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firedrake-install
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firedrake-install
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#! /usr/bin/env python3
import logging
import platform
import subprocess
import sys
import os
import shutil
from argparse import ArgumentParser, RawDescriptionHelpFormatter
import argparse
from collections import OrderedDict
import atexit
import json
import pprint
import shlex
from glob import iglob
from itertools import chain
import re
import importlib
try:
from pkg_resources.extern.packaging.version import Version, InvalidVersion
except ModuleNotFoundError:
from packaging.version import Version, InvalidVersion
osname = platform.uname().system
arch = platform.uname().machine
# Packages which we wish to ensure are always recompiled
wheel_blacklist = ["mpi4py", "randomgen", "numpy"]
# Packages for which we set CC=mpicc, CXX=mpicxx, F90=mpif90.
parallel_packages = ["h5py", "petsc4py", "slepc", "slepc4py", "PyOP2", "libsupermesh", "firedrake"]
# Firedrake application installation shortcuts.
firedrake_apps = {
"gusto": ("""Atmospheric dynamical core library. http://firedrakeproject.org/gusto""",
"git+ssh://github.com/firedrakeproject/gusto.git@main#egg=gusto"),
"thetis": ("""Coastal ocean model. http://thetisproject.org""",
"git+ssh://github.com/thetisproject/thetis#egg=thetis"),
"icepack": ("""Glacier and ice sheet model. https://icepack.github.io""",
"git+ssh://github.com/icepack/icepack.git#egg=icepack"),
"irksome": ("""Implicit Runge-Kutta methods. https://github.com/firedrakeproject/Irksome/""",
"git+ssh://github.com/firedrakeproject/Irksome.git#egg=Irksome"),
"femlium": ("""Interactive visualization of finite element simulations on geographic maps with folium. https://femlium.github.io/""",
"git+ssh://github.com/FEMlium/FEMlium.git@main#egg=FEMlium"),
"fascd": ("""Full approximation scheme constraint decomposition solver for variational inequalities. https://bitbucket.org/pefarrell/fascd""",
"git+ssh://bitbucket.org/pefarrell/fascd.git@master#egg=fascd"),
"defcon": ("""Deflated continuation algorithm for bifurcation analysis. https://bitbucket.org/pefarrell/defcon""",
"git+ssh://bitbucket.org/pefarrell/defcon.git@master#egg=defcon"),
"gadopt": ("""Geodynamic Adjoint Optimization Platform. http://g-adopt.github.io""",
"git+ssh://github.com/g-adopt/g-adopt.git@master#egg=gadopt"),
"asQ": ("""ParaDiag parallel-in-time methods. http://firedrakeproject.org/asQ""",
"git+ssh://github.com/firedrakeproject/asQ.git@master#egg=asQ"),
}
class InstallError(Exception):
# Exception for generic install problems.
pass
class FiredrakeConfiguration(dict):
"""A dictionary extended to facilitate the storage of Firedrake
configuration information."""
def __init__(self, args=None):
super(FiredrakeConfiguration, self).__init__()
'''A record of the persistent options in force.'''
self["options"] = {}
'''Relevant environment variables.'''
self["environment"] = {}
'''Additional packages installed via the plugin interface.'''
self["additions"] = []
if args:
for o in self._persistent_options:
if o in args.__dict__.keys():
self["options"][o] = args.__dict__[o]
_persistent_options = ["package_manager",
"minimal_petsc", "mpicc", "mpicxx", "mpif90", "mpiexec", "disable_ssh",
"honour_petsc_dir", "with_parmetis",
"slepc", "packages", "honour_pythonpath",
"opencascade", "tinyasm", "torch",
"petsc_int_type", "cache_dir", "complex", "remove_build_files", "with_blas", "netgen"]
def deep_update(this, that):
from collections import abc
for k, v in that.items():
if isinstance(v, abc.Mapping) and k in this.keys():
this[k] = deep_update(this.get(k, {}), v)
else:
this[k] = v
return this
if os.path.basename(__file__) == "firedrake-install":
mode = "install"
logfile_directory = os.path.abspath(os.getcwd())
logfile_mode = "w"
elif os.path.basename(__file__) == "firedrake-update":
mode = "update"
os.chdir(os.path.dirname(os.path.realpath(__file__)) + "/../..")
try:
logfile_directory = os.environ["VIRTUAL_ENV"]
except KeyError:
quit("Unable to retrieve venv name from the environment.\n Please ensure the venv is active before running firedrake-update.")
logfile_mode = "a" if "--no-update-script" in sys.argv else "w"
else:
sys.exit("Script must be invoked either as firedrake-install or firedrake-update")
# Set up logging
# Log to file at DEBUG level
if ("-h" in sys.argv) or ("--help" in sys.argv):
# Don't log if help displayed to avoid overwriting an existing log
logfile = os.devnull
else:
logfile = os.path.join(logfile_directory, 'firedrake-%s.log' % mode)
logging.basicConfig(level=logging.DEBUG,
format='%(asctime)s %(levelname)-6s %(message)s',
filename=logfile,
filemode=logfile_mode)
# Log to console at INFO level
console = logging.StreamHandler()
console.setLevel(logging.INFO)
formatter = logging.Formatter('%(message)s')
console.setFormatter(formatter)
logging.getLogger().addHandler(console)
log = logging.getLogger()
log.info("Running %s" % " ".join(sys.argv))
if sys.version_info >= (3, 12):
print("""\nCan not install Firedrake with Python 3.12 at the moment:
Some wheels are not yet available for Python 3.12 for some required package(s).
