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Model: EPFLiGHT/Meditron3-Gemma2-9B Source: Original Platform
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README.md
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---
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language:
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- en
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license: gemma
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base_model:
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- google/gemma-2-9b-it
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pipeline_tag: text-generation
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tags:
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- medical
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new_version: EPFLiGHT/Gemma-3-27B-MeditronFO
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---
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### Model Card: Gemma2 Meditron-3[9B]
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**Model Type:** Large Language Model (LLM)
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**Specialization:** Medicine
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**Focus:** General purpose including limited resource and humanitarian settings
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**Description:**
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Meditron is a suite of large language models specialized in clinical medicine. The models are co-designed with a diverse range of expert clinicians and humanitarian practitioners. Its training emphasizes equitable representation, contextual diversity, and actionable real-world evidence-based guidelines. We make a particular effort to represent limited-resource and humanitarian settings, neglected populations, and diseases. This release is trained on Gemma2[9B] base model and has the nomenclature Gemma2 Meditron-3[9B].
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#### Model details
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- **Developed by:** [OpenMeditron intiative](https://huggingface.co/OpenMeditron)
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- **Model type:** Causal decoder-only transformer language model
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- **Language(s):** English (mainly)
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- **Finetuned from model:** [Gemma2-9B](https://huggingface.co/google/gemma-2-9B)
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- **Input:** Text only
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- **Output:** Text only
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- **Status:** This is a static model trained on an offline dataset. Future versions of the tuned models will be released as we enhance model's performance.
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#### Uses
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Meditron-3 is a research-only model to study and evaluate the potential of LLMs in enhancing clinical decision-making and access to evidence-based medical information.
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#### Direct Use
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Meditron-3 is a research-only model. It is not validated for medical use (see disclaimer below).
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#### Downstream Use
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Meditron-3 is a suite of foundation models that have NOT been fine-tuned or instruction-tuned. However, these models can be adapted to specific downstream tasks or applications using techniques such as Reinforcement Learning from Human Feedback (RLHF) or Direct Preference Optimization (DPO). In our evaluation of the models, we have used two different methods for downstream question-answering tasks:
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1. In-context learning with k demonstrations added to the prompt.
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2. Model fine-tuning for Q&A tasks using specific training datasets.
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#### Training Data
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This new data mixture comprises expert-curated publicly available data and combines various sources:
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- **Clinical Guidelines:** a dataset of internationally-recognized clinical practice guidelines from various healthcare-related sources across the world, including hospitals and international organizations.
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- **Peer-Reviewed Medical Publications:** full-text medical articles.
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- **Synthetic Differential Diagnoses:** synthetic conversation like data for differential diagnosis.
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- **Replay Data:** general domain pretraining data sampled from multiple state of the art pretraining and instruction tuning.
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- **LLM-enhanced Medical MCQ:** medical multiple-choice questions enriched with LLMs.
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Additional information about the datasets will be included in the Meditron-3 publication.
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#### Evaluation
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| Model Name | MedmcQA | MedQA | PubmedQA | Average |
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|-----------------------------|---------|--------|----------|---------|
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| google/gemma-2-9b | 56.60 | 63.32 | 76.80 | 65.57 |
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| gemMeditron-2-9b | 57.21 | 63.79 | 77.00 | 66.00 |
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| Difference (gemMeditron vs.)| 0.61 | 0.47 | 0.20 | 0.43 |
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| Model Name | AfrimedQA |
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|-----------------------------|-----------|
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| google/gemma-2-9b | 51.25 |
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| gemMeditron-2-9b | 58.23 |
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| Difference (gemMeditron vs.)| 6.98 |
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We evaluated Meditron on medical multiple-choice questions using [lm-harness](https://github.com/EleutherAI/lm-evaluation-harness) for reproducibility.
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While MCQs are valuable for assessing exam-like performance, they fall short of capturing the model's real-world utility, especially in terms of contextual adaptation in under-represented settings. Medicine is not multiple choice and we need to go beyond accuracy to assess finer-grained issues like empathy, alignment to local guidelines, structure, completeness and safety. To address this, we have developed a platform to collect feedback directly from experts to continuously adapt to the changing contexts of clinical practice.
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#### Paper
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The Meditron-3 publication is currently in progress and will be released at a later date.
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#### Legal Disclaimer
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THIS SOFTWARE AND MODEL ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS, OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES, OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT, OR OTHERWISE, ARISING FROM, OUT OF, OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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These models are a research tool intended for use in the field of computational linguistics and medicine. They are not intended to be used as diagnostic tools or for clinical decision-making without appropriate validation and regulatory approval. The content and data provided with the models do not replace the expertise of healthcare professionals. Healthcare professionals should use their professional judgment in evaluating the outputs of the Gemma models. Patients should not use the model outputs for self-diagnosis or treatment without consulting a qualified healthcare provider.
