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View Code? Open in Web Editor NEWImplementation of Learning Gradient Fields for Molecular Conformation Generation (ICML 2021).
License: MIT License
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shichence unixjunkie yingli2009 superxiang tiger-tiger ziqiaomeng thegodone alexgcsa jxzhangjhu truongquocchien yidongsong xuty-007 qcxia20 chifengwoo alexjli general-synthesis hojinyoo chrisallenming rnaimehaom yuh8 chaoqu12 paulie-ai lyndonlens xingxinglikecode damondengxin yansonggu zhuxiaohai fyjun2071 cuidachao yukiycu rich-xgk itcd bondrewd smile-ttxpconfgf's Issues
The conformation generated is 2D and how to make sure it is a proper conformer as output?
Hello
Thank you for your work and it is useful for fast generating conformers.
I just have a small technical issue here and want to ask.
So I tried to run the default generating conformers using smiles for any random molecule as input.
I tried to run the template command for benzene "python -u script/gen.py --config_path ./config/qm9_default.yml --generator ConfGF --smiles c1ccccc1“
and "python -u script/gen.py --config_path ./config/qm9_default.yml --generator ConfGFDist --smiles c1ccccc1"
but the output rdmol reading from the .pkl files are both 2D and do not contain 3D coordinates.
As first, I though it is benzene and it might be flat.
Then I tried a random example like CCCC, "python -u script/gen.py --config_path ./config/qm9_default.yml --generator ConfGF --smiles CCCC" and the output is also 2D unless I embed it using Rdkit, but if I use Rdkit to embed, then it will change the coordinates of the output and the conformer is actually refine by Rkdit, as shown below:
"(confgf) popzq@GPUSrv:~/桌面/ConfGF-main/Diamond/qm9_default$ python
Python 3.7.16 (default, Jan 17 2023, 22:20:44)
[GCC 11.2.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
import pandas as pd
data = pd.read_pickle('ConfGF_CCCC.pkl')
print(data)
Data(atom_type=[14], bond_edge_index=[2, 26], d_gen=[128, 1], d_recover=[128, 1], edge_index=[2, 128], edge_length=[128, 1], edge_name=[128], edge_order=[128], edge_type=[128], is_bond=[128], num_pos_gen=[1], num_pos_traj=[1], pos=[14, 3], pos_gen=[14, 3], pos_traj=[70000, 3], rdmol=<rdkit.Chem.rdchem.Mol object at 0x7fa28856d8f0>, smiles="CCCC")
from rdkit import Chem
from rdkit.Chem import rdMolDescriptors
rdmol_object = data.rdmol
conf = rdmol_object.GetConformer()
Traceback (most recent call last):
File "", line 1, in
ValueError: Bad Conformer Id
positions = conf.GetPositions()
Traceback (most recent call last):
File "", line 1, in
NameError: name 'conf' is not defined
AllChem.EmbedMolecule(rdmol_object, randomSeed=42)
Traceback (most recent call last):
File "", line 1, in
NameError: name 'AllChem' is not defined
from rdkit import AllChem
Traceback (most recent call last):
File "", line 1, in
ImportError: cannot import name 'AllChem' from 'rdkit' (/home/popzq/anaconda3/envs/confgf/lib/python3.7/site-packages/rdkit/init.py)
from rdkit.Chem import AllChem
AllChem.EmbedMolecule(rdmol_object, randomSeed=42)
0
conf = rdmol_object.GetConformer()
positions = conf.GetPositions()
if positions.shape[1] == 3:
print("The molecule has 3D coordinates.")
else:
print("The molecule has 2D coordinates.")
...
The molecule has 3D coordinates.
"
I was just wondering, is there any way I can get the original model generating 3D output, instead of using Rkdit to generate a conformer? Is that any issue I might miss in running this model?
Multiple Conformers
Hi, after running the following two commands:
python -u script/gen.py --config_path ./config/drugs_default.yml --generator ConfGF --smiles c1ccccc1
python -u script/gen.py --config_path ./config/drugs_default.yml --generator ConfGFDist --smiles c1ccccc1
I noticed only one .pkl file is generated by each command - is it possible to generate more conformers for one given smiles?
