diff --git a/nemo_skills/evaluation/fill_majority_answer.py b/nemo_skills/evaluation/fill_majority_answer.py
index 8ef3b14cd..cd6e5e7d3 100644
--- a/nemo_skills/evaluation/fill_majority_answer.py
+++ b/nemo_skills/evaluation/fill_majority_answer.py
@@ -14,6 +14,7 @@
 
 import json
 import logging
+import shutil
 import sys
 from collections import Counter
 from itertools import zip_longest
@@ -75,7 +76,7 @@ def fill_majority_answer(cfg: FillMajorityAnswerConfig):
     new_answers = []
     all_predictions = []
     for idx, predictions in enumerate(tqdm(zip_longest(*file_handles))):
-        data = read_predictions(predictions)
+        data = read_predictions(predictions, idx, file_handles)
         for elem in data:
             if 'predicted_answer' not in elem:
                 elem['predicted_answer'] = extract_answer(elem['generation'])
@@ -106,8 +107,12 @@ def fill_majority_answer(cfg: FillMajorityAnswerConfig):
     for file_handle in file_handles:
         file_handle.close()
 
-    # writing the majority answers back to the files
-    file_handles = [open(file, "wt", encoding="utf-8") for file in unroll_files(cfg.input_files)]
+    # TODO: change to instead write to a fully new set of files
+    # Create temp filenames and open temp files for writing
+    input_files = unroll_files(cfg.input_files)
+    temp_files = [f"{file}-tmp" for file in input_files]
+    file_handles = [open(temp_file, "wt", encoding="utf-8") for temp_file in temp_files]
+
     for idx, predictions in enumerate(all_predictions):
         for lidx, handle in enumerate(file_handles):
             if cfg.ignore_if_not_none and predictions[lidx][cfg.fill_key] is not None:
@@ -118,7 +123,6 @@ def fill_majority_answer(cfg: FillMajorityAnswerConfig):
                 predictions[lidx]["majority_votes"], predictions[lidx]["total_votes"] = new_answers[idx][1]
             else:
                 predictions[lidx]["answer_rm_score"] = new_answers[idx][1]
-            # this is just a string match check, so for full correctness need to rerun the evaluator
             if cfg.fill_is_correct:
                 predictions[lidx]["is_correct"] = (
                     predictions[lidx]["predicted_answer"] == predictions[lidx]["expected_answer"]
@@ -127,8 +131,14 @@ def fill_majority_answer(cfg: FillMajorityAnswerConfig):
                 predictions[lidx].pop("is_correct")
             handle.write(json.dumps(predictions[lidx]) + "\n")
 
-    for file_handle in file_handles:
-        file_handle.close()
+    # Close all files before moving
+    for handle in file_handles:
+        handle.close()
+
+    # Move temp files to original files
+    input_files = unroll_files(cfg.input_files)
+    for temp_file, orig_file in zip(temp_files, input_files):
+        shutil.move(temp_file, orig_file)
 
 
 HELP_MESSAGE = get_help_message(FillMajorityAnswerConfig)
diff --git a/nemo_skills/evaluation/metrics/compute_metrics.py b/nemo_skills/evaluation/metrics/compute_metrics.py
index 1a4e5b289..3f89b5cb1 100644
--- a/nemo_skills/evaluation/metrics/compute_metrics.py
+++ b/nemo_skills/evaluation/metrics/compute_metrics.py
@@ -53,7 +53,7 @@ def compute_metrics(self, input_files):
             for idx, predictions in enumerate(zip_longest(*file_handles)):
                 if idx == self.max_samples:
                     break
-                data = read_predictions(predictions)
+                data = read_predictions(predictions, idx, file_handles)
                 # checking if we need to create a new metrics calculator
                 data_subset = data[0].get('subset_for_metrics', 'all')
                 if data_subset not in self.calculators:
diff --git a/nemo_skills/evaluation/metrics/utils.py b/nemo_skills/evaluation/metrics/utils.py
index fb6f3c120..2771a2330 100644
--- a/nemo_skills/evaluation/metrics/utils.py
+++ b/nemo_skills/evaluation/metrics/utils.py
@@ -12,12 +12,19 @@
 # See the License for the specific lang
 
 import json
+import logging
 
+LOG = logging.getLogger(__file__)
 
