diff --git a/examples/audio/process_audio.py b/examples/audio/process_audio.py
index 8657d53ef957..d34461937284 100644
--- a/examples/audio/process_audio.py
+++ b/examples/audio/process_audio.py
@@ -176,6 +176,7 @@ def main(cfg: ProcessConfig) -> ProcessConfig:
             raise RuntimeError('Model does not have a sampler')
 
     if cfg.audio_dir is not None:
+        input_dir = cfg.audio_dir
         filepaths = list(glob.glob(os.path.join(cfg.audio_dir, f"**/*.{cfg.audio_type}"), recursive=True))
     else:
         # get filenames from manifest
@@ -193,6 +194,15 @@ def main(cfg: ProcessConfig) -> ProcessConfig:
                     audio_file = manifest_dir / audio_file
                 filepaths.append(str(audio_file.absolute()))
 
+        # common path for all files
+        common_path = os.path.commonpath(filepaths)
+        if Path(common_path).is_relative_to(manifest_dir):
+            # if all paths are relative to the manifest, use manifest dir as input dir
+            input_dir = manifest_dir
+        else:
+            # use the parent of the common path as input dir
+            input_dir = Path(common_path).parent
+
     if cfg.max_utts is not None:
         # Limit the number of utterances to process
         filepaths = filepaths[: cfg.max_utts]
@@ -238,6 +248,7 @@ def autocast():
                 batch_size=cfg.batch_size,
                 num_workers=cfg.num_workers,
                 input_channel_selector=cfg.input_channel_selector,
+                input_dir=input_dir,
             )
 
     logging.info(f"Finished processing {len(filepaths)} files!")
diff --git a/nemo/collections/audio/models/audio_to_audio.py b/nemo/collections/audio/models/audio_to_audio.py
index 60c16f756f58..57b4c9d48119 100644
--- a/nemo/collections/audio/models/audio_to_audio.py
+++ b/nemo/collections/audio/models/audio_to_audio.py
@@ -332,6 +332,7 @@ def process(
         batch_size: int = 1,
         num_workers: Optional[int] = None,
         input_channel_selector: Optional[ChannelSelectorType] = None,
+        input_dir: Optional[str] = None,
     ) -> List[str]:
         """
         Takes paths to audio files and returns a list of paths to processed
@@ -344,6 +345,7 @@ def process(
             num_workers: Number of workers for the dataloader
             input_channel_selector (int | Iterable[int] | str): select a single channel or a subset of channels from multi-channel audio.
                             If set to `'average'`, it performs averaging across channels. Disabled if set to `None`. Defaults to `None`.
+            input_dir: Optional, directory that contains the input files. If provided, the output directory will mirror the input directory structure.
 
         Returns:
             Paths to processed audio signals.
@@ -413,9 +415,17 @@ def process(
 
                     for example_idx in range(processed_batch.size(0)):
                         # This assumes the data loader is not shuffling files
-                        file_name = os.path.basename(paths2audio_files[file_idx])
+                        if input_dir is not None:
+                            # Make sure the output has the same directory structure as the input
+                            filepath_relative = os.path.relpath(paths2audio_files[file_idx], start=input_dir)
+                        else:
+                            # Input dir is not provided, save files in the output directory
+                            filepath_relative = os.path.basename(paths2audio_files[file_idx])
                         # Prepare output file
-                        output_file = os.path.join(output_dir, f'processed_{file_name}')
+                        output_file = os.path.join(output_dir, filepath_relative)
+                        # Create output dir if necessary
+                        if not os.path.isdir(os.path.dirname(output_file)):
+                            os.makedirs(os.path.dirname(output_file))
                         # Crop the output signal to the actual length
                         output_signal = processed_batch[example_idx, :, : input_length[example_idx]].cpu().numpy()
                         # Write audio
diff --git a/nemo/collections/llm/gpt/data/packed_sequence.py b/nemo/collections/llm/gpt/data/packed_sequence.py
index 345489ea0b63..1f43bce99e62 100644
--- a/nemo/collections/llm/gpt/data/packed_sequence.py
+++ b/nemo/collections/llm/gpt/data/packed_sequence.py
@@ -78,7 +78,7 @@ def prepare_packed_sequence_data(
     sequences, histogram = create_hist(dataset, max_seq_length)
 
     assignments = create_packing_strategy(histogram, packed_sequence_size, packing_algorithm)
-    output_data = fill_packing_strategy(assignments, sequences, packed_sequence_size)
+    output_data = fill_packing_strategy(assignments, sequences, packed_sequence_size, tokenizer.eos_id)
 