An error on "Generate conformations of a molecule by feeding its SMILES into the model"
I have downloaded ckpt from google driver provided by authors, and then tried to "Generate conformations of a molecule by feeding its SMILES into the model".
The ckpt was placed at XXX/ConfGF/confgf/train/qm9_default/checkpoint284 or XXX/ConfGF/confgf/train/qm9_default.
However, both pathes had this error occurred: FileNotFoundError: [Errno 2] No such file or directory: 'XXX/ConfGF/confgf/train/qm9_default/checkpoint284'
Hope to get your kindly help!
"The 'data' object was created by an older version of PyG. "
Hi!
thank you for sharing your work
When I ues google colab
run"python -u script/gen.py --config_path ./config/qm9_default.yml --generator ConfGF --smiles c1ccccc1"
it returned an error :RuntimeError: The 'data' object was created by an older version of PyG. If this error occurred while loading an already existing dataset, remove the 'processed/' directory in the dataset's root folder and try again.
could you please tell me how to fix this?
whole output:
Let's use 1 GPUs!
Using device cuda:0 as main device
{'train': {'batch_size': 128, 'seed': 2021, 'epochs': 300, 'shuffle': True, 'resume_train': False, 'eval': True, 'num_workers': 0, 'gpus': [0], 'anneal_power': 2.0, 'save': True, 'save_path': '/home/shichenc/scratch/confgf/train', 'resume_checkpoint': None, 'resume_epoch': None, 'log_interval': 400, 'optimizer': {'type': 'Adam', 'lr': 0.001, 'weight_decay': 0.0, 'dropout': 0.0}, 'scheduler': {'type': 'plateau', 'factor': 0.6, 'patience': 10, 'min_lr': '1e-4'}, 'device': device(type='cuda', index=0)}, 'test': {'init_checkpoint': '/home/shichenc/scratch/confgf/train/qm9_default', 'output_path': '/home/shichenc/scratch/confgf/test/qm9_default', 'epoch': 284, 'gen': {'dg_step_size': 3.0, 'dg_num_steps': 1000, 'steps_d': 100, 'step_lr_d': 2e-06, 'steps_pos': 100, 'step_lr_pos': 2.4e-06, 'clip': 1000, 'min_sigma': 0.0, 'verbose': 1}}, 'data': {'base_path': '/content/', 'dataset': 'qm9', 'train_set': 'train_data_40k.pkl', 'val_set': 'val_data_5k.pkl', 'test_set': 'test_data_200.pkl'}, 'model': {'name': 'qm9_default', 'hidden_dim': 256, 'num_convs': 4, 'sigma_begin': 10, 'sigma_end': 0.01, 'num_noise_level': 50, 'order': 3, 'mlp_act': 'relu', 'gnn_act': 'relu', 'cutoff': 10.0, 'short_cut': True, 'concat_hidden': False, 'noise_type': 'symmetry', 'edge_encoder': 'mlp'}}
set seed for random, numpy and torch
loading data from /content/qm9_processed
train size : 0 || val size: 0 || test size: 24068
loading data done!
got 200 molecules with 24068 confs
Traceback (most recent call last):
File "script/gen.py", line 92, in
test_data = dataset.GEOMDataset_PackedConf(data=test_data, transform=transform)
File "/content/ConfGF/confgf/dataset/dataset.py", line 449, in init
self._pack_data_by_mol()
File "/content/ConfGF/confgf/dataset/dataset.py", line 469, in _pack_data_by_mol
data = copy.deepcopy(v[0])
File "/usr/local/lib/python3.7/copy.py", line 161, in deepcopy
y = copier(memo)
File "/usr/local/lib/python3.7/site-packages/torch_geometric/data/data.py", line 392, in deepcopy
out._store._parent = out
File "/usr/local/lib/python3.7/site-packages/torch_geometric/data/data.py", line 358, in getattr
"The 'data' object was created by an older version of PyG. "
RuntimeError: The 'data' object was created by an older version of PyG. If this error occurred while loading an already existing dataset, remove the 'processed/' directory in the dataset's root folder and try again.
