Merge pull request #112 from cindytsai/Refactor

All done!!! FINALLY!

Author: cindytsai

.clang-format

@@ -1,44 +1,49 @@
 ---
 BasedOnStyle: Google
-AccessModifierOffset: '-4'
+AccessModifierOffset: -1
 AlignAfterOpenBracket: Align
-AlignConsecutiveMacros: 'true'
+AlignConsecutiveMacros: true
 AlignEscapedNewlines: Right
 AlignOperands: 'true'
-AlignTrailingComments: 'true'
-AllowAllConstructorInitializersOnNextLine: 'true'
-AllowShortCaseLabelsOnASingleLine: 'false'
-AlwaysBreakBeforeMultilineStrings: 'false'
+AlignTrailingComments: true
+AllowAllArgumentsOnNextLine: true
+AllowAllConstructorInitializersOnNextLine: true
+AllowShortCaseLabelsOnASingleLine: false
+AlwaysBreakBeforeMultilineStrings: false
 AlwaysBreakTemplateDeclarations: 'Yes'
+BinPackArguments: false
+BinPackParameters: 'true'
 BreakBeforeBraces: Attach
+BreakBeforeTernaryOperators: true
 BreakConstructorInitializers: BeforeColon
 BreakInheritanceList: AfterColon
-ColumnLimit: '120'
+ColumnLimit: 90
 CommentPragmas: '''^  *'''
-CompactNamespaces: 'false'
-IndentCaseLabels: 'true'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+DerivePointerAlignment: false
+IndentCaseLabels: true
 IndentPPDirectives: None
-IndentWidth: '4'
-KeepEmptyLinesAtTheStartOfBlocks: 'false'
+IndentWidth: 2
+KeepEmptyLinesAtTheStartOfBlocks: false
 Language: Cpp
-DerivePointerAlignment: false
-ReflowComments: 'true'
-SpaceAfterCStyleCast: 'false'
-SpaceAfterLogicalNot: 'false'
-SpaceAfterTemplateKeyword: 'false'
-SpaceBeforeAssignmentOperators: 'true'
-SpaceBeforeCtorInitializerColon: 'true'
-SpaceBeforeInheritanceColon: 'true'
+ReflowComments: true
+SpaceAfterCStyleCast: false
+SpaceAfterLogicalNot: false
+SpaceAfterTemplateKeyword: false
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
 SpaceBeforeParens: ControlStatements
-SpaceBeforeRangeBasedForLoopColon: 'true'
-SpaceInEmptyParentheses: 'false'
-SpacesBeforeTrailingComments: '2'
-SpacesInAngles: 'false'
-SpacesInCStyleCastParentheses: 'false'
-SpacesInContainerLiterals: 'false'
-SpacesInParentheses: 'false'
-SpacesInSquareBrackets: 'false'
-Standard: Cpp11
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 2
+SpacesInAngles: false
+SpacesInCStyleCastParentheses: false
+SpacesInContainerLiterals: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard: c++14
 UseTab: Never
 
 ...

.github/Notes.md

@@ -1,16 +1,14 @@
 # GitHub Action
 
-## Usage of Each Folder
+## File Structure
 - **tests**: Store test related files. 
   - Test file will be run as inline python script in `libyt/example.cpp`. File name ends with `Test`.
 - **tools**: Miscellaneous.
 - **workflows**: Store GitHub Action yaml script.
 
-## Tests
+## Workflows
 
-### DataIO
-- **Workflows**: `.github/workflows/build-test.yml`
-- **Test File**: `.github/tests/DataIOTest.py`
-- **Description**:
-  - Check if `libyt/example` can successfully run in fake serial (`mpirun -np 1`) and in parallel using `mpirun`.
-  - Check if data read by `libyt` is the same as data original in C++ array.
+- `cmake-build-test.yml`: Build different options of libyt on different os.
+- `example-test-run.yml`: Make sure the AMR example can run in parallel and in serial modes.
+- `unit-test.yml`: Run unit tests. Since some of the units have MPI coupled in them, we need to run the tests in parallel mode and in serial mode. For parallel mode, `openmpi` and `mpich` are tested. For serial mode, `Python3.7` ~ `Python3.14` are tested. All of them have a combination with `-DUSE_PYBIND11=ON` and `-DUSE_PYBIND11=OFF` options.
+- `memory-profile.yml`: Run memory profiling tests using valgrind.

