Development

NOTICE

@@ -1,6 +1,6 @@
 Copyright (c) 2023 UChicago Argonne, LLC and contributors. All rights reserved.
 
-Title: BoxKit (SF-23-0)
+Title: BoxKit (SF-23-067)
 
 By: Argonne National Laboratory ARGONNE NATIONAL LABORATORY, WITH A
 FACILITY IN THE STATE OF ILLINOIS, IS OWNED BY THE UNITED STATES

boxkit/__meta__.py

@@ -1,7 +1,7 @@
 """Metadata for BoxKit package"""
 
 __pkgname__ = "BoxKit"
-__version__ = "2023.06.5"
+__version__ = "2023.06.7"
 __authors__ = "Akash Dhruv"
 __license__ = "Apache License"
 __copyright__ = "Copyright (c) Akash Dhruv 2023. All Rights Reserved."

boxkit/resources/read/_flash.py

@@ -70,14 +70,24 @@ def read_flash(
 
     # Create block attributes
     block_attributes = get_blk_attributes(
-        (lblock for lblock in range(nblocks)), inputfile, nxb, nyb, nzb
+        (lblock for lblock in range(nblocks)),
+        inputfile["block size"][:],
+        inputfile["bounding box"][:],
+        inputfile["refine level"][:],
+        inputfile["node type"][:],
+        inputfile["processor number"][:],
+        nxb,
+        nyb,
+        nzb,
     )
 
     return data_attributes, block_attributes
 
 
 @Action
-def get_blk_attributes(lblock, inputfile, nxb, nyb, nzb):
+def get_blk_attributes(
+    lblock, block_size, bounding_box, refine_level, node_type, proc_num, nxb, nyb, nzb
+):  # pylint: disable=too-many-arguments
     """
     lblock: block number
     inputfile: HDF5 file handle
@@ -87,27 +97,19 @@ def get_blk_attributes(lblock, inputfile, nxb, nyb, nzb):
     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],
+        "dx": block_size[lblock][0] / nxb,
+        "dy": (1.0 if block_size[lblock][1] == 0.0 else block_size[lblock][1] / nyb),
+        "dz": (1.0 if block_size[lblock][2] == 0.0 else block_size[lblock][2] / nzb),
+        "xmin": bounding_box[lblock][0][0],
+        "ymin": bounding_box[lblock][1][0],
+        "zmin": bounding_box[lblock][2][0],
+        "xmax": bounding_box[lblock][0][1],
+        "ymax": bounding_box[lblock][1][1],
+        "zmax": bounding_box[lblock][2][1],
         "tag": lblock,
-        "level": inputfile["refine level"][lblock],
-        "leaf": bool(inputfile["node type"][lblock] == 1),
-        "inputproc": inputfile["processor number"][lblock],
+        "level": refine_level[lblock],
+        "leaf": bool(node_type[lblock] == 1),
+        "inputproc": proc_num[lblock],
     }
 
     return block_dict

tests/acadia/__main__.py

@@ -1,7 +1,11 @@
 """Run the test suite."""
 
+import os
+import io
 import sys
+import contextlib
 import unittest
+from datetime import date
 
 
 def main():
@@ -12,7 +16,17 @@ def main():
     for test in tests:
         suite.addTest(unittest.defaultTestLoader.loadTestsFromName(test))
 
-    res = unittest.TextTestRunner().run(suite).wasSuccessful()
+    with io.StringIO() as buf:
+        with contextlib.redirect_stdout(buf):
+            res = unittest.TextTestRunner(stream=buf).run(suite).wasSuccessful()
+
+        print(buf.getvalue())
+
+        with open(
+            f"{os.path.dirname(__file__)}/archive/{str(date.today())}.log", "w"
+        ) as bufOut:
+            print(buf.getvalue(), file=bufOut)
+
     rc = 0 if res else 1
     sys.exit(rc)
 