Code on property prediction experiments
I failed to use Psi4 to reproduce the Property Prediction experiments and the results are very different in the order of magnitude. Can you release the code for property prediction experiments and the randomly selected 30 molecule smiles?
Grad Error!
When I run the code train.py, some error occurred in "default_runner.py", specifically, loss.backward()
The followings are the detail debug information:
RuntimeError: one of the variables needed for gradient computation has been modified by an inplace operation: [torch.cuda.FloatTensor [2507, 256]], which is output 0 of ReluBackward0, is at version 1; expected version 0 instead. Hint: the backtrace further above shows the operation that failed to compute its gradient. The variable in question was changed in there or anywhere later. Good luck!
I can find where the grad have been modified? Anyone meet this issue? Thank you for your help!
My environments are:
Unable to recreate the environment
Hi, I'm using Miniconda3 Linux 64-bit - Python 3.7 version. I tried both the methods given in the repository to set up the environment but the installation failed while downloading pytorch-geometric libraries.
The pip installations in yml file fails every time with the following message:
Installing pip dependencies: \ Ran pip subprocess with arguments:
['/home/dhruv/miniconda3/envs/confgf/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt', '--exists-action=b']
Pip subprocess output:
Looking in indexes: https://pypi.org/simple, https://dev-pypi.aganitha.ai/
Looking in links: https://pytorch-geometric.com/whl/torch-1.7.0+cpu.html
Collecting ase==3.21.1
Downloading ase-3.21.1-py3-none-any.whl (2.2 MB)
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Downloading dataclasses-0.6-py3-none-any.whl (14 kB)
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Downloading future-0.18.2.tar.gz (829 kB)
Collecting googledrivedownloader==0.4
Downloading googledrivedownloader-0.4-py2.py3-none-any.whl (3.9 kB)
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Downloading torch_cluster-1.6.0.tar.gz (43 kB)
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Using cached torch_scatter-2.1.0.tar.gz (106 kB)
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Downloading torch_sparse-0.6.16.tar.gz (208 kB)
Collecting torch-spline-conv
Downloading https://data.pyg.org/whl/torch-1.7.0%2Bcpu/torch_spline_conv-1.2.1-cp37-cp37m-linux_x86_64.whl (135 kB)
Collecting urllib3==1.26.5
Downloading urllib3-1.26.5-py2.py3-none-any.whl (138 kB)
Requirement already satisfied: matplotlib>=2.0.0 in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from ase==3.21.1->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 2)) (3.3.4)
Requirement already satisfied: numpy>=1.11.3 in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from ase==3.21.1->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 2)) (1.20.2)
Requirement already satisfied: scipy>=0.18.1 in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from ase==3.21.1->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 2)) (1.6.2)
Requirement already satisfied: six in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from isodate==0.6.0->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 10)) (1.15.0)
Requirement already satisfied: setuptools in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from numba==0.53.1->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 14)) (52.0.0.post20210125)
Requirement already satisfied: networkx in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from python-louvain==0.13->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 15)) (2.5)
Requirement already satisfied: pyparsing in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from rdflib==5.0.0->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 17)) (2.4.7)
Requirement already satisfied: certifi>=2017.4.17 in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from requests==2.25.1->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 18)) (2021.5.30)
Requirement already satisfied: torch in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from torch-geometric==1.6.3->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 20)) (1.7.0)
Requirement already satisfied: tqdm in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from torch-geometric==1.6.3->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 20)) (4.59.0)
Requirement already satisfied: scikit-learn in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from torch-geometric==1.6.3->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 20)) (0.24.2)
Requirement already satisfied: pandas in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from torch-geometric==1.6.3->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 20)) (1.2.4)
