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##
# Copyright 2009-2021 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
#
# https://github.com/easybuilders/easybuild
#
# EasyBuild is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation v2.
#
# EasyBuild is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with EasyBuild. If not, see <http://www.gnu.org/licenses/>.
##
"""
EasyBuild support for building and installing numpy, implemented as an easyblock
@author: Stijn De Weirdt (Ghent University)
@author: Dries Verdegem (Ghent University)
@author: Kenneth Hoste (Ghent University)
@author: Pieter De Baets (Ghent University)
@author: Jens Timmerman (Ghent University)
"""
import glob
import os
import re
import tempfile
import easybuild.tools.environment as env
import easybuild.tools.toolchain as toolchain
from easybuild.easyblocks.generic.fortranpythonpackage import FortranPythonPackage
from easybuild.easyblocks.generic.pythonpackage import det_pylibdir
from easybuild.framework.easyconfig import CUSTOM
from easybuild.tools.build_log import EasyBuildError
from easybuild.tools.filetools import change_dir, mkdir, read_file, remove_dir
from easybuild.tools.modules import get_software_root
from easybuild.tools.run import run_cmd
from distutils.version import LooseVersion
class EB_numpy(FortranPythonPackage):
"""Support for installing the numpy Python package as part of a Python installation."""
@staticmethod
def extra_options():
"""Easyconfig parameters specific to numpy."""
extra_vars = ({
'blas_test_time_limit': [500, "Time limit (in ms) for 1000x1000 matrix dot product BLAS test", CUSTOM],
'ignore_test_result': [True, "Run numpy test suite, but ignore test result (only log)", CUSTOM],
})
return FortranPythonPackage.extra_options(extra_vars=extra_vars)
def __init__(self, *args, **kwargs):
"""Initialize numpy-specific class variables."""
super(EB_numpy, self).__init__(*args, **kwargs)
self.sitecfg = None
self.sitecfgfn = 'site.cfg'
self.testinstall = True
def configure_step(self):
"""Configure numpy build by composing site.cfg contents."""
# see e.g. https://github.com/numpy/numpy/pull/2809/files
self.sitecfg = '\n'.join([
"[DEFAULT]",
"library_dirs = %(libs)s",
"include_dirs= %(includes)s",
"search_static_first=True",
])
if get_software_root("imkl"):
if self.toolchain.comp_family() == toolchain.GCC:
# see https://software.intel.com/en-us/articles/numpyscipy-with-intel-mkl,
# section Building with GNU Compiler chain
extrasiteconfig = '\n'.join([
"[mkl]",
"lapack_libs = ",
"mkl_libs = mkl_rt",
])
else:
extrasiteconfig = '\n'.join([
"[mkl]",
"lapack_libs = %(lapack)s",
"mkl_libs = %(blas)s",
])
else:
# [atlas] the only real alternative, even for non-ATLAS BLAS libs (e.g., OpenBLAS, ACML, ...)
# using only the [blas] and [lapack] sections results in sub-optimal builds that don't provide _dotblas.so;
# it does require a CBLAS interface to be available for the BLAS library being used
# e.g. for ACML, the CBLAS module providing a C interface needs to be used
extrasiteconfig = '\n'.join([
"[atlas]",
"atlas_libs = %(lapack)s",
"[lapack]",
"lapack_libs = %(lapack)s", # required by scipy, that uses numpy's site.cfg
])
blas = None
lapack = None
fft = None
if get_software_root("imkl"):
# with IMKL, no spaces and use '-Wl:'
# redefine 'Wl,' to 'Wl:' so that the patch file can do its job
def get_libs_for_mkl(varname):
"""Get list of libraries as required for MKL patch file."""
libs = self.toolchain.variables['LIB%s' % varname].copy()
libs.try_remove(['pthread', 'dl'])
tweaks = {
'prefix': '',
'prefix_begin_end': '-Wl:',
'separator': ',',
'separator_begin_end': ',',
}
libs.try_function_on_element('change', kwargs=tweaks)
libs.SEPARATOR = ','
return str(libs) # str causes list concatenation and adding prefixes & separators
blas = get_libs_for_mkl('BLAS_MT')
lapack = get_libs_for_mkl('LAPACK_MT')
fft = get_libs_for_mkl('FFT')
# make sure the patch file is there
# we check for a typical characteristic of a patch file that cooperates with the above
# not fool-proof, but better than enforcing a particular patch filename
patch_found = False
patch_wl_regex = re.compile(r"replace\(':',\s*','\)")
for patch in self.patches:
# patches are either strings (extension) or dicts (easyblock)
if isinstance(patch, dict):
patch = patch['path']
if patch_wl_regex.search(read_file(patch)):
patch_found = True
break
if not patch_found:
raise EasyBuildError("Building numpy on top of Intel MKL requires a patch to "
"handle -Wl linker flags correctly, which doesn't seem to be there.")