tests/acadia/archive/2023-06-27.log

@@ -0,0 +1,40 @@
+
+-------------------------Running: boiling.TestBoiling.test_data_pointers_3D-------------------------
+
+boiling.TestBoiling.test_data_pointers_3D: 0.058s
+.
+-------------------------Running: boiling.TestBoiling.test_mergeblocks_3D-------------------------
+
+[cpu_count]: 8 [cpu_avail]: 2 [mem_avail]: 8.17 GB [cpu_usage]: 78.1% [mem_usage]: 48.9%
+run-loky:boxkit.api._mergeblocks.map_blk_to_merged_dset
+[boxkit.mergeblocks.map_dataset_block]: 0.305s
+[boxkit.mergeblocks]: 0.327s
+boiling.TestBoiling.test_mergeblocks_3D: 0.478s
+.
+-------------------------Running: boiling.TestBoiling.test_neighbors_3D-------------------------
+
+boiling.TestBoiling.test_neighbors_3D: 0.096s
+.
+-------------------------Running: boiling.TestBoiling.test_regionprops_3D-------------------------
+
+run-loky:boxkit.api._regionprops.skimage_props_blk
+boxkit.regionprops: 2.187s
+boiling.TestBoiling.test_regionprops_3D: 2.26s
+.
+-------------------------Running: boiling.TestBoiling.test_slice_3D-------------------------
+
+boiling.TestBoiling.test_slice_3D: 0.061s
+.
+-------------------------Running: heater.TestHeater.test_neighbors_oneblk_2D-------------------------
+
+heater.TestHeater.test_neighbors_oneblk_2D: 0.002s
+.
+-------------------------Running: heater.TestHeater.test_regionprops_oneblk_2D-------------------------
+
+heater.TestHeater.test_regionprops_oneblk_2D: 0.05s
+.
+----------------------------------------------------------------------
+Ran 7 tests in 3.006s
+
+OK
+

tests/sedona/__main__.py

@@ -1,7 +1,11 @@
 """Run the test suite."""
 
+import os
+import io
 import sys
+import contextlib
 import unittest
+from datetime import date
 
 
 def main():
@@ -12,7 +16,17 @@ def main():
     for test in tests:
         suite.addTest(unittest.defaultTestLoader.loadTestsFromName(test))
 
-    res = unittest.TextTestRunner().run(suite).wasSuccessful()
+    with io.StringIO() as buf:
+        with contextlib.redirect_stdout(buf):
+            res = unittest.TextTestRunner(stream=buf).run(suite).wasSuccessful()
+
+        print(buf.getvalue())
+
+        with open(
+            f"{os.path.dirname(__file__)}/archive/{str(date.today())}.log", "w"
+        ) as bufOut:
+            print(buf.getvalue(), file=bufOut)
+
     rc = 0 if res else 1
     sys.exit(rc)
 

