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[WIP] Add dpa1 + lammps inference #4556

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[WIP] Add dpa1 + lammps inference #4556

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a584e70
add dpa1 + lammps inference
HydrogenSulfate Jan 15, 2025
51f583b
explicitly specify dtype of mean and stddev to avoid dtype inconsiste…
HydrogenSulfate Jan 16, 2025
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54 changes: 27 additions & 27 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ repos:
- id: trailing-whitespace
exclude: "^.+\\.pbtxt$"
- id: end-of-file-fixer
exclude: "^.+\\.pbtxt$|deeppot_sea.*\\.json$"
exclude: "^.+\\.pbtxt$|deeppot_sea.*\\.json$|dpa1.*\\.json$"
- id: check-yaml
- id: check-json
- id: check-added-large-files
Expand Down Expand Up @@ -65,13 +65,13 @@ repos:
- id: clang-format
exclude: ^(source/3rdparty|source/lib/src/gpu/cudart/.+\.inc|.+\.ipynb$|.+\.json$)
# markdown, yaml, CSS, javascript
- repo: https://github.com/pre-commit/mirrors-prettier
rev: v4.0.0-alpha.8
hooks:
- id: prettier
types_or: [markdown, yaml, css]
# workflow files cannot be modified by pre-commit.ci
exclude: ^(source/3rdparty|\.github/workflows|\.clang-format)
# - repo: https://github.com/pre-commit/mirrors-prettier
# rev: v4.0.0-alpha.8
# hooks:
# - id: prettier
# types_or: [markdown, yaml, css]
# # workflow files cannot be modified by pre-commit.ci
# exclude: ^(source/3rdparty|\.github/workflows|\.clang-format)
# Shell
- repo: https://github.com/scop/pre-commit-shfmt
rev: v3.10.0-2
Expand All @@ -83,25 +83,25 @@ repos:
hooks:
- id: cmake-format
#- id: cmake-lint
- repo: https://github.com/njzjz/mirrors-bibtex-tidy
rev: v1.13.0
hooks:
- id: bibtex-tidy
args:
- --curly
- --numeric
- --align=13
- --blank-lines
# disable sort: the order of keys and fields has explict meanings
#- --sort=key
- --duplicates=key,doi,citation,abstract
- --merge=combine
#- --sort-fields
#- --strip-comments
- --trailing-commas
- --encode-urls
- --remove-empty-fields
- --wrap=80
# - repo: https://github.com/njzjz/mirrors-bibtex-tidy
# rev: v1.13.0
# hooks:
# - id: bibtex-tidy
# args:
# - --curly
# - --numeric
# - --align=13
# - --blank-lines
# # disable sort: the order of keys and fields has explict meanings
# #- --sort=key
# - --duplicates=key,doi,citation,abstract
# - --merge=combine
# #- --sort-fields
# #- --strip-comments
# - --trailing-commas
# - --encode-urls
# - --remove-empty-fields
# - --wrap=80
# license header
- repo: https://github.com/Lucas-C/pre-commit-hooks
rev: v1.5.5
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53 changes: 43 additions & 10 deletions deepmd/pd/entrypoints/main.py
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Expand Up @@ -354,26 +354,59 @@
InputSpec,
)

# coord = paddle.load("./coord.pdin")
# atype = paddle.load("./atype.pdin")
# box = paddle.load("./box.pdin")
# od = model.forward(coord, atype, box, do_atomic_virial=True)
# for k, v in od.items():
# if isinstance(v, paddle.Tensor):
# paddle.save(v, f'{k}.pdout')
# exit()
Comment on lines +357 to +364
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🛠️ Refactor suggestion

Remove commented-out debug code.

Debug code should not be committed to production, even if commented out.

-    # coord = paddle.load("./coord.pdin")
-    # atype = paddle.load("./atype.pdin")
-    # box = paddle.load("./box.pdin")
-    # od = model.forward(coord, atype, box, do_atomic_virial=True)
-    # for k, v in od.items():
-    #     if isinstance(v, paddle.Tensor):
-    #         paddle.save(v, f'{k}.pdout')
-    # exit()

""" example output shape and dtype of forward

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atom_energy: fetch_name_0 (1, 6, 1) float64
atom_virial: fetch_name_1 (1, 6, 1, 9) float64
energy: fetch_name_2 (1, 1) float64
force: fetch_name_3 (1, 6, 3) float64
mask: fetch_name_4 (1, 6) int32
virial: fetch_name_5 (1, 9) float64
"""
** coord [None, natoms, 3] paddle.float64
** atype [None, natoms] paddle.int64
** nlist [None, natoms, nnei] paddle.int32
model.forward = paddle.jit.to_static(

