oh-my-batch 0.5.1__tar.gz → 0.5.3__tar.gz

{oh_my_batch-0.5.1 → oh_my_batch-0.5.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: oh-my-batch
-Version: 0.5.1
+Version: 0.5.3
 Summary: 
 License: GPL
 Author: weihong.xu
@@ -37,6 +37,9 @@ pip install oh-my-batch
 
 ## Examples
 * [TESLA workflow](./examples/tesla/): A customizable active learning workflow for training machine learning potentials.
+* [TESLA PIMD workflow](./examples/tesla-pimd/): A customizable active learning workflow for training machine learning potentials with path integral molecular dynamics.
+* [LAMMPS benchmark](./examples/lammps-benchmark/): Find out the best MPI and OpenMP setup for LAMMPS through benchmarking.
+
 
 ## Use cases
 

{oh_my_batch-0.5.1 → oh_my_batch-0.5.3}/README.md

@@ -19,6 +19,9 @@ pip install oh-my-batch
 
 ## Examples
 * [TESLA workflow](./examples/tesla/): A customizable active learning workflow for training machine learning potentials.
+* [TESLA PIMD workflow](./examples/tesla-pimd/): A customizable active learning workflow for training machine learning potentials with path integral molecular dynamics.
+* [LAMMPS benchmark](./examples/lammps-benchmark/): Find out the best MPI and OpenMP setup for LAMMPS through benchmarking.
+
 
 ## Use cases
 

{oh_my_batch-0.5.1 → oh_my_batch-0.5.3}/oh_my_batch/batch.py

@@ -2,7 +2,6 @@ import shlex
 import os
 
 from .util import split_list, ensure_dir, expand_globs, mode_translate
-from .assets import get_asset
 
 
 class BatchMaker:

{oh_my_batch-0.5.1 → oh_my_batch-0.5.3}/oh_my_batch/combo.py

@@ -1,5 +1,6 @@
 from itertools import product
 from string import Template
+import traceback
 import random
 import json
 import os
@@ -164,7 +165,7 @@ class ComboMaker:
         return self
 
     def make_files(self, file: str, template: str, delimiter='@', mode=None, encoding='utf-8',
-                   extra_vars_from_file=None):
+                   extra_vars_from_file=None, ignore_error=False):
         """
         Make files from template against each combo
         The template file can include variables with delimiter.
@@ -181,6 +182,7 @@ class ComboMaker:
         :param mode: File mode, e.g. 755, 644, ...
         :param encoding: File encoding
         :param extra_vars_from_file: Load extra variables from json file, which can be used in template
+        :param ignore_error: If True, ignore error when making files
         """
         _delimiter = delimiter
 
@@ -189,24 +191,31 @@ class ComboMaker:
 
         combos = self._make_combos()
         for i, combo in enumerate(combos):
-            _template = template.format(i=i, **combo)
-            with open(_template, 'r') as f:
-                template_text = f.read()
-
-            if extra_vars_from_file is not None:
-                _vars_file = extra_vars_from_file.format(i=i, **combo)
-                with open(_vars_file, 'r') as f:
-                    extra_vars = json.load(f)
-            else:
-                extra_vars = {}
-            text = _Template(template_text).safe_substitute(combo, **extra_vars)
-            _file = file.format(i=i, **combo)
-            ensure_dir(_file)
-
-            with open(_file, 'w', encoding=encoding) as f:
-                f.write(text)
-            if mode is not None:
-                os.chmod(_file, mode_translate(str(mode)))
+            try:
+                _template = template.format(i=i, **combo)
+                with open(_template, 'r') as f:
+                    template_text = f.read()
+
+                if extra_vars_from_file is not None:
+                    _vars_file = extra_vars_from_file.format(i=i, **combo)
+                    with open(_vars_file, 'r') as f:
+                        extra_vars = json.load(f)
+                else:
+                    extra_vars = {}
+                text = _Template(template_text).safe_substitute(combo, **extra_vars)
+                _file = file.format(i=i, **combo)
+                ensure_dir(_file)
+
+                with open(_file, 'w', encoding=encoding) as f:
+                    f.write(text)
+                if mode is not None:
+                    os.chmod(_file, mode_translate(str(mode)))
+            except Exception as e:
+                if ignore_error:
+                    print(f"Error during making file, ignore: {e}")
+                    traceback.print_exc()
+                else:
+                    raise e
         return self
 
     def print(self, *line: str, file: str = '', mode=None, encoding='utf-8'):
@@ -254,6 +263,9 @@ class ComboMaker:
         return self
 
     def show_combos(self):
+        """
+        Show all combos in a human-readable format for debugging
+        """
         combos = self._make_combos()
         if not combos:
             print("No combos")

{oh_my_batch-0.5.1 → oh_my_batch-0.5.3}/oh_my_batch/job.py

@@ -87,14 +87,15 @@ class BaseJobManager:
                 break
 
             time.sleep(interval)
+
+        error = False
         for job in jobs:
-            error = False
             if not JobState.is_success(job['state']):
                 logger.error('Job %s failed', job['script'])
                 error = True
-        if error:
+        if error and not wait:
             raise RuntimeError('Some jobs failed')
-    
+
     def wait(self, *job_ids, timeout=None, interval=10):
         """
         Wait for jobs to finish
@@ -135,7 +136,7 @@ class BaseJobManager:
 
     def _update_state(self, jobs: List[dict]):
         raise NotImplementedError
-    
+
     def _submit_job(self, job: dict, submit_opts: str):
         raise NotImplementedError
 
@@ -170,7 +171,7 @@ class Slurm(BaseJobManager):
                     break
             else:
                 logger.error('Job %s not found in sacct output', job['id'])
-        return jobs 
+        return jobs
 
     def _submit_job(self, job:dict, submit_opts:str):
         submit_cmd = f'{self._sbatch_bin} {submit_opts} {job["script"]}'

{oh_my_batch-0.5.1 → oh_my_batch-0.5.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "oh-my-batch"
-version = "0.5.1"
+version = "0.5.3"
 description = ""
 authors = ["weihong.xu <xuweihong.cn@gmail.com>"]
 license = "GPL"