ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

use the log file with 1 proc in serial runs, removed examples/bpm/impact/brokenDump

Browse Source
This commit is contained in:
Trung Nguyen
2024-08-28 12:57:58 -05:00
parent a59ac7ec86
commit f5ffb28a1f
2 changed files with 54 additions and 3945 deletions
Download Patch File Download Diff File Expand all files Collapse all files

3914
examples/bpm/impact/brokenDump
View File

File diff suppressed because it is too large Load Diff

85
tools/regression-tests/run_tests.py
View File

@ -1,6 +1,6 @@
#!/usr/bin/env python3
'''
UPDATE: August 13, 2024:
UPDATE: August 28, 2024:
Launching the LAMMPS binary under testing using a configuration defined in a yaml file (e.g. config.yaml).
Comparing the output thermo with that in the existing log file (with the same nprocs)
+ data in the log files are extracted and converted into yaml data structure
@ -13,6 +13,8 @@ With the current features, users can:
+ specify tolerances for individual quantities for any input script to override the global values
+ launch tests with `mpirun` with all supported command line features (multiple procs, multiple paritions, and suffices)
+ skip certain input files (whose names match specified patterns) if not interested, or packaged not installed, or no reference log file exists
+ set a timeout for every input script run if they may take too long
+ skip numerical checks if the goal is just to check if the runs do not fail
+ simplify the main LAMMPS builds, as long as a LAMMPS binary is available
+ keep track of the testing progress to resume the testing from the last checkpoint (skipping completed runs)
+ distribute the input list across multiple processes via multiprocessing, or
@ -49,16 +51,10 @@ Example usage:
--list-subfolders=list_subfolders1.txt --output-file=output1.txt --progress-file=progress1.yaml \
--log-file=run1.log
4) Specify a list of example input scripts
4) Specify a list of example input scripts (e.g. obtained from running tools/regression-tests/get-quick-list.py)
python3 run_tests.py --lmp-bin=/path/to/lmp_binary --config-file=/path/to/config/file/config.yaml \
--list-input=input-list-1.txt --output-file=output1.txt --progress-file=progress1.yaml \
--log-file=run1.log
The example subfolders can also be loaded from a text file list_subfolders1.txt:
python3 run_tests.py --lmp-bin=/path/to/lmp_binary --config-file=/path/to/config/file/config.yaml \
--list-subfolders=list_subfolders1.txt --output-file=output1.txt --progress-file=progress1.yaml \
--log-file=run1.log
--list-input=input_list.txt
5) Test a LAMMPS binary with the whole top-level /examples folder in a LAMMPS source tree
python3 run_tests.py --lmp-bin=/path/to/lmp_binary --examples-top-level=/path/to/lammps/examples
@ -248,7 +244,8 @@ def iterate(lmp_binary, input_folder, input_list, config, results, progress_file
if fnmatch.fnmatch(file, pattern):
p = file.rsplit('.', 1)
if p[1].isnumeric():
if use_valgrind == True:
# if using valgrind or running in serial, then use the log file with 1 proc
if use_valgrind == True or config['mpiexec'] == "":
if int(p[1]) == 1:
max_np = int(p[1])
ref_logfile_exist = True
@ -263,10 +260,11 @@ def iterate(lmp_binary, input_folder, input_list, config, results, progress_file
# if there is no ref log file and not running with valgrind
if ref_logfile_exist == False and use_valgrind == False:
max_np = 4
# if the maximum number of procs is different from the value in the configuration file
# then override the setting for this input script
saved_nprocs = config['nprocs']
# if the maximum number of procs is different from the value in the configuration file
# then override the setting for this particular input script
if max_np != int(config['nprocs']):
config['nprocs'] = str(max_np)