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THE INFORMATION IS NOT INTENDED FOR CLINICAL DECISION-MAKING, IS NOT INTENDED TO BE USED IN THE DIAGNOSIS OR TREATMENT OF PATIENTS, AND MAY NOT BE USEFUL OR APPROPRIATE FOR ANY CLINICAL PURPOSE.
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UNDER NO CIRCUMSTANCES CAN USERS USE THE NAME “YALE” OR "EPFL" OR “YALE UNIVERSITY,” OR ANY AFFILIATED INSTITUTION NOR ANY VARIATION OR ADAPTATION THEREOF, NOR ANY TRADEMARK, TRADENAME OR OTHER DESIGNATION OWNED BY YALE, NOR THE NAMES OF ANY OF ITS TRUSTEES, OFFICERS, FACULTY, STUDENTS, EMPLOYEES OR AGENTS, FOR ANY PURPOSE WITHOUT THE PRIOR WRITTEN CONSENT OF YALE IN EACH INSTANCE, SUCH CONSENT TO BE GRANTED OR WITHHELD BY YALE IN ITS SOLE DISCRETION.
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Meditron3-Gemma2 [9B] is licensed under the Gemma License.
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This model is provided under the terms of the Gemma Model License Agreement, as issued by Google LLC. By using or distributing this model, you agree to comply with the terms of that license.
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Disclaimer: This model is provided "as-is" without warranties or conditions of any kind, either express or implied. Google and any contributors disclaim all liability for any damages resulting from use of the model.
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For more information, visit: https://ai.google.dev/gemma
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3
scheduler.pt
Normal file
3
scheduler.pt
Normal file
@@ -0,0 +1,3 @@
|
||||
version https://git-lfs.github.com/spec/v1
|
||||
oid sha256:758f4eace6f016664eef18abbb90d12c3202d90801733cb2037bc1899719f46d
|
||||
size 1064
|
||||
34
special_tokens_map.json
Normal file
34
special_tokens_map.json
Normal file
@@ -0,0 +1,34 @@
|
||||
{
|
||||
"additional_special_tokens": [
|
||||
"<start_of_turn>",
|
||||
"<end_of_turn>"
