5e5fe3e03ba14da8f629f62db12df962 Mon Sep 17 00:00:00 2001 From: Benjamin Meyers Date: Wed, 8 Mar 2023 06:59:35 -0500 Subject: Update and fix py-meldmd (#35783) * Update/fix py-meldmd; update openmm * Restrict filter_file based on openmm version * Updates based on Adam's feedback * [@spackbot] updating style on behalf of meyersbs * Break up long filter_file Co-authored-by: Adam J. Stewart --------- Co-authored-by: Adam J. Stewart --- var/spack/repos/builtin/packages/openmm/package.py | 22 +++++++- .../repos/builtin/packages/py-meldmd/package.py | 64 +++++++++++++++++++++- 2 files changed, 80 insertions(+), 6 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/openmm/package.py b/var/spack/repos/builtin/packages/openmm/package.py index aa7c1c1b63..3b8329fdea 100644 --- a/var/spack/repos/builtin/packages/openmm/package.py +++ b/var/spack/repos/builtin/packages/openmm/package.py @@ -3,8 +3,6 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -import os - from spack.package import * @@ -49,8 +47,26 @@ class Openmm(CMakePackage, CudaPackage): "wrappers/python/CMakeLists.txt", ) + def setup_build_environment(self, env): + spec = self.spec + if "+cuda" in spec: + env.set("OPENMM_CUDA_COMPILER", self.spec["cuda"].prefix.bin.nvcc) + env.set("CUDA_HOST_COMPILER", self.compiler.cxx) + def setup_run_environment(self, env): spec = self.spec if "+cuda" in spec: env.set("OPENMM_CUDA_COMPILER", self.spec["cuda"].prefix.bin.nvcc) - env.prepend_path("PATH", os.path.dirname(self.compiler.cc)) + env.set("CUDA_HOST_COMPILER", self.compiler.cxx) + + def setup_dependent_run_environment(self, env, dependent_spec): + spec = self.spec + if "+cuda" in spec: + env.set("OPENMM_CUDA_COMPILER", self.spec["cuda"].prefix.bin.nvcc) + env.set("CUDA_HOST_COMPILER", self.compiler.cxx) + + def setup_dependent_build_environment(self, env, dependent_spec): + spec = self.spec + if "+cuda" in spec: + env.set("OPENMM_CUDA_COMPILER", self.spec["cuda"].prefix.bin.nvcc) + env.set("CUDA_HOST_COMPILER", self.compiler.cxx) diff --git a/var/spack/repos/builtin/packages/py-meldmd/package.py b/var/spack/repos/builtin/packages/py-meldmd/package.py index 12c90783e8..7fdefa4bd9 100644 --- a/var/spack/repos/builtin/packages/py-meldmd/package.py +++ b/var/spack/repos/builtin/packages/py-meldmd/package.py @@ -3,26 +3,84 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) +import os + from spack.package import * -class PyMeldmd(PythonPackage, CudaPackage): +class PyMeldmd(CMakePackage, PythonExtension, CudaPackage): """MELD is a tool for inferring the structure of biomolecules from sparse, ambiguous, or noisy data.""" homepage = "http://meldmd.org/" url = "https://github.com/maccallumlab/meld/archive/refs/tags/0.4.20.tar.gz" + version("0.6.1", sha256="aae8e5bfbdacc1e6de61768a3298314c51575cda477a511e98dc11f5730fd918") version("0.4.20", sha256="8c8d2b713f8dc0ecc137d19945b3957e12063c8dda569696e47c8820eeac6c92") + extends("python") + depends_on("python@3.6:", type=("build", "run")) depends_on("py-setuptools", type="build") depends_on("amber") - depends_on("openmm") + depends_on("openmm+cuda") depends_on("py-netcdf4", type=("build", "run")) - depends_on("py-numpy", type=("build", "run")) + # Meld uses np.bool, deprecated in py-numpy@1.24.0 + # https://numpy.org/devdocs/release/1.24.0-notes.html + depends_on("py-numpy@:1.23", type=("build", "run")) depends_on("py-scipy", type=("build", "run")) depends_on("py-scikit-learn", type=("build", "run")) depends_on("py-parmed", type=("build", "run")) depends_on("py-tqdm", type=("build", "run")) depends_on("py-mpi4py", type=("build", "run")) + depends_on("py-pip", type="build") + + # C++ / CUDA + depends_on("eigen", type="link") + depends_on("swig@4.0", type="build") + + def cmake_args(self): + args = [] + args.append("-DOPENMM_DIR={0}".format(self.spec["openmm"].prefix)) + return args + + root_cmakelists_dir = "plugin" + + @run_after("install") + def install_python(self): + args = std_pip_args + ["--prefix=" + prefix, "."] + pip(*args) + with working_dir(join_path(self.build_directory, "python")): + make("MeldPluginPatch") + pip(*args) + for _, _, files in os.walk(self.spec["openmm"].prefix.lib.plugins): + for f in files: + os.symlink( + join_path(self.spec["openmm"].prefix.lib.plugins, f), + join_path(self.prefix.lib.plugins, f), + ) + + def patch(self): + filter_file( + "# Compile the Python module.", + "# Compile the Python module.\n" + 'add_custom_target(MeldPluginPatch DEPENDS "${WRAP_FILE}")', + "plugin/python/CMakeLists.txt", + string=True, + ) + # Fixed, but not versioned yet: + # https://github.com/maccallumlab/meld/commit/afe4b0c199e3562d112af7825f8839e76067039c + filter_file( + "MAXFLOAT", "FLT_MAX", "plugin/platforms/cuda/src/kernels/computeMeld.cu", string=True + ) + # API Change: https://github.com/openmm/openmm/releases/tag/7.6.0 + if self.spec.satisfies("^openmm@7.6.0:"): + filter_file("simtk.openmm", "openmm", "plugin/python/meldplugin.i", string=True) + + def setup_run_environment(self, env): + env.set("OPENMM_PLUGIN_DIR", self.prefix.lib.plugins) + + @run_after("install") + @on_package_attributes(run_tests=True) + def install_test(self): + python("-m", "meld.test_install") -- cgit v1.2.3-60-g2f50