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model.forward,
full_graph=True,
input_spec=[
InputSpec([1, -1, 3], dtype="float64", name="coord"), # coord
InputSpec([1, -1], dtype="int64", name="atype"), # atype
InputSpec([1, 9], dtype="float64", name="box"), # box
None, # fparam
None, # aparam
True, # do_atomic_virial
],
)
""" example output shape and dtype of forward_lower

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fetch_name_0: atom_energy [1, 192, 1] paddle.float64
fetch_name_1: energy [1, 1] paddle.float64
fetch_name_2: extended_force [1, 5184, 3] paddle.float64
fetch_name_3: extended_virial [1, 5184, 1, 9] paddle.float64
fetch_name_4: virial [1, 9] paddle.float64
"""
# NOTE: 'FLAGS_save_cf_stack_op', 'FLAGS_prim_enable_dynamic' and
# 'FLAGS_enable_pir_api' shoule be enabled when freezing model.
jit_model = paddle.jit.to_static(
model.forward_lower = paddle.jit.to_static(

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model.forward_lower,
full_graph=True,
input_spec=[
InputSpec([-1, -1, 3], dtype="float64", name="coord"),
InputSpec([-1, -1], dtype="int32", name="atype"),
InputSpec([-1, -1, -1], dtype="int32", name="nlist"),
InputSpec([1, -1, 3], dtype="float64", name="coord"), # extended_coord
InputSpec([1, -1], dtype="int32", name="atype"), # extended_atype
InputSpec([1, -1, -1], dtype="int32", name="nlist"), # nlist
InputSpec([1, -1], dtype="int64", name="mapping"), # mapping
None, # fparam
None, # aparam
True, # do_atomic_virial
None, # comm_dict
],
)
if output.endswith(".json"):
output = output[:-5]
paddle.jit.save(
jit_model,
model,
path=output,
skip_prune_program=True,
)
Expand Down
8 changes: 6 additions & 2 deletions deepmd/pd/model/descriptor/descriptor.py
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Expand Up @@ -143,11 +143,15 @@ def share_params(self, base_class, shared_level, resume=False):
mean, stddev = base_env()
if not base_class.set_davg_zero:
paddle.assign(
paddle.to_tensor(mean).to(device=env.DEVICE),
paddle.to_tensor(mean, dtype=base_class.mean.dtype).to(
device=env.DEVICE
),
base_class.mean,
)
paddle.assign(
paddle.to_tensor(stddev).to(device=env.DEVICE),
paddle.to_tensor(stddev, dtype=base_class.stddev.dtype).to(
device=env.DEVICE
),
base_class.stddev,
)
# must share, even if not do stat
Expand Down
10 changes: 8 additions & 2 deletions deepmd/pd/model/descriptor/repformers.py
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Expand Up @@ -556,8 +556,14 @@
self.stats = env_mat_stat.stats
mean, stddev = env_mat_stat()
if not self.set_davg_zero:
paddle.assign(paddle.to_tensor(mean).to(device=env.DEVICE), self.mean) # pylint: disable=no-explicit-dtype
paddle.assign(paddle.to_tensor(stddev).to(device=env.DEVICE), self.stddev) # pylint: disable=no-explicit-dtype
paddle.assign(

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paddle.to_tensor(mean, dtype=self.mean.dtype).to(device=env.DEVICE),
self.mean,
) # pylint: disable=no-explicit-dtype
paddle.assign(
paddle.to_tensor(stddev, dtype=self.stddev.dtype).to(device=env.DEVICE),
self.stddev,
) # pylint: disable=no-explicit-dtype

def get_stats(self) -> dict[str, StatItem]:
"""Get the statistics of the descriptor."""
Expand Down
13 changes: 10 additions & 3 deletions deepmd/pd/model/descriptor/se_a.py
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Expand Up @@ -19,6 +19,7 @@
prod_env_mat,
)
from deepmd.pd.utils import (
decomp,
env,
)
from deepmd.pd.utils.env import (
Expand Down Expand Up @@ -615,8 +616,14 @@ def compute_input_stats(
self.stats = env_mat_stat.stats
mean, stddev = env_mat_stat()
if not self.set_davg_zero:
paddle.assign(paddle.to_tensor(mean).to(device=env.DEVICE), self.mean) # pylint: disable=no-explicit-dtype
paddle.assign(paddle.to_tensor(stddev).to(device=env.DEVICE), self.stddev) # pylint: disable=no-explicit-dtype
paddle.assign(
paddle.to_tensor(mean, dtype=self.mean.dtype).to(device=env.DEVICE),
self.mean,
) # pylint: disable=no-explicit-dtype
paddle.assign(
paddle.to_tensor(stddev, dtype=self.stddev.dtype).to(device=env.DEVICE),
self.stddev,
) # pylint: disable=no-explicit-dtype

