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Merge branch 'master' into gpu
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‎.github/workflows/ci.yml‎

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name: CI
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# Trigger the workflow on push or pull request,
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# but only for the master branch
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on:
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push:
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branches:
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- master
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pull_request:
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branches:
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- master
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jobs:
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test:
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runs-on: ubuntu-latest
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env:
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CC: mpicc
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PETSC_CONFIGURE_OPTIONS: --with-debugging=1
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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- name: Install system dependencies
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shell: bash
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run: |
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sudo apt install \
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build-essential python3-dev git python3-pip libopenmpi-dev \
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openmpi-bin libblas-dev liblapack-dev gfortran
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- name: Set correct Python version
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uses: actions/setup-python@v2
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with:
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python-version: '3.6'
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# xargs is used to force installation of requirements in the order we specified.
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# pip 20.2 needed for loopy install to work.
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- name: Install Python dependencies
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shell: bash
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run: |
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pip install pip==20.2
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xargs -l1 pip install < requirements-ext.txt
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xargs -l1 pip install < requirements-git.txt
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pip install pulp
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pip install -U flake8
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- name: Install PyOP2
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shell: bash
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run: pip install -e .
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- name: Do tests
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shell: bash
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run: |
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make lint
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py.test test -v --tb=native

‎.github/workflows/gh-pages.yml‎

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name: Build Website
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on:
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push:
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branches:
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- master
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jobs:
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gh-pages:
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runs-on: ubuntu-latest
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env:
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CC: mpicc
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PETSC_CONFIGURE_OPTIONS: --with-debugging=1
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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- name: Install system dependencies
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shell: bash
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run: |
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sudo apt install \
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build-essential python3-dev git python3-pip libopenmpi-dev \
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openmpi-bin libblas-dev liblapack-dev gfortran
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- name: Set correct Python version
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uses: actions/setup-python@v2
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with:
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python-version: '3.6'
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# xargs is used to force installation of requirements in the order we specified.
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# pip 20.2 needed for loopy install to work.
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- name: Install Python dependencies
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shell: bash
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run: |
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pip install pip==20.2
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xargs -l1 pip install < requirements-ext.txt
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xargs -l1 pip install < requirements-git.txt
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pip install pulp sphinx
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pip install -U flake8
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- name: Install PyOP2
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shell: bash
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run: pip install -e .
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- name: Build documentation
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shell: bash
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run: make -C doc/sphinx html
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- name: Upload to GitHub Pages
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uses: crazy-max/ghaction-github-pages@v2.2.0
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with:
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build_dir: doc/sphinx/build/html
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jekyll: false
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.mailmap‎

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@@ -16,3 +16,4 @@ Andrew McRae <a.t.t.mcrae@bath.ac.uk> <dorugeber@users.noreply.github.com>
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Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk> <lawrence.mitchell@ed.ac.uk>
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Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk> <wence@gmx.li>
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Kaho Sato <kahosato93@gmail.com>
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Reuben W. Nixon-Hill <reuben.nixon-hill10@imperial.ac.uk> <ReubenHill@users.noreply.github.com>

‎.travis.yml‎

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This file was deleted.

‎AUTHORS‎

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@@ -20,4 +20,4 @@ Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk>
2020
Florian Rathgeber <florian.rathgeber@gmail.com>
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Francis Russell <francis@unchartedbackwaters.co.uk>
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Kaho Sato <kahosato93@gmail.com>
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Reuben W. Hill <reuben.hill10@imperial.ac.uk>
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Reuben W. Nixon-Hill <reuben.nixon-hill10@imperial.ac.uk>

‎doc/sphinx/Makefile‎

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@@ -20,7 +20,6 @@ devhelp epub latex latexpdf text man changes linkcheck doctest gettext apidoc
2020

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help:
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@echo "Please use \`make <target>' where <target> is one of"
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@echo " livehtml to make HTML files and point livereload server at them"
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@echo " html to make standalone HTML files"
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@echo " dirhtml to make HTML files named index.html in directories"
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@echo " singlehtml to make a single large HTML file"
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clean:
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-rm -rf $(BUILDDIR)/*
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livehtml:
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python server.py
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buildhtml:
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$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
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‎doc/sphinx/server.py‎