Requirement already satisfied: pillow>=6.2.0 in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from matplotlib>=2.0.0->ase==3.21.1->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 2)) (8.2.0)
Requirement already satisfied: cycler>=0.10 in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from matplotlib>=2.0.0->ase==3.21.1->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 2)) (0.10.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from matplotlib>=2.0.0->ase==3.21.1->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 2)) (1.3.1)
Requirement already satisfied: python-dateutil>=2.1 in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from matplotlib>=2.0.0->ase==3.21.1->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 2)) (2.8.1)
Requirement already satisfied: decorator>=4.3.0 in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from networkx->python-louvain==0.13->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 15)) (5.0.9)
Requirement already satisfied: pytz>=2017.3 in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from pandas->torch-geometric==1.6.3->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 20)) (2021.1)
Requirement already satisfied: joblib>=0.11 in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from scikit-learn->torch-geometric==1.6.3->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 20)) (1.0.1)
Requirement already satisfied: threadpoolctl>=2.0.0 in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from scikit-learn->torch-geometric==1.6.3->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 20)) (2.1.0)
Requirement already satisfied: typing_extensions in /home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages (from torch->torch-geometric==1.6.3->-r /home/dhruv/work/github/ConfGF/condaenv.ze5v_33c.requirements.txt (line 20)) (3.7.4.3)
Building wheels for collected packages: future, python-louvain, pyyaml, torch-geometric, torch-cluster, torch-scatter, torch-sparse
Building wheel for future (setup.py): started
Building wheel for future (setup.py): finished with status 'done'
Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=b727b0996b69214b156ea5c5f0c4b078531a34d5c575ea43ee2cb7a5de0c2df5
Stored in directory: /home/dhruv/.cache/pip/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
Building wheel for python-louvain (setup.py): started
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Created wheel for python-louvain: filename=python_louvain-0.13-py3-none-any.whl size=9222 sha256=f83375b047416d12159160eb6227c42eb1198fbed2c9b250e3f841c383d40864
Stored in directory: /home/dhruv/.cache/pip/wheels/dd/6b/3b/87539deabac63a68ec34be2867308907d0544e11ba4d4e728d
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Created wheel for pyyaml: filename=PyYAML-5.3.1-cp37-cp37m-linux_x86_64.whl size=44620 sha256=09eb08962d8ef3f2d25c78a9b4afa201884836d3ee22d075911783cc0933143d
Stored in directory: /home/dhruv/.cache/pip/wheels/5e/03/1e/e1e954795d6f35dfc7b637fe2277bff021303bd9570ecea653
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Created wheel for torch-geometric: filename=torch_geometric-1.6.3-py3-none-any.whl size=322718 sha256=25c46ccfc3a092560d35fb7bc961532fc35db2cdc01f6ec465a47048a5b0ddd4
Stored in directory: /home/dhruv/.cache/pip/wheels/9f/98/e2/5e1e57b8ac9f135413e7d3b0399761e9243194864b4ffcf3d7
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Created wheel for torch-cluster: filename=torch_cluster-1.6.0-cp37-cp37m-linux_x86_64.whl size=1075923 sha256=f28afb2f78e285bd13f6264a5f5b6997c5c61f9e6b036720cc5bc114f9cdf120
Stored in directory: /home/dhruv/.cache/pip/wheels/bc/c7/3e/258dd72b35d7a459264143ad5bfe97b9dc5eef90069ca2f13f
Building wheel for torch-scatter (setup.py): started
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Running setup.py clean for torch-scatter
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Building wheel for torch-sparse (setup.py): finished with status 'done'
Created wheel for torch-sparse: filename=torch_sparse-0.6.16-cp37-cp37m-linux_x86_64.whl size=1740317 sha256=47ccd7b7a5ce0ade79ea5d4ca660534999a5895a6647c265207bc667b72a7cfa
Stored in directory: /home/dhruv/.cache/pip/wheels/92/8d/17/1517bf0318b8343b665b7aadf906dff4bc8967d82cacc17992
Successfully built future python-louvain pyyaml torch-geometric torch-cluster torch-sparse
Failed to build torch-scatter
Installing collected packages: urllib3, markupsafe, llvmlite, isodate, idna, future, dataclasses, chardet, cached-property, requests, rdflib, python-louvain, numba, jinja2, h5py, googledrivedownloader, ase, torch-spline-conv, torch-sparse, torch-scatter, torch-geometric, torch-cluster, pyyaml
Running setup.py install for torch-scatter: started
Running setup.py install for torch-scatter: still running...