@ -318,6 +316,41 @@ def iterate(lmp_binary, input_folder, input_list, config, results, progress_file
test_id = test_id + 1
continue
# check if a log.lammps file exists in the current folder
if os.path.isfile("log.lammps") == False:
logger.info(f" ERROR: No log.lammps generated with {input_test} with return code {returncode}.\n")
logger.info(f" Output:")
logger.info(f" {output}")
logger.info(f" Error:\n{error}")
progress.write(f"{input}: {{ folder: {input_folder}, status: \"error, no log.lammps\" }}\n")
progress.close()
num_error = num_error + 1
test_id = test_id + 1
continue
else:
# save a copy of the log file for further inspection
cmd_str = f"cp log.lammps log.{basename}.{nprocs}"
p = subprocess.run(cmd_str, shell=True, text=True, capture_output=True)
# if skip numerical checks, then skip the rest
if skip_numerical_check == True:
msg = "completed, skipping numerical checks"
if use_valgrind == True:
if "All heap blocks were freed" in error:
msg += ", no memory leak"
else:
msg += ", memory leaks detected"
num_memleak = num_memleak + 1
result.status = msg
results.append(result)
progress.write(f"{input}: {{ folder: {input_folder}, status: \"{msg}\" }}\n")
progress.close()
# count the number of completed runs
num_completed = num_completed + 1
test_id = test_id + 1
continue
# if there is no ERROR in the output, but there is no Total wall time printed out
if "Total wall time" not in output:
logger.info(f" ERROR: no Total wall time in the output.\n")
@ -342,22 +375,6 @@ def iterate(lmp_binary, input_folder, input_list, config, results, progress_file
test_id = test_id + 1
continue
# check if a log.lammps file exists in the current folder
if os.path.isfile("log.lammps") == False:
logger.info(f" ERROR: No log.lammps generated with {input_test} with return code {returncode}.\n")
logger.info(f" Output:")
logger.info(f" {output}")
logger.info(f" Error:\n{error}")
progress.write(f"{input}: {{ folder: {input_folder}, status: \"error, no log.lammps\" }}\n")
progress.close()
num_error = num_error + 1
test_id = test_id + 1
continue
else:
# save a copy of the log file for further inspection
cmd_str = f"cp log.lammps log.{basename}.{nprocs}"
p = subprocess.run(cmd_str, shell=True, text=True, capture_output=True)
# parse thermo output in log.lammps from the run
thermo = extract_data_to_yaml("log.lammps")
num_runs = len(thermo)
@ -724,9 +741,12 @@ def get_lammps_build_configuration(lmp_binary):
'''
def execute(lmp_binary, config, input_file_name, generate_ref_yaml=False):
cmd_str = ""
# check if mpiexec/mpirun is used
if config['mpiexec']:
cmd_str += config['mpiexec'] + " " + config['mpiexec_numproc_flag'] + " " + config['nprocs'] + " "
cmd_str += lmp_binary + " -in " + input_file_name + " " + config['args']
logger.info(f" Executing: {cmd_str}")
# set a timeout (in seconds) for each run
timeout = 60
@ -739,7 +759,7 @@ def execute(lmp_binary, config, input_file_name, generate_ref_yaml=False):
return cmd_str, p.stdout, p.stderr, p.returncode
except subprocess.TimeoutExpired:
msg = f" Timeout for {cmd_str} ({timeout} s) expired"
msg = f" Timeout for: {cmd_str} ({timeout}s expired)"
logger.info(msg)
print(msg)
@ -886,6 +906,8 @@ if __name__ == "__main__":
parser.add_argument("--progress-file",dest="progress_file", default=progress_file, help="Progress file")
parser.add_argument("--analyze",dest="analyze", action='store_true', default=False,
help="Analyze the testing folders and report statistics, not running the tests")
parser.add_argument("--skip-numerical-check",dest="skip_numerical_check", action='store_true', default=False,
help="Generating reference data")
args = parser.parse_args()
@ -907,6 +929,7 @@ if __name__ == "__main__":
verbose = args.verbose
log_file = args.logfile
analyze = args.analyze
skip_numerical_check = args.skip_numerical_check
resume = args.resume
progress_file = args.progress_file