     # save output data
     np.save(output_path, output_data)
diff --git a/nemo/deploy/nlp/__init__.py b/nemo/deploy/nlp/__init__.py
index 5ebbe6816664..633544e300ed 100644
--- a/nemo/deploy/nlp/__init__.py
+++ b/nemo/deploy/nlp/__init__.py
@@ -12,15 +12,5 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-use_query_llm = True
-try:
-    from nemo.deploy.nlp.query_llm import NemoQueryLLM, NemoQueryLLMPyTorch
-except Exception:
-    use_query_llm = False
-
-use_megatron_llm = True
-try:
-    from nemo.deploy.nlp.megatronllm_deployable import MegatronLLMDeployable
-except Exception:
-    use_megatron_llm = False
+from nemo.deploy.nlp.megatronllm_deployable import MegatronLLMDeployable
+from nemo.deploy.nlp.query_llm import NemoQueryLLM, NemoQueryLLMPyTorch
diff --git a/nemo/utils/sequence_packing_utils.py b/nemo/utils/sequence_packing_utils.py
index 2ca03ce44b67..647a0401bd5b 100644
--- a/nemo/utils/sequence_packing_utils.py
+++ b/nemo/utils/sequence_packing_utils.py
@@ -176,7 +176,7 @@ def create_packing_strategy(
 
 
 def fill_packing_strategy(
-    assignments: List[List[int]], sequences: Dict[int, List[Dict]], pack_size: int
+    assignments: List[List[int]], sequences: Dict[int, List[Dict]], pack_size: int, pad_id: int
 ) -> List[Dict]:
     """
     Fills the packing strategy with actual sequence data based on assignments and sequence information.
@@ -192,6 +192,7 @@ def fill_packing_strategy(
           sequences: A dictionary where keys are sequence lengths and values are lists of corresponding sequences
                       from the dataset (output of 'create_hist').
           pack_size: The maximum capacity of each bin.
+          pad_id: The tokenizer's padding token.
 
     Returns:
           output_data: A list of dictionaries, where each dictionary represents a packed sequence with its input IDs,
@@ -205,7 +206,13 @@ def fill_packing_strategy(
             input_ids = np.array([x['input_ids'] for x in per_seq_data])[perm].tolist()
             try:
                 loss_mask = np.array(
-                    [[idx >= x['answer_start_idx'] for idx in range(len(x['input_ids']))] for x in per_seq_data]
+                    [
+                        [
+                            idx >= x['answer_start_idx'] and x['input_ids'][idx] != pad_id
+                            for idx in range(len(x['input_ids']))
+                        ]
+                        for x in per_seq_data
+                    ]
                 )[perm].tolist()
             except KeyError:
                 loss_mask = None
diff --git a/scripts/dataset_processing/add_noise.py b/scripts/dataset_processing/add_noise.py
index 2aefc8b03974..e273d0de0af2 100644
--- a/scripts/dataset_processing/add_noise.py
+++ b/scripts/dataset_processing/add_noise.py
@@ -131,12 +131,15 @@ def add_noise(infile, snrs, noise_manifest, out_dir, num_workers=1):
 def main():
     parser = argparse.ArgumentParser()
     parser.add_argument(
-        "--input_manifest", type=str, required=True, help="clean test set",
+        "--input_manifest",
+        type=str,
+        required=True,
+        help="clean test set",
     )
     parser.add_argument("--noise_manifest", type=str, required=True, help="path to noise manifest file")
     parser.add_argument("--out_dir", type=str, required=True, help="destination directory for audio and manifests")
     parser.add_argument("--snrs", type=int, nargs="+", default=[0, 10, 20, 30])
-    parser.add_argument("--seed", type=int, default=42)
+    parser.add_argument("--seed", type=int, default=None)
     parser.add_argument("--num_workers", default=1, type=int)
     parser.add_argument("--sample_rate", default=16000, type=int)
     parser.add_argument(
diff --git a/scripts/deploy/nlp/query_inframework.py b/scripts/deploy/nlp/query_inframework.py
index e77ab72a1f04..a62e09fa071d 100644
--- a/scripts/deploy/nlp/query_inframework.py
+++ b/scripts/deploy/nlp/query_inframework.py
@@ -15,7 +15,7 @@
 import argparse
 import sys
 
-from nemo.deploy.nlp.query_llm import NemoQueryLLMPyTorch
+from nemo.deploy.nlp import NemoQueryLLMPyTorch
 
 
 def get_args(argv):
diff --git a/scripts/llm/llama3_pretraining.py b/scripts/llm/pretraining.py
similarity index 80%
rename from scripts/llm/llama3_pretraining.py
rename to scripts/llm/pretraining.py
index a5ca3a496a88..1b4a33832a56 100644
--- a/scripts/llm/llama3_pretraining.py
+++ b/scripts/llm/pretraining.py
@@ -13,8 +13,8 @@
 # limitations under the License.
 