Running setup.py install for torch-scatter: finished with status 'error'
Pip subprocess error:
ERROR: Command errored out with exit status 1:
command: /home/dhruv/miniconda3/envs/confgf/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-uny9vo1m/torch-scatter_9fc63357621946e09c129266a2493a1f/setup.py'"'"'; __file__='"'"'/tmp/pip-install-uny9vo1m/torch-scatter_9fc63357621946e09c129266a2493a1f/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-hm_a50e0
cwd: /tmp/pip-install-uny9vo1m/torch-scatter_9fc63357621946e09c129266a2493a1f/
Complete output (285 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/torch_scatter
copying torch_scatter/segment_coo.py -> build/lib.linux-x86_64-3.7/torch_scatter
copying torch_scatter/scatter.py -> build/lib.linux-x86_64-3.7/torch_scatter
copying torch_scatter/utils.py -> build/lib.linux-x86_64-3.7/torch_scatter
copying torch_scatter/__init__.py -> build/lib.linux-x86_64-3.7/torch_scatter
copying torch_scatter/segment_csr.py -> build/lib.linux-x86_64-3.7/torch_scatter
copying torch_scatter/placeholder.py -> build/lib.linux-x86_64-3.7/torch_scatter
creating build/lib.linux-x86_64-3.7/torch_scatter/composite
copying torch_scatter/composite/logsumexp.py -> build/lib.linux-x86_64-3.7/torch_scatter/composite
copying torch_scatter/composite/std.py -> build/lib.linux-x86_64-3.7/torch_scatter/composite
copying torch_scatter/composite/__init__.py -> build/lib.linux-x86_64-3.7/torch_scatter/composite
copying torch_scatter/composite/softmax.py -> build/lib.linux-x86_64-3.7/torch_scatter/composite
running egg_info
writing torch_scatter.egg-info/PKG-INFO
writing dependency_links to torch_scatter.egg-info/dependency_links.txt
writing requirements to torch_scatter.egg-info/requires.txt
writing top-level names to torch_scatter.egg-info/top_level.txt
reading manifest file 'torch_scatter.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*' found under directory 'test'
writing manifest file 'torch_scatter.egg-info/SOURCES.txt'
running build_ext
building 'torch_scatter._segment_coo_cpu' extension
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/csrc
creating build/temp.linux-x86_64-3.7/csrc/cpu
gcc -pthread -B /home/dhruv/miniconda3/envs/confgf/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DWITH_PYTHON -Icsrc -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/TH -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/THC -I/home/dhruv/miniconda3/envs/confgf/include/python3.7m -c csrc/segment_coo.cpp -o build/temp.linux-x86_64-3.7/csrc/segment_coo.o -O3 -Wno-sign-compare -DAT_PARALLEL_OPENMP -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=_segment_coo_cpu -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/dhruv/miniconda3/envs/confgf/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DWITH_PYTHON -Icsrc -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/TH -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/THC -I/home/dhruv/miniconda3/envs/confgf/include/python3.7m -c csrc/cpu/segment_coo_cpu.cpp -o build/temp.linux-x86_64-3.7/csrc/cpu/segment_coo_cpu.o -O3 -Wno-sign-compare -DAT_PARALLEL_OPENMP -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=_segment_coo_cpu -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
g++ -pthread -shared -B /home/dhruv/miniconda3/envs/confgf/compiler_compat -L/home/dhruv/miniconda3/envs/confgf/lib -Wl,-rpath=/home/dhruv/miniconda3/envs/confgf/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/csrc/segment_coo.o build/temp.linux-x86_64-3.7/csrc/cpu/segment_coo_cpu.o -L/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/lib -lc10 -ltorch -ltorch_cpu -ltorch_python -o build/lib.linux-x86_64-3.7/torch_scatter/_segment_coo_cpu.so -s
building 'torch_scatter._segment_coo_cuda' extension
creating build/temp.linux-x86_64-3.7/csrc/cuda