Please install with Python 3.11 (or an earlier version >= 3.8).""")
sys.exit(1)
elif sys.version_info < (3, 9) and osname == "Darwin" and arch == "arm64":
print("""
Installing Firedrake on Mac Arm (M1 or M2) requires at least Python 3.9 since
some required package(s) are not available for earlier Python versions.""")
elif sys.version_info < (3, 8):
if mode == "install":
print("""\nInstalling Firedrake requires Python 3, at least version 3.8.
You should run firedrake-install with python3.""")
if mode == "update":
if hasattr(sys, "real_prefix"):
# sys.real_prefix exists iff we are in an active virtualenv.
#
# Existing install trying to update past the py2/py3 barrier
print("""\nFiredrake is now Python 3 only. You cannot upgrade your existing installation.
Please follow the instructions at http://www.firedrakeproject.org/download.html to reinstall.""")
sys.exit(1)
else:
# Accidentally (?) running firedrake-update with python2.
print("""\nfiredrake-update must be run with Python 3, did you accidentally use Python 2?""")
sys.exit(1)
branches = {}
def resolve_doi_branches(doi):
import requests
import hashlib
log.info("Installing Firedrake components specified by {}".format(doi))
# Zenodo updated their API to use elastic search so simply querying with
# ?q=doi:10.5281/zenodo.<id> now returns multiple results (not ideal)
# Instead use
# /<id>
# as documented here https://developers.zenodo.org/#retrieve
id_ = doi.split('.')[-1]
response = requests.get("https://zenodo.org/api/records/{}".format(id_))
if not response.ok:
log.error("Unable to obtain Zenodo record for doi {}".format(doi))
log.error("Response was {}".format(response.json()))
sys.exit(1)
record = response.json()
files = record["files"]
try:
componentjson, = (f for f in files if f["key"] == "components.json")
except ValueError:
log.error("Expecting to find exactly one 'components.json' in record")
sys.exit(1)
download = requests.get(componentjson["links"]["self"])
if download.status_code >= 400:
log.error("Unable to download 'components.json'")
log.error("Response was {}".format(download.json()))
sys.exit(1)
# component response has checksum as "md5:HEXDIGEST", strip the md5.
if hashlib.md5(download.content).hexdigest() != componentjson["checksum"][4:]:
log.error("Download failed checksum, expecting {expect}, got {got}".format(
expect=componentjson["checksum"][4:],
got=hashlib.md5(download.content).hexdigest()))
sys.exit(1)
componentjson = download.json()
branches = {}
for record in componentjson["components"]:
commit = record["commit"]
component = record["component"]
package = component[component.find("/")+1:].lower()
branches[package] = commit
log.info("Using commit {commit} for component {comp}".format(
commit=commit, comp=component))
return branches
def honour_petsc_dir_get_petsc_dir():
try:
petsc_dir = os.environ["PETSC_DIR"]
except KeyError:
raise InstallError("Unable to find installed PETSc (did you forget to set PETSC_DIR?)")
petsc_arch = os.environ.get("PETSC_ARCH", "")
return petsc_dir, petsc_arch
def honour_petsc_dir_fetch_petscconf(name):
# Return the line in "petscconf.h" that starts with name.
petsc_dir, petsc_arch = honour_petsc_dir_get_petsc_dir()
petscconf_h = os.path.join(petsc_dir, petsc_arch, "include", "petscconf.h")
with open(petscconf_h) as fh:
for line in fh.readlines():
if line.startswith(name):
return line
def honour_petsc_dir_get_petsc_int_type():
line = honour_petsc_dir_fetch_petscconf("#define PETSC_USE_64BIT_INDICES")
if line and line.split()[2] == '1':
return "int64"
else:
return "int32"
def honour_petsc_dir_get_petsc_packages():
line = honour_petsc_dir_fetch_petscconf("#define PETSC_HAVE_PACKAGES")
return set(line.split()[2].strip().strip(':"').split(':'))
if mode == "install":
# Handle command line arguments.
parser = ArgumentParser(description="""Install firedrake and its dependencies.""",
epilog="""The install process has three steps.
1. Any required system packages are installed using brew (MacOS) or apt (Ubuntu
and similar Linux systems). On a Linux system without apt, the installation
will fail if a dependency is not found.
2. A set of standard and/or third party Python packages is installed to the
specified install location.
3. The core set of Python packages is downloaded to ./firedrake/src/ and
installed to the specified location.
The install creates a venv in ./firedrake (or in ./name where name is the
parameter given to --venv-name) and installs inside that venv.
