Fix #839: Make jobid 1-based.

Yank/commands/script.py

@@ -35,7 +35,7 @@
 
 Optional Arguments:
   --jobid=INTEGER               You can run only a subset of the experiments by specifying jobid and njobs, where
-                                0 <= job_id <= n_jobs-1. In this case, njobs must be specified as well and YANK will
+                                1 <= job_id <= n_jobs. In this case, njobs must be specified as well and YANK will
                                 run only 1/n_jobs of the experiments. This can be used to run several separate YANK
                                 executions in parallel starting from the same script.
   --njobs=INTEGER               Specify the total number of parallel executions. jobid has to be specified too.

Yank/experiment.py

@@ -502,7 +502,7 @@ class ExperimentBuilder(object):
         can load it later by using :func:`parse` (default is None).
     job_id : None or int
         If you want to split the experiments among different executions,
-        you can set this to an integer 0 <= job_id <= n_jobs-1, and this
+        you can set this to an integer 1 <= job_id <= n_jobs, and this
         :class:`ExperimentBuilder` will run only 1/n_jobs of the experiments.
     n_jobs : None or int
         If ``job_id`` is specified, this is the total number of jobs that
@@ -606,8 +606,8 @@ def __init__(self, script=None, job_id=None, n_jobs=None):
         if job_id is not None:
             if n_jobs is None:
                 raise ValueError('n_jobs must be specified together with job_id')
-            if not 0 <= job_id <= n_jobs:
-                raise ValueError('job_id must be between 0 and n_jobs ({})'.format(n_jobs))
+            if not 1 <= job_id <= n_jobs:
+                raise ValueError('job_id must be between 1 and n_jobs ({})'.format(n_jobs))
 
         self._job_id = job_id
         self._n_jobs = n_jobs
@@ -1021,7 +1021,10 @@ def _expand_experiments(self):
 
             # Loop over all combinations
             for name, combination in experiment.named_combinations(separator='_', max_name_length=50):
-                if self._job_id is None or experiment_id % self._n_jobs == self._job_id:
+                # Both self._job_id and self._job_id-1 work (self._job_id is 1-based),
+                # but we use the latter just because it makes it easier to identify in
+                # advance which job ids are associated to which experiments.
+                if self._job_id is None or experiment_id % self._n_jobs == self._job_id-1:
                     yield os.path.join(output_dir, name), combination
                 experiment_id += 1
 

Yank/tests/test_experiment.py

@@ -1875,11 +1875,11 @@ def test_expand_experiments():
     experiment_systems = utils.CombinatorialLeaf(['explicit-system', 'implicit-system', 'hydration-system'])
     template_script['experiments']['system'] = experiment_systems
 
-    exp_builder = ExperimentBuilder(script=template_script, job_id=0, n_jobs=2)
+    exp_builder = ExperimentBuilder(script=template_script, job_id=1, n_jobs=2)
     experiments = list(exp_builder._expand_experiments())
     assert len(experiments) == 2
 
-    exp_builder = ExperimentBuilder(script=template_script, job_id=1, n_jobs=2)
+    exp_builder = ExperimentBuilder(script=template_script, job_id=2, n_jobs=2)
     experiments = list(exp_builder._expand_experiments())
     assert len(experiments) == 1