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‎doc/sphinx/source/conf.py‎

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# Add any Sphinx extension module names here, as strings. They can be extensions
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# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
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extensions = ['sphinx.ext.autodoc', 'sphinx.ext.todo', 'sphinx.ext.pngmath']
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extensions = ['sphinx.ext.autodoc', 'sphinx.ext.todo', 'sphinx.ext.imgmath']
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autodoc_default_flags = ['members', 'undoc-members']
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# Both the class’ and the __init__ method’s docstring are concatenated and
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# inserted into the class definition
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# built documents.
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#
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# The short X.Y version.
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execfile("../../../pyop2/version.py")
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version = '%d.%d' % __version_info__[0:2] # noqa: pulled from pyop2/version.py
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version = '2020.0'
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# The full version, including alpha/beta/rc tags.
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release = __version__ # noqa: pulled from pyop2/version.py
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release = version
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# The language for content autogenerated by Sphinx. Refer to documentation
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# for a list of supported languages.

‎doc/sphinx/source/index.rst‎

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Welcome to PyOP2's documentation!
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=================================
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.. warning::
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The prose documentation contained here is significantly out-of-date and thus
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contains many inaccuracies. It is, nevertheless, quite a useful resource for
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people new to PyOP2. Please read with care.
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The API documentation, however, is updated regularly and can be considered
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accurate.
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Contents:
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.. toctree::

‎pyop2/base.py‎

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self._global = global_
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self._globalset = GlobalSet(comm=self.comm)
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self._name = "gdset_#x%x" % id(self)
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10531054
@classmethod
10541055
def _cache_key(cls, *args):
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13831384
multiplication / division by a scalar.
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"""
13851386

1387+
_zero_kernels = {}
1388+
"""Class-level cache for zero kernels."""
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1390+
_modes = [READ, WRITE, RW, INC, MIN, MAX]
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@cached_property
13871393
def pack(self):
13881394
from pyop2.codegen.builder import DatPack
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return DatPack
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1391-
_modes = [READ, WRITE, RW, INC, MIN, MAX]
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13931397
@validate_type(('dataset', (DataCarrier, DataSet, Set), DataSetTypeError),
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('name', str, NameTypeError))
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@validate_dtype(('dtype', None, DataTypeError))
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loop = loops.get(iterset, None)
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15931597
if loop is None:
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import islpy as isl
1595-
import pymbolic.primitives as p
1596-
1597-
inames = isl.make_zero_and_vars(["i"])
1598-
domain = (inames[0].le_set(inames["i"])) & (inames["i"].lt_set(inames[0] + self.cdim))
1599-
x = p.Variable("dat")
1600-
i = p.Variable("i")
1601-
insn = loopy.Assignment(x.index(i), 0, within_inames=frozenset(["i"]))
1602-
data = loopy.GlobalArg("dat", dtype=self.dtype, shape=(self.cdim,))
1603-
knl = loopy.make_function([domain], [insn], [data], name="zero")
1604-
1605-
knl = Kernel(knl, 'zero')
1598+
try:
1599+
knl = self._zero_kernels[(self.dtype, self.cdim)]
1600+
except KeyError:
1601+
import islpy as isl
1602+
import pymbolic.primitives as p
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inames = isl.make_zero_and_vars(["i"])
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domain = (inames[0].le_set(inames["i"])) & (inames["i"].lt_set(inames[0] + self.cdim))
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x = p.Variable("dat")
1607+
i = p.Variable("i")
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insn = loopy.Assignment(x.index(i), 0, within_inames=frozenset(["i"]))
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data = loopy.GlobalArg("dat", dtype=self.dtype, shape=(self.cdim,))
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knl = loopy.make_function([domain], [insn], [data], name="zero")
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knl = Kernel(knl, 'zero')
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self._zero_kernels[(self.dtype, self.cdim)] = knl
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loop = _make_object('ParLoop', knl,
16071615
iterset,
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self(WRITE))
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34153423
code = code.gencode()
34163424
if isinstance(code, loopy.LoopKernel):
34173425
from loopy.tools import LoopyKeyBuilder
3418-
from pytools.persistent_dict import new_hash
3419-
key_hash = new_hash()
3426+
from hashlib import sha256
3427+
key_hash = sha256()
34203428
code.update_persistent_hash(key_hash, LoopyKeyBuilder())
34213429
code = key_hash.hexdigest()
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hashee = (str(code) + name + str(sorted(opts.items())) + str(include_dirs)

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