gcc -pthread -B /home/dhruv/miniconda3/envs/confgf/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DWITH_PYTHON -DWITH_CUDA -Icsrc -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/TH -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/THC -I/usr/local/cuda/include -I/home/dhruv/miniconda3/envs/confgf/include/python3.7m -c csrc/segment_coo.cpp -o build/temp.linux-x86_64-3.7/csrc/segment_coo.o -O3 -Wno-sign-compare -DAT_PARALLEL_OPENMP -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=_segment_coo_cuda -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/dhruv/miniconda3/envs/confgf/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DWITH_PYTHON -DWITH_CUDA -Icsrc -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/TH -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/THC -I/usr/local/cuda/include -I/home/dhruv/miniconda3/envs/confgf/include/python3.7m -c csrc/cpu/segment_coo_cpu.cpp -o build/temp.linux-x86_64-3.7/csrc/cpu/segment_coo_cpu.o -O3 -Wno-sign-compare -DAT_PARALLEL_OPENMP -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=_segment_coo_cuda -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
/usr/local/cuda/bin/nvcc -DWITH_PYTHON -DWITH_CUDA -Icsrc -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/TH -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/THC -I/usr/local/cuda/include -I/home/dhruv/miniconda3/envs/confgf/include/python3.7m -c csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/) -o build/temp.linux-x86_64-3.7/csrc/cuda/segment_coo_cuda.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options '-fPIC' -O3 --expt-relaxed-constexpr -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=_segment_coo_cuda -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_61,code=sm_61 -std=c++14
/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning #68-D: integer conversion resulted in a change of sign
/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning #68-D: integer conversion resulted in a change of sign
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(70): error: no instance of overloaded function "__ldg" matches the argument list
argument types are: (c10::BFloat16 *)
detected during instantiation of "void segment_coo_arg_kernel(const scalar_t *, at::cuda::detail::TensorInfo<int64_t, int>, scalar_t *, int64_t *, size_t, size_t) [with scalar_t=c10::BFloat16]"
(217): here
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(146): error: no instance of overloaded function "__ldg" matches the argument list
argument types are: (c10::BFloat16 *)
detected during instantiation of "void segment_coo_arg_broadcast_kernel(const scalar_t *, at::cuda::detail::TensorInfo<int64_t, int>, scalar_t *, int64_t *, size_t, size_t, size_t) [with scalar_t=c10::BFloat16]"
(217): here
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(299): error: no instance of overloaded function "__ldg" matches the argument list
argument types are: (const c10::BFloat16 *)
detected during instantiation of "void gather_coo_kernel(const scalar_t *, at::cuda::detail::TensorInfo<int64_t, int>, scalar_t *, size_t, size_t) [with scalar_t=c10::BFloat16]"
(368): here
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(321): error: no instance of overloaded function "__ldg" matches the argument list
argument types are: (const c10::BFloat16 *)
detected during instantiation of "void gather_coo_broadcast_kernel(const scalar_t *, at::cuda::detail::TensorInfo<int64_t, int>, scalar_t *, size_t, size_t, size_t) [with scalar_t=c10::BFloat16]"
(368): here
58 errors detected in the compilation of "csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)".
error: command '/usr/local/cuda/bin/nvcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for torch-scatter
ERROR: Command errored out with exit status 1:
command: /home/dhruv/miniconda3/envs/confgf/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-uny9vo1m/torch-scatter_9fc63357621946e09c129266a2493a1f/setup.py'"'"'; __file__='"'"'/tmp/pip-install-uny9vo1m/torch-scatter_9fc63357621946e09c129266a2493a1f/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-2zf8xclq/install-record.txt --single-version-externally-managed --compile --install-headers /home/dhruv/miniconda3/envs/confgf/include/python3.7m/torch-scatter
cwd: /tmp/pip-install-uny9vo1m/torch-scatter_9fc63357621946e09c129266a2493a1f/
Complete output (285 lines):
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/torch_scatter
copying torch_scatter/segment_coo.py -> build/lib.linux-x86_64-3.7/torch_scatter