 # NOTE: This script is only an example of using NeMo with NeMo-Run's APIs and is subject to change without notice.
-# This script is used for pretraining a Llama3 model, specifically for the 8b or 70b model variants, on local and slurm executors.
-# It uses NeMo 2.0 recipes (https://github.com/NVIDIA/NeMo/blob/main/nemo/collections/llm/recipes/llama3_8b.py#L74) and NeMo-Run (https://github.com/NVIDIA/NeMo-Run) to configure and execute the runs.
+# This script is used for pretraining on local and slurm executors.
+# It uses NeMo 2.0 recipes (https://github.com/NVIDIA/NeMo/blob/main/nemo/collections/llm/recipes/) and NeMo-Run (https://github.com/NVIDIA/NeMo-Run) to configure and execute the runs.
 
 import argparse
 from functools import partial
@@ -26,12 +26,12 @@
 
 
 def get_parser():
-    parser = argparse.ArgumentParser(description="Llama3 Pretraining")
+    parser = argparse.ArgumentParser(description="NeMo2.0 Pretraining")
     parser.add_argument(
-        "--size",
+        "--recipe",
         type=str,
-        default="8b",
-        help="Choose llama3 model size 70b/8b",
+        default="llama3_8b",
+        help="Choose NeMo 2.0 recipe. Recipes are named in the format of <model_name>_<model_size>(_<long_sequenth_length> or other special settings)",
     )
     parser.add_argument(
         "--tag",
@@ -66,7 +66,7 @@ def slurm_executor(
     time: str = "01:00:00",
     custom_mounts: Optional[list[str]] = None,
     custom_env_vars: Optional[dict[str, str]] = None,
-    container_image: str = "nvcr.io/nvidia/nemo:dev",
+    container_image: str = "nvcr.io/nvidia/nemo:24.09",
     retries: int = 0,
 ) -> run.SlurmExecutor:
     if not (user and host and remote_job_dir and account and partition and nodes and devices):
@@ -102,7 +102,7 @@ def slurm_executor(
         mem="0",
         exclusive=True,
         gres="gpu:8",
-        packager=run.GitArchivePackager(subpath="examples/llm/run"),
+        packager=run.GitArchivePackager(),
     )
 
     executor.container_image = container_image
@@ -134,28 +134,14 @@ def main():
     if args.tag and not args.tag.startswith("-"):
         args.tag = "-" + args.tag
 
-    MODEL_SIZE_MAPPING: dict[str, dict[str, Any]] = {
-        "8b": {
-            "exp_name": "llama3-8b",
-            "nemo": {
-                "pretrain": partial(llm.llama3_8b.pretrain_recipe, num_nodes=1, num_gpus_per_node=8),
-            },
-        },
-        "70b": {
-            "exp_name": "llama3-70b",
-            "nemo": {
-                "pretrain": partial(llm.llama3_70b.pretrain_recipe, num_nodes=128, num_gpus_per_node=8),
-            },
-        },
-    }
-
-    exp_name = MODEL_SIZE_MAPPING[args.size]["exp_name"]
+    exp_name = args.recipe
 
     # Uses configs from NeMo directly
-    pretrain = MODEL_SIZE_MAPPING[args.size]["nemo"]["pretrain"](
-        name=exp_name,
-        ckpt_dir="/nemo_run/checkpoints",
-    )
+    assert hasattr(
+        llm, args.recipe
+    ), f"Recipe named {args.recipe} not found. General format is <model_name>_<model_size>(_<long_sequenth_length> or other special settings)"
+    pretrain_recipe = getattr(llm, args.recipe).pretrain_recipe
+    pretrain = partial(pretrain_recipe)(name=exp_name, dir="/nemo_run/checkpoints")
 