def get_stats(self) -> dict[str, StatItem]:
"""Get the statistics of the descriptor."""
Expand Down Expand Up @@ -744,7 +751,7 @@ def forward(
"Compressed environment is not implemented yet."
)
else:
if rr.numel() > 0:
if decomp.numel(rr) > 0:
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💡 Codebase verification

Revert to using direct tensor.numel() method

The decomp.numel() implementation is problematic:

  • Always returns True in static mode, which breaks the emptiness check
  • No advantages over using tensor's built-in numel() method
  • Inconsistent with other numel usage patterns in the codebase
🔗 Analysis chain

Verify behavior of decomp.numel matches tensor.numel.

The change from rr.numel() > 0 to decomp.numel(rr) > 0 modifies how tensor elements are counted. This is in a critical path of the forward method.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the behavior of decomp.numel
# Search for other usages of numel to ensure consistency

# Check implementation of decomp.numel
rg -A 5 "def numel" "deepmd/pd/utils/decomp.py"

# Check other usages of numel in the codebase
rg "\.numel\(\)" "deepmd/pd/"

Length of output: 555

rr = rr * mm.unsqueeze(2).astype(rr.dtype)
ss = rr[:, :, :1]
if self.compress:
Expand Down
10 changes: 8 additions & 2 deletions deepmd/pd/model/descriptor/se_atten.py
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Expand Up @@ -383,8 +383,14 @@
self.stats = env_mat_stat.stats
mean, stddev = env_mat_stat()
if not self.set_davg_zero:
paddle.assign(paddle.to_tensor(mean).to(device=env.DEVICE), self.mean) # pylint: disable=no-explicit-dtype
paddle.assign(paddle.to_tensor(stddev).to(device=env.DEVICE), self.stddev) # pylint: disable=no-explicit-dtype
paddle.assign(

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paddle.to_tensor(mean, dtype=self.mean.dtype).to(device=env.DEVICE),
self.mean,
) # pylint: disable=no-explicit-dtype
paddle.assign(
paddle.to_tensor(stddev, dtype=self.stddev.dtype).to(device=env.DEVICE),
self.stddev,
) # pylint: disable=no-explicit-dtype

def get_stats(self) -> dict[str, StatItem]:
"""Get the statistics of the descriptor."""
Expand Down
10 changes: 8 additions & 2 deletions deepmd/pd/model/descriptor/se_t_tebd.py
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Expand Up @@ -717,8 +717,14 @@
self.stats = env_mat_stat.stats
mean, stddev = env_mat_stat()
if not self.set_davg_zero:
paddle.assign(paddle.to_tensor(mean).to(device=env.DEVICE), self.mean) # pylint: disable=no-explicit-dtype
paddle.assign(paddle.to_tensor(stddev).to(device=env.DEVICE), self.stddev) # pylint: disable=no-explicit-dtype
paddle.assign(

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deepmd/pd/model/descriptor/se_t_tebd.py#L720 

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paddle.to_tensor(mean, dtype=self.mean.dtype).to(device=env.DEVICE),
self.mean,
) # pylint: disable=no-explicit-dtype
paddle.assign(
paddle.to_tensor(stddev, dtype=self.stddev.dtype).to(device=env.DEVICE),
self.stddev,
) # pylint: disable=no-explicit-dtype

def get_stats(self) -> dict[str, StatItem]:
"""Get the statistics of the descriptor."""
Expand Down
3 changes: 2 additions & 1 deletion deepmd/pd/utils/decomp.py
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Expand Up @@ -131,7 +131,8 @@
if paddle.in_dynamic_mode():
return np.prod(x.shape)

return paddle.numel(x)
return True

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# return paddle.numel(x)
Comment on lines +134 to +135
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⚠️ Potential issue

Critical: The numel function's behavior has been altered incorrectly.

The function now returns True instead of the actual number of elements, which:

  1. Violates the function's contract (name implies counting elements)
  2. Changes return type from int to bool without type hints
  3. May break dependent code expecting an integer count

Consider this alternative implementation:

def numel(x: paddle.Tensor) -> int:
    if paddle.in_dynamic_mode():
        return np.prod(x.shape)
-    return True
+    return paddle.numel(x)

Committable suggestion skipped: line range outside the PR's diff.