|
||||
],
|
||||
"bos_token": {
|
||||
"content": "<bos>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false
|
||||
},
|
||||
"eos_token": {
|
||||
"content": "<eos>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false
|
||||
},
|
||||
"pad_token": {
|
||||
"content": "<pad>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false
|
||||
},
|
||||
"unk_token": {
|
||||
"content": "<unk>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false
|
||||
}
|
||||
}
|
||||
3
tokenizer.json
Normal file
3
tokenizer.json
Normal file
@@ -0,0 +1,3 @@
|
||||
version https://git-lfs.github.com/spec/v1
|
||||
oid sha256:5f7eee611703c5ce5d1eee32d9cdcfe465647b8aff0c1dfb3bed7ad7dbb05060
|
||||
size 34362873
|
||||
3
tokenizer.model
Normal file
3
tokenizer.model
Normal file
@@ -0,0 +1,3 @@
|
||||
version https://git-lfs.github.com/spec/v1
|
||||
oid sha256:61a7b147390c64585d6c3543dd6fc636906c9af3865a5548f27f31aee1d4c8e2
|
||||
size 4241003
|
||||
2013
tokenizer_config.json
Normal file
2013
tokenizer_config.json
Normal file
File diff suppressed because it is too large
Load Diff
33759
trainer_state.json
Normal file
33759
trainer_state.json
Normal file
File diff suppressed because it is too large
Load Diff
3
training_args.bin
Normal file
3
training_args.bin
Normal file
@@ -0,0 +1,3 @@
|
||||
version https://git-lfs.github.com/spec/v1
|
||||
oid sha256:43af283256885474e3076c6237c19580d8d2fe0397ba9a2caf163b6ca1d49ef7
|
||||
size 8504
|
||||
592
zero_to_fp32.py
Normal file
592
zero_to_fp32.py
Normal file
@@ -0,0 +1,592 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
# Copyright (c) Microsoft Corporation.
|
||||
# SPDX-License-Identifier: Apache-2.0
|
||||
|
||||
# DeepSpeed Team
|
||||
|
||||
# This script extracts fp32 consolidated weights from a zero 1, 2 and 3 DeepSpeed checkpoints. It gets
|
||||
# copied into the top level checkpoint dir, so the user can easily do the conversion at any point in
|
||||
# the future. Once extracted, the weights don't require DeepSpeed and can be used in any
|
||||
# application.
|
||||
#
|
||||
# example: python zero_to_fp32.py . pytorch_model.bin
|
||||
|
||||
import argparse
|
||||
import torch
|
||||
import glob
|
||||
import math
|
||||
import os
|
||||
import re
|
||||
from collections import OrderedDict
|
||||
from dataclasses import dataclass
|
||||
|
||||
# while this script doesn't use deepspeed to recover data, since the checkpoints are pickled with
|
||||
# DeepSpeed data structures it has to be available in the current python environment.
|
||||
from deepspeed.utils import logger
|
||||
from deepspeed.checkpoint.constants import (DS_VERSION, OPTIMIZER_STATE_DICT, SINGLE_PARTITION_OF_FP32_GROUPS,
|
||||
FP32_FLAT_GROUPS, ZERO_STAGE, PARTITION_COUNT, PARAM_SHAPES, BUFFER_NAMES,
|
||||
FROZEN_PARAM_SHAPES, FROZEN_PARAM_FRAGMENTS)
|
||||
|
||||
|
||||
@dataclass
|
||||
class zero_model_state:
|
||||
buffers: dict()
|
||||
param_shapes: dict()
|
||||
shared_params: list
|
||||
ds_version: int
|
||||
frozen_param_shapes: dict()
|
||||
frozen_param_fragments: dict()
|
||||
|
||||
|
||||
debug = 0
|
||||
|
||||
# load to cpu
|
||||
device = torch.device('cpu')
|
||||
|
||||
|
||||
def atoi(text):
|
||||
return int(text) if text.isdigit() else text
|
||||
|
||||
|
||||
def natural_keys(text):
|
||||
'''
|
||||
alist.sort(key=natural_keys) sorts in human order
|
||||
http://nedbatchelder.com/blog/200712/human_sorting.html
|
||||
(See Toothy's implementation in the comments)
|
||||
'''
|
||||
return [atoi(c) for c in re.split(r'(\d+)', text)]
|
||||
|
||||
|
||||
def get_model_state_file(checkpoint_dir, zero_stage):
|
||||
if not os.path.isdir(checkpoint_dir):
|
||||
raise FileNotFoundError(f"Directory '{checkpoint_dir}' doesn't exist")
|
||||
|
||||
# there should be only one file
|
||||
if zero_stage <= 2:
|
||||
file = os.path.join(checkpoint_dir, "mp_rank_00_model_states.pt")
|
||||
elif zero_stage == 3:
|
||||
file = os.path.join(checkpoint_dir, "zero_pp_rank_0_mp_rank_00_model_states.pt")
|
||||
|
||||
if not os.path.exists(file):
|
||||
raise FileNotFoundError(f"can't find model states file at '{file}'")
|
||||
|
||||
return file
|
||||
|
||||
|
||||
def get_checkpoint_files(checkpoint_dir, glob_pattern):
|
||||
# XXX: need to test that this simple glob rule works for multi-node setup too
|
||||
ckpt_files = sorted(glob.glob(os.path.join(checkpoint_dir, glob_pattern)), key=natural_keys)
|
||||
|
||||
if len(ckpt_files) == 0:
|
||||
raise FileNotFoundError(f"can't find {glob_pattern} files in directory '{checkpoint_dir}'")
|
||||
|
||||
return ckpt_files
|
||||
|
||||
|
||||
def get_optim_files(checkpoint_dir):
|
||||
return get_checkpoint_files(checkpoint_dir, "*_optim_states.pt")
|
||||
|
||||
|
||||
def get_model_state_files(checkpoint_dir):
|
||||
return get_checkpoint_files(checkpoint_dir, "*_model_states.pt")
|
||||
|
||||
|
||||
def parse_model_states(files):
|
||||
zero_model_states = []
|
||||
for file in files:
|
||||
state_dict = torch.load(file, map_location=device)
|
||||
|
||||
if BUFFER_NAMES not in state_dict:
|
||||
raise ValueError(f"{file} is not a model state checkpoint")
|
||||
buffer_names = state_dict[BUFFER_NAMES]
|
||||
if debug:
|
||||
print("Found buffers:", buffer_names)
|
||||
|
||||
# recover just the buffers while restoring them to fp32 if they were saved in fp16
|
||||
buffers = {k: v.float() for k, v in state_dict["module"].items() if k in buffer_names}
|
||||
param_shapes = state_dict[PARAM_SHAPES]
|
||||
|
||||
# collect parameters that are included in param_shapes
|
