Handled error runs where log.lammps is not created (e.g. using more MPI procs than the number of physical CPUs)
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Trung Nguyen
@ -199,12 +199,7 @@ def execute(lmp_binary, config, input_file_name, generate_ref_yaml=False):
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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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output = p.stdout
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# process output to handle failed runs
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return cmd_str, output
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return cmd_str, p.stdout, p.stderr, p.returncode
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'''
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attempt to plug in the REG markers before each run command
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@ -309,66 +304,71 @@ def iterate(lmp_binary, input_list, config, results, removeAnnotatedInput=False)
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# then override the setting for this input script
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saved_nprocs = config['nprocs']
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if max_np != int(config['nprocs']):
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config['nprocs'] = str(max_np)
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config['nprocs'] = str(max_np)
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if logfile_exist:
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thermo_ref = extract_data_to_yaml(thermo_ref_file)
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num_runs_ref = len(thermo_ref)
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else:
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print(f"Cannot find reference log file with {pattern}.")
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# try to 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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thermo_ref = extract_data_to_yaml(thermo_ref_file)
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num_runs_ref = len(thermo_ref)
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else:
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print(f"SKIPPED: {thermo_ref_file} does not exist in the working directory.")
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result.status = "skipped"
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results.append(result)
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continue
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else:
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print(f"Cannot find reference log file with {pattern}.")
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# try to 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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num_runs_ref = len(thermo_ref)
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else:
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print(f"SKIPPED: {thermo_ref_file} does not exist in the working directory.")
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result.status = "skipped"
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results.append(result)
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continue
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# using the LAMMPS python module (for single-proc runs)
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# lmp = lammps()
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# lmp.file(input_test)
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# or more customizable with config.yaml
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cmd_str, output = execute(lmp_binary, config, input_test)
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cmd_str, output, error, returncode = execute(lmp_binary, config, input_test)
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# restore the nprocs value in the configuration
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config['nprocs'] = saved_nprocs
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# process thermo output
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if returncode != 0:
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print(f"ERROR: Failed with {input_test}. Check the log file for the run output.\n")
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logger.info(f"\n{error}")
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continue
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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"ERROR: Failed with {input_test}. Check the log file for the run output.\n")
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#print(f"{output}")
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logger.info(f"The run terminated with the following output:\n")
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logger.info(f"\n{output}")
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result.status = "error"
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results.append(result)
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continue
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print(f"ERROR: Failed with {input_test}. Check the log file for the run output.\n")
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#print(f"{output}")
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logger.info(f"The run terminated with the following output:\n")
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logger.info(f"\n{output}")
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result.status = "error"
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results.append(result)
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continue
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print(f"Comparing thermo output from log.lammps with the reference log file {thermo_ref_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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result.status = "error"
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results.append(result)
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continue
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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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result.status = "error"
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results.append(result)
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continue
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# comparing output vs reference values
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width = 20
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if verbose == True:
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print("Quantities".ljust(width) + "Output".center(width) + "Reference".center(width) +
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print("Quantities".ljust(width) + "Output".center(width) + "Reference".center(width) +
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"Abs Diff Check".center(width) + "Rel Diff Check".center(width))
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# check if overrides for this input scipt is specified
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overrides = {}
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if 'overrides' in config:
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if input_test in config['overrides']:
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overrides = config['overrides'][input_test]
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if input_test in config['overrides']:
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overrides = config['overrides'][input_test]
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# iterate through all num_runs
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@ -469,9 +469,6 @@ def iterate(lmp_binary, input_list, config, results, removeAnnotatedInput=False)
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'''
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if __name__ == "__main__":
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logger = logging.getLogger(__name__)
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logging.basicConfig(filename='run.log', level=logging.INFO)
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# default values
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lmp_binary = ""
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configFileName = "config.yaml"
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@ -479,18 +476,20 @@ if __name__ == "__main__":
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genref = False
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verbose = False
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output_file = "output.xml"
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log_file = "run.log"
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# parse the arguments
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parser = ArgumentParser()
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parser.add_argument("--lmp-bin", dest="lmp_binary", default="", help="LAMMPS binary")
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parser.add_argument("--config-file", dest="config_file", default="config.yaml",
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parser.add_argument("--config-file", dest="config_file", default=configFileName,
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help="Configuration YAML file")
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parser.add_argument("--example-folders", dest="example_folders", default="", help="Example subfolders")
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parser.add_argument("--gen-ref",dest="genref", action='store_true', default=False,
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help="Generating reference data")
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parser.add_argument("--verbose",dest="verbose", action='store_true', default=False,
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help="Verbose output")
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parser.add_argument("--output",dest="output", default="output.xml", help="Output file")
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parser.add_argument("--output",dest="output", default=output_file, help="Output file")
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parser.add_argument("--logfile",dest="logfile", default=log_file, help="Log file")
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args = parser.parse_args()
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@ -503,6 +502,11 @@ if __name__ == "__main__":
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print(example_subfolders)
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genref = args.genref
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verbose = args.verbose
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log_file = args.logfile
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# logging
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logger = logging.getLogger(__name__)
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logging.basicConfig(filename=log_file, level=logging.INFO, filemode="w")
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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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@ -530,7 +534,7 @@ if __name__ == "__main__":
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inplace_input = True
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test_cases = []
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# if the example folders are not specified from the command-line argument -example-folders
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# if the example folders are not specified from the command-line argument --example-folders
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if len(example_subfolders) == 0:
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example_subfolders.append("../../examples/melt")
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example_subfolders.append('../../examples/flow')
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@ -595,6 +599,9 @@ if __name__ == "__main__":
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if 'RIGID' in packages:
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example_subfolders.append('../../examples/rigid')
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if 'SNAP' in packages:
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example_subfolders.append('../../examples/snap')
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if 'SRD' in packages:
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example_subfolders.append('../../examples/srd')
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