Instructions to use dnagpt/laya-bio-models with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Laya
How to use dnagpt/laya-bio-models with Laya:
# No code snippets available yet for this library. # To use this model, check the repository files and the library's documentation. # Want to help? PRs adding snippets are welcome at: # https://github.com/huggingface/huggingface.js
- Notebooks
- Google Colab
- Kaggle
File size: 14,916 Bytes
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"""Measure full-parameter Laya supervised-CE memory on a single GPU.
This is an engineering probe only. It uses synthetic token ids (every position is
attended, length 1024), so it does not produce a biological result. The probe loads
the fixed local typed-decisions checkpoint, keeps parameters in FP32, uses BF16 CUDA
autocast, enables gradient checkpointing on the ModernBERT encoder, and runs AdamW
updates for micro-batches 4 and 8. The decision head's ``act_head`` is frozen because
this CE probe has no action target. Laya's ``head_checkpointing`` attribute is only a
configuration flag; it is deliberately not counted as checkpointing here.
"""
from __future__ import annotations
import argparse
import gc
import json
import os
import subprocess
import sys
import time
from pathlib import Path
from typing import Any
import torch
import torch.nn.functional as F
from safetensors.torch import load_file
def parse_args() -> argparse.Namespace:
p = argparse.ArgumentParser()
p.add_argument("--model-dir", default="artifacts/laya_model")
p.add_argument("--laya-repo", default="vendor/laya")
p.add_argument("--output", default="artifacts/laya_memory_probe.json")
p.add_argument("--seq-len", type=int, default=1024)
p.add_argument("--updates", type=int, default=3)
p.add_argument("--lr", type=float, default=2e-5)
p.add_argument("--seed", type=int, default=20260922)
p.add_argument("--micro-batches", type=int, nargs="+", default=[4, 8])
return p.parse_args()
def driver_info() -> dict[str, Any]:
"""Read driver details without making nvidia-smi a hard dependency."""
info: dict[str, Any] = {}
try:
out = subprocess.check_output(
[
"nvidia-smi",
"--query-gpu=index,name,memory.total,driver_version",
"--format=csv,noheader,nounits",
],
text=True,
stderr=subprocess.STDOUT,
).strip()
rows = []
for line in out.splitlines():
fields = [x.strip() for x in line.split(",")]
if len(fields) >= 4:
rows.append(
{
"index": fields[0],
"name": fields[1],
"memory_total_mib": fields[2],
"driver_version": fields[3],
}
)
info["nvidia_smi"] = rows
except (OSError, subprocess.CalledProcessError) as exc:
info["nvidia_smi_error"] = str(exc)
return info
def import_laya(repo: str):
repo_path = str(Path(repo).resolve())
if repo_path not in sys.path:
sys.path.insert(0, repo_path)
from laya.common import build_model
return build_model
def load_fixed_model(model_dir: Path, build_model, device: torch.device):
"""Build and load on CPU first, then move one copy to the GPU."""
with (model_dir / "rl_agent_config.json").open(encoding="utf-8") as fh:
cfg = json.load(fh)
encoder_dir = model_dir / "encoder"
model = build_model(cfg, encoder_dir=str(encoder_dir))
# safetensors is explicitly read on CPU. Loading into the CPU model first
# avoids a transient second full model allocation on the GPU.
state = load_file(str(model_dir / "model.safetensors"), device="cpu")
model.load_state_dict(state, strict=True)
del state
gc.collect()
# This is the real activation checkpointing switch for ModernBERT. The
# DecisionModel.head_checkpointing attribute is not used by its forward pass.
model.encoder.gradient_checkpointing_enable(
gradient_checkpointing_kwargs={"use_reentrant": False}
)
model.to(device)
model.train()
# There is no action supervision in this CE objective. Keep act_head out of
# autograd and report that it was frozen rather than pretending it was trained.
for parameter in model.act_head.parameters():
parameter.requires_grad_(False)
model.act_head.eval()
return model, cfg
def memory_snapshot(device: torch.device) -> dict[str, float]:
return {
"allocated_gib": float(torch.cuda.memory_allocated(device) / 2**30),
"reserved_gib": float(torch.cuda.memory_reserved(device) / 2**30),
"max_allocated_gib": float(torch.cuda.max_memory_allocated(device) / 2**30),
"max_reserved_gib": float(torch.cuda.max_memory_reserved(device) / 2**30),
}
def assert_finite_gradients(model: torch.nn.Module) -> tuple[float, int]:
finite_count = 0
squared = None
for parameter in model.parameters():
if not parameter.requires_grad or parameter.grad is None:
continue
assert torch.isfinite(parameter.grad).all().item(), "non-finite gradient"
finite_count += 1
value = parameter.grad.detach().float().norm(2)
squared = value * value if squared is None else squared + value * value
assert finite_count > 0, "no trainable parameter received a gradient"
grad_norm = float(torch.sqrt(squared).detach().cpu())
assert torch.isfinite(torch.tensor(grad_norm)), "non-finite aggregate gradient norm"
return grad_norm, finite_count
def run_trial(
model: torch.nn.Module,
device: torch.device,
micro_batch: int,
seq_len: int,
updates: int,
lr: float,
seed: int,
) -> dict[str, Any]:
# Parameters remain FP32; BF16 is used only by CUDA autocast.
parameter_dtypes = sorted({str(p.dtype) for p in model.parameters()})
assert parameter_dtypes == ["torch.float32"], parameter_dtypes
assert torch.cuda.is_bf16_supported(), "the requested BF16 CUDA autocast is unavailable"
model.train()
model.act_head.eval()
optimizer = torch.optim.AdamW(
[p for p in model.parameters() if p.requires_grad], lr=lr, weight_decay=0.01
)
optimizer.zero_grad(set_to_none=True)
vocab_size = int(model.encoder.config.vocab_size)
rng = torch.Generator(device="cpu").manual_seed(seed)
input_ids_cpu = torch.randint(
0, vocab_size, (micro_batch, seq_len), generator=rng, dtype=torch.long
)
attention_cpu = torch.ones((micro_batch, seq_len), dtype=torch.long)
# Two valid choice markers. Their token values are irrelevant to the memory probe.
marker_pos_cpu = torch.tensor([[0, 1]] * micro_batch, dtype=torch.long)
marker_mask_cpu = torch.ones((micro_batch, 2), dtype=torch.bool)
qtype_cpu = torch.zeros(micro_batch, dtype=torch.long)
labels_cpu = torch.arange(micro_batch, dtype=torch.long) % 2
torch.cuda.reset_peak_memory_stats(device)
update_records: list[dict[str, Any]] = []
sync_times: list[float] = []
t_total_start = time.perf_counter()
for update in range(updates):
# Include host-to-device copies outside the measured synchronized model step.
batch = {
"input_ids": input_ids_cpu.to(device, non_blocking=True),
"attention_mask": attention_cpu.to(device, non_blocking=True),
"marker_pos": marker_pos_cpu.to(device, non_blocking=True),
"marker_mask": marker_mask_cpu.to(device, non_blocking=True),
"qtype": qtype_cpu.to(device, non_blocking=True),
"labels": labels_cpu.to(device, non_blocking=True),
}
pre_t = time.perf_counter()
torch.cuda.synchronize(device)
sync_times.append(time.perf_counter() - pre_t)
compute_t = time.perf_counter()
with torch.autocast(device_type="cuda", dtype=torch.bfloat16):
logits, _ = model(
batch["input_ids"],
batch["attention_mask"],
batch["marker_pos"],
batch["marker_mask"],
batch["qtype"],
)
logits = logits.masked_fill(~batch["marker_mask"], -1e4)
loss = F.cross_entropy(logits, batch["labels"])
assert torch.isfinite(loss).item(), "non-finite loss"
loss.backward()
grad_norm, finite_grad_tensors = assert_finite_gradients(model)
clipped_norm = torch.nn.utils.clip_grad_norm_(
[p for p in model.parameters() if p.requires_grad], 1.0
)
assert torch.isfinite(clipped_norm).item(), "non-finite clipped gradient norm"
optimizer.step()
optimizer.zero_grad(set_to_none=True)
post_t = time.perf_counter()
torch.cuda.synchronize(device)
sync_times.append(time.perf_counter() - post_t)
wall_seconds = time.perf_counter() - compute_t
state_tensors = sum(
1 for state in optimizer.state.values() for key in ("exp_avg", "exp_avg_sq") if key in state
)
snap = memory_snapshot(device)
update_records.append(
{
"optimizer_update": update + 1,
"loss": float(loss.detach().cpu()),
"grad_norm_before_clip": grad_norm,
"clipped_grad_norm": float(clipped_norm.detach().cpu()),
"finite_gradient_tensors": finite_grad_tensors,
"adam_state_tensors": state_tensors,
"wall_seconds_with_synchronize": wall_seconds,
"memory": snap,
}
)
print(
f"[memory-probe] microbatch={micro_batch} update={update + 1}/{updates} "
f"loss={float(loss.detach().cpu()):.5f} grad={grad_norm:.3f} "
f"max_alloc={snap['max_allocated_gib']:.2f}GiB "
f"max_reserved={snap['max_reserved_gib']:.2f}GiB",
flush=True,
)
del batch, logits, loss
total_seconds = time.perf_counter() - t_total_start
final = memory_snapshot(device)
return {
"micro_batch": micro_batch,
"seq_len": seq_len,
"attention_all_ones": True,
"updates": updates,
"parameter_dtypes": parameter_dtypes,
"autocast_dtype": "torch.bfloat16",
"encoder_gradient_checkpointing": bool(
