From afd3462338afa4f86794431a3be484ee9260d76b Mon Sep 17 00:00:00 2001
From: Martin Bauer <martin.bauer@fau.de>
Date: Thu, 1 Feb 2018 10:05:02 +0100
Subject: [PATCH] Ported most of the tutorials/demos/benchmarks
---
datahandling/datahandling_interface.py | 3 ++-
datahandling/parallel_datahandling.py | 8 ++++++--
datahandling/serial_datahandling.py | 18 +++++++-----------
jupytersetup.py | 4 ++++
slicing.py | 8 ++++++++
5 files changed, 27 insertions(+), 14 deletions(-)
diff --git a/datahandling/datahandling_interface.py b/datahandling/datahandling_interface.py
index b2faa156c..2a537206d 100644
--- a/datahandling/datahandling_interface.py
+++ b/datahandling/datahandling_interface.py
@@ -102,7 +102,7 @@ class DataHandling(ABC):
"""
@abstractmethod
- def gatherArray(self, name, sliceObj=None, allGather=False):
+ def gatherArray(self, name, sliceObj=None, allGather=False, ghostLayers=False):
"""
Gathers part of the domain on a local process. Whenever possible use 'access' instead, since this method copies
the distributed data to a single process which is inefficient and may exhaust the available memory
@@ -110,6 +110,7 @@ class DataHandling(ABC):
:param name: name of the array to gather
:param sliceObj: slice expression of the rectangular sub-part that should be gathered
:param allGather: if False only the root process receives the result, if True all processes
+ :param ghostLayers: number of outer ghost layers to include (only available for serial data handlings)
:return: gathered field that does not include any ghost layers, or None if gathered on another process
"""
diff --git a/datahandling/parallel_datahandling.py b/datahandling/parallel_datahandling.py
index d8d558cdc..08000b8b2 100644
--- a/datahandling/parallel_datahandling.py
+++ b/datahandling/parallel_datahandling.py
@@ -4,7 +4,7 @@ from pystencils.datahandling.datahandling_interface import DataHandling
from pystencils.parallel.blockiteration import slicedBlockIteration, blockIteration
from pystencils.utils import DotDict
import waLBerla as wlb
-
+import warnings
class ParallelDataHandling(DataHandling):
GPU_DATA_PREFIX = "gpu_"
@@ -152,7 +152,11 @@ class ParallelDataHandling(DataHandling):
else:
yield from blockIteration(self.blocks, ghostLayers, self.dim, prefix)
- def gatherArray(self, name, sliceObj=None, allGather=False):
+ def gatherArray(self, name, sliceObj=None, allGather=False, ghostLayers=False):
+ if ghostLayers is not False:
+ warnings.warn("gatherArray with ghost layers is only supported in serial datahandling. "
+ "Array without ghost layers is returned")
+
if sliceObj is None:
sliceObj = tuple([slice(None, None, None)] * self.dim)
if self.dim == 2:
diff --git a/datahandling/serial_datahandling.py b/datahandling/serial_datahandling.py
index 1662462a8..d422e76a6 100644
--- a/datahandling/serial_datahandling.py
+++ b/datahandling/serial_datahandling.py
@@ -16,13 +16,6 @@ except ImportError:
class SerialDataHandling(DataHandling):
- class _PassThroughContextManager:
- def __init__(self, arr):
- self.arr = arr
-
- def __enter__(self, *args, **kwargs):
- return self.arr
-
def __init__(self, domainSize, defaultGhostLayers=1, defaultLayout='SoA', periodicity=False):
"""
Creates a data handling for single node simulations
@@ -98,7 +91,6 @@ class SerialDataHandling(DataHandling):
indexDimensions = 0
layoutTuple = spatialLayoutStringToTuple(layout, self.dim)
-
# cpuArr is always created - since there is no createPycudaArrayWithLayout()
cpuArr = createNumpyArrayWithLayout(layout=layoutTuple, **kwargs)
if cpu:
@@ -162,11 +154,15 @@ class SerialDataHandling(DataHandling):
offset = tuple(s.start - ghostLayers for s in sliceObj)
yield SerialBlock(iterDict, offset, sliceObj)
- def gatherArray(self, name, sliceObj=None, **kwargs):
- gls = self._fieldInformation[name]['ghostLayers']
+ def gatherArray(self, name, sliceObj=None, ghostLayers=False, **kwargs):
+ glToRemove = self._fieldInformation[name]['ghostLayers']
+ if isinstance(ghostLayers, int):
+ glToRemove -= ghostLayers
+ if ghostLayers is True:
+ glToRemove = 0
arr = self.cpuArrays[name]
indDimensions = self.fields[name].indexDimensions
- arr = removeGhostLayers(arr, indexDimensions=indDimensions, ghostLayers=gls)
+ arr = removeGhostLayers(arr, indexDimensions=indDimensions, ghostLayers=glToRemove)
if sliceObj is not None:
sliceObj = normalizeSlice(sliceObj, arr.shape[:-indDimensions] if indDimensions > 0 else arr.shape)
diff --git a/jupytersetup.py b/jupytersetup.py
index f390c9c4b..1e46d707c 100644
--- a/jupytersetup.py
+++ b/jupytersetup.py
@@ -4,6 +4,7 @@ from IPython.display import HTML
from tempfile import NamedTemporaryFile
import base64
from IPython import get_ipython
+import sympy as sp
def log_progress(sequence, every=None, size=None, name='Items'):
@@ -176,4 +177,7 @@ def setDisplayMode(mode):
ipython = get_ipython()
if ipython:
setDisplayMode('imageupdate')
+ ipython.magic("config InlineBackend.rc = { }")
ipython.magic("matplotlib inline")
+ plt.rc('figure', figsize=(16, 6))
+ sp.init_printing()
diff --git a/slicing.py b/slicing.py
index f22ad411b..200cb0305 100644
--- a/slicing.py
+++ b/slicing.py
@@ -9,6 +9,14 @@ class SliceMaker(object):
makeSlice = SliceMaker()
+class SlicedGetter(object):
+ def __init__(self, functionReturningArray):
+ self._functionReturningArray = functionReturningArray
+
+ def __getitem__(self, item):
+ return self._functionReturningArray(item)
+
+
def normalizeSlice(slices, sizes):
"""Converts slices with floating point and/or negative entries to integer slices"""
--
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