else:
# unless Intel MKL is used, $ATLAS should be set to take full control,
# and to make sure a fully optimized version is built, including _dotblas.so
# which is critical for decent performance of the numpy.dot (matrix dot product) function!
env.setvar('ATLAS', '1')
lapack = ', '.join([x for x in self.toolchain.get_variable('LIBLAPACK_MT', typ=list) if x != "pthread"])
fft = ', '.join(self.toolchain.get_variable('LIBFFT', typ=list))
libs = ':'.join(self.toolchain.get_variable('LDFLAGS', typ=list))
includes = ':'.join(self.toolchain.get_variable('CPPFLAGS', typ=list))
# CBLAS is required for ACML, because it doesn't offer a C interface to BLAS
if get_software_root('ACML'):
cblasroot = get_software_root('CBLAS')
if cblasroot:
lapack = ', '.join([lapack, "cblas"])
cblaslib = os.path.join(cblasroot, 'lib')
# with numpy as extension, CBLAS might not be included in LDFLAGS because it's not part of a toolchain
if cblaslib not in libs:
libs = ':'.join([libs, cblaslib])
else:
raise EasyBuildError("CBLAS is required next to ACML to provide a C interface to BLAS, "
"but it's not loaded.")
if fft:
extrasiteconfig += "\n[fftw]\nlibraries = %s" % fft
suitesparseroot = get_software_root('SuiteSparse')
if suitesparseroot:
amddir = os.path.join(suitesparseroot, 'AMD')
umfpackdir = os.path.join(suitesparseroot, 'UMFPACK')
if not os.path.exists(amddir) or not os.path.exists(umfpackdir):
raise EasyBuildError("Expected SuiteSparse subdirectories are not both there: %s, %s",
amddir, umfpackdir)
else:
extrasiteconfig += '\n'.join([
"[amd]",
"library_dirs = %s" % os.path.join(amddir, 'Lib'),
"include_dirs = %s" % os.path.join(amddir, 'Include'),
"amd_libs = amd",
"[umfpack]",
"library_dirs = %s" % os.path.join(umfpackdir, 'Lib'),
"include_dirs = %s" % os.path.join(umfpackdir, 'Include'),
"umfpack_libs = umfpack",
])
self.sitecfg = '\n'.join([self.sitecfg, extrasiteconfig])
self.sitecfg = self.sitecfg % {
'blas': blas,
'lapack': lapack,
'libs': libs,
'includes': includes,
}
super(EB_numpy, self).configure_step()
# check configuration (for debugging purposes)
cmd = "%s setup.py config" % self.python_cmd
run_cmd(cmd, log_all=True, simple=True)
def test_step(self):
"""Run available numpy unit tests, and more."""
# determine command to use to run numpy test suite,
# and whether test results should be ignored or not
if self.cfg['ignore_test_result']:
test_code = 'numpy.test(verbose=2)'
else:
if LooseVersion(self.version) >= LooseVersion('1.15'):
# Numpy 1.15+ returns a True on success. Hence invert to get a failure value
test_code = 'sys.exit(not numpy.test(verbose=2))'
else:
# Return value is a TextTestResult. Check the errors member for any error
test_code = 'sys.exit(len(numpy.test(verbose=2).errors) > 0)'
# Prepend imports
test_code = "import sys; import numpy; " + test_code
# LDFLAGS should not be set when testing numpy/scipy, because it overwrites whatever numpy/scipy sets
# see http://projects.scipy.org/numpy/ticket/182
self.testcmd = "unset LDFLAGS && cd .. && %%(python)s -c '%s'" % test_code
super(EB_numpy, self).test_step()
# temporarily install numpy, it doesn't alow to be used straight from the source dir
tmpdir = tempfile.mkdtemp()
abs_pylibdirs = [os.path.join(tmpdir, pylibdir) for pylibdir in self.all_pylibdirs]
for pylibdir in abs_pylibdirs:
mkdir(pylibdir, parents=True)
pythonpath = "export PYTHONPATH=%s &&" % os.pathsep.join(abs_pylibdirs + ['$PYTHONPATH'])
cmd = self.compose_install_command(tmpdir, extrapath=pythonpath)
run_cmd(cmd, log_all=True, simple=True, verbose=False)
try:
pwd = os.getcwd()
os.chdir(tmpdir)
except OSError as err:
raise EasyBuildError("Faild to change to %s: %s", tmpdir, err)
# evaluate performance of numpy.dot (3 runs, 3 loops each)
size = 1000
cmd = ' '.join([
pythonpath,
'%s -m timeit -n 3 -r 3' % self.python_cmd,
'-s "import numpy; x = numpy.random.random((%(size)d, %(size)d))"' % {'size': size},
'"numpy.dot(x, x.T)"',
])
(out, ec) = run_cmd(cmd, simple=False)
self.log.debug("Test output: %s" % out)
# fetch result
time_msec = None
msec_re = re.compile(r"\d+ loops, best of \d+: (?P<time>[0-9.]+) msec per loop")
res = msec_re.search(out)
if res:
time_msec = float(res.group('time'))
else:
sec_re = re.compile(r"\d+ loops, best of \d+: (?P<time>[0-9.]+) sec per loop")
res = sec_re.search(out)
if res:
time_msec = 1000 * float(res.group('time'))
elif self.dry_run:
# use fake value during dry run
time_msec = 123
self.log.warning("Using fake value for time required for %dx%d matrix dot product under dry run: %s",
size, size, time_msec)
else:
raise EasyBuildError("Failed to determine time for numpy.dot test run.")