The installer will ensure that the required configuration options are
passed to PETSc. In addition, any configure options which you provide
in the PETSC_CONFIGURE_OPTIONS environment variable will be
honoured.""",
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument("--slepc", action="store_true",
help="Install SLEPc along with PETSc.")
parser.add_argument("--opencascade", action="store_true",
help="Install OpenCASCADE for CAD integration.")
parser.add_argument("--tinyasm", action="store_true",
help="Install TinyASM as backend for ASMPatchPC.")
parser.add_argument("--torch", const="cpu", default=False, nargs='?', choices=["cpu", "cuda"],
help="Install PyTorch for a CPU or CUDA backend (default: CPU).")
parser.add_argument("--disable-ssh", action="store_true",
help="Do not attempt to use ssh to clone git repositories: fall immediately back to https.")
parser.add_argument("--no-package-manager", action='store_false', dest="package_manager",
help="Do not attempt to use apt or homebrew to install operating system packages on which we depend.")
group = parser.add_mutually_exclusive_group()
group.add_argument("--minimal-petsc", action="store_true",
help="Minimise the set of petsc dependencies installed. This creates faster build times (useful for build testing).")
group.add_argument("--with-parmetis", action="store_true",
help="Install PETSc with ParMETIS? (Non-free license, see http://glaros.dtc.umn.edu/gkhome/metis/parmetis/download)")
parser.add_argument("--honour-petsc-dir", action="store_true",
help="Usually it is best to let Firedrake build its own PETSc. If you wish to use another PETSc, set PETSC_DIR and pass this option.")
parser.add_argument("--petsc-int-type", choices=["int32", "int64"],
default="int32", type=str,
help="The integer type used by PETSc. Use int64 if you need to solve problems with more than 2 billion degrees of freedom. Only takes effect if firedrake-install builds PETSc.")
parser.add_argument("--honour-pythonpath", action="store_true",
help="Pointing to external Python packages is usually a user error. Set this option if you know that you want PYTHONPATH set.")
parser.add_argument("--rebuild-script", action="store_true",
help="Only rebuild the firedrake-install script. Use this option if your firedrake-install script is broken and a fix has been released in upstream Firedrake. You will need to specify any other options which you wish to be honoured by your new update script.")
parser.add_argument("--doi", type=str, nargs=1,
help="Install a set of components matching a particular Zenodo DOI. The record should have been created with firedrake-zenodo.")
# Used for testing if Zenodo broke the API
# Tries to resolve to a known DOI and immediately exits.
parser.add_argument("--test-doi-resolution", action="store_true",
help=argparse.SUPPRESS)
parser.add_argument("--package-branch", type=str, nargs=2, action="append", metavar=("PACKAGE", "BRANCH"),
help="Specify which branch of a package to use. This takes two arguments, the package name and the branch.")
parser.add_argument("--verbose", "-v", action="store_true", help="Produce more verbose debugging output.")
parser.add_argument("--mpicc", type=str,
action="store", default=None,
help="C compiler to use when building with MPI. If not set, MPICH will be downloaded and used.")
parser.add_argument("--mpicxx", type=str,
action="store", default=None,
help="C++ compiler to use when building with MPI. If not set, MPICH will be downloaded and used.")
parser.add_argument("--mpif90", type=str,
action="store", default=None,
help="Fortran compiler to use when building with MPI. If not set, MPICH will be downloaded and used.")
parser.add_argument("--mpiexec", type=str,
action="store", default=None,
help="MPI launcher. If not set, MPICH will be downloaded and used.")
parser.add_argument("--show-petsc-configure-options", action="store_true",
help="Print out the configure options passed to PETSc and exit")
parser.add_argument("--show-dependencies", action="store_true",
help="Print out the package manager used and packages installed/required.")
parser.add_argument("--venv-name", default="firedrake",
type=str, action="store",
help="Name of the venv to create and the name of the install directory relative to this install script (default is 'firedrake' with directory ./firedrake)")
parser.add_argument("--install", action="append", dest="packages",
help="Additional packages to be installed. The address should be in format vcs+protocol://repo_url/#egg=pkg&subdirectory=pkg_dir . Some additional packages have shortcut install options for more information see --install-help.")
parser.add_argument("--pip-install", action="append", dest="pip_packages",
help="Pip install additional packages into the venv")
parser.add_argument("--install-help", action="store_true",
help="Provide information on packages which can be installed using shortcut names.")
parser.add_argument("--cache-dir", type=str,
action="store",
help="Directory to use for disk caches of compiled code (default is the .cache subdirectory of the Firedrake installation).")
parser.add_argument("--complex", action="store_true",
help="Installs the complex version of Firedrake; rebuilds PETSc in complex mode.")
parser.add_argument("--documentation-dependencies", action="store_true",
help="Install the dependencies required to build the documentation")
parser.add_argument("--remove-build-files", action="store_true",
help="Cleans up build artefacts from Firedrake venv. Unless you really cannot spare the disk space, this option is not recommended")
parser.add_argument("--with-blas", default=("download" if osname == "Darwin" else None),
help="Specify path to system BLAS directory. Use '--with-blas=download' to download openblas")
parser.add_argument("--netgen", action="store_true",
help="Install NGSolve/Netgen and ngsPETSc.")
parser.add_argument("--no-vtk", action="store_true",
help="Do not install VTK into the Firedrake virtualenv")
args = parser.parse_args()
# If the user has set any MPI info, they must set them all
if args.mpicc or args.mpicxx or args.mpif90 or args.mpiexec:
if not (args.mpicc and args.mpicxx and args.mpif90 and args.mpiexec):
log.error("If you set any MPI information, you must set all of {mpicc, mpicxx, mpif90, mpiexec}.")