||||
param_names = []
|
||||
for s in param_shapes:
|
||||
for name in s.keys():
|
||||
param_names.append(name)
|
||||
|
||||
# update with frozen parameters
|
||||
frozen_param_shapes = state_dict.get(FROZEN_PARAM_SHAPES, None)
|
||||
if frozen_param_shapes is not None:
|
||||
if debug:
|
||||
print(f"Found frozen_param_shapes: {frozen_param_shapes}")
|
||||
param_names += list(frozen_param_shapes.keys())
|
||||
|
||||
# handle shared params
|
||||
shared_params = [[k, v] for k, v in state_dict["shared_params"].items()]
|
||||
|
||||
ds_version = state_dict.get(DS_VERSION, None)
|
||||
|
||||
frozen_param_fragments = state_dict.get(FROZEN_PARAM_FRAGMENTS, None)
|
||||
|
||||
z_model_state = zero_model_state(buffers=buffers,
|
||||
param_shapes=param_shapes,
|
||||
shared_params=shared_params,
|
||||
ds_version=ds_version,
|
||||
frozen_param_shapes=frozen_param_shapes,
|
||||
frozen_param_fragments=frozen_param_fragments)
|
||||
zero_model_states.append(z_model_state)
|
||||
|
||||
return zero_model_states
|
||||
|
||||
|
||||
def parse_optim_states(files, ds_checkpoint_dir):
|
||||
|
||||
total_files = len(files)
|
||||
state_dicts = []
|
||||
for f in files:
|
||||
state_dict = torch.load(f, map_location=device)
|
||||
# immediately discard the potentially huge 2 optimizer states as we only care for fp32 master weights
|
||||
# and also handle the case where it was already removed by another helper script
|
||||
state_dict["optimizer_state_dict"].pop("optimizer_state_dict", None)
|
||||
state_dicts.append(state_dict)
|
||||
|
||||
if not ZERO_STAGE in state_dicts[0][OPTIMIZER_STATE_DICT]:
|
||||
raise ValueError(f"{files[0]} is not a zero checkpoint")
|
||||
zero_stage = state_dicts[0][OPTIMIZER_STATE_DICT][ZERO_STAGE]
|
||||
world_size = state_dicts[0][OPTIMIZER_STATE_DICT][PARTITION_COUNT]
|
||||
|
||||
# For ZeRO-2 each param group can have different partition_count as data parallelism for expert
|
||||
# parameters can be different from data parallelism for non-expert parameters. So we can just
|
||||
# use the max of the partition_count to get the dp world_size.
|
||||
|
||||
if type(world_size) is list:
|
||||
world_size = max(world_size)
|
||||
|
||||
if world_size != total_files:
|
||||
raise ValueError(
|
||||
f"Expected {world_size} of '*_optim_states.pt' under '{ds_checkpoint_dir}' but found {total_files} files. "
|
||||
"Possibly due to an overwrite of an old checkpoint, or a checkpoint didn't get saved by one or more processes."
|
||||
)
|
||||
|
||||
# the groups are named differently in each stage
|
||||
if zero_stage <= 2:
|
||||
fp32_groups_key = SINGLE_PARTITION_OF_FP32_GROUPS
|
||||
elif zero_stage == 3:
|
||||
fp32_groups_key = FP32_FLAT_GROUPS
|
||||
else:
|
||||
raise ValueError(f"unknown zero stage {zero_stage}")
|
||||
|
||||
if zero_stage <= 2:
|
||||
fp32_flat_groups = [state_dicts[i][OPTIMIZER_STATE_DICT][fp32_groups_key] for i in range(len(state_dicts))]
|
||||
elif zero_stage == 3:
|
||||
# if there is more than one param group, there will be multiple flattened tensors - one
|
||||
# flattened tensor per group - for simplicity merge them into a single tensor
|
||||
#
|
||||
# XXX: could make the script more memory efficient for when there are multiple groups - it
|
||||
# will require matching the sub-lists of param_shapes for each param group flattened tensor
|
||||
|
||||
fp32_flat_groups = [
|
||||
torch.cat(state_dicts[i][OPTIMIZER_STATE_DICT][fp32_groups_key], 0) for i in range(len(state_dicts))
|
||||
]
|
||||
|
||||
return zero_stage, world_size, fp32_flat_groups
|
||||
|
||||
|
||||
def _get_fp32_state_dict_from_zero_checkpoint(ds_checkpoint_dir):
|
||||
"""
|
||||
Returns fp32 state_dict reconstructed from ds checkpoint
|
||||
|
||||
Args:
|
||||
- ``ds_checkpoint_dir``: path to the deepspeed checkpoint folder (where the optimizer files are)
|
||||
|
||||
"""
|
||||
print(f"Processing zero checkpoint '{ds_checkpoint_dir}'")
|
||||
|
||||
optim_files = get_optim_files(ds_checkpoint_dir)
|
||||
zero_stage, world_size, fp32_flat_groups = parse_optim_states(optim_files, ds_checkpoint_dir)
|
||||
print(f"Detected checkpoint of type zero stage {zero_stage}, world_size: {world_size}")
|
||||
|
||||
model_files = get_model_state_files(ds_checkpoint_dir)
|
||||
|
||||
zero_model_states = parse_model_states(model_files)
|
||||
print(f'Parsing checkpoint created by deepspeed=={zero_model_states[0].ds_version}')
|
||||
|
||||
if zero_stage <= 2:
|
||||
return _get_fp32_state_dict_from_zero2_checkpoint(world_size, fp32_flat_groups, zero_model_states)
|
||||
elif zero_stage == 3:
|
||||
return _get_fp32_state_dict_from_zero3_checkpoint(world_size, fp32_flat_groups, zero_model_states)
|
||||
|
||||
|
||||
def _zero2_merge_frozen_params(state_dict, zero_model_states):
|
||||
if zero_model_states[0].frozen_param_shapes is None or len(zero_model_states[0].frozen_param_shapes) == 0:
|
||||
return
|
||||
|
||||
frozen_param_shapes = zero_model_states[0].frozen_param_shapes
|
||||
frozen_param_fragments = zero_model_states[0].frozen_param_fragments
|
||||
|
||||
if debug:
|
||||
num_elem = sum(s.numel() for s in frozen_param_shapes.values())
|
||||
print(f'rank 0: {FROZEN_PARAM_SHAPES}.numel = {num_elem}')
|
||||
|
||||
wanted_params = len(frozen_param_shapes)
|
||||
wanted_numel = sum(s.numel() for s in frozen_param_shapes.values())
|
||||
avail_numel = sum([p.numel() for p in frozen_param_fragments.values()])
|
||||
print(f'Frozen params: Have {avail_numel} numels to process.')
