enable generating new reference log files if desirable
This commit is contained in:
Trung Nguyen
@ -157,6 +157,8 @@ def iterate(lmp_binary, input_folder, input_list, config, results, progress_file
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using_markers = False
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EPSILON = np.float64(config['epsilon'])
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nugget = float(config['nugget'])
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genref = config['genref']
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compiler = config['compiler']
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use_valgrind = False
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if 'valgrind' in config['mpiexec']:
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use_valgrind = True
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@ -325,7 +327,7 @@ def iterate(lmp_binary, input_folder, input_list, config, results, progress_file
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config['nprocs'] = saved_nprocs
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# check if the output contains ERROR
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# there might not be a log.lammps generated at this point, or only log.lammps contains only the date line
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# there might not be a log file generated at this point, or only the log file contains only the date line
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if "ERROR" in output:
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error_line = ""
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for line in output.split('\n'):
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@ -357,16 +359,18 @@ def iterate(lmp_binary, input_folder, input_list, config, results, progress_file
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test_id = test_id + 1
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continue
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# check if a log.lammps file exists in the current folder
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if os.path.isfile("log.lammps") == False:
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msg = f" failed, no log.lammps generated with {input_test} with return code {returncode}.\n"
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# check if a log file log.{basename}.{nprocs} exists in the current folder
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logfilename = f"log.{basename}.{nprocs}"
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if os.path.isfile(logfilename) == False:
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msg = f" failed, no log.{basename}.{nprocs} generated with {input_test} with return code {returncode}.\n"
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print(msg)
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logger.info(msg)
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logger.info(f" Output:")
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logger.info(f" {output}")
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logger.info(f" Error:\n{error}")
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msg = f"{input}: {{ folder: {input_folder}, status: \"failed, no log.lammps\", walltime: {walltime} }}\n"
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msg = f"{input}: {{ folder: {input_folder}, status: \"failed, no log file generated\", walltime: {walltime} }}\n"
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progress.write(msg)
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progress.close()
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failure.write(msg)
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@ -375,9 +379,14 @@ def iterate(lmp_binary, input_folder, input_list, config, results, progress_file
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test_id = test_id + 1
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continue
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else:
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# save a copy of the log file for further inspection
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cmd_str = f"cp log.lammps log.{basename}.{nprocs}"
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p = subprocess.run(cmd_str, shell=True, text=True, capture_output=True)
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# generate a new log file whose name has the format of log.{date}.{basename}.{compiler}.{nprocs}
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if genref == True:
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dmy = datetime.datetime.now()
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date = dmy.strftime("%d%b%y")
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# assume g++ for now, but is be available from running "lmp_binary -h"
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compiler = "g++"
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cmd_str = f"cp log.{basename}.{nprocs} log.{date}.{basename}.{compiler}.{nprocs}"
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p = subprocess.run(cmd_str, shell=True, text=True, capture_output=True)
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# if skip numerical checks, then skip the rest
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if skip_numerical_check == True:
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@ -795,6 +804,7 @@ def get_lammps_build_configuration(lmp_binary):
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reading = False
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operating_system = ""
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GitInfo = ""
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compiler = "g++"
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row = 0
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for line in output:
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if line != "":
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@ -810,7 +820,11 @@ def get_lammps_build_configuration(lmp_binary):
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operating_system = line
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if "Git info" in line:
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GitInfo = line
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if "Compiler" in line:
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if "GNU" in line:
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compiler = "g++"
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if "Intel" in line:
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compiler = "icc"
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row += 1
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packages = packages.strip()
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@ -824,20 +838,24 @@ def get_lammps_build_configuration(lmp_binary):
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row += 1
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return packages.split(" "), operating_system, GitInfo, compile_flags
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return packages.split(" "), operating_system, GitInfo, compile_flags, compiler
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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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TODO:
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- generate new reference values if needed
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'''
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def execute(lmp_binary, config, input_file_name, generate_ref_yaml=False):
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def execute(lmp_binary, config, input_file_name, generate_ref=False):
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cmd_str = ""
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# check if mpiexec/mpirun is used
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if config['mpiexec']:
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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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# write to a log file with format log.{basename}.{nprocs}
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basename = input_file_name[3:]
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logfilename = f"log.{basename}.{config['nprocs']}"
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cmd_str += lmp_binary + " -in " + input_file_name + " " + config['args'] + " -log " + logfilename
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logger.info(f" Executing: {cmd_str}")
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# set a timeout (in seconds) for each run
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@ -1325,10 +1343,11 @@ if __name__ == "__main__":
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lmp_binary = os.path.abspath(config['lmp_binary'])
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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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packages, operating_system, GitInfo, compile_flags, compiler = get_lammps_build_configuration(lmp_binary)
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print("\nLAMMPS build info:")
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print(f" - {operating_system}")
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print(f" - {GitInfo}")
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print(f" - Compiler: {compiler}")
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print(f" - Active compile flags: {compile_flags}")
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print(f" - List of {len(packages)} installed packages:")
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all_pkgs = ""
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@ -1336,6 +1355,10 @@ if __name__ == "__main__":
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all_pkgs += p + " "
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print(all_pkgs)
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# augment config with additional keys
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config['compiler'] = compiler
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config['genref'] = genref
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all_results = []
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# save current working dir
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