Added function to extract output from an existing log file into a yaml data structure, working on in place testing
This commit is contained in:
Trung Nguyen
@ -38,12 +38,11 @@ Original plan: using the LAMMPS Python module
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#from lammps import lammps
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import os
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import sys
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import fnmatch
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import re, yaml
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import numpy as np
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import subprocess
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import sys
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from argparse import ArgumentParser
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try:
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@ -95,6 +94,47 @@ def extract_thermo(yamlFileName):
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return thermo
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'''
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Convert an existing log.lammps file into a thermo yaml style log
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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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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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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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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 += "..."
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#print(docs)
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# load the docs into a YAML data struture
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thermo = list(yaml.load_all(docs, Loader=Loader))
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return thermo
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'''
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return the list of installed packages
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'''
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@ -174,6 +214,8 @@ def iterate(input_list, config, removeAnnotatedInput=False):
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EPSILON = np.float64(config['epsilon'])
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nugget = float(config['nugget'])
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nprocs = int(config['nprocs'])
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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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@ -221,60 +263,75 @@ def iterate(input_list, config, removeAnnotatedInput=False):
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print(f"Number of runs: {num_runs}")
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# read in the thermo yaml output
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thermo_ref_file = 'thermo.' + input + '.yaml'
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file_exist = os.path.isfile(thermo_ref_file)
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if file_exist == True:
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thermo_ref = extract_thermo(thermo_ref_file)
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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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irun = 0
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num_fields = len(thermo[irun]['keywords'])
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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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thermo_step = nthermo_steps - 1
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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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quantity = thermo[0]['keywords'][i]
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# check if a log file exists in the current folder
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logfile_exist = False
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pattern = f'log.*.{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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val = thermo[irun]['data'][thermo_step][i]
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ref = thermo_ref[irun]['data'][thermo_step][i]
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abs_diff = abs(float(val) - float(ref))
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if abs(float(ref)) > EPSILON:
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rel_diff = abs(float(val) - float(ref))/abs(float(ref))
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else:
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rel_diff = abs(float(val) - float(ref))/abs(float(ref)+nugget)
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abs_diff_check = "PASSED"
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rel_diff_check = "PASSED"
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if quantity in config['tolerance']:
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if abs_diff > float(config['tolerance'][quantity]['abs']):
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abs_diff_check = "FAILED"
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num_abs_failed = num_abs_failed + 1
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if rel_diff > float(config['tolerance'][quantity]['rel']):
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rel_diff_check = "FAILED"
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num_rel_failed = num_rel_failed + 1
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else:
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abs_diff_check = "N/A"
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rel_diff_check = "N/A"
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print(f"{thermo[irun]['keywords'][i].ljust(width)} {str(val).rjust(20)} {str(ref).rjust(20)} {abs_diff_check.rjust(20)} {rel_diff_check.rjust(20)}")
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if num_abs_failed > 0:
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print(f"{num_abs_failed} abs checks failed")
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elif num_rel_failed > 0:
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print(f"{num_rel_failed} rel checks failed")
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else:
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print("All checks passed. (N/A means tolerance not defined in the config file.)")
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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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else:
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print(f"SKIPPED: {thermo_ref_file} does not exist")
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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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file_exist = os.path.isfile(thermo_ref_file)
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if file_exist == True:
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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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# 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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irun = 0
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num_fields = len(thermo[irun]['keywords'])
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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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thermo_step = nthermo_steps - 1
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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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quantity = thermo[0]['keywords'][i]
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val = thermo[irun]['data'][thermo_step][i]
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ref = thermo_ref[irun]['data'][thermo_step][i]
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abs_diff = abs(float(val) - float(ref))
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if abs(float(ref)) > EPSILON:
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rel_diff = abs(float(val) - float(ref))/abs(float(ref))
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else:
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rel_diff = abs(float(val) - float(ref))/abs(float(ref)+nugget)
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abs_diff_check = "PASSED"
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rel_diff_check = "PASSED"
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if quantity in config['tolerance']:
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if abs_diff > float(config['tolerance'][quantity]['abs']):
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abs_diff_check = "FAILED"
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num_abs_failed = num_abs_failed + 1
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if rel_diff > float(config['tolerance'][quantity]['rel']):
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rel_diff_check = "FAILED"
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num_rel_failed = num_rel_failed + 1
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else:
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abs_diff_check = "N/A"
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rel_diff_check = "N/A"
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print(f"{thermo[irun]['keywords'][i].ljust(width)} {str(val).rjust(20)} {str(ref).rjust(20)} {abs_diff_check.rjust(20)} {rel_diff_check.rjust(20)}")
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if num_abs_failed > 0:
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print(f"{num_abs_failed} abs checks failed")
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elif num_rel_failed > 0:
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print(f"{num_rel_failed} rel checks failed")
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else:
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print("All checks passed. (N/A means tolerance not defined in the config file.)")
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print("-"*(5*width+4))
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test_id = test_id + 1
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@ -324,8 +381,8 @@ if __name__ == "__main__":
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lmp_binary = config['lmp_binary']
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packages, OS, GitInfo = get_lammps_build_configuration(lmp_binary)
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print(OS)
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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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@ -334,12 +391,12 @@ if __name__ == "__main__":
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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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#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 = False
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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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@ -366,9 +423,9 @@ if __name__ == "__main__":
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print("List of input scripts:")
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print(input_list)
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# iterate through the input scripts
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iterate(input_list)
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iterate(input_list, config)
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# unlink the symbolic link
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cmd_str = "unlink lmp"
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@ -379,6 +436,8 @@ if __name__ == "__main__":
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else:
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# or using the input scripts in the working directory
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#input_list=['in.lj', 'in.rhodo', 'in.eam']
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input_list=['in.lj']
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input_list=['in.lj', 'in.rhodo', 'in.eam']
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iterate(input_list, config)
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