|
||||
print(f'Frozen params: Need {wanted_numel} numels in {wanted_params} params')
|
||||
|
||||
total_params = 0
|
||||
total_numel = 0
|
||||
for name, shape in frozen_param_shapes.items():
|
||||
total_params += 1
|
||||
unpartitioned_numel = shape.numel()
|
||||
total_numel += unpartitioned_numel
|
||||
|
||||
state_dict[name] = frozen_param_fragments[name]
|
||||
|
||||
if debug:
|
||||
print(f"{name} full shape: {shape} unpartitioned numel {unpartitioned_numel} ")
|
||||
|
||||
print(f"Reconstructed Frozen fp32 state dict with {total_params} params {total_numel} elements")
|
||||
|
||||
|
||||
def _has_callable(obj, fn):
|
||||
attr = getattr(obj, fn, None)
|
||||
return callable(attr)
|
||||
|
||||
|
||||
def _zero2_merge_trainable_params(state_dict, world_size, fp32_flat_groups, zero_model_states):
|
||||
param_shapes = zero_model_states[0].param_shapes
|
||||
|
||||
# Reconstruction protocol:
|
||||
#
|
||||
# XXX: document this
|
||||
|
||||
if debug:
|
||||
for i in range(world_size):
|
||||
for j in range(len(fp32_flat_groups[0])):
|
||||
print(f"{FP32_FLAT_GROUPS}[{i}][{j}].shape={fp32_flat_groups[i][j].shape}")
|
||||
|
||||
# XXX: memory usage doubles here (zero2)
|
||||
num_param_groups = len(fp32_flat_groups[0])
|
||||
merged_single_partition_of_fp32_groups = []
|
||||
for i in range(num_param_groups):
|
||||
merged_partitions = [sd[i] for sd in fp32_flat_groups]
|
||||
full_single_fp32_vector = torch.cat(merged_partitions, 0)
|
||||
merged_single_partition_of_fp32_groups.append(full_single_fp32_vector)
|
||||
avail_numel = sum(
|
||||
[full_single_fp32_vector.numel() for full_single_fp32_vector in merged_single_partition_of_fp32_groups])
|
||||
|
||||
if debug:
|
||||
wanted_params = sum([len(shapes) for shapes in param_shapes])
|
||||
wanted_numel = sum([sum(shape.numel() for shape in shapes.values()) for shapes in param_shapes])
|
||||
# not asserting if there is a mismatch due to possible padding
|
||||
print(f"Have {avail_numel} numels to process.")
|
||||
print(f"Need {wanted_numel} numels in {wanted_params} params.")
|
||||
|
||||
# params
|
||||
# XXX: for huge models that can't fit into the host's RAM we will have to recode this to support
|
||||
# out-of-core computing solution
|
||||
total_numel = 0
|
||||
total_params = 0
|
||||
for shapes, full_single_fp32_vector in zip(param_shapes, merged_single_partition_of_fp32_groups):
|
||||
offset = 0
|
||||
avail_numel = full_single_fp32_vector.numel()
|
||||
for name, shape in shapes.items():
|
||||
|
||||
unpartitioned_numel = shape.numel() if _has_callable(shape, 'numel') else math.prod(shape)
|
||||
total_numel += unpartitioned_numel
|
||||
total_params += 1
|
||||
|
||||
if debug:
|
||||
print(f"{name} full shape: {shape} unpartitioned numel {unpartitioned_numel} ")
|
||||
state_dict[name] = full_single_fp32_vector.narrow(0, offset, unpartitioned_numel).view(shape)
|
||||
offset += unpartitioned_numel
|
||||
|
||||
# Z2 started to align to 2*world_size to improve nccl performance. Therefore both offset and
|
||||
# avail_numel can differ by anywhere between 0..2*world_size. Due to two unrelated complex
|
||||
# paddings performed in the code it's almost impossible to predict the exact numbers w/o the
|
||||
# live optimizer object, so we are checking that the numbers are within the right range
|
||||
align_to = 2 * world_size
|
||||
|
||||
def zero2_align(x):
|
||||
return align_to * math.ceil(x / align_to)
|
||||
|
||||
if debug:
|
||||
print(f"original offset={offset}, avail_numel={avail_numel}")
|
||||
|
||||
offset = zero2_align(offset)
|
||||
avail_numel = zero2_align(avail_numel)
|
||||
|
||||
if debug:
|
||||
print(f"aligned offset={offset}, avail_numel={avail_numel}")
|
||||
|
||||
# Sanity check
|
||||
if offset != avail_numel:
|
||||
raise ValueError(f"consumed {offset} numels out of {avail_numel} - something is wrong")
|
||||
|
||||
