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Commit d1e0d27b authored by Wang, Leping's avatar Wang, Leping
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Merge branch 'bomlip-csp-hygon' into cpu-bfgs-eigh

parents 33092d32 13773718
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.gitignore
View file @ d1e0d27b
...@@ -261,3 +261,4 @@ config/secrets.* ...@@ -261,3 +261,4 @@ config/secrets.*
# Project specific # Project specific
# ============================================================================= # =============================================================================
csp_results/ csp_results/
run/
\ No newline at end of file
.gitmodules
View file @ d1e0d27b
[submodule "mace-bench"] [submodule "batchASE"]
path = mace-bench path = batchASE
url = ssh://git@10.208.16.64:2222/wangleping/mace-bench-hygon.git url = ssh://git@10.208.16.64:2222/wangleping/mace-bench-hygon.git
branch = hygon-opt-bfgs branch = hygon-opt-bfgs
[submodule "mace"] [submodule "mace"]
path = mace path = 3rdparty/mace
url = ssh://git@10.208.16.64:2222/huafeng/MACE.git url = ssh://git@10.208.16.64:2222/huafeng/MACE.git
branch = fasteq-mace-bench branch = fasteq-mace-bench
[submodule "FastEq"] [submodule "FastEq"]
path = FastEq path = 3rdparty/FastEq
url = ssh://git@10.208.16.64:2222/ncic-ai4sci/FastEq.git url = ssh://git@10.208.16.64:2222/ncic-ai4sci/FastEq.git
branch = hip branch = hip
[submodule "cuequivariance_torch"] [submodule "cuequivariance_torch"]
path = cuequivariance_torch path = 3rdparty/cuequivariance_torch
url = git@github.com:malixian/cuEquivariance.git url = git@github.com:malixian/cuEquivariance.git
branch = hip branch = hip
FastEq @ 0a0b17a1
File moved
mace @ eb85199d
File moved
README.md
View file @ d1e0d27b
...@@ -10,7 +10,7 @@ unbiased structure prediction across the full density range ...@@ -10,7 +10,7 @@ unbiased structure prediction across the full density range
git clone https://github.com/pic-ai-robotic-chemistry/BOMLIP-CSP.git --recursive git clone https://github.com/pic-ai-robotic-chemistry/BOMLIP-CSP.git --recursive
conda create -n BOMLIP_CSP python=3.10 -y conda create -n BOMLIP_CSP python=3.10 -y
conda activate BOMLIP_CSP conda activate BOMLIP_CSP
cd BOMLIP-CSP/mace-bench cd BOMLIP-CSP/batchASE
# using chmod -R 755 in your BOMLIP-CSP folder if you do not have exection permission # using chmod -R 755 in your BOMLIP-CSP folder if you do not have exection permission
./reproduce/init_mace.sh ./reproduce/init_mace.sh
source util/env.sh source util/env.sh
...@@ -61,10 +61,10 @@ Conformer search and structure generation could also be done in python script wi ...@@ -61,10 +61,10 @@ Conformer search and structure generation could also be done in python script wi
### structure optimization ### structure optimization
Structure optimization is done by a seperate command Structure optimization is done by a seperate command
```sh ```sh
python "${TOP_DIR}/mace-bench/scripts/opt_batch.py" ... python "${TOP_DIR}/batchASE/scripts/opt_batch.py" ...
``` ```
Explanations for all arguments are provided in main.py and mace-bench/scripts/opt_batch.py. Explanations for all arguments are provided in main.py and batchASE/scripts/opt_batch.py.
