Bugfixed optimize_hyperparams.py

hyperparameter_search/optimize_hyperparams.py

@@ -69,7 +69,10 @@ def main(args):
         ranges_dict = yaml.load(fh, yaml.FullLoader)
 
     # Generate dbs
-    with open(args.kmer_list, 'r') as fh: kmer_list = [k.strip() for k in fh.readlines() if len(k.strip())]
+    with open(args.kmer_list, 'r') as fh:
+        kmer_list = [k.strip() for k in fh.readlines() if len(k.strip())]
+
+    kmer_list = kmer_list[:2]
     db_dir = parse_output_path(f'{args.out_dir}dbs/')
     logs_dir = parse_output_path(f'{args.out_dir}logs/')
 
@@ -108,30 +111,26 @@ def main(args):
                     "--directoryperdb", "--fork", "--journal",
                     "--logpath", f"{args.out_dir}mongodb_log.log"])
 
-    try:
-        # start worker processses
-        worker_cmd_list = ["hyperopt-mongo-worker", "--mongo=localhost:1234/db"]
-        worker_list = [subprocess.Popen(worker_cmd_list,
-                                        stdout=open(os.devnull, 'wb'),
-                                        stderr=open(os.devnull, 'wb'))
-                       for _ in range(args.hyperopt_parallel_jobs)]
-
-        # minimize objective
-        trials = MongoTrials('mongo://localhost:1234/db/jobs')
-        # trials = hp.Trials()
-        out_param_dict = hp.fmin(fmin_objective,
-                                 space=space,
-                                 algo=hp.tpe.suggest,
-                                 trials=trials,
-                                 max_evals=args.hyperopt_iters,
-                                 max_queue_len=args.hyperopt_parallel_jobs)
-        for worker in worker_list:
-            worker.terminate()
-        subprocess.run(['mongod', '--shutdown', '--dbpath', mongodb_pth])
-    except Exception as e:
-        print(f'Had to exit: {e}')
-        subprocess.run(['mongod', '--shutdown', '--dbpath', mongodb_pth])  # todo can't this be done more elegantly?
 
+    # start worker processses
+    worker_cmd_list = ["hyperopt-mongo-worker", "--mongo=localhost:1234/db"]
+    worker_list = [subprocess.Popen(worker_cmd_list,
+                                    stdout=open(os.devnull, 'wb'),
+                                    stderr=open(os.devnull, 'wb'))
+                   for _ in range(args.hyperopt_parallel_jobs)]
+
+    # minimize objective
+    trials = MongoTrials('mongo://localhost:1234/db/jobs', exp_key='test_1')
+    out_param_dict = hp.fmin(fmin_objective,
+                             space=space,
+                             algo=hp.tpe.suggest,
+                             trials=trials,
+                             max_evals=args.hyperopt_iters)
+    for worker in worker_list:
+        worker.terminate()
+    subprocess.run(['mongod', '--shutdown', '--dbpath', mongodb_pth])
+
+    print(out_param_dict)
     for p in out_param_dict:
         if ranges_dict['variable'][p]['type'] == 'int': out_param_dict[p] = int(out_param_dict[p])
     for p in ranges_dict['nonvariable']: out_param_dict[p] = ranges_dict['nonvariable'][p]