print(f"Reconstructed fp32 state dict with {total_params} params {total_numel} elements")
|
||||
|
||||
|
||||
def _get_fp32_state_dict_from_zero2_checkpoint(world_size, fp32_flat_groups, zero_model_states):
|
||||
state_dict = OrderedDict()
|
||||
|
||||
# buffers
|
||||
buffers = zero_model_states[0].buffers
|
||||
state_dict.update(buffers)
|
||||
if debug:
|
||||
print(f"added {len(buffers)} buffers")
|
||||
|
||||
_zero2_merge_frozen_params(state_dict, zero_model_states)
|
||||
|
||||
_zero2_merge_trainable_params(state_dict, world_size, fp32_flat_groups, zero_model_states)
|
||||
|
||||
# recover shared parameters
|
||||
for pair in zero_model_states[0].shared_params:
|
||||
if pair[1] in state_dict:
|
||||
state_dict[pair[0]] = state_dict[pair[1]]
|
||||
|
||||
return state_dict
|
||||
|
||||
|
||||
def zero3_partitioned_param_info(unpartitioned_numel, world_size):
|
||||
remainder = unpartitioned_numel % world_size
|
||||
padding_numel = (world_size - remainder) if remainder else 0
|
||||
partitioned_numel = math.ceil(unpartitioned_numel / world_size)
|
||||
return partitioned_numel, padding_numel
|
||||
|
||||
|
||||
def _zero3_merge_frozen_params(state_dict, world_size, zero_model_states):
|
||||
if zero_model_states[0].frozen_param_shapes is None or len(zero_model_states[0].frozen_param_shapes) == 0:
|
||||
return
|
||||
|
||||
if debug:
|
||||
for i in range(world_size):
|
||||
num_elem = sum(s.numel() for s in zero_model_states[i].frozen_param_fragments.values())
|
||||
print(f'rank {i}: {FROZEN_PARAM_SHAPES}.numel = {num_elem}')
|
||||
|
||||
frozen_param_shapes = zero_model_states[0].frozen_param_shapes
|
||||
wanted_params = len(frozen_param_shapes)
|
||||
wanted_numel = sum(s.numel() for s in frozen_param_shapes.values())
|
||||
avail_numel = sum([p.numel() for p in zero_model_states[0].frozen_param_fragments.values()]) * world_size
|
||||
print(f'Frozen params: Have {avail_numel} numels to process.')
|
||||
print(f'Frozen params: Need {wanted_numel} numels in {wanted_params} params')
|
||||
|
||||
total_params = 0
|
||||
total_numel = 0
|
||||
for name, shape in zero_model_states[0].frozen_param_shapes.items():
|
||||
total_params += 1
|
||||
unpartitioned_numel = shape.numel()
|
||||
total_numel += unpartitioned_numel
|
||||
|
||||
param_frags = tuple(model_state.frozen_param_fragments[name] for model_state in zero_model_states)
|
||||
state_dict[name] = torch.cat(param_frags, 0).narrow(0, 0, unpartitioned_numel).view(shape)
|
||||
|
||||
partitioned_numel, partitioned_padding_numel = zero3_partitioned_param_info(unpartitioned_numel, world_size)
|
||||
|
||||
if debug:
|
||||
print(
|
||||
f"Frozen params: {total_params} {name} full shape: {shape} partition0 numel={partitioned_numel} partitioned_padding_numel={partitioned_padding_numel}"
|
||||
)
|
||||
|
||||
print(f"Reconstructed Frozen fp32 state dict with {total_params} params {total_numel} elements")
|
||||
|
||||
|
||||
def _zero3_merge_trainable_params(state_dict, world_size, fp32_flat_groups, zero_model_states):
|
||||
param_shapes = zero_model_states[0].param_shapes
|
||||
avail_numel = fp32_flat_groups[0].numel() * world_size
|
||||
# Reconstruction protocol: For zero3 we need to zip the partitions together at boundary of each
|
||||
# param, re-consolidating each param, while dealing with padding if any
|
||||
|
||||
# merge list of dicts, preserving order
|
||||
param_shapes = {k: v for d in param_shapes for k, v in d.items()}
|
||||
|
||||
if debug:
|
||||
for i in range(world_size):
|
||||
print(f"{FP32_FLAT_GROUPS}[{i}].shape={fp32_flat_groups[i].shape}")
|
||||
|
||||
wanted_params = len(param_shapes)
|
||||
wanted_numel = sum(shape.numel() for shape in param_shapes.values())
|
||||
# not asserting if there is a mismatch due to possible padding
|
||||
avail_numel = fp32_flat_groups[0].numel() * world_size
|
||||
print(f"Trainable params: Have {avail_numel} numels to process.")