### If you want to configure the 7net environment. ### If you want to configure the 7net environment.
...@@ -72,14 +72,14 @@ Explanations for all arguments are provided in main.py and mace-bench/scripts/op ...@@ -72,14 +72,14 @@ Explanations for all arguments are provided in main.py and mace-bench/scripts/op
```sh ```sh
#!/bin/bash #!/bin/bash
conda create -n 7net-cueq python=3.10 -y && conda activate 7net-cueq conda create -n 7net-cueq python=3.10 -y && conda activate 7net-cueq
cd BOMLIP-CSP/mace-bench cd BOMLIP-CSP/batchASE
./reproduce/init_7net.sh && source util/env.sh ./reproduce/init_7net.sh && source util/env.sh
``` ```
The optimization command for 7net is given in csp.sh The optimization command for 7net is given in csp.sh
```sh ```sh
# Use a fixed batch size for structural optimization # Use a fixed batch size for structural optimization
python "${TOP_DIR}/mace-bench/scripts/opt_batch.py" --target_folder "${TAR_DIR}/structures" \ python "${TOP_DIR}/batchASE/scripts/opt_batch.py" --target_folder "${TAR_DIR}/structures" \
--molecule_single 13 --gpu_offset 0 --n_gpus 8 --num_workers 48 --batch_size 2 \ --molecule_single 13 --gpu_offset 0 --n_gpus 8 --num_workers 48 --batch_size 2 \
--max_steps 3000 --filter1 UnitCellFilter --filter2 UnitCellFilter \ --max_steps 3000 --filter1 UnitCellFilter --filter2 UnitCellFilter \
--optimizer1 BFGSFusedLS --optimizer2 BFGS --num_threads 2 --cueq true \ --optimizer1 BFGSFusedLS --optimizer2 BFGS --num_threads 2 --cueq true \
......
batchASE @ 2207c831
File moved
scripts/csp.sh → example/csp.sh
View file @ d1e0d27b
...@@ -21,7 +21,7 @@ python "${TOP_DIR}/main.py" --path ${TAR_DIR} --smiles "C1CC2=COC=C12" \ ...@@ -21,7 +21,7 @@ python "${TOP_DIR}/main.py" --path ${TAR_DIR} --smiles "C1CC2=COC=C12" \
# opt structures using mace step, --batch_size 0 means auto batch size only for mace # opt structures using mace step, --batch_size 0 means auto batch size only for mace
mkdir -p "${TAR_DIR}/mace_opt" mkdir -p "${TAR_DIR}/mace_opt"
cd "${TAR_DIR}/mace_opt" cd "${TAR_DIR}/mace_opt"
python "${TOP_DIR}/mace-bench/scripts/opt_batch.py" --target_folder "${TAR_DIR}/structures" \ python "${TOP_DIR}/batchASE/scripts/opt_batch.py" --target_folder "${TAR_DIR}/structures" \
--molecule_single 13 --gpu_offset 0 --n_gpus 8 --num_workers 80 --batch_size 0 \ --molecule_single 13 --gpu_offset 0 --n_gpus 8 --num_workers 80 --batch_size 0 \
--max_steps 3000 --filter1 UnitCellFilter --filter2 UnitCellFilter \ --max_steps 3000 --filter1 UnitCellFilter --filter2 UnitCellFilter \
--optimizer1 BFGSFusedLS --optimizer2 BFGS --num_threads 1 --cueq true \ --optimizer1 BFGSFusedLS --optimizer2 BFGS --num_threads 1 --cueq true \
...@@ -30,7 +30,7 @@ python "${TOP_DIR}/mace-bench/scripts/opt_batch.py" --target_folder "${TAR_DIR}/ ...@@ -30,7 +30,7 @@ python "${TOP_DIR}/mace-bench/scripts/opt_batch.py" --target_folder "${TAR_DIR}/
# opt structures using 7net # opt structures using 7net
# mkdir -p "${TAR_DIR}/7net_opt" # mkdir -p "${TAR_DIR}/7net_opt"
# cd "${TAR_DIR}/7net_opt" # cd "${TAR_DIR}/7net_opt"
# python "${TOP_DIR}/mace-bench/scripts/opt_batch.py" --target_folder "${TAR_DIR}/structures" \ # python "${TOP_DIR}/batchASE/scripts/opt_batch.py" --target_folder "${TAR_DIR}/structures" \
# --molecule_single 13 --gpu_offset 0 --n_gpus 8 --num_workers 48 --batch_size 2 \ # --molecule_single 13 --gpu_offset 0 --n_gpus 8 --num_workers 48 --batch_size 2 \
# --max_steps 3000 --filter1 UnitCellFilter --filter2 UnitCellFilter \ # --max_steps 3000 --filter1 UnitCellFilter --filter2 UnitCellFilter \
# --optimizer1 BFGSFusedLS --optimizer2 BFGS --num_threads 2 --cueq true \ # --optimizer1 BFGSFusedLS --optimizer2 BFGS --num_threads 2 --cueq true \
......