sys.exit(1)
if args.package_branch:
branches = {package.lower(): branch for package, branch in args.package_branch}
if args.test_doi_resolution:
actual = resolve_doi_branches("10.5281/zenodo.1322546")
expect = {'coffee': '87e50785d3a05b111f5423a66d461cd44cc4bdc9',
'finat': 'aa74fd499304c8363a4520555fd62ef21e8e5e1f',
'fiat': '184601a46c24fb5cbf8fd7961d22b16dd26890e7',
'firedrake': '6a30b64da01eb587dcc0e04e8e6b84fe4839bdb7',
'petsc': '413f72f04f5cb0a010c85e03ed029573ff6d4c63',
'petsc4py': 'ac2690070a80211dfdbab04634bdb3496c14ca0a',
'tsfc': 'fe9973eaacaa205fd491cd1cc9b3743b93a3d076',
'ufl': 'c5eb7fbe89c1091132479c081e6fa9c182191dcc',
'pyop2': '741a21ba9a62cb67c0aa300a2e199436ea8cb61c'}
if actual != expect:
log.error("Unable to resolve DOI correctly.")
log.error("You'll need to figure out how Zenodo have changed their API.")
sys.exit(1)
else:
log.info("DOI resolution test passed.")
sys.exit(0)
if args.doi:
branches = resolve_doi_branches(args.doi[0])
if args.honour_petsc_dir:
petsc_int_type = honour_petsc_dir_get_petsc_int_type()
if petsc_int_type != args.petsc_int_type:
petsc_dir, petsc_arch = honour_petsc_dir_get_petsc_dir()
log.warning("Provided PETSc (PETSC_DIR=%s, PETSC_ARCH=%s) was compiled for %s, but given --petsc-int-type = %s: setting --petsc-int-type %s." % (petsc_dir, petsc_arch, petsc_int_type, args.petsc_int_type, petsc_int_type))
args.petsc_int_type = petsc_int_type
args.prefix = False # Disabled as untested
args.packages = args.packages or []
config = FiredrakeConfiguration(args)
else:
# This duplicates code from firedrake_configuration in order to avoid the module dependency and allow for installation recovery.
try:
with open(os.path.join(os.environ["VIRTUAL_ENV"],
".configuration.json"), "r") as f:
config = json.load(f)
except FileNotFoundError:
# Fall back to the old location.
import firedrake_configuration
config = firedrake_configuration.get_config()
if config is None:
raise InstallError("Failed to find existing Firedrake configuration")
parser = ArgumentParser(description="""Update this firedrake install to the latest versions of all packages.""",
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument("--no-update-script", action="store_false", dest="update_script",
help="Do not update script before updating Firedrake.")
parser.add_argument("--rebuild", action="store_true",
help="Rebuild all packages even if no new version is available. Usually petsc and petsc4py are only rebuilt if they change. All other packages are always rebuilt.")
parser.add_argument("--rebuild-script", action="store_true",
help="Only rebuild the firedrake-install script. Use this option if your firedrake-install script is broken and a fix has been released in upstream Firedrake. You will need to specify any other options which you wish to be honoured by your new update script.")
parser.add_argument("--slepc", action="store_true", dest="slepc", default=config["options"]["slepc"],
help="Install SLEPc along with PETSc")
parser.add_argument("--opencascade", action="store_true", dest="opencascade", default=config["options"].get("opencascade", False),
help="Install OpenCASCADE for CAD integration.")
parser.add_argument("--tinyasm", action="store_true", dest="tinyasm", default=config["options"].get("tinyasm", False),
help="Install TinyASM as backend for ASMPatchPC.")
parser.add_argument("--torch", const="cpu", nargs='?', choices=["cpu", "cuda"], default=config["options"].get("torch", False),
help="Install PyTorch for a CPU or CUDA backend (default: CPU).")
parser.add_argument("--honour-petsc-dir", action="store_true",
default=config["options"]["honour_petsc_dir"],
help="Usually it is best to let Firedrake build its own PETSc. If you wish to use another PETSc, set PETSC_DIR and pass this option.")
parser.add_argument("--petsc-int-type", choices=["int32", "int64"],
default=config["options"]["petsc_int_type"], type=str,
help="The integer type used by PETSc. Use int64 if you need to solve problems with more than 2 billion degrees of freedom. Only takes effect if firedrake-install builds PETSc.")
parser.add_argument("--honour-pythonpath", action="store_true", default=config["options"].get("honour_pythonpath", False),
help="Pointing to external Python packages is usually a user error. Set this option if you know that you want PYTHONPATH set.")
parser.add_argument("--clean", action='store_true',
help="Delete any remnants of obsolete Firedrake components.")
parser.add_argument("--verbose", "-v", action="store_true", help="Produce more verbose debugging output.")
parser.add_argument("--install", action="append", dest="packages", default=config["options"].get("packages", []),
help="Additional packages to be installed. The address should be in format vcs+protocol://repo_url/#egg=pkg&subdirectory=pkg_dir. Some additional packages have shortcut install options for more information see --install-help.")
parser.add_argument("--pip-install", action="append", dest="pip_packages",
help="Pip install additional packages into the venv")
parser.add_argument("--install-help", action="store_true",
help="Provide information on packages which can be installed using shortcut names.")
parser.add_argument("--cache-dir", type=str,
action="store", default=config["options"].get("cache_dir", ""),
help="Directory to use for disk caches of compiled code (default is the .cache subdirectory of the Firedrake installation).")
complex_group = parser.add_mutually_exclusive_group()
complex_group.add_argument("--complex", action="store_true",
help="Updates to the complex version of Firedrake; rebuilds PETSc in complex mode.")