|
||||
print(f"Trainable params: Need {wanted_numel} numels in {wanted_params} params.")
|
||||
|
||||
# params
|
||||
# XXX: for huge models that can't fit into the host's RAM we will have to recode this to support
|
||||
# out-of-core computing solution
|
||||
offset = 0
|
||||
total_numel = 0
|
||||
total_params = 0
|
||||
for name, shape in param_shapes.items():
|
||||
|
||||
unpartitioned_numel = shape.numel()
|
||||
total_numel += unpartitioned_numel
|
||||
total_params += 1
|
||||
|
||||
partitioned_numel, partitioned_padding_numel = zero3_partitioned_param_info(unpartitioned_numel, world_size)
|
||||
|
||||
if debug:
|
||||
print(
|
||||
f"Trainable params: {total_params} {name} full shape: {shape} partition0 numel={partitioned_numel} partitioned_padding_numel={partitioned_padding_numel}"
|
||||
)
|
||||
|
||||
# XXX: memory usage doubles here
|
||||
state_dict[name] = torch.cat(
|
||||
tuple(fp32_flat_groups[i].narrow(0, offset, partitioned_numel) for i in range(world_size)),
|
||||
0).narrow(0, 0, unpartitioned_numel).view(shape)
|
||||
offset += partitioned_numel
|
||||
|
||||
offset *= world_size
|
||||
|
||||
# Sanity check
|
||||
if offset != avail_numel:
|
||||
raise ValueError(f"consumed {offset} numels out of {avail_numel} - something is wrong")
|
||||
|
||||
print(f"Reconstructed Trainable fp32 state dict with {total_params} params {total_numel} elements")
|
||||
|
||||
|
||||
def _get_fp32_state_dict_from_zero3_checkpoint(world_size, fp32_flat_groups, zero_model_states):
|
||||
state_dict = OrderedDict()
|
||||
|
||||
# buffers
|
||||
buffers = zero_model_states[0].buffers
|
||||
state_dict.update(buffers)
|
||||
if debug:
|
||||
print(f"added {len(buffers)} buffers")
|
||||
|
||||
_zero3_merge_frozen_params(state_dict, world_size, zero_model_states)
|
||||
|
||||
_zero3_merge_trainable_params(state_dict, world_size, fp32_flat_groups, zero_model_states)
|
||||
|
||||
# recover shared parameters
|
||||
for pair in zero_model_states[0].shared_params:
|
||||
if pair[1] in state_dict:
|
||||
state_dict[pair[0]] = state_dict[pair[1]]
|
||||
|
||||
return state_dict
|
||||
|
||||
|
||||
def get_fp32_state_dict_from_zero_checkpoint(checkpoint_dir, tag=None):
|
||||
"""
|
||||
Convert ZeRO 2 or 3 checkpoint into a single fp32 consolidated state_dict that can be loaded with
|
||||
``load_state_dict()`` and used for training without DeepSpeed or shared with others, for example
|
||||
via a model hub.
|
||||
|
||||
Args:
|
||||
- ``checkpoint_dir``: path to the desired checkpoint folder
|
||||
- ``tag``: checkpoint tag used as a unique identifier for checkpoint. If not provided will attempt to load tag in 'latest' file. e.g., ``global_step14``
|
||||
|
||||
Returns:
|
||||
- pytorch ``state_dict``
|
||||
|
||||
Note: this approach may not work if your application doesn't have sufficient free CPU memory and
|
||||
you may need to use the offline approach using the ``zero_to_fp32.py`` script that is saved with
|
||||
the checkpoint.
|
||||
|
||||
A typical usage might be ::
|
||||
|
||||
from deepspeed.utils.zero_to_fp32 import get_fp32_state_dict_from_zero_checkpoint
|
||||
# do the training and checkpoint saving
|
||||
state_dict = get_fp32_state_dict_from_zero_checkpoint(checkpoint_dir) # already on cpu
|
||||
model = model.cpu() # move to cpu
|
||||
model.load_state_dict(state_dict)
|
||||
# submit to model hub or save the model to share with others
|
||||
|
||||
In this example the ``model`` will no longer be usable in the deepspeed context of the same
|
||||
application. i.e. you will need to re-initialize the deepspeed engine, since
|
||||
``model.load_state_dict(state_dict)`` will remove all the deepspeed magic from it.
|
||||
|
||||
If you want it all done for you, use ``load_state_dict_from_zero_checkpoint`` instead.