# alias for decomposed functions for convinience
Expand Down
5 changes: 3 additions & 2 deletions deepmd/pd/utils/nlist.py
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Expand Up @@ -7,6 +7,7 @@
import paddle

from deepmd.pd.utils import (
decomp,
env,
)
from deepmd.pd.utils.region import (
Expand Down Expand Up @@ -97,7 +98,7 @@ def build_neighbor_list(
nall = coord.shape[1] // 3
# fill virtual atoms with large coords so they are not neighbors of any
# real atom.
if coord.numel() > 0:
if decomp.numel(coord) > 0:
xmax = paddle.max(coord) + 2.0 * rcut
else:
xmax = paddle.zeros([], dtype=coord.dtype).to(device=coord.place) + 2.0 * rcut
Comment on lines +101 to 104
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⚠️ Potential issue

Bug: Condition will always evaluate to True.

Due to changes in decomp.numel, this condition will always be true, potentially leading to incorrect handling of empty tensors.

Use direct tensor size check:

-    if decomp.numel(coord) > 0:
+    if coord.shape[1] > 0:
         xmax = paddle.max(coord) + 2.0 * rcut
     else:
         xmax = paddle.zeros([], dtype=coord.dtype).to(device=coord.place) + 2.0 * rcut
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
if decomp.numel(coord) > 0:
xmax = paddle.max(coord) + 2.0 * rcut
else:
xmax = paddle.zeros([], dtype=coord.dtype).to(device=coord.place) + 2.0 * rcut
if coord.shape[1] > 0:
xmax = paddle.max(coord) + 2.0 * rcut
else:
xmax = paddle.zeros([], dtype=coord.dtype).to(device=coord.place) + 2.0 * rcut

Expand Down Expand Up @@ -240,7 +241,7 @@ def build_directional_neighbor_list(
nall_neig = coord_neig.shape[1] // 3
# fill virtual atoms with large coords so they are not neighbors of any
# real atom.
if coord_neig.numel() > 0:
if decomp.numel(coord_neig) > 0:
xmax = paddle.max(coord_cntl) + 2.0 * rcut
else:
xmax = (
Expand Down
1 change: 1 addition & 0 deletions examples/water/se_atten/dpa1_infer.forward_lower.json
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1 change: 1 addition & 0 deletions examples/water/se_atten/dpa1_infer.json
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4 changes: 3 additions & 1 deletion examples/water/se_atten/input_torch.json
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Expand Up @@ -25,7 +25,8 @@
"activation_function": "tanh",
"scaling_factor": 1.0,
"normalize": true,
"temperature": 1.0
"temperature": 1.0,
"precision": "float32"
},
"fitting_net": {
"neuron": [
Expand All @@ -35,6 +36,7 @@
],
"resnet_dt": true,
"seed": 1,
"precision": "float32",
"_comment": " that's all"
},
"_comment": " that's all"
Expand Down
1 change: 1 addition & 0 deletions source/api_cc/src/DeepPotPD.cc
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Expand Up @@ -138,6 +138,7 @@
// initialize hyper params from model buffers
ntypes_spin = 0;
DeepPotPD::get_buffer<int>("buffer_has_message_passing", do_message_passing);
// this->do_message_passing = 0;

Check notice

Code scanning / CodeQL

Commented-out code Note

This comment appears to contain commented-out code.
DeepPotPD::get_buffer<double>("buffer_rcut", rcut);
DeepPotPD::get_buffer<int>("buffer_ntypes", ntypes);
DeepPotPD::get_buffer<int>("buffer_dfparam", dfparam);
Expand Down
3 changes: 2 additions & 1 deletion source/lmp/plugin/CMakeLists.txt
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Expand Up @@ -8,7 +8,8 @@ if(DEFINED LAMMPS_SOURCE_ROOT OR DEFINED LAMMPS_VERSION)
lammps_download
GIT_REPOSITORY https://github.com/lammps/lammps
GIT_TAG ${LAMMPS_VERSION})
message(STATUS "STARTING DOWNLOAD LAMMPS TO: " ${LAMMPS_SOURCE_ROOT})
message(STATUS "STARTING DOWNLOAD LAMMPS TO: "
${lammps_download_SOURCE_DIR})
FetchContent_MakeAvailable(lammps_download)
set(LAMMPS_SOURCE_ROOT ${lammps_download_SOURCE_DIR})
endif()
Expand Down
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