Merge pull request NHERI-SimCenter#401 from bsaakash/master

abs - surrogate-aided Bayesian calibration

Author: fmckenna

modules/performFEM/OpenSees/createOpenSeesDriver.cpp

@@ -229,6 +229,7 @@ int main(int argc, const char **argv) {
 
     dpreproCommand = remoteDir + std::string("/applications/performUQ/templateSub/simCenterSub");
     openSeesCommand = std::string("/home1/00477/tg457427/bin/OpenSees");
+    // openSeesCommand = std::string("/opt/apps/intel24/impi21/opensees/3.7.1/bin/OpenSees");
     pythonCommand = std::string("python3");
 
   }

modules/performUQ/UCSD_UQ/UCSD_UQ.py

@@ -30,27 +30,28 @@ def main(args):  # noqa: D103
         else:
             pythonCommand = 'python3'  # noqa: N806
 
-        mainScriptDir = os.path.dirname(os.path.realpath(__file__))  # noqa: PTH120, N806
-        mainScript = os.path.join(mainScriptDir, 'mainscript.py')  # noqa: PTH118, N806
-        templateDir = os.getcwd()  # noqa: PTH109, N806
-        tmpSimCenterDir = str(Path(templateDir).parents[0])  # noqa: N806
-
         # Change permission of driver file
         os.chmod(driverFile, stat.S_IXUSR | stat.S_IRUSR | stat.S_IXOTH)  # noqa: PTH101
         st = os.stat(driverFile)  # noqa: PTH116
         os.chmod(driverFile, st.st_mode | stat.S_IEXEC)  # noqa: PTH101
         driverFile = './' + driverFile  # noqa: N806
-        print('WORKFLOW: ' + driverFile)  # noqa: T201
+
+        template_dir = Path.cwd()
+        tmp_simcenter_dir = template_dir.parent
+
+        main_script_dir = Path(__file__).parent
+        main_script = main_script_dir / 'mainscript.py'
 
         command = (
-            f'"{pythonCommand}" "{mainScript}" "{tmpSimCenterDir}"'
-            f' "{templateDir}" {runType} {driverFile} {workflowInput}'
+            f'"{pythonCommand}" "{main_script!s}" "{tmp_simcenter_dir!s}"'
+            f' "{template_dir!s}" {runType} {driverFile} {workflowInput}'
         )
+
         print(command)  # noqa: T201
 
         command_list = shlex.split(command)
 
-        err_file = Path(tmpSimCenterDir) / 'UCSD_UQ.err'
+        err_file = tmp_simcenter_dir / 'UCSD_UQ.err'
         err_file.touch()
 
         try:

modules/performUQ/UCSD_UQ/mainscript.py

@@ -1,81 +1,139 @@
-"""authors: Mukesh Kumar Ramancha, Maitreya Manoj Kurumbhati, Prof. J.P. Conte, Aakash Bangalore Satish*
-affiliation: University of California, San Diego, *SimCenter, University of California, Berkeley
-
-"""  # noqa: INP001, D205, D400
-
-# ======================================================================================================================
+"""
+module: mainscript.py.
+
+This script executes an uncertainty quantification (UQ) analysis based on an input JSON file.
+It dynamically selects the appropriate UQ method in the UCSD_UQ engine and executes the corresponding script.
+
+### Functionality:
+- Adds the `common` directory to `sys.path` to allow importing necessary modules.
+- Parses command-line arguments for necessary paths and parameters.
+- Reads and validates the JSON input file.
+- Determines the appropriate UQ script to run based on `uqType` and `useApproximation` flags.
+- Constructs the command and executes the selected script.
+- Captures errors and logs them to `UCSD_UQ.err`.
+
+### Usage:
+```sh
+python script.py /path/to/working /path/to/template runningLocal driver input.json
+```
+
+### Arguments:
+1. `working_dir` (Path): Path to the working directory where computations are performed.
+2. `template_dir` (Path): Path to the template directory containing the input JSON file.
+3. `run_type` (str): Execution mode (`runningLocal` or `runningRemote`).
+4. `driver_file` (str): Name of the driver file.
+5. `input_file` (Path): Name of the JSON input file.
+
+### Error Handling:
+- If an invalid JSON file is provided, the script exits with an error.
+- If an unknown UQ type is encountered, the script exits with an error.
+- If an exception occurs during execution, the error is logged in `UCSD_UQ.err`.
+
+"""
+
+import argparse
 import json
-import shlex
 import sys
 import traceback
 from pathlib import Path
 
-path_to_common_uq = Path(__file__).parent.parent / 'common'
-sys.path.append(str(path_to_common_uq))
+# Dynamically add 'common' directory to sys.path
+path_to_common_uq = Path(__file__).resolve().parent.parent / 'common'
+if path_to_common_uq not in sys.path:
+    sys.path.insert(0, str(path_to_common_uq))
 
 
-# ======================================================================================================================
-def main(input_args):  # noqa: D103
-    # # Initialize analysis
-    # path_to_UCSD_UQ_directory = Path(input_args[2]).resolve().parent
-    # path_to_working_directory = Path(input_args[3]).resolve()
-    # path_to_template_directory = Path(input_args[4]).resolve()
-    # run_type = input_args[5]  # either "runningLocal" or "runningRemote"
-    # driver_file_name = input_args[6]
-    # input_file_name = input_args[7]
+def parse_args():
+    """Parse command-line arguments."""
+    parser = argparse.ArgumentParser(description='Run UQ analysis.')
+    parser.add_argument('working_dir', type=Path, help='Path to working directory')
+    parser.add_argument('template_dir', type=Path, help='Path to template directory')
+    parser.add_argument(
+        'run_type', choices=['runningLocal', 'runningRemote'], help='Run type'
+    )
+    parser.add_argument('driver_file', help='Driver file name')
+    parser.add_argument('input_file', type=Path, help='Input JSON file')
+    return parser.parse_args()
+
 