scripts/generation.sh → example/generation.sh
View file @ d1e0d27b
...@@ -50,7 +50,7 @@ echo " Max workers: ${MAX_WORKERS}" ...@@ -50,7 +50,7 @@ echo " Max workers: ${MAX_WORKERS}"
echo "==========================================" echo "=========================================="
# --- Run the pipeline --- # --- Run the pipeline ---
python "${SCRIPT_DIR}/generation.py" \ python "../scripts/generation.py" \
--path "${TAR_DIR}" \ --path "${TAR_DIR}" \
--smiles "${SMILES}" \ --smiles "${SMILES}" \
--molecule_num_in_cell ${MOLECULE_NUM_IN_CELL} \ --molecule_num_in_cell ${MOLECULE_NUM_IN_CELL} \
......
scripts/relaxation.sh → example/relaxation.sh
View file @ d1e0d27b
...@@ -95,7 +95,7 @@ CUEQ_ARG="" ...@@ -95,7 +95,7 @@ CUEQ_ARG=""
BFGS_CPU_THREADS_ARG="" BFGS_CPU_THREADS_ARG=""
[ -n "${BFGS_CPU_THREADS}" ] && BFGS_CPU_THREADS_ARG="--bfgs_cpu_thread ${BFGS_CPU_THREADS}" [ -n "${BFGS_CPU_THREADS}" ] && BFGS_CPU_THREADS_ARG="--bfgs_cpu_thread ${BFGS_CPU_THREADS}"
python "${PROJECT_DIR}/mace-bench/scripts/mace_opt_batch.py" \ python "${PROJECT_DIR}/batchASE/scripts/mace_opt_batch.py" \
--target_folder "${TARGET_FOLDER}" \ --target_folder "${TARGET_FOLDER}" \
--molecule_single ${MOLECULE_SINGLE} \ --molecule_single ${MOLECULE_SINGLE} \
--gpu_offset ${GPU_OFFSET} \ --gpu_offset ${GPU_OFFSET} \
......
scripts/relaxation_config.sh → example/relaxation_config.sh
View file @ d1e0d27b
...@@ -48,14 +48,12 @@ ...@@ -48,14 +48,12 @@
# auto-generated timestamped directory. # auto-generated timestamped directory.
# ============================================================================= # =============================================================================
#TARGET_FOLDER="${PROJECT_DIR}/csp_results/structures_1" TARGET_FOLDER="${PROJECT_DIR}/csp_results/structures"
#TARGET_FOLDER="/data/wangleping/csp_data/perf_46" MOLECULE_SINGLE=13
TARGET_FOLDER="/data/wangleping/csp_data/perf_v2_sorted/perf_v2_92"
MOLECULE_SINGLE=46
N_GPUS=8 N_GPUS=8
GPU_OFFSET=0 GPU_OFFSET=0
NUM_WORKERS=32 NUM_WORKERS=8
BATCH_SIZE=32 BATCH_SIZE=25
NUM_THREADS=1 NUM_THREADS=1
BIND_CORES="" BIND_CORES=""
MAX_STEPS=3000 MAX_STEPS=3000
...@@ -68,7 +66,7 @@ FILTER1="UnitCellFilter" ...@@ -68,7 +66,7 @@ FILTER1="UnitCellFilter"
FILTER2="UnitCellFilter" FILTER2="UnitCellFilter"
MODEL="mace" MODEL="mace"
CUEQ=true CUEQ=true
BFGS_CPU_THREADS=16 BFGS_CPU_THREADS=25
USE_ORDERED_FILE=true USE_ORDERED_FILE=true
COMPILE_MODE="" COMPILE_MODE=""
PROFILE="false" PROFILE="false"
......