.github/tests/test-DataIO/DataIOTest.py

@@ -1,13 +1,17 @@
 import yt
 import yt_libyt
-from mpi4py import MPI
 import pandas as pd
 import numpy as np
 
 yt.enable_parallelism()
 step = 0
-comm = MPI.COMM_WORLD
-myrank = comm.Get_rank()
+
+try:
+    from mpi4py import MPI
+    comm = MPI.COMM_WORLD
+    myrank = comm.Get_rank()
+except ImportError:
+    myrank = 0
 
 class DataIOTestFailed(Exception):
     """
@@ -69,7 +73,7 @@ def test_function():
         # Compare them, if bigger than criteria, raise an error
         diff = np.sum(np.absolute(sim_data - data_io)) / (dimensions[0] * dimensions[1] * dimensions[2])
         if diff > DataIOTestFailed.criteria:
-            err_msg = "On MPI rank {}, step {}, density grid (id={}) is different from simulation data {}.\n" \
+            err_msg = "On rank {}, step {}, density grid (id={}) is different from simulation data {}.\n" \
                       "DataIOTest FAILED.\n".format("%d" % myrank, "%d" % step, "%d" % gid, "%.10e" % diff)
             raise DataIOTestFailed(err_msg)
 

.github/tools/combine_valgrind_snapshot.py

@@ -0,0 +1,78 @@
+import os
+import argparse
+
+class Bcolors:
+    HEADER = '\033[95m'
+    OKBLUE = '\033[94m'
+    OKCYAN = '\033[96m'
+    OKGREEN = '\033[92m'
+    WARNING = '\033[93m'
+    FAIL = '\033[91m'
+    ENDC = '\033[0m'
+    BOLD = '\033[1m'
+    UNDERLINE = '\033[4m'
+
+def combine_detailed_snapshot(filebase: str, combined_filename: str, mpi_rank: int, iter_total: int):
+    """combined_detailed_snapshot
+    Combined individual detailed snapshots dumped by valgrind,
+    so that it can be visualized in massif-visualizer in a time series.
+    The time series starts at t = 0.
+    """
+
+    snapshot_flag = """#-----------\nsnapshot={}\n#-----------\n"""
+    combined_filename_suffix = ".mem_prof"
+
+    # make sure the combined_filename ends with .mem_prof
+    if not combined_filename.endswith(combined_filename_suffix):
+        combined_filename += combined_filename_suffix
+
+    # make sure the file does not exist
+    if os.path.exists(combined_filename):
+        print(f"{Bcolors.FAIL}File {combined_filename} already exists {Bcolors.ENDC}")
+        raise "File already exists"
+
+    # write the combined file
+    with open(combined_filename, "a") as f_combined:
+
+        for t in range(iter_total):
+
+            # read raw file
+            filename = filebase.format(mpi_rank, t)
+            with open(filename, "r") as f:
+                raw = f.read()
+                print(f"Reading file {Bcolors.WARNING} {filename} {Bcolors.ENDC} ... done")
+
+            # ignore the heading in the file except the first one,
+            # and we also need to append our own flag
+            if t != 0:
+                # write the snapshot flag
+                f_combined.write(snapshot_flag.format(t))
+
+                # ignore the heading and the snapshot flag
+                pos = raw.find(snapshot_flag.format(0))
+                pos = pos + len(snapshot_flag.format(0))
+                f_combined.write(raw[pos:-1])
+                f_combined.write("\n")
+
+            else:
+                f_combined.write(raw)
+
+    print(f"Writing file to {Bcolors.OKGREEN} {combined_filename} {Bcolors.ENDC} ... done")
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser(description="Combine detailed snapshots dumped by valgrind")
+    parser.add_argument('--tag', metavar='tag', type=str, nargs=1,
+                        help='Tag, e.g., "BeforeFree_rank0_time0.mem_prof" has tag "BeforeFree"')
+    parser.add_argument('--mpi_size', metavar='mpi_size', type=int, nargs=1,
+                        help='MPI size')
+    parser.add_argument('--total_time_steps', metavar='time_steps', type=int, nargs=1,
+                        help='Total number of time steps')
+    args = parser.parse_args()
+
+    # Call combine_detailed_snapshot
+    file_base_name = args.tag[0] + "_rank{}_time{}.mem_prof"
+    combined_file_name = args.tag[0] + "_rank{}.mem_prof"
+
+    for r in range(args.mpi_size[0]):
+        combine_detailed_snapshot(file_base_name, combined_file_name.format(r), r, args.total_time_steps[0])

