diff --git a/LICENSE b/LICENSE index 3976164f..b9cce6c1 100644 --- a/LICENSE +++ b/LICENSE @@ -1,13 +1,185 @@ -Copyright 2022 Akash Dhruv - -Licensed under the Apache License, Version 2.0 (the "License"); -you may not use this file except in compliance with the License. -You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an "AS IS" BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. +Apache Open-Source License + +Version 2.0, January 2004 + + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS + + + +**************************************************************************************************** +DISCLAIMER + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +************************************************************************************************* diff --git a/NOTICE b/NOTICE new file mode 100644 index 00000000..025a347b --- /dev/null +++ b/NOTICE @@ -0,0 +1,20 @@ +Copyright © 2023 Akash Dhruv and UChicago Argonne, LLC All right reserved + +Title: BoxKit + +By: Argonne National Laboratory ARGONNE NATIONAL LABORATORY, WITH A +FACILITY IN THE STATE OF ILLINOIS, IS OWNED BY THE UNITED STATES +GOVERNMENT, AND OPERATED BY UCHICAGO ARGONNE, LLC UNDER PROVISION OF A +CONTRACT WITH THE DEPARTMENT OF ENERGY. + +Licensed under the Apache License, Version 2.0 (the "License"). A copy +of the License is included in the file LICENSE. You may also obtain a +copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. diff --git a/boxkit/api/_read.py b/boxkit/api/_read.py index 41881b67..77150fe7 100644 --- a/boxkit/api/_read.py +++ b/boxkit/api/_read.py @@ -13,6 +13,8 @@ def read_dataset( force_memmap=False, nthreads=1, backend="serial", + monitor=False, + batch="auto", ): # pylint: disable=too-many-arguments disable=too-many-locals """ Create a dataset from a file @@ -28,6 +30,14 @@ def read_dataset( server : server dictionary + force_memamp : flag + + nthreads : integer + + backend : string parameter for parallel backend + + monitor : flag + (see tests/boiling.py and tests/heater.py for references) Returns @@ -41,7 +51,9 @@ def read_dataset( if not storage: storage = "numpy-memmap" - data_attributes, block_attributes = resources.read.options[source](filename, server) + data_attributes, block_attributes = resources.read.options[source]( + filename, server, nthreads, batch, monitor, backend + ) data = library.Data(storage=storage, **data_attributes) blocklist = [library.Block(data, **attributes) for attributes in block_attributes] diff --git a/boxkit/library/_block.py b/boxkit/library/_block.py index 7159624e..f3ba17cb 100644 --- a/boxkit/library/_block.py +++ b/boxkit/library/_block.py @@ -5,22 +5,26 @@ class Block: # pylint: disable=too-many-instance-attributes - """Default class for a Block. + """ + Class for storing block metadata Parameters ---------- - data : data object - attributes : dictionary - { 'dx' : grid spacing in x dir - 'dy' : grid spacing in y dir - 'dz' : grid spacing in z dir - 'xmin' : low bound in x dir - 'ymin' : low bound in y dir - 'zmin' : low bound in z dir - 'xmax' : high bound in x dir - 'ymax' : high bound in y dir - 'zmax' : high bound in z dir - 'tag' : block ID } + data : Boxkit Data object + attributes : Dictionary of attributes + + .. code-block:: + + 'dx' : grid spacing x direction + 'dy' : grid spacing y direction + 'dz' : grid spacing z direction + 'xmin' : low bound x direction + 'ymin' : low bound y direction + 'zmin' : low bound z direction + 'xmax' : high bound x direction + 'ymax' : high bound y direction + 'zmax' : high bound z direction + 'tag' : block ID """ type_ = "default" diff --git a/boxkit/library/_data.py b/boxkit/library/_data.py index a1cf5681..5d16caac 100644 --- a/boxkit/library/_data.py +++ b/boxkit/library/_data.py @@ -29,28 +29,32 @@ class Data(_DataBase): # pylint: disable=too-many-instance-attributes - """Default class to store data""" + """ + Class to store handles for physical data + + Parameters + ---------- + attributes : Dictionary of attributes + .. code-block:: + + 'nblocks' : total number of blocks, + 'nxb' : number of grid points per block x direction, + 'nyb' : number of grid points per block y direction, + 'nzb' : number of grid points per block z direction, + 'xguard' : number of guard cells x direction, + 'yguard' : number of guard cells y direction, + 'zguard' : number of guard cells z direction, + 'inputfile' : hdf5 inputfile default (None), + 'remotefile': sftp remote file default (None), + 'variables' : dictionary of variables default ({}), + 'storage' : ('numpy', 'zarr', 'dask', 'pyarrow') + """ type_ = "default" def __init__(self, **attributes): - """Initialize the class object - - Parameters - ---------- - attributes : dictionary - { 'nblocks' : total number of blocks, - 'nxb' : number of grid points per block in x dir, - 'nyb' : number of grid points per block in y dir, - 'nzb' : number of grid points per block in z dir, - 'xguard' : number of guard cells in x dir, - 'yguard' : number of guard cells in y dir, - 'zguard' : number of guard cells in z dir, - 'inputfile' : hdf5 inputfile default (None), - 'remotefile': sftp remote file default (None), - 'variables' : dictionary of variables default ({}), - 'storage' : ('numpy', 'zarr', 'dask', 'pyarrow')} - """ + """Initialize the class object""" + super().__init__() self.nblocks = 1 diff --git a/boxkit/resources/read/_flash.py b/boxkit/resources/read/_flash.py index f9916882..a8389df2 100644 --- a/boxkit/resources/read/_flash.py +++ b/boxkit/resources/read/_flash.py @@ -3,8 +3,12 @@ import h5py import h5pickle +from boxkit.library import Action -def read_flash(filename, server): + +def read_flash( + filename, server, nthreads, batch, monitor, backend +): # pylint: disable=too-many-locals disable=too-many-arguments """ Read dataset from FLASH output file @@ -59,32 +63,51 @@ def read_flash(filename, server): "variables": variables, } + get_blk_attributes.nthreads = nthreads + get_blk_attributes.backend = backend + get_blk_attributes.batch = batch + get_blk_attributes.monitor = monitor + # Create block attributes - block_attributes = [ - { - "dx": inputfile["block size"][lblock][0] / nxb, - "dy": ( - 1.0 - if inputfile["block size"][lblock][1] == 0.0 - else inputfile["block size"][lblock][1] / nyb - ), - "dz": ( - 1.0 - if inputfile["block size"][lblock][2] == 0.0 - else inputfile["block size"][lblock][2] / nzb - ), - "xmin": inputfile["bounding box"][lblock][0][0], - "ymin": inputfile["bounding box"][lblock][1][0], - "zmin": inputfile["bounding box"][lblock][2][0], - "xmax": inputfile["bounding box"][lblock][0][1], - "ymax": inputfile["bounding box"][lblock][1][1], - "zmax": inputfile["bounding box"][lblock][2][1], - "tag": lblock, - "level": inputfile["refine level"][lblock], - "leaf": bool(inputfile["node type"][lblock] == 1), - "inputproc": inputfile["processor number"][lblock], - } - for lblock in range(nblocks) - ] + block_attributes = get_blk_attributes( + (lblock for lblock in range(nblocks)), inputfile, nxb, nyb, nzb + ) return data_attributes, block_attributes + + +@Action +def get_blk_attributes(lblock, inputfile, nxb, nyb, nzb): + """ + lblock: block number + inputfile: HDF5 file handle + + Returns + ------- + block_dict + """ + block_dict = { + "dx": inputfile["block size"][lblock][0] / nxb, + "dy": ( + 1.0 + if inputfile["block size"][lblock][1] == 0.0 + else inputfile["block size"][lblock][1] / nyb + ), + "dz": ( + 1.0 + if inputfile["block size"][lblock][2] == 0.0 + else inputfile["block size"][lblock][2] / nzb + ), + "xmin": inputfile["bounding box"][lblock][0][0], + "ymin": inputfile["bounding box"][lblock][1][0], + "zmin": inputfile["bounding box"][lblock][2][0], + "xmax": inputfile["bounding box"][lblock][0][1], + "ymax": inputfile["bounding box"][lblock][1][1], + "zmax": inputfile["bounding box"][lblock][2][1], + "tag": lblock, + "level": inputfile["refine level"][lblock], + "leaf": bool(inputfile["node type"][lblock] == 1), + "inputproc": inputfile["processor number"][lblock], + } + + return block_dict diff --git a/boxkit/resources/read/_sample.py b/boxkit/resources/read/_sample.py index 196c99f1..67d2626d 100644 --- a/boxkit/resources/read/_sample.py +++ b/boxkit/resources/read/_sample.py @@ -3,7 +3,9 @@ import h5pickle as h5py -def read_test_sample(filename, server): # pylint: disable=too-many-locals +def read_test_sample( + filename, server, nthreads, batch, monitor, backend +): # pylint: disable=too-many-locals disable=too-many-arguments disable=unused-argument """ Read dataset from BoxKit test sample diff --git a/docs/boxkit.library._block.html b/docs/boxkit.library._block.html index 49070bf4..8064b860 100644 --- a/docs/boxkit.library._block.html +++ b/docs/boxkit.library._block.html @@ -86,23 +86,23 @@
class boxkit.library._block.Block(data=None, **attributes)