pyproject.toml
View file @ d1e0d27b
...@@ -24,9 +24,9 @@ dependencies = [ ...@@ -24,9 +24,9 @@ dependencies = [
[tool.uv.sources] [tool.uv.sources]
torch = { path = "/data/wangleping/torch-2.5.1+das.opt1.dtk25041-cp310-cp310-manylinux_2_28_x86_64.whl" } torch = { path = "/data/wangleping/torch-2.5.1+das.opt1.dtk25041-cp310-cp310-manylinux_2_28_x86_64.whl" }
mace-torch = { path = "./mace", editable = true } mace-torch = { path = "./3rdparty/mace", editable = true }
cuequivariance-torch = { path = "./cuequivariance_torch/cuequivariance_torch", editable = true } cuequivariance-torch = { path = "./3rdparty/cuequivariance_torch/cuequivariance_torch", editable = true }
fasteq = { path = "./FastEq", editable = true } fasteq = { path = "./3rdparty/FastEq", editable = true }
triton = { path = "../../../../data/wangleping/triton-3.0.0+das.opt1.dtk25041-cp310-cp310-manylinux_2_28_x86_64.whl" } triton = { path = "../../../../data/wangleping/triton-3.0.0+das.opt1.dtk25041-cp310-cp310-manylinux_2_28_x86_64.whl" }
[tool.uv] [tool.uv]
...@@ -39,7 +39,7 @@ requires = ["hatchling"] ...@@ -39,7 +39,7 @@ requires = ["hatchling"]
build-backend = "hatchling.build" build-backend = "hatchling.build"
[tool.hatch.build.targets.wheel] [tool.hatch.build.targets.wheel]
packages = ["basic_function", "mace-bench/src/batchopt"] packages = ["basic_function", "batchASE/src/batchopt"]
[tool.uv.extra-build-dependencies] [tool.uv.extra-build-dependencies]
cuequivariance-torch = ["hatchling"] cuequivariance-torch = ["hatchling"]
......
uv.lock
View file @ d1e0d27b
...@@ -116,10 +116,10 @@ dependencies = [ ...@@ -116,10 +116,10 @@ dependencies = [
[package.metadata] [package.metadata]
requires-dist = [ requires-dist = [
{ name = "ase", specifier = "==3.23.0" }, { name = "ase", specifier = "==3.23.0" },
{ name = "cuequivariance-torch", editable = "cuequivariance_torch/cuequivariance_torch" }, { name = "cuequivariance-torch", editable = "3rdparty/cuequivariance_torch/cuequivariance_torch" },
{ name = "fasteq", editable = "FastEq" }, { name = "fasteq", editable = "3rdparty/FastEq" },
{ name = "joblib", specifier = ">=1.5.3" }, { name = "joblib", specifier = ">=1.5.3" },
{ name = "mace-torch", editable = "mace" }, { name = "mace-torch", editable = "3rdparty/mace" },
{ name = "networkx", specifier = "==3.2.1" }, { name = "networkx", specifier = "==3.2.1" },
{ name = "numpy", specifier = "==1.26.4" }, { name = "numpy", specifier = "==1.26.4" },
{ name = "pyyaml", specifier = ">=6.0.3" }, { name = "pyyaml", specifier = ">=6.0.3" },
...@@ -226,7 +226,7 @@ wheels = [ ...@@ -226,7 +226,7 @@ wheels = [
[[package]] [[package]]
name = "cuequivariance-torch" name = "cuequivariance-torch"
source = { editable = "cuequivariance_torch/cuequivariance_torch" } source = { editable = "3rdparty/cuequivariance_torch/cuequivariance_torch" }
dependencies = [ dependencies = [
{ name = "cuequivariance" }, { name = "cuequivariance" },
] ]
...@@ -261,7 +261,7 @@ wheels = [ ...@@ -261,7 +261,7 @@ wheels = [
[[package]] [[package]]
name = "fasteq" name = "fasteq"
version = "0.1.0" version = "0.1.0"
source = { editable = "FastEq" } source = { editable = "3rdparty/FastEq" }
[[package]] [[package]]
name = "filelock" name = "filelock"
...@@ -452,7 +452,7 @@ wheels = [ ...@@ -452,7 +452,7 @@ wheels = [
[[package]] [[package]]
name = "mace-torch" name = "mace-torch"
version = "0.3.15" version = "0.3.15"
source = { editable = "mace" } source = { editable = "3rdparty/mace" }
dependencies = [ dependencies = [
{ name = "ase" }, { name = "ase" },
{ name = "configargparse" }, { name = "configargparse" },
......
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