.github/tools/conclude_memory_profile.py

@@ -0,0 +1,83 @@
+import os
+import argparse
+
+
+class Bcolors:
+    HEADER = '\033[95m'
+    OKBLUE = '\033[94m'
+    OKCYAN = '\033[96m'
+    OKGREEN = '\033[92m'
+    WARNING = '\033[93m'
+    FAIL = '\033[91m'
+    ENDC = '\033[0m'
+    BOLD = '\033[1m'
+    UNDERLINE = '\033[4m'
+
+
+def extract_value_from_file(folder: str or None, filename: str, attribute: str) -> dict:
+    """extract_value_from_file
+    Assume attribute in a file is in a format 'attribute=value'.
+    """
+
+    file_full_name = filename if folder is None else os.path.join(folder, filename)
+
+    # make sure file exist and read the file
+    if not os.path.exists(file_full_name):
+        print(f"{Bcolors.FAIL}File {file_full_name} does not exist {Bcolors.ENDC}")
+        raise "No such file"
+    with open(file_full_name, "r") as f:
+        raw = f.read()
+        print(f"Reading file {Bcolors.WARNING} {file_full_name} {Bcolors.ENDC} ... done")
+
+    # find all the matching attribute
+    found = -1
+    extract_value = []
+    while True:
+        # find matching attributes
+        found = raw.find(attribute, found + 1)
+        if found < 0:
+            break
+
+        found_newline = raw.find("\n", found)
+        extract_value.append(int(raw[found + len(attribute) + 1: found_newline]))
+
+    results = dict()
+    results[attribute] = extract_value
+    results[attribute + "_diff"] = [extract_value[i] - extract_value[i - 1] for i in range(1, len(extract_value))]
+    print(f"Extracting attribute {Bcolors.OKGREEN} {attribute} {Bcolors.ENDC} in {file_full_name}  ... done")
+
+    return results
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser(description="Combine detailed snapshots dumped by valgrind")
+    parser.add_argument('--title', metavar='title', type=str, nargs=1,
+                        help='Title')
+    parser.add_argument('--folder', metavar='folder', type=str, nargs=1,
+                        help='Folder where the files are stored. (optional)')
+    parser.add_argument('--tags', metavar='tags', type=str, nargs='*',
+                        help='A list of tags, e.g., "BeforeFree_rank0.mem_prof" has tag "BeforeFree"')
+    parser.add_argument('--attr', metavar='attr', type=str, nargs=1,
+                        help='Attribute to extract in valgrind massif dump.')
+    parser.add_argument('--mpi_size', metavar='mpi_size', type=int, nargs=1,
+                        help='MPI size')
+    parser.add_argument('--output_filename', metavar='output_filename', type=str, nargs=1,
+                        help='Output to file.')
+    args = parser.parse_args()
+
+    # Extract value and write to file
+    with open(args.output_filename[0], "a") as f:
+        f.write("#### " + args.title[0] + "\n\n")
+    for tag in args.tags:
+        for r in range(args.mpi_size[0]):
+            filename = tag + "_rank{}.mem_prof".format(r)
+            if args.folder is not None:
+                attr_value = extract_value_from_file(args.folder[0], filename, args.attr[0])
+            else:
+                attr_value = extract_value_from_file(None, filename, args.attr[0])
+
+            for key in attr_value:
+                with open(args.output_filename[0], "a") as f:
+                    f.write("**{}({}_rank{})**: ".format(key, tag, r) + str(attr_value[key]) + "\n")
+    with open(args.output_filename[0], "a") as f:
+        f.write("\n---\n\n")