-def read_predictions(predictions):
+
+def read_predictions(predictions, line_idx, file_handles):
     data = []
-    for prediction in predictions:
-        prediction_dict = json.loads(prediction)
+    for file_idx, prediction in enumerate(predictions):
+        try:
+            prediction_dict = json.loads(prediction)
+        except Exception as e:
+            LOG.error(f"Error reading line %s in file %s: %s", line_idx + 1, file_handles[file_idx].name, e)
+            raise
         data.append(prediction_dict)
 
     return data
diff --git a/nemo_skills/pipeline/utils.py b/nemo_skills/pipeline/utils.py
index c5f4529d9..e302d6e52 100644
--- a/nemo_skills/pipeline/utils.py
+++ b/nemo_skills/pipeline/utils.py
@@ -19,6 +19,7 @@
 import sys
 import tarfile
 from dataclasses import dataclass
+from functools import lru_cache
 from pathlib import Path
 from typing import Optional
 
@@ -52,6 +53,9 @@ def get_unmounted_path(cluster_config, path):
     raise ValueError(f"The path '{path}' is not mounted. Check cluster config.")
 
 
+# caching the status assuming it doesn't change while experiment is being scheduled
+# otherwise this results in too many ssh calls
+@lru_cache
 def get_exp_handles(expname: str, ignore_finished=True, ignore_exp_not_exists=True) -> list[str]:
     """Will return the handles of the tasks in the experiment.
 
@@ -68,7 +72,7 @@ def _get_handles(exp):
         handles = []
         for job in exp.jobs:
             if not ignore_finished or (
-                job.status(exp._runner) in [AppState.RUNNING, AppState.PENDING, AppState.SUBMITTED]
+                job.status(exp._runner) in [AppState.RUNNING, AppState.PENDING, AppState.SUBMITTED, AppState.UNKNOWN]
             ):
                 handles.append(job.handle)
                 continue
@@ -314,8 +318,27 @@ def get_cluster_config(cluster=None, config_dir=None):
     return read_config(config_file)
 
 
+@lru_cache
+def _get_tunnel_cached(
+    job_dir: str,
+    host: str,
+    user: str,
+    identity: str | None = None,
+    shell: str | None = None,
+    pre_command: str | None = None,
+):
+    return run.SSHTunnel(
+        host=host,
+        user=user,
+        identity=identity,
+        shell=shell,
+        pre_command=pre_command,
+        job_dir=job_dir,
+    )
+
+
 def get_tunnel(cluster_config):
-    return run.SSHTunnel(**cluster_config["ssh_tunnel"])
+    return _get_tunnel_cached(**cluster_config["ssh_tunnel"])
 
 
 # Helper class and function to support streaming updates
@@ -429,7 +452,8 @@ def cluster_upload(tunnel: SSHTunnel, local_file: str, remote_dir: str, verbose:
     print(f"\nTransfer complete")
 
 
-def get_packager(extra_package_dirs: list[str] | None = None):
+@lru_cache
+def get_packager(extra_package_dirs: tuple[str] | None = None):
     """Will check if we are running from a git repo and use git packager or default packager otherwise."""
     nemo_skills_dir = Path(__file__).absolute().parents[1]
 
@@ -607,13 +631,15 @@ def get_executor(
     partition=None,
     time_min=None,
     dependencies=None,
-    extra_package_dirs: list[str] | None = None,
+    extra_package_dirs: tuple[str] | None = None,
     slurm_kwargs: dict | None = None,
 ):
     env_vars = get_env_variables(cluster_config)
     config_mounts = get_mounts_from_config(cluster_config, env_vars)
 