complex_group.add_argument("--real", action="store_true",
help="Updates to the real version of Firedrake; rebuilds PETSc in real mode.")
parser.add_argument("--documentation-dependencies", action="store_true",
help="Install the dependencies required to build the documentation")
parser.add_argument("--show-dependencies", action="store_true",
help="Print out the package manager used and packages installed/required.")
parser.add_argument("--remove-build-files", action="store_true",
help="Cleans up build artefacts from Firedrake venv. Unless you really cannot spare the disk space, this option is not recommended")
parser.add_argument("--with-blas", default=("download" if osname == "Darwin" else None),
help="Specify path to system BLAS directory. Use '--with-blas=download' to download openblas")
parser.add_argument("--netgen", action="store_true", dest="netgen", default=config["options"].get("netgen", False),
help="Install Netgen.")
args = parser.parse_args()
args.packages = list(set(args.packages)) # remove duplicates
if args.honour_petsc_dir != config["options"]["honour_petsc_dir"]:
log.error("You installed Firedrake with --honour-petsc-dir=%s, but are trying to update it with --honour-petsc-dir=%s." % (config["options"]["honour_petsc_dir"], args.honour_petsc_dir))
exit(1)
if args.honour_petsc_dir:
# Set int_type to the one found in petscconf.h
petsc_int_type = honour_petsc_dir_get_petsc_int_type()
if petsc_int_type != args.petsc_int_type:
petsc_dir, petsc_arch = honour_petsc_dir_get_petsc_dir()
log.warning("Provided PETSc (PETSC_DIR=%s, PETSC_ARCH=%s) was compiled for %s, but given --petsc-int-type = %s: setting --petsc-int-type %s." % (petsc_dir, petsc_arch, petsc_int_type, args.petsc_int_type, petsc_int_type))
args.petsc_int_type = petsc_int_type
petsc_int_type_changed = False
if config["options"]["petsc_int_type"] != args.petsc_int_type:
petsc_int_type_changed = True
args.rebuild = True
if config["options"].get("with_blas") is not None:
if config["options"].get("with_blas") != args.with_blas:
# Rebuild if BLAS library explicitly changed at command line
args.rebuild = True
else:
# Prevent deep_update overwriting BLAS options if they exist in the config, but are unspecified at the command line
args.with_blas = config["options"].get("with_blas")
petsc_complex_type_changed = False
previously_complex = config["options"].get("complex", False)
now_complex = not args.real and (args.complex or previously_complex)
if previously_complex != now_complex:
petsc_complex_type_changed = True
args.rebuild = True
args.complex = now_complex
config = deep_update(config, FiredrakeConfiguration(args))
if args.install_help:
help_string = """
You can install the following packages by passing --install shortname
where shortname is one of the names given below:
"""
componentformat = "|{:10}|{:70}|\n"
header = componentformat.format("Name", "Description")
line = "-" * (len(header) - 1) + "\n"
help_string += line + header + line
for package, d in firedrake_apps.items():
help_string += componentformat.format(package, d[0])
help_string += line
print(help_string)
sys.exit(0)
def sniff_compiler(exe):
"""Obtain the correct compiler class by calling the compiler executable.
Attempt to determine the compiler version number.
:arg cpp: If set to True will use the C++ compiler rather than
the C compiler to determine the version number.
:arg exe: String with name or path to compiler executable
:returns: A compiler class
"""
# NAME
try:
output = subprocess.run(
[exe, "--version"],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
check=True,
encoding="utf-8"
).stdout
except (subprocess.CalledProcessError, UnicodeDecodeError):
output = ""
# Find the name of the compiler family
if output.startswith("gcc") or output.startswith("g++") or output.startswith("GNU"):
name = "GNU"
elif output.startswith("clang"):
name = "clang"
elif output.startswith("Apple LLVM") or output.startswith("Apple clang"):
name = "clang"
elif output.startswith("icc"):
name = "Intel"
elif "Cray" in output.split("\n")[0]:
# Cray is more awkward eg:
# Cray clang version 11.0.4 (<some_hash>)
# gcc (GCC) 9.3.0 20200312 (Cray Inc.)
name = "Cray"
else:
name = "unknown"
# VERSION
version = None
for dumpstring in ["-dumpfullversion", "-dumpversion"]:
try:
output = subprocess.run(
[exe, dumpstring],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
check=True,
encoding="utf-8"
).stdout
version = Version(output)
break
except (subprocess.CalledProcessError, UnicodeDecodeError, InvalidVersion):
continue
return name, version
# Temporary catch for tigerlake processors with gcc/g++/gfortran 9.3
if platform.system() == "Linux" and mode == "install":
# Get the cpu information
try:
cpuinfostring = subprocess.run(
["lscpu"],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
check=True,
encoding="utf-8"
).stdout
except (subprocess.CalledProcessError, UnicodeDecodeError):
output = ""
# Check if it is a tigerlake processor ie: "i3-11", "i5-11", "i7-11"
if any(bad_cpu in cpuinfostring for bad_cpu in ["i3-11", "i5-11", "i7-11"]):
# Get the compiler names and versions
try:
cc = sniff_compiler(args.mpicc or "gcc")
cxx = sniff_compiler(args.mpicxx or "g++")
fortran = sniff_compiler(args.mpif90 or "gfortran")
# Check if the combination is a problem
if any(map(lambda compiler: compiler[0] == "GNU" and compiler[1] < Version("9.4"), [cc, cxx, fortran])):
log.info(
"\nUsing a Tiger Lake (or newer) CPU with gcc, g++ and gfortran version<=9.3 is not possible."