-    # Initialize analysis
-    path_to_UCSD_UQ_directory = Path(input_args[0]).resolve().parent  # noqa: N806, F841
-    path_to_working_directory = Path(input_args[1]).resolve()
-    path_to_template_directory = Path(input_args[2]).resolve()
-    run_type = input_args[3]  # either "runningLocal" or "runningRemote"
-    driver_file_name = input_args[4]
-    input_file_name = input_args[5]
+def load_json(file_path):
+    """Load and validate JSON input."""
+    try:
+        with file_path.open(encoding='utf-8') as f:
+            data = json.load(f)
+    except json.JSONDecodeError as e:
+        sys.stderr.write(f'ERROR: Invalid JSON format in {file_path}:\n{e}\n')
+        sys.exit(1)
 
-    Path('dakotaTab.out').unlink(missing_ok=True)
-    Path('dakotaTabPrior.out').unlink(missing_ok=True)
+    if 'UQ' not in data:
+        sys.stderr.write(f"ERROR: Missing 'UQ' key in input JSON: {file_path}\n")
+        sys.exit(1)
 
-    input_file_full_path = path_to_template_directory / input_file_name
+    return data
 
-    with open(input_file_full_path, encoding='utf-8') as f:  # noqa: PTH123
-        inputs = json.load(f)
 
-    uq_inputs = inputs['UQ']
-    if uq_inputs['uqType'] == 'Metropolis Within Gibbs Sampler':
-        import mainscript_hierarchical_bayesian
+def select_uq_script(uq_inputs):
+    """Determine which UQ script to run."""
+    uq_methods = {
+        'Metropolis Within Gibbs Sampler': 'mainscript_hierarchical_bayesian',
+    }
 
-        main_function = mainscript_hierarchical_bayesian.main
-    else:
-        import mainscript_tmcmc
+    module_name = uq_methods.get(uq_inputs['uqType'], 'mainscript_tmcmc')
+    if uq_inputs.get('useApproximation'):
+        module_name = 'gp_ab_algorithm'
 
-        main_function = mainscript_tmcmc.main
+    try:
+        module = __import__(module_name)
+    except ImportError:
+        sys.stderr.write(
+            f'ERROR: Could not import {module_name}. Ensure the script exists.\n'
+        )
+        sys.exit(1)
 
-    command = (
-        f'"{path_to_working_directory}" "{path_to_template_directory}" '
-        f'{run_type} "{driver_file_name}" "{input_file_full_path}"'
-    )
-    command_list = shlex.split(command)
+    return module.main
 
-    # Check if 'UCSD_UQ.err' exists, and create it if not
-    err_file = path_to_working_directory / 'UCSD_UQ.err'
 
-    if not err_file.exists():
-        err_file.touch()  # Create the file
+def main():
+    """Run UQ analysis."""
+    args = parse_args()
+
+    # Ensure output error file exists
+    err_file = args.working_dir / 'UCSD_UQ.err'
+    err_file.touch(exist_ok=True)
+
+    # Remove any previous output files
+    (args.working_dir / 'dakotaTab.out').unlink(missing_ok=True)
+    (args.working_dir / 'dakotaTabPrior.out').unlink(missing_ok=True)
+
+    # Load JSON input file
+    inputs = load_json(args.template_dir / args.input_file)
+    uq_inputs = inputs['UQ']
+
+    # Select the appropriate UQ script
+    main_function = select_uq_script(uq_inputs)
+
+    # Construct the command
+    command = [
+        str(args.working_dir),
+        str(args.template_dir),
+        args.run_type,
+        args.driver_file,
+        str(args.template_dir / args.input_file),
+    ]
 
-    # Try running the main_function and catch any exceptions
     try:
-        main_function(command_list)
-    except Exception:  # noqa: BLE001
-        # Write the exception message to the .err file
+        main_function(command)
+    except Exception:
+        err_msg = f'ERROR: An exception occurred:\n{traceback.format_exc()}\n'
         with err_file.open('a') as f:
-            f.write('ERROR: An exception occurred:\n')
-            f.write(f'{traceback.format_exc()}\n')
+            f.write(err_msg)
+        sys.stderr.write(err_msg)
 
+        if args.run_type == 'runningRemote':
+            from mpi4py import MPI
 
-# ======================================================================================================================
+            MPI.COMM_WORLD.Abort(1)
 
-if __name__ == '__main__':
-    input_args = sys.argv
-    main(input_args)
 
-# ======================================================================================================================
+if __name__ == '__main__':
+    main()

modules/performUQ/common/CMakeLists.txt

@@ -23,4 +23,9 @@ simcenter_add_python_script(SCRIPT gp_ab_algorithm.py)
 simcenter_add_python_script(SCRIPT gp_model.py)
 simcenter_add_python_script(SCRIPT principal_component_analysis.py)
 simcenter_add_python_script(SCRIPT space_filling_doe.py)
-simcenter_add_python_script(SCRIPT tmcmc.py)
+simcenter_add_python_script(SCRIPT tmcmc.py)
+simcenter_add_python_script(SCRIPT safer_cholesky.py)
+simcenter_add_python_script(SCRIPT kernel_density_estimation.py)
+simcenter_add_python_script(SCRIPT config_utilities.py)
+simcenter_add_python_script(SCRIPT logging_utilities.py)
+simcenter_add_python_script(SCRIPT log_likelihood_functions.py)