Cleaned up and tested with micelle and melt under examples
This commit is contained in:
Trung Nguyen
@ -1,12 +1,18 @@
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'''
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UPDATE: Dec 10, 2023:
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UPDATE: Jan 30, 2024:
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Launching the LAMMPS binary under testing using a configuration defined in a yaml file (e.g. config.yaml).
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Comparing the output thermo with that in the existing log file (with the same nprocs)
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+ data in the log files are extracted and converted into yaml data structure
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+ using the in place input scripts, no need to add REG markers to the input scripts
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This way we can:
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+ launch tests with mpirun with multiple procs
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+ specify what LAMMPS binary version to test
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+ simplify the build configuration
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Example usage:
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python3 run_tests.py --lmp-bin=/path/to/lmp_binary --config-file=config.yaml --gen-ref=False
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1) Simple use:
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python3 run_tests.py --lmp-bin=/path/to/lmp_binary
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2) Use a custom testing configuration
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python3 run_tests.py --lmp-bin=/path/to/lmp_binary --config-file=/path/to/config/file/config.yaml
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--------------------------------------------------------------------------------------------------------------
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@ -99,39 +105,37 @@ def extract_thermo(yamlFileName):
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inputFileName = a provided log file in an examples folder (e.g. examples/melt/log.8Apr21.melt.g++.4)
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return a YAML data structure as if loaded from a thermo yaml file
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'''
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def convert_log_to_yaml(inputFileName):
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def extract_data_to_yaml(inputFileName):
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with open(inputFileName, 'r') as file:
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data = file.read()
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lines = data.splitlines()
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reading = False
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data = []
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docs = ""
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for line in lines:
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if "Step" in line:
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line.strip()
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keywords = line.split()
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reading = True
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docs += "---\n"
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docs += str("keywords: [")
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for word in enumerate(keywords):
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docs += "'" + word[1] + "', "
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docs += "]\n"
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docs += "data:\n"
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if "Loop" in line:
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reading = False
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break
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if reading == True and "Step" not in line:
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data.append(line.split())
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docs = "---\n"
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docs += str("keywords: [")
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for word in enumerate(keywords):
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docs += "'" + word[1] + "', "
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docs += "]\n"
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docs += "data:\n"
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for line in enumerate(data):
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docs += " - ["
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for field in enumerate(line[1]):
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docs += field[1] + ", "
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docs += "]\n"
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docs += "...\n"
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docs += "..."
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#print(docs)
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if reading == True and "Step" not in line:
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data = line.split()
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docs += " - ["
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for field in enumerate(data):
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docs += field[1] + ", "
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docs += "]\n"
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# load the docs into a YAML data struture
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#print(docs)
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thermo = list(yaml.load_all(docs, Loader=Loader))
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return thermo
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@ -153,13 +157,22 @@ def get_lammps_build_configuration(lmp_binary):
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packages = l.strip()
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break
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if "OS:" in l:
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OS = l
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operating_system = l
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if "Git info" in l:
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GitInfo = l
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row += 1
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return packages.split(" "), OS, GitInfo
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row = 0
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compile_flags = ""
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for l in output:
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if l != "":
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if "-DLAMMPS" in l:
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compile_flags += " " + l.strip()
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row += 1
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return packages.split(" "), operating_system, GitInfo, compile_flags
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'''
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launch LAMMPS using the configuration defined in the dictionary config with an input file
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@ -170,7 +183,7 @@ def get_lammps_build_configuration(lmp_binary):
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def execute(lmp_binary, config, input_file_name, generate_ref_yaml=False):
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cmd_str = config['mpiexec'] + " " + config['mpiexec_numproc_flag'] + " " + config['nprocs'] + " "
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cmd_str += lmp_binary + " -in " + input_file_name + " " + config['args']
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print(f"Execute: {cmd_str}")
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print(f"Executing: {cmd_str}")
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p = subprocess.run(cmd_str, shell=True, text=True, capture_output=True)
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output = p.stdout.split('\n')
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@ -218,31 +231,35 @@ def iterate(input_list, config, removeAnnotatedInput=False):
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num_tests = len(input_list)
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test_id = 0
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# iterative over the input scripts
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using_markers = False
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# iterate over the input scripts
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for input in input_list:
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input_test = 'test.' + input
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if os.path.isfile(input) == True:
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if has_markers(input):
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process_markers(input, input_test)
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else:
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print(f"SKIPPED: {input} does not have REG markers")
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continue
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input_markers = input + '.markers'
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# if the .test file with the REG markers does not exist
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# attempt to plug in the REG markers before each run command
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if os.path.isfile(input_markers) == False:
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cmd_str = "cp " + input + " " + input_markers
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os.system(cmd_str)
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generate_markers(input, input_markers)
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process_markers(input_markers, input_test)
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# input.test should be ready for testing without markers but with the inserted thermo lines
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str_t = "\nRunning " + input + f" ({test_id+1}/{num_tests})"
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if using_markers == True:
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input_test = 'test.' + input
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if os.path.isfile(input) == True:
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if has_markers(input):
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process_markers(input, input_test)
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else:
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print(f"WARNING: {input} does not have REG markers")
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input_markers = input + '.markers'
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# if the input file with the REG markers does not exist
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# attempt to plug in the REG markers before each run command
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if os.path.isfile(input_markers) == False:
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cmd_str = "cp " + input + " " + input_markers
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os.system(cmd_str)
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generate_markers(input, input_markers)
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process_markers(input_markers, input_test)
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str_t = "\nRunning " + input_test + f" ({test_id+1}/{num_tests})"
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else:
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input_test = input
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str_t = "\nRunning " + input_test + f" ({test_id+1}/{num_tests})"
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print(str_t)
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print(f"-"*len(str_t))
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@ -254,26 +271,26 @@ def iterate(input_list, config, removeAnnotatedInput=False):
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execute(lmp_binary, config, input_test)
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# process thermo output
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thermo = extract_thermo("log.lammps")
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#thermo = extract_thermo("log.lammps")
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thermo = extract_data_to_yaml("log.lammps")
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num_runs = len(thermo)
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if num_runs == 0:
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print(f"Failed with {input_test}\n")
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print(f"Failed with {input_test}. Check if the run with this input script completed normally.\n")
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continue
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print(f"Number of runs: {num_runs}")
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# check if a log file exists in the current folder
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# check if a log file exists in the current folder: log.[date].basename.[nprocs]
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basename = input_test.replace('in.','')
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logfile_exist = False
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pattern = f'log.*.{nprocs}'
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pattern = f'log.*.{basename}.*.{nprocs}'
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for file in os.listdir('.'):
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if fnmatch.fnmatch(file, pattern):
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logfile_exist = True
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break
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if logfile_exist:
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print(f"reading {file}")
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thermo_ref = convert_log_to_yaml(file)
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thermo_ref = extract_data_to_yaml(file)
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num_runs_ref = len(thermo_ref)
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else:
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# read in the thermo yaml output from the working directory
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thermo_ref_file = 'thermo.' + input + '.yaml'
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@ -282,8 +299,13 @@ def iterate(input_list, config, removeAnnotatedInput=False):
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thermo_ref = extract_thermo(thermo_ref_file)
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else:
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print(f"SKIPPED: {thermo_ref_file} does not exist")
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return
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continue
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print(f"Comparing thermo output from log.lammps with the reference log {file}")
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if num_runs != num_runs_ref:
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print(f"ERROR: Number of runs in log.lammps ({num_runs}) is not the same as that in the reference log ({num_runs_ref})")
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continue
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# comparing output vs reference values
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width = 20
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print("Quantities".ljust(width) + "Output".center(width) + "Reference".center(width) + "Abs Diff Check".center(width) + "Rel Diff Check".center(width))
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@ -292,9 +314,9 @@ def iterate(input_list, config, removeAnnotatedInput=False):
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# get the total number of the thermo output lines
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nthermo_steps = len(thermo[irun]['data'])
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# get the output at thelast timestep
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# get the output at the last timestep
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thermo_step = nthermo_steps - 1
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print(f"nthermo_steps = {nthermo_steps}")
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#print(f"nthermo_steps = {nthermo_steps}")
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num_abs_failed = 0
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num_rel_failed = 0
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for i in range(num_fields):
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@ -370,7 +392,8 @@ if __name__ == "__main__":
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# read in the configuration of the tests
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with open(configFileName, 'r') as f:
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config = yaml.load(f, Loader=Loader)
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print(f"Using the testing configuration defined in {configFileName}")
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absolute_path = os.path.abspath(configFileName)
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print(f"Regression tests with settings defined in {absolute_path}")
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# check if lmp_binary is specified in the config yaml
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if lmp_binary == "":
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@ -380,23 +403,25 @@ if __name__ == "__main__":
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else:
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lmp_binary = config['lmp_binary']
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packages, operating_system, GitInfo = get_lammps_build_configuration(lmp_binary)
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print(operating_system)
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print(GitInfo)
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print(f"List of installed packages: {packages}")
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# print out the binary info
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packages, operating_system, GitInfo, compile_flags = get_lammps_build_configuration(lmp_binary)
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print("LAMMPS build info:")
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print(f"- {operating_system}")
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print(f"- {GitInfo}")
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print(f"- Active compile flags: {compile_flags}")
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print(f"- List of installed packages: {packages}")
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# Using inplace input scripts
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# Using in place input scripts
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inplace_input = True
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example_subfolders = []
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example_subfolders.append("../../examples/melt")
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#if 'MOLECULE' in packages:
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# molecule_package = True
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# example_subfolders.append('../../examples/micelle')
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# append the example subfolders depending on the installed packages
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if 'MOLECULE' in packages:
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molecule_package = True
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example_subfolders.append('../../examples/micelle')
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inplace_input = True
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if inplace_input == True:
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# save current working dir
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@ -409,7 +434,7 @@ if __name__ == "__main__":
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for directory in example_subfolders:
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print("Entering " + directory)
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print("\nEntering " + directory)
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os.chdir(directory)
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# create a symbolic link to the lammps binary at the present directory
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