" Please install at least gcc, g++ and gfortran version 9.4.0 or later"
)
sys.exit(1)
except (subprocess.CalledProcessError, FileNotFoundError):
log.info(
"\nFailed to sniff compiler version, perhaps there is no compiler installed.\n"
"You can ignore this if you are not using a Tiger Lake (or newer) CPU with gcc, g++ or gfortran version<=9.3\n"
)
@atexit.register
def print_log_location():
log.info("\n\n%s log saved in %s" % (mode.capitalize(), logfile))
class directory(object):
"""Context manager that executes body in a given directory"""
def __init__(self, dir):
self.dir = os.path.abspath(dir)
def __enter__(self):
self.olddir = os.path.abspath(os.getcwd())
log.debug("Old path '%s'" % self.olddir)
log.debug("Pushing path '%s'" % self.dir)
os.chdir(self.dir)
def __exit__(self, *args):
log.debug("Popping path '%s'" % self.dir)
os.chdir(self.olddir)
log.debug("New path '%s'" % self.olddir)
class environment(object):
def __init__(self, **env):
self.old = os.environ.copy()
self.new = env
def __enter__(self):
os.environ.update(self.new)
def __exit__(self, *args):
os.environ = self.old
options = config["options"]
# Apply short cut package names. pyadjoint shoud no longer turn up the packages list because it is a hard dependency.
options["packages"] = [firedrake_apps.get(p, (None, p))[1] for p in options["packages"] if not p.endswith("pyadjoint")]
# Record of obsolete packages which --clean should remove from old installs.
old_git_packages = ["dolfin-adjoint", "libadjoint"]
if mode == "install":
firedrake_env = os.path.abspath(args.venv_name)
else:
firedrake_env = os.environ["VIRTUAL_ENV"]
if "cache_dir" not in config["options"] or not config["options"]["cache_dir"]:
config["options"]["cache_dir"] = os.path.join(firedrake_env, ".cache")
# venv install
python = "%s/bin/python" % firedrake_env
# Use the pip from the venv
pip = [python, "-m", "pip"]
pipinstall = pip + ["install",
"--no-build-isolation",
"--no-binary", ",".join(wheel_blacklist)]
if mode == "install":
# "petsc4py" is in `branches` when we are explicitly asking for a petsc4py
# branch that lives in firedrake-project/petsc4py. This happens when we do:
# python3 firedrake-install --doi some_old_zenodo_doi ...
# or:
# python3 firedrake-install --package-branch petsc4py some_old_branch ...
use_petsc4py_in_petsc = "petsc4py" not in branches
use_slepc4py_in_slepc = "slepc4py" not in branches
else:
use_petsc4py_in_petsc = True
use_slepc4py_in_slepc = True
# This context manager should be used whenever arguments should be temporarily added to pipinstall.
class pipargs(object):
def __init__(self, *args):
self.args = args
def __enter__(self):
self.save = pipinstall.copy()
pipinstall.extend(self.args)
def __exit__(self, *args, **kwargs):
global pipinstall
pipinstall = self.save
def check_call(arguments):
try:
log.debug("Running command '%s'", " ".join(arguments))
log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode())
except subprocess.CalledProcessError as e:
log.debug(e.output.decode())
raise
def check_output(args):
try:
log.debug("Running command '%s'", " ".join(args))
return subprocess.check_output(args, stderr=subprocess.STDOUT, env=os.environ).decode()
except subprocess.CalledProcessError as e:
log.debug(e.output.decode())
raise
pyinstall = [python, "setup.py", "install"]
if "PYTHONPATH" in os.environ and not args.honour_pythonpath:
quit("""The PYTHONPATH environment variable is set. This is probably an error.
If you really want to use your own Python packages, please run again with the
--honour-pythonpath option.
""")
def brew_gcc_libdir():
brew_gcc_prefix = check_output(["brew", "--prefix", "gcc"])[:-1]
brew_gcc_info = json.loads(check_output(["brew", "info", "--json", "gcc"])[:-1])
gcc_major_version = brew_gcc_info[0]["installed"][0]["version"].split(".")[0]
return brew_gcc_prefix + "/lib/gcc/" + gcc_major_version
# See .github/workflows/docker.yml to see the PETSc options used on CI.
# Edit these as appropriate if PETSc external packages are added or removed.
def get_minimal_petsc_packages():
pkgs = set()
# File format
pkgs.add("hdf5")
# Parallel mesh partitioner
pkgs.add("ptscotch")
# Sparse direct solver
pkgs.add("scalapack") # Needed for mumps
pkgs.add("mumps")
return pkgs
def get_petsc_options(minimal=False):
# The logic in this function is getting out of hand...
petsc_options = {"--with-fortran-bindings=0",
"--with-debugging=0",
"--with-shared-libraries=1",
"--with-c2html=0",
# Parser generator
"--download-bison"}
for pkg in get_minimal_petsc_packages():
petsc_options.add("--download-" + pkg)
if osname == "Darwin":
petsc_options.add("--with-x=0")
# These three lines are used to inspect the MacOS Command Line Tools (CLT) version
cmd = ["pkgutil", "--pkg-info=com.apple.pkg.CLTools_Executables"]
output = subprocess.run(cmd, stdout=subprocess.PIPE, encoding="UTF-8")
clt = {k.strip(): v.strip() for k, v in [line.split(':') for line in output.stdout.split('\n') if line]}
elif osname == "Linux":