# make sure we observe decent performance
if time_msec < self.cfg['blas_test_time_limit']:
self.log.info("Time for %dx%d matrix dot product: %d msec < %d msec => OK",
size, size, time_msec, self.cfg['blas_test_time_limit'])
else:
raise EasyBuildError("Time for %dx%d matrix dot product: %d msec >= %d msec => ERROR",
size, size, time_msec, self.cfg['blas_test_time_limit'])
try:
os.chdir(pwd)
remove_dir(tmpdir)
except OSError as err:
raise EasyBuildError("Failed to change back to %s: %s", pwd, err)
def install_step(self):
"""Install numpy and remove numpy build dir, so scipy doesn't find it by accident."""
super(EB_numpy, self).install_step()
builddir = os.path.join(self.builddir, "numpy")
try:
if os.path.isdir(builddir):
os.chdir(self.builddir)
remove_dir(builddir)
else:
self.log.debug("build dir %s already clean" % builddir)
except OSError as err:
raise EasyBuildError("Failed to clean up numpy build dir %s: %s", builddir, err)
def run(self):
"""Install numpy as an extension"""
super(EB_numpy, self).run()
return self.make_module_extra_numpy_include()
def sanity_check_step(self, *args, **kwargs):
"""Custom sanity check for numpy."""
# can't use self.pylibdir here, need to determine path on the fly using currently active 'python' command;
# this is important for numpy installations for multiple Python version (via multi_deps)
custom_paths = {
'files': [],
'dirs': [det_pylibdir()],
}
custom_commands = []
if LooseVersion(self.version) >= LooseVersion("1.10"):
# generic check to see whether numpy v1.10.x and up was built against a CBLAS-enabled library
# cfr. https://github.com/numpy/numpy/issues/6675#issuecomment-162601149
blas_check_pytxt = '; '.join([
"import sys",
"import numpy",
"blas_ok = 'HAVE_CBLAS' in dict(numpy.__config__.blas_opt_info['define_macros'])",
"sys.exit((1, 0)[blas_ok])",
])
custom_commands.append('python -c "%s"' % blas_check_pytxt)
else:
# _dotblas is required for decent performance of numpy.dot(), but only there in numpy 1.9.x and older
custom_commands.append("python -c 'import numpy.core._dotblas'")
return super(EB_numpy, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)
def make_module_extra_numpy_include(self):
"""
Return update statements for $CPATH specifically for numpy
"""
numpy_core_subdir = os.path.join('numpy', 'core')
numpy_core_dirs = []
cwd = change_dir(self.installdir)
for pylibdir in self.all_pylibdirs:
numpy_core_dirs.extend(glob.glob(os.path.join(pylibdir, numpy_core_subdir)))
numpy_core_dirs.extend(glob.glob(os.path.join(pylibdir, 'numpy*.egg', numpy_core_subdir)))
change_dir(cwd)
txt = ''
for numpy_core_dir in numpy_core_dirs:
txt += self.module_generator.prepend_paths('CPATH', os.path.join(numpy_core_dir, 'include'))
for lib_env_var in ('LD_LIBRARY_PATH', 'LIBRARY_PATH'):
txt += self.module_generator.prepend_paths(lib_env_var, os.path.join(numpy_core_dir, 'lib'))
return txt
def make_module_extra(self):
"""
Add additional update statements in module file specific to numpy
"""
txt = super(EB_numpy, self).make_module_extra()
txt += self.make_module_extra_numpy_include()
return txt