tests/sedona/archive/2023-06-27.log

@@ -0,0 +1,83 @@
+
+-------------------------Running: boiling.TestBoiling.test_data_pointers_3D-------------------------
+
+boiling.TestBoiling.test_data_pointers_3D: 0.615s
+.
+-------------------------Running: boiling.TestBoiling.test_mean_temporal_3D-------------------------
+
+[boxkit.mean_temporal.mean_blk_list]: 1.823s
+[boxkit.mean_temporal]: 1.992s
+[cpu_count]: 24 [cpu_avail]: 20 [mem_avail]: 25.85 GB [cpu_usage]: 18.6% [mem_usage]: 17.3%
+run-loky:boxkit.api._mergeblocks.map_blk_to_merged_dset
+[boxkit.mergeblocks.map_dataset_block]: 0.231s
+[boxkit.mergeblocks]: 0.261s
+boiling.TestBoiling.test_mean_temporal_3D: 2.888s
+.
+-------------------------Running: boiling.TestBoiling.test_mergeblocks_3D-------------------------
+
+[cpu_count]: 24 [cpu_avail]: 21 [mem_avail]: 25.87 GB [cpu_usage]: 15.6% [mem_usage]: 17.2%
+run-loky:boxkit.api._mergeblocks.map_blk_to_merged_dset
+[boxkit.mergeblocks.map_dataset_block]: 0.218s
+[boxkit.mergeblocks]: 0.239s
+boiling.TestBoiling.test_mergeblocks_3D: 0.372s
+.
+-------------------------Running: boiling.TestBoiling.test_neighbors_3D-------------------------
+
+boiling.TestBoiling.test_neighbors_3D: 0.904s
+.
+-------------------------Running: boiling.TestBoiling.test_regionprops_3D-------------------------
+
+run-loky:boxkit.api._regionprops.skimage_props_blk
+run-loky:boxkit.api._regionprops.skimage_props_blk
+run-loky:boxkit.api._regionprops.skimage_props_blk
+run-loky:boxkit.api._regionprops.skimage_props_blk
+run-loky:boxkit.api._regionprops.skimage_props_blk
+run-loky:boxkit.api._regionprops.skimage_props_blk
+boxkit.regionprops: 2.388s
+boiling.TestBoiling.test_regionprops_3D: 3.34s
+.
+-------------------------Running: boiling.TestBoiling.test_slice_3D-------------------------
+
+boiling.TestBoiling.test_slice_3D: 0.661s
+.
+-------------------------Running: heater.TestHeater.test_neighbors_oneblk_2D-------------------------
+
+heater.TestHeater.test_neighbors_oneblk_2D: 0.037s
+
+.
+-------------------------Running: heater.TestHeater.test_regionprops_blocks_2D-------------------------
+
+heater.TestHeater.test_regionprops_blocks_2D: 1.602s
+
+.
+-------------------------Running: heater.TestHeater.test_regionprops_oneblk_2D-------------------------
+
+heater.TestHeater.test_regionprops_oneblk_2D: 0.185s
+
+.
+-------------------------Running: application.TestApplication.test_flowx-------------------------
+
+run-loky:flowx.imbound._interface.utils._shapely_search._search_block
+Search time:  2.0188839435577393
+[fill guardcells time]:  0.024975061416625977
+.
+-------------------------Running: astrophysics.TestAstrophysics.test_read_nthreads_12_3D-------------------------
+
+run-loky:boxkit.resources.read._flash.get_blk_attributes
+Dataset:
+ - type         : <class 'boxkit.library._dataset.Dataset'>
+ - file         : <HDF5 file "25m_3d_32km_hdf5_plt_cnt_1000" (mode r)>
+ - keys         : ['dens', 'temp', 'velx', 'vely', 'ye  ', 'fe54', 'fe56', 'o16 ', 'si28', 'entr', 'enuc', 'cr48', 'cr56', 'fe52', 'ni56', 'pres', 'c12 ', 's32 ', 'gpot', 'gamc', 'dtbn', 'velz']
+ - dtype	: [<class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>, <class 'h5pickle.Dataset'>]
+ - bound(z-y-x) : [-10000000000.0, 10000000000.0] x [-10000000000.0, 10000000000.0] x [-10000000000.0, 10000000000.0]
+ - shape(z-y-x) : 8 x 8 x 8
+ - guard(z-y-x) : 0 x 0 x 0
+ - nblocks      : 90200
+ - dtype        : {'dens': <class 'h5pickle.Dataset'>, 'temp': <class 'h5pickle.Dataset'>, 'velx': <class 'h5pickle.Dataset'>, 'vely': <class 'h5pickle.Dataset'>, 'ye  ': <class 'h5pickle.Dataset'>, 'fe54': <class 'h5pickle.Dataset'>, 'fe56': <class 'h5pickle.Dataset'>, 'o16 ': <class 'h5pickle.Dataset'>, 'si28': <class 'h5pickle.Dataset'>, 'entr': <class 'h5pickle.Dataset'>, 'enuc': <class 'h5pickle.Dataset'>, 'cr48': <class 'h5pickle.Dataset'>, 'cr56': <class 'h5pickle.Dataset'>, 'fe52': <class 'h5pickle.Dataset'>, 'ni56': <class 'h5pickle.Dataset'>, 'pres': <class 'h5pickle.Dataset'>, 'c12 ': <class 'h5pickle.Dataset'>, 's32 ': <class 'h5pickle.Dataset'>, 'gpot': <class 'h5pickle.Dataset'>, 'gamc': <class 'h5pickle.Dataset'>, 'dtbn': <class 'h5pickle.Dataset'>, 'velz': <class 'h5pickle.Dataset'>}
+astrophysics.TestAstrophysics.test_read_nthreads_12_3D: 4.612s
+.
+----------------------------------------------------------------------
+Ran 11 tests in 17.356s
+
+OK
+

tests/sedona/astrophysics.py

@@ -61,6 +61,7 @@ def test_read_nthreads_12_3D(self):
             for filename in self.filenames
         ]
         for dataset in dataframes:
+            print(dataset)
             dataset.purge()
 
     def tearDown(self):