# PETSc requires cmake version 3.18.1 or higher.
petsc_options.add("--download-cmake")
if (not options["minimal_petsc"]) and (not minimal):
# Another sparse direct solver
petsc_options.add("--download-superlu_dist")
petsc_options.add("--with-zlib")
# File formats
petsc_options.add("--download-netcdf")
petsc_options.add("--download-pnetcdf")
# Sparse direct solvers
petsc_options.add("--download-suitesparse")
petsc_options.add("--download-pastix")
# Required by pastix
petsc_options.add("--download-hwloc")
if osname == "Darwin":
petsc_options.add("--download-hwloc-configure-arguments=--disable-opencl")
# Serial mesh partitioner
petsc_options.add("--download-metis")
if options.get("with_parmetis", None):
# Non-free license.
petsc_options.add("--download-parmetis")
if options["petsc_int_type"] != "int32":
petsc_options.add("--with-64-bit-indices")
if options["complex"]:
petsc_options.add('--with-scalar-type=complex')
else:
# AMG
petsc_options.add("--download-hypre")
if options.get("mpiexec") is not None:
petsc_options.add("--with-mpiexec={}".format(options["mpiexec"]))
petsc_options.add("--with-cc={}".format(options["mpicc"]))
petsc_options.add("--with-cxx={}".format(options["mpicxx"]))
petsc_options.add("--with-fc={}".format(options["mpif90"]))
else:
# Download mpich if the user does not tell us about an MPI.
petsc_options.add("--download-mpich")
if osname == "Darwin":
petsc_options.add("--download-mpich-configure-arguments=--disable-opencl")
if options.get("with_blas") == "download":
# Download openblas if the user specifies.
petsc_options.add("--download-openblas")
petsc_options.add("--download-openblas-make-options='USE_THREAD=0 USE_LOCKING=1 USE_OPENMP=0'")
if osname == "Darwin":
petsc_options.add("--CFLAGS=-Wno-implicit-function-declaration")
if Version(clt["version"]) >= Version("15"):
# CLT >= 15 requires legacy linking behaviour
petsc_options.add("--LDFLAGS=-Wl,-ld_classic")
elif options.get("with_blas") is not None:
petsc_options.add("--with-blaslapack-dir={}".format(options["with_blas"]))
if osname == "Darwin":
petsc_options.add("--CFLAGS=-I{}/include -Wno-implicit-function-declaration".format(options["with_blas"]))
if Version(clt["version"]) >= Version("15"):
# CLT >= 15 requires legacy linking behaviour
petsc_options.add("--LDFLAGS=-Wl,-ld_classic,-rpath,{0}/lib -L{0}/lib".format(options["with_blas"]))
else:
petsc_options.add("--CFLAGS=-I{}/include".format(options["with_blas"]))
petsc_options.add("--LDFLAGS=-Wl,-rpath,{0}/lib -L{0}/lib".format(options["with_blas"]))
elif osname == "Darwin":
brew_blas_prefix = check_output(["brew", "--prefix", "openblas"])[:-1]
petsc_options.add("--with-blaslapack-dir={}".format(brew_blas_prefix))
petsc_options.add("--CFLAGS=-I{}/include -Wno-implicit-function-declaration".format(brew_blas_prefix))
if Version(clt["version"]) >= Version("15"):
# CLT >= 15 requires legacy linking behaviour
petsc_options.add("--LDFLAGS=-Wl,-ld_classic,-rpath,{0}/lib -L{0}/lib -L{1}".format(brew_blas_prefix, brew_gcc_libdir()))
else:
petsc_options.add("--LDFLAGS=-Wl,-rpath,{0}/lib -L{0}/lib -L{1}".format(brew_blas_prefix, brew_gcc_libdir()))
if not minimal:
for option in shlex.split(os.environ.get("PETSC_CONFIGURE_OPTIONS", "")):
if option.startswith("--with-hdf5-dir"):
petsc_options.discard("--download-hdf5")
os.environ["HDF5_DIR"] = option.replace("--with-hdf5-dir=", "")
petsc_options.add(option)
if "HDF5_DIR" in os.environ and "--download-hdf5" in petsc_options:
del os.environ["HDF5_DIR"]
log.info("\nWarning: HDF5_DIR environment variable set, but ignored; "
"use PETSC_CONFIGURE_OPTIONS=\"--with-hdf5-dir=$HDF5_DIR\" "
"to have PETSc built against $HDF5_DIR.")
return list(petsc_options)
def get_petsc_config():
petsc_dir, petsc_arch = get_petsc_dir()
with open(os.path.join(petsc_dir, petsc_arch, "include", "petscconfiginfo.h")) as fh:
for line in fh.readlines():
if line.startswith("static const char *petscconfigureoptions"):
info = line.split("=", maxsplit=1)[1].strip(' ";\n').split('--')[1:]
break
return ["--" + arg for arg in info]
if mode == "update" and petsc_int_type_changed:
log.warning("""Force rebuilding all packages because PETSc int type changed""")
if mode == "update" and petsc_complex_type_changed:
log.warning("""Force rebuilding all packages because PETSc scalar type changed between real and complex""")
def brew_install(name, options=None):
arguments = [name]
if options:
arguments = options + arguments
if args.verbose:
arguments = ["--verbose"] + arguments
check_call(["brew", "install"] + arguments)
def apt_check(name):
log.info("Checking for presence of package %s..." % name)
# Note that subprocess return codes have the opposite logical
# meanings to those of Python variables.
try:
check_call(["dpkg-query", "-s", name])
log.info(" installed.")