Bases: object

-

Default class for a Block.

+

Class for storing block metadata

Parameters
    -

  • data (data object) –

    • -

  • attributes (dictionary) –

    -
    { ‘dx’grid spacing in x dir

    ’dy’ : grid spacing in y dir -‘dz’ : grid spacing in z dir -‘xmin’ : low bound in x dir -‘ymin’ : low bound in y dir -‘zmin’ : low bound in z dir -‘xmax’ : high bound in x dir -‘ymax’ : high bound in y dir -‘zmax’ : high bound in z dir -‘tag’ : block ID }

    -
    -
    +

  • data (Boxkit Data object) –

    • +

  • attributes (Dictionary of attributes) – 

    'dx'   : grid spacing x direction
+'dy'   : grid spacing y direction
+'dz'   : grid spacing z direction
+'xmin' : low  bound x direction
+'ymin' : low  bound y direction
+'zmin' : low  bound z direction
+'xmax' : high bound x direction
+'ymax' : high bound y direction
+'zmax' : high bound z direction
+'tag'  : block ID
+
    +

diff --git a/docs/boxkit.library._data.html b/docs/boxkit.library._data.html index 8da92f62..1db0d9c5 100644 --- a/docs/boxkit.library._data.html +++ b/docs/boxkit.library._data.html @@ -86,7 +86,25 @@
class boxkit.library._data.Data(**attributes)

Bases: boxkit.cbox.lib.library.Data

-

Default class to store data

+

Class to store handles for physical data

+
+
Parameters
+

attributes (Dictionary of attributes) – 

'nblocks'   : total number of blocks,
+'nxb'       : number of grid points per block x direction,
+'nyb'       : number of grid points per block y direction,
+'nzb'       : number of grid points per block z direction,
+'xguard'    : number of guard cells x direction,
+'yguard'    : number of guard cells y direction,
+'zguard'    : number of guard cells z direction,
+'inputfile' : hdf5 inputfile default (None),
+'remotefile': sftp remote file default (None),
+'variables' : dictionary of variables default ({}),
+'storage'   : ('numpy', 'zarr', 'dask', 'pyarrow')
+
+
+