     mounts = mounts or config_mounts
+    if extra_package_dirs is not None:
+        extra_package_dirs = tuple(extra_package_dirs)
     packager = get_packager(extra_package_dirs=extra_package_dirs)
     if cluster_config["executor"] == "local":
         if num_nodes > 1:
diff --git a/nemo_skills/prompt/utils.py b/nemo_skills/prompt/utils.py
index 623a8b67b..c286140ea 100644
--- a/nemo_skills/prompt/utils.py
+++ b/nemo_skills/prompt/utils.py
@@ -266,14 +266,20 @@ def fill(
             return prompt_string
         else:
             if multi_turn_key is None:
-                messages = [
-                    {"role": "system", "content": self.config.system},
-                    {"role": "user", "content": self.build_user_message(input_dict)},
-                ]
+                if self.config.system:
+                    messages = [
+                        {"role": "system", "content": self.config.system},
+                    ]
+                else:
+                    messages = []
+                messages.append({"role": "user", "content": self.build_user_message(input_dict)})
                 if generation and include_generation:
                     messages.append({"role": "assistant", "content": generation})
             else:
-                messages = [{"role": "system", "content": self.config.system}]
+                if self.config.system:
+                    messages = [{"role": "system", "content": self.config.system}]
+                else:
+                    messages = []
                 for turn in input_dict[multi_turn_key][:-1]:
                     messages.append({"role": "user", "content": self.build_user_message(turn)})
                     messages.append({"role": "assistant", "content": turn["assistant"]})
diff --git a/tests/test_prompts.py b/tests/test_prompts.py
index 649321c0f..c3a321c7a 100644
--- a/tests/test_prompts.py
+++ b/tests/test_prompts.py
@@ -205,7 +205,6 @@ def test_generic_codegen_prompt():
     prompt = get_prompt('generic/codegen')
 
     expected_prompt = [
-        {'role': 'system', 'content': ''},
         {
             'role': 'user',
             'content': '''
@@ -228,7 +227,6 @@ def test_generic_default_prompt():
     prompt = get_prompt('generic/default')
 
     expected_prompt = [
-        {'role': 'system', 'content': ''},
         {
             'role': 'user',
             'content': 'How are you?',
@@ -911,10 +909,6 @@ def test_judge_math():
     prompt = get_prompt('judge/math')
 
     expected_prompt = [
-        {
-            'role': 'system',
-            'content': '',
-        },
         {
             'role': 'user',
             'content': '''
@@ -1012,10 +1006,6 @@ def test_judge_check_contamination():
     prompt = get_prompt('judge/check-contamination')
 
     expected_prompt = [
-        {
-            'role': 'system',
-            'content': '',
-        },
         {
             'role': 'user',
             'content': '''
@@ -1209,6 +1199,7 @@ def test_generic_lean4_fewshot_prompt():
         == expected_prompt
     )
 
+
 def test_mmlu_pro_llama_few_shot_prompt():
     prompt = get_prompt('llama3-instruct/mmlu_pro', 'llama3-instruct', 'mmlu_pro_few_shot_llama_math')
     expected_prompt = """<|begin_of_text|><|start_header_id|>system<|end_header_id|>
@@ -1340,10 +1331,10 @@ def test_mmlu_pro_llama_few_shot_prompt():
 """
 
     inputs = {
-        'question' : 'If the half-life of a radioactive substance is 8 years, how long will it take, in years, for two thirds of the substance to decay?',
-        'options' :'A. 22.45\nB. 12.21\nC. 12.68\nD. 7.69\nE. 16.89\nF. 20.76\nG. 4.68\nH. 14.12\nI. 10.33\nJ. 18.34',
+        'question': 'If the half-life of a radioactive substance is 8 years, how long will it take, in years, for two thirds of the substance to decay?',
+        'options': 'A. 22.45\nB. 12.21\nC. 12.68\nD. 7.69\nE. 16.89\nF. 20.76\nG. 4.68\nH. 14.12\nI. 10.33\nJ. 18.34',
     }
-    assert (prompt.fill(inputs) == expected_prompt)
+    assert prompt.fill(inputs) == expected_prompt
 
 
 def test_mmlu_pro_tigerlab_few_shot_prompt():
@@ -1441,10 +1432,9 @@ def test_mmlu_pro_tigerlab_few_shot_prompt():
 
 """
     inputs = {
-        'question' : "What is the square root of 81 squared?",
-        'options' : "A. 9^2\nB. 27\nC. 81^2\nD. 729\nE. 6561\nF. 12\nG. 162\nH. 243\nI. 81\nJ. 9",
-        "subset_for_metrics": "other"
+        'question': "What is the square root of 81 squared?",
+        'options': "A. 9^2\nB. 27\nC. 81^2\nD. 729\nE. 6561\nF. 12\nG. 162\nH. 243\nI. 81\nJ. 9",
+        "subset_for_metrics": "other",
     }
     print(prompt.fill(inputs))
     assert prompt.fill(inputs) == expected_prompt
-