return True
except subprocess.CalledProcessError:
log.info(" missing.")
return False
def apt_install(names):
log.info("Installing missing packages: %s." % ", ".join(names))
if sys.stdin.isatty():
subprocess.check_call(["sudo", "apt-get", "install"] + names)
else:
log.info("Non-interactive stdin detected; installing without prompts")
subprocess.check_call(["sudo", "apt-get", "-y", "install"] + names)
def split_requirements_url(url):
name = url.split(".git")[0].split("#")[0].split("/")[-1]
spliturl = url.split("://")[1].split("#")[0].split("@")
try:
plain_url, branch = spliturl
except ValueError:
plain_url = spliturl[0]
branch = "master"
return name, plain_url, branch
def git_url(plain_url, protocol):
if protocol == "ssh":
return "git@%s:%s" % tuple(plain_url.split("/", 1))
elif protocol == "https":
return "https://%s" % plain_url
else:
raise ValueError("Unknown git protocol: %s" % protocol)
def git_clone(url):
name, plain_url, branch = split_requirements_url(url)
if name == "petsc" and args.honour_petsc_dir:
log.info("Using existing PETSc installation\n")
return name
elif name == "petsc4py" and use_petsc4py_in_petsc:
log.info("Not cloning petsc4py from firedrake-project repo: using petsc4py in PETSc source tree.\n")
return name
log.info("Cloning %s\n" % name)
branch = branches.get(name.lower(), branch)
try:
if options["disable_ssh"]:
raise InstallError("Skipping ssh clone because --disable-ssh")
# note: so far only loopy requires submodule
check_call(["git", "clone", "-q", "--recursive", git_url(plain_url, "ssh")])
log.info("Successfully cloned repository %s" % name)
except (subprocess.CalledProcessError, InstallError):
if not options["disable_ssh"]:
log.warning("Failed to clone %s using ssh, falling back to https." % name)
try:
check_call(["git", "clone", "-q", "--recursive", git_url(plain_url, "https")])
log.info("Successfully cloned repository %s." % name)
except subprocess.CalledProcessError:
log.error("Failed to clone %s branch %s." % (name, branch))
raise
with directory(name):
try:
log.info("Checking out branch %s" % branch)
check_call(["git", "checkout", "-q", branch])
log.info("Successfully checked out branch %s" % branch)
except subprocess.CalledProcessError:
log.error("Failed to check out branch %s" % branch)
raise
try:
log.info("Updating submodules.")
check_call(["git", "submodule", "update", "--recursive"])
log.info("Successfully updated submodules.")
except subprocess.CalledProcessError:
log.error("Failed to update submodules.")
raise
return name
def list_cloned_dependencies(name):
log.info("Finding dependencies of %s\n" % name)
deps = OrderedDict()
try:
for dep in open(name + "/requirements-git.txt", "r"):
name = split_requirements_url(dep.strip())[0]
deps[name] = dep.strip()
except IOError:
pass
return deps
def clone_dependencies(name):
log.info("Cloning the dependencies of %s" % name)
deps = []
try:
for dep in open(name + "/requirements-git.txt", "r"):
deps.append(git_clone(dep.strip()))
except IOError:
pass
return deps
def git_update(name, url=None):
# Update the named git repo and return true if the current branch actually changed.
log.info("Updating the git repository for %s" % name)
with directory(name):
git_sha = check_output(["git", "rev-parse", "HEAD"])
# Ensure remotes get updated if and when we move repositories.
if url:
_, plain_url, branch = split_requirements_url(url)
current_url = check_output(["git", "remote", "-v"]).split()[1]
current_branch = check_output(["git", "rev-parse", "--abbrev-ref", "HEAD"]).strip()
protocol = "https" if current_url.startswith("https") else "ssh"
new_url = git_url(plain_url, protocol)
# Ensure we only change from bitbucket to github and not the reverse.
if (new_url != current_url
and ("bitbucket.org" in current_url)
and ("github.com/firedrakeproject" in plain_url
or "github.com/dolfin-adjoint" in plain_url)):
log.info("Updating git remote for %s" % name)
check_call(["git", "remote", "set-url", "origin", new_url])
# Ensure we only switch loopy branch if loopy is on firedrake and not on a feature branch.
elif name == "loopy" and current_branch != branch and current_branch == "firedrake":
log.info("Updating loopy branch to main")
check_call(["git", "checkout", "-q", branch])
check_call(["git", "pull", "--recurse-submodules"])
git_sha_new = check_output(["git", "rev-parse", "HEAD"])
return git_sha != git_sha_new
def run_pip(args):
check_call(pip + args)
def run_pip_install(pipargs):
# Make pip verbose when logging, so we see what the
# subprocesses wrote out.
# Particularly important for debugging petsc fails.
with environment(**blas):
pipargs = ["-vvv"] + pipargs
check_call(pipinstall + pipargs)