+
+
_create_dask_objects()
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BoxKit","boxkit package","boxkit.api package","boxkit.api._create module","boxkit.api._mean module","boxkit.api._mergeblocks module","boxkit.api._read module","boxkit.api._regionprops module","boxkit.api._resfilter module","boxkit.library package","boxkit.library._action module","boxkit.library._block module","boxkit.library._data module","boxkit.library._dataset module","boxkit.library._execute module","boxkit.library._monitor module","boxkit.library._region module","boxkit.library._resources module","boxkit.library._server module","boxkit.library._slice module","boxkit.library._timer module","boxkit.resources package","boxkit.resources.read package","boxkit.resources.read._flash module","boxkit.resources.read._sample module","Welcome to BoxKit\u2019s documentation!","Astrophysics Example 1","Pool Boiling Gravity"],titleterms:{"0":[],"1":26,"25m_3d_32km_hdf5_plt_cnt_1000":[],"8x8x8":[],"90200":[],"import":[],In:[],The:[],_action:10,_block:11,_creat:3,_data:12,_dataset:13,_execut:14,_flash:23,_mean:4,_mergeblock:5,_monitor:15,_read:6,_region:16,_regionprop:7,_resfilt:8,_resourc:17,_sampl:24,_server:18,_slice:19,_timer:20,after:[],along:[],api:[2,3,4,5,6,7,8],ar:[],astrophys:26,block:[],boil:27,boxkit:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25],can:[],citat:0,contain:[],content:25,contribut:0,creat:[],data:[],dataset:[],dimension:[],document:25,each:[],environ:[],exampl:26,extract:[],file:[],flash:[],from:[],graviti:27,hdf5:[],help:0,icon:0,indic:25,inform:[],instal:0,kei:[],librari:[9,10,11,12,13,14,15,16,17,18,19,20],list:[],locat:[],loop:[],modul:[3,4,5,6,7,8,10,11,12,13,14,15,16,17,18,19,20,23,24],next:[],now:[],output:[],over:[],overview:0,packag:[1,2,9,21,22],pars:[],perform:[],pool:27,print:[],probe:[],python:[],read:[22,23,24],requir:[],resourc:[21,22,23,24],right:[],s:25,simpl:[],simul:[],size:[],slice:[],statement:[],step:[],submodul:[2,9,22],subpackag:[1,21],support:0,tabl:25,test:0,thi:[],three:[],tutori:0,us:[],usag:0,variabl:[],we:[],welcom:25,work:[],x:[],y:[]}}) \ No newline at end of file diff --git a/paper/paper.md b/paper/paper.md index e7cdf9a6..2280adc0 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -120,7 +120,9 @@ packages available in Python shown by dotted lines in \autoref{fig:workflow}. # Acknowledgements -We acknowledge contributions from Laboratory Directed Research and Development -(LDRD) program supported by Argonne National Laboratory [@argonne]. +This material is based upon work supported by Laboratory Directed Research +and Development (LDRD) funding from Argonne National Laboratory, provided by +the Director, Office of Science, of the U.S. Department of Energy under Contract +No. DE-AC02-06CH11357. # References diff --git a/tests/sedona/__main__.py b/tests/sedona/__main__.py index b0b86937..6c2abc99 100644 --- a/tests/sedona/__main__.py +++ b/tests/sedona/__main__.py @@ -5,7 +5,7 @@ def main(): - tests = ["boiling", "heater", "application"] + tests = ["boiling", "heater", "application", "astrophysics"] suite = unittest.TestSuite() diff --git a/tests/sedona/astrophysics.py b/tests/sedona/astrophysics.py new file mode 100644 index 00000000..1f71a24f --- /dev/null +++ b/tests/sedona/astrophysics.py @@ -0,0 +1,72 @@ +"""Tests for `boxkit/api`.""" + +import os +import time +import unittest +import pymorton +import numpy +import boxkit +from boxkit.library import Monitor, Timer + + +class TestAstrophysics(unittest.TestCase): + """boxkit unit test for 3D astrophysics data""" + + def setUp(self): + """ + Setup test parameters + + timestart : tag start time + basedir : base directory of the input data + filetags : list of file tags + prefix : prefix for input file + filenames : list of filenames generated from basedir, prefix and filetags + + """ + print( + f"\n-------------------------Running: {self.id()}-------------------------\n" + ) + self.timer = Timer(self.id()) + + basedir = ( + os.getenv("HOME") + "/Box/Jarvis-DataShare/Bubble-Box-Sample/astrophysics/" + ) + filetags = [1000] + prefix = "25m_3d_32km_hdf5_plt_cnt_" + self.filenames = [ + "".join([basedir, prefix, str(filetag).zfill(4)]) for filetag in filetags + ] + + # def test_read_nthreads_4_3D(self): + # """ + # Test read dataset with 4 threads + # """ + # dataframes = [ + # boxkit.read_dataset( + # filename, source="flash", nthreads=4, backend="loky", monitor=True + # ) + # for filename in self.filenames + # ] + # for dataset in dataframes: + # dataset.purge() + + def test_read_nthreads_12_3D(self): + """ + Test read dataset with 12 threads + """ + dataframes = [ + boxkit.read_dataset( + filename, source="flash", nthreads=12, backend="loky", monitor=True + ) + for filename in self.filenames + ] + for dataset in dataframes: + dataset.purge() + + def tearDown(self): + """Clean up and timing""" + del self.timer + + +if __name__ == "__main__": + unittest.main()