|
||||
|
||||
"""
|
||||
if tag is None:
|
||||
latest_path = os.path.join(checkpoint_dir, 'latest')
|
||||
if os.path.isfile(latest_path):
|
||||
with open(latest_path, 'r') as fd:
|
||||
tag = fd.read().strip()
|
||||
else:
|
||||
raise ValueError(f"Unable to find 'latest' file at {latest_path}")
|
||||
|
||||
ds_checkpoint_dir = os.path.join(checkpoint_dir, tag)
|
||||
|
||||
if not os.path.isdir(ds_checkpoint_dir):
|
||||
raise FileNotFoundError(f"Directory '{ds_checkpoint_dir}' doesn't exist")
|
||||
|
||||
return _get_fp32_state_dict_from_zero_checkpoint(ds_checkpoint_dir)
|
||||
|
||||
|
||||
def convert_zero_checkpoint_to_fp32_state_dict(checkpoint_dir, output_file, tag=None):
|
||||
"""
|
||||
Convert ZeRO 2 or 3 checkpoint into a single fp32 consolidated ``state_dict`` file that can be
|
||||
loaded with ``torch.load(file)`` + ``load_state_dict()`` and used for training without DeepSpeed.
|
||||
|
||||
Args:
|
||||
- ``checkpoint_dir``: path to the desired checkpoint folder. (one that contains the tag-folder, like ``global_step14``)
|
||||
- ``output_file``: path to the pytorch fp32 state_dict output file (e.g. path/pytorch_model.bin)
|
||||
- ``tag``: checkpoint tag used as a unique identifier for checkpoint. If not provided will attempt to load tag in the file named ``latest`` in the checkpoint folder, e.g., ``global_step14``
|
||||
"""
|
||||
|
||||
state_dict = get_fp32_state_dict_from_zero_checkpoint(checkpoint_dir, tag)
|
||||
print(f"Saving fp32 state dict to {output_file}")
|
||||
torch.save(state_dict, output_file)
|
||||
|
||||
|
||||
def load_state_dict_from_zero_checkpoint(model, checkpoint_dir, tag=None):
|
||||
"""
|
||||
1. Put the provided model to cpu
|
||||
2. Convert ZeRO 2 or 3 checkpoint into a single fp32 consolidated ``state_dict``
|
||||
3. Load it into the provided model
|
||||
|
||||
Args:
|
||||
- ``model``: the model object to update
|
||||
- ``checkpoint_dir``: path to the desired checkpoint folder. (one that contains the tag-folder, like ``global_step14``)
|
||||
- ``tag``: checkpoint tag used as a unique identifier for checkpoint. If not provided will attempt to load tag in the file named ``latest`` in the checkpoint folder, e.g., ``global_step14``
|
||||
|
||||
Returns:
|
||||
- ``model`: modified model
|
||||
|
||||
Make sure you have plenty of CPU memory available before you call this function. If you don't
|
||||
have enough use the ``zero_to_fp32.py`` utility to do the conversion. You will find it
|
||||
conveniently placed for you in the checkpoint folder.
|
||||
|
||||
A typical usage might be ::
|
||||
|
||||
from deepspeed.utils.zero_to_fp32 import load_state_dict_from_zero_checkpoint
|
||||
model = load_state_dict_from_zero_checkpoint(trainer.model, checkpoint_dir)
|
||||
# submit to model hub or save the model to share with others
|
||||
|
||||
Note, that once this was run, the ``model`` will no longer be usable in the deepspeed context
|
||||
of the same application. i.e. you will need to re-initialize the deepspeed engine, since
|
||||
``model.load_state_dict(state_dict)`` will remove all the deepspeed magic from it.
|
||||
|
||||
"""
|
||||
logger.info(f"Extracting fp32 weights")
|
||||
state_dict = get_fp32_state_dict_from_zero_checkpoint(checkpoint_dir, tag)
|
||||
|
||||
logger.info(f"Overwriting model with fp32 weights")
|
||||
model = model.cpu()
|
||||
model.load_state_dict(state_dict, strict=False)
|
||||
|
||||
return model
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
|
||||
parser = argparse.ArgumentParser()
|
||||
parser.add_argument("checkpoint_dir",
|
||||
type=str,
|
||||
help="path to the desired checkpoint folder, e.g., path/checkpoint-12")
|
||||
parser.add_argument(
|
||||
"output_file",
|
||||
type=str,
|
||||
help="path to the pytorch fp32 state_dict output file (e.g. path/checkpoint-12/pytorch_model.bin)")
|
||||
parser.add_argument("-t",
|
||||
"--tag",
|
||||
type=str,
|
||||
default=None,
|
||||
help="checkpoint tag used as a unique identifier for checkpoint. e.g., global_step1")
|
||||
parser.add_argument("-d", "--debug", action='store_true', help="enable debug")
|
||||
args = parser.parse_args()
|
||||
|
||||
debug = args.debug
|
||||
|
||||
convert_zero_checkpoint_to_fp32_state_dict(args.checkpoint_dir, args.output_file, tag=args.tag)
|
||||
Reference in New Issue
Block a user