[macOS} Only a few output files created when PolyChord runs through Cobaya

[kabeleh]

I would like to assess a cosmological model (implemented into CLASS) using Cobaya and PolyChord. Eventually, it should run on a cluster, but for initial testing I was hoping to use my MacBook Air (M4).

When I run Cobaya with

sampler:
  polychord: {}

it should use the default values

write_resume: True
read_resume: True
write_stats: True
write_live: True
write_dead: True
write_prior: True

yet, the only output that gets created are the following files/folders:

• .updated.yaml
• .input.yaml
• _clusters/ an empty folder
• _polychord_raw/ a folder containing an empty folder clusters/ and the file _phys_live.txt

Would the other files (stats, resume, dead, prior) only get created when a specific threshold with live points is found or should those get created right on launching the run? How could I investigate what prevents the creation? I doubt it's a permission issue, since two folders and one file are successfully created.

I had some issues installing PolyChord and solved them by just hard-coding the correct compiler into setup.py. Maybe this broke something?

I manually added

env["HOME"] = os.environ.get("HOME", os.path.expanduser("~"))

to CustomBuildPy and forced check_compiler to return gcc-15, as this is the gcc version I used to compile MPI.

"""
Python interface to PolyChord

Polychord is a tool to solve high dimensional problems.
"""

from setuptools import setup, Extension, find_packages, Distribution
from setuptools.command.build_py import build_py as _build_py
from distutils.command.clean import clean as _clean

import os, sys, subprocess, shutil

import numpy


def check_compiler(default_CC="gcc"):
    """Checks what compiler is being used (clang, intel, or gcc)."""

    CC = default_CC if "CC" not in os.environ else os.environ["CC"]
    CC_version = (
        subprocess.check_output([CC, "-v"], stderr=subprocess.STDOUT)
        .decode("utf-8")
        .lower()
    )

    if "clang" in CC_version:
        CC_family = "clang"
    elif "icc" in CC_version:
        CC_family = "intel"
    elif "gcc" in CC_version:
        CC_family = "gcc"
    else:
        print("Warning: unrecognised compiler: {}".format(CC_version))
        CC_family = ""

    CC_family = "gcc-15"

    return CC_family


NAME = "pypolychord"
DOCLINES = (__doc__ or "").split("\n")


# Deal with annoying differences between clang and the other compilers
CC_FAMILY = check_compiler()
CPPRUNTIMELIB_FLAG = []
RPATH_FLAG = []

if CC_FAMILY == "clang":
    CPPRUNTIMELIB_FLAG += ["-stdlib=libc++"]
    if sys.platform == "darwin":
        # macOS idiosyncrasies
        CPPRUNTIMELIB_FLAG += ["-mmacosx-version-min=10.9"]

if sys.platform != "darwin":
    # Set RPATH on Linux machines
    RPATH_FLAG += ["-Wl,-rpath,$ORIGIN/pypolychord/lib"]


def readme():
    with open("pypolychord_README.rst") as f:
        return f.read()


def get_version(short=False):
    with open("src/polychord/feedback.f90") as f:
        for line in f:
            if "version" in line:
                return line[44:50]


class DistributionWithOption(Distribution, object):
    def __init__(self, *args, **kwargs):
        self.global_options = self.global_options + [
            ("no-mpi", None, "Don't compile with MPI support."),
            ("debug-flags", None, "Compile in debug mode."),
        ]
        self.no_mpi = None
        self.debug_flags = None
        super(DistributionWithOption, self).__init__(*args, **kwargs)


class CustomBuildPy(_build_py, object):
    def run(self):
        env = {}
        env["HOME"] = os.environ.get("HOME", os.path.expanduser("~"))
        env["PATH"] = os.environ["PATH"]
        if self.distribution.no_mpi is None:
            env["MPI"] = "1"
            # These need to be set so that build_ext uses the right compilers
            cc_compiler = (
                subprocess.check_output(["make", "print_CC"]).decode("utf-8").strip()
            )
            os.environ["CC"] = cc_compiler

            cxx_compiler = (
                subprocess.check_output(["make", "print_CXX"]).decode("utf-8").strip()
            )
            os.environ["CXX"] = cxx_compiler
        else:
            env["MPI"] = "0"

        if self.distribution.debug_flags is not None:
            self.distribution.ext_modules[0].extra_compile_args += ["-g", "-O0"]
            env["DEBUG"] = "1"

        BASE_PATH = os.path.dirname(os.path.abspath(__file__))
        env["PWD"] = BASE_PATH
        env.update({k: os.environ[k] for k in ["CC", "CXX", "FC"] if k in os.environ})
        subprocess.check_call(["make", "-e", "libchord.so"], env=env, cwd=BASE_PATH)
        if not os.path.isdir("pypolychord/lib/"):
            os.makedirs(os.path.join(BASE_PATH, "pypolychord/lib/"))
        shutil.copy(
            os.path.join(BASE_PATH, "lib/libchord.so"),
            os.path.join(BASE_PATH, "pypolychord/lib/"),
        )
        self.run_command("build_ext")
        return super(CustomBuildPy, self).run()


class CustomClean(_clean):
    def run(self):
        subprocess.run(["make", "veryclean"], check=True, env=os.environ)
        return super().run()


if "--no-mpi" in sys.argv:
    NAME += "_nompi"
    DOCLINES[1] = DOCLINES[1] + " (cannot be used with MPI)"

pypolychord_module = Extension(
    name="_pypolychord",
    library_dirs=["lib"],
    include_dirs=["src/polychord", numpy.get_include()],
    libraries=[
        "chord",
    ],
    extra_link_args=RPATH_FLAG + CPPRUNTIMELIB_FLAG,
    extra_compile_args=["-std=c++11"] + RPATH_FLAG + CPPRUNTIMELIB_FLAG,
    runtime_library_dirs=["lib"],
    sources=["pypolychord/_pypolychord.cpp"],
)

setup(
    name=NAME,
    version=get_version(),
    description="Python interface to PolyChord " + get_version(),
    url="https://ccpforge.cse.rl.ac.uk/gf/project/polychord/",
    author="Will Handley",
    author_email="wh260@cam.ac.uk",
    license="PolyChord",
    packages=find_packages(),
    install_requires=["numpy", "scipy"],
    extras_require={"plotting": "getdist"},
    distclass=DistributionWithOption,
    ext_modules=[pypolychord_module],
    cmdclass={"build_py": CustomBuildPy, "clean": CustomClean},
    package_data={"": ["lib/libchord.so"]},
    include_package_data=True,
    zip_safe=False,
)