     # Overwrite the dataloader in the recipe to use your custom dataloader.
     # dataloader = set_your_custom_dataloader
diff --git a/scripts/nlp_language_modeling/prepare_packed_ft_dataset.py b/scripts/nlp_language_modeling/prepare_packed_ft_dataset.py
index 19a3e6a78228..9b0a2cb60131 100644
--- a/scripts/nlp_language_modeling/prepare_packed_ft_dataset.py
+++ b/scripts/nlp_language_modeling/prepare_packed_ft_dataset.py
@@ -131,6 +131,7 @@ def tokenize_dataset(cfg: 'DictConfig'):
 
     max_seq_length = dataset.max_seq_length
     pad_id = dataset.tokenizer.eos_id
+    tokenizer = dataset.tokenizer
     pad_seq_length_to_mult = dataset.pad_seq_length_to_mult
     dataset = np.array([dataset[i] for i in range(len(dataset))])
     if cp_size > 1:
@@ -162,7 +163,7 @@ def pre_pad_dataset(data, max_seq_length, max_length_to_pad, pad_id):
         for data in dataset:
             max_length_to_pad = min(max_seq_length, ceil_to_nearest(len(data['input_ids']), pad_seq_length_to_mult))
             pre_pad_dataset(data, max_seq_length, max_length_to_pad, pad_id)
-    return dataset
+    return dataset, tokenizer
 
 
 @dataclass
@@ -187,11 +188,11 @@ def from_config(self, cfg: 'DictConfig'):
 )
 def main(cfg: 'DictConfig') -> None:
     args = PackingArgs().from_config(cfg)
-    dataset = tokenize_dataset(cfg)
+    dataset, tokenizer = tokenize_dataset(cfg)
     sequences, histogram = create_hist(dataset, cfg.model.data.train_ds.max_seq_length)
     for pack_size in args.pack_sizes:
         assignments = create_packing_strategy(histogram, pack_size, args.packing_algorithm)
-        output_data = fill_packing_strategy(assignments, sequences, pack_size)
+        output_data = fill_packing_strategy(assignments, sequences, pack_size, tokenizer.eos_id)
 
         # save output data
         os.makedirs(args.output_dir, exist_ok=True)
diff --git a/tests/deploy/nemo_deploy.py b/tests/deploy/nemo_deploy.py
index 23db7c4f01f3..45f2bae3425e 100644
--- a/tests/deploy/nemo_deploy.py
+++ b/tests/deploy/nemo_deploy.py
@@ -21,7 +21,7 @@
 
 import torch
 
-from nemo.deploy.nlp.megatronllm_deployable import MegatronLLMDeployable
+from nemo.deploy.nlp import MegatronLLMDeployable
 from tests.infer_data_path import get_infer_test_data
 
 run_export_tests = True
diff --git a/tests/export/nemo_export.py b/tests/export/nemo_export.py
index df6a68828d41..cb2b3619e4d3 100644
--- a/tests/export/nemo_export.py
+++ b/tests/export/nemo_export.py
@@ -43,7 +43,8 @@
     from nemo.deploy.nlp import MegatronLLMDeployable, NemoQueryLLMPyTorch
 except Exception as e:
     LOGGER.warning(
-        f"Cannot import MegatronLLMDeployable, in-framework inference will not be available. {type(e).__name__}: {e}"
+        "Cannot import MegatronLLMDeployable or NemoQueryLLMPyTorch,"
+        f" in-framework inference will not be available. {type(e).__name__}: {e}"
     )
     in_framework_supported = False
 
@@ -104,12 +105,7 @@ def get_accuracy_with_lambada(model, nq, task_ids, lora_uids, test_data_path):
             all_expected_outputs.append(expected_output)
             if model is not None:
 
-                in_framework_model = False
-                if in_framework_supported:
-                    if isinstance(model, MegatronLLMDeployable):
-                        in_framework_model = True
-
-                if in_framework_model:
+                if in_framework_supported and isinstance(model, MegatronLLMDeployable):
                     model_output = model.generate(
                         inputs=[prompt],
                         length_params={"min_length": 1, "max_length": 1},
@@ -153,7 +149,7 @@ def get_accuracy_with_lambada(model, nq, task_ids, lora_uids, test_data_path):
                     correct_answers_relaxed += 1
 
             if nq is not None:
-                if isinstance(nq, NemoQueryLLMPyTorch):
+                if in_framework_supported and isinstance(nq, NemoQueryLLMPyTorch):
                     deployed_output = nq.query_llm(
                         prompts=[prompt],
                         max_length=1,