getattr(model.encoder, "is_gradient_checkpointing", False)
),
"head_checkpointing_attribute": bool(getattr(model, "head_checkpointing", False)),
"head_checkpointing_used": False,
"act_head_frozen": all(not p.requires_grad for p in model.act_head.parameters()),
"total_seconds": total_seconds,
"synchronize_seconds": {
"count": len(sync_times),
"sum": float(sum(sync_times)),
"max": float(max(sync_times) if sync_times else 0.0),
},
"updates_detail": update_records,
"final_memory": final,
"peak_memory": {
"max_allocated_gib": max(x["memory"]["max_allocated_gib"] for x in update_records),
"max_reserved_gib": max(x["memory"]["max_reserved_gib"] for x in update_records),
},
"assertions": {
"finite_loss_each_update": True,
"finite_gradients_each_update": True,
"adam_states_present_after_update_1": update_records[0]["adam_state_tensors"] > 0,
},
}
def main() -> None:
args = parse_args()
if not torch.cuda.is_available():
raise RuntimeError("CUDA is unavailable; the GPU should be enabled before this probe")
assert args.seq_len == 1024, "the requested probe is defined for 1024-token inputs"
device = torch.device("cuda:0")
torch.manual_seed(args.seed)
torch.cuda.manual_seed_all(args.seed)
model_dir = Path(args.model_dir)
output = Path(args.output)
output.parent.mkdir(parents=True, exist_ok=True)
build_model = import_laya(args.laya_repo)
props = torch.cuda.get_device_properties(device)
result: dict[str, Any] = {
"probe": "laya_full_supervised_ce_memory",
"synthetic_inputs_only": True,
"model_dir": str(model_dir),
"laya_repo": str(Path(args.laya_repo).resolve()),
"gpu": {
"index": 0,
"name": props.name,
"total_memory_gib": float(props.total_memory / 2**30),
"cuda_runtime": torch.version.cuda,
"torch": torch.__version__,
**driver_info(),
},
"config": {
"seq_len": args.seq_len,
"updates": args.updates,
"micro_batches": args.micro_batches,
"lr": args.lr,
"seed": args.seed,
"optimizer": "AdamW",
"parameters": "FP32",
"autocast": "BF16",
"encoder_gradient_checkpointing": True,
"no_cpt": True,
},
"trials": [],
}
for micro_batch in args.micro_batches:
# Each trial gets a fresh model and optimizer, ensuring the second trial's
# peak is not contaminated by the first trial's Adam state.
torch.cuda.empty_cache()
torch.cuda.reset_peak_memory_stats(device)
model = None
try:
model, cfg = load_fixed_model(model_dir, build_model, device)
result["checkpoint"] = {
"encoder": cfg.get("encoder"),
"max_len": cfg.get("max_len"),
"head_max_len": cfg.get("head_max_len"),
"vocab_size": int(model.encoder.config.vocab_size),
}
loaded = memory_snapshot(device)
trial = run_trial(
model,
device,
micro_batch,
args.seq_len,
args.updates,
args.lr,
args.seed + micro_batch,
)
trial["model_loaded_memory"] = loaded
result["trials"].append(trial)
except torch.cuda.OutOfMemoryError as exc:
torch.cuda.empty_cache()
result["trials"].append(
{
"micro_batch": micro_batch,
"status": "oom",
"error": str(exc),
"memory_at_oom": memory_snapshot(device),
}
)
print(f"[memory-probe] microbatch={micro_batch} OOM", flush=True)
finally:
del model
gc.collect()
torch.cuda.empty_cache()
torch.cuda.synchronize(device)
result["status"] = "ok" if all(t.get("status", "ok") == "ok" for t in result["trials"]) else "partial"
output.write_text(json.dumps(result, indent=2) + "\n", encoding="utf-8")
print("[memory-probe] summary", flush=True)
for trial in result["trials"]:
if trial.get("status") == "oom":
print(f" microbatch={trial['micro_batch']}: OOM", flush=True)
else:
peak = trial["peak_memory"]
print(
f" microbatch={trial['micro_batch']}: "
f"max_alloc={peak['max_allocated_gib']:.2f} GiB, "
f"max_reserved={peak['max_reserved_gib']:.2f} GiB, "
f"updates={trial['updates']}",
flush=True,
)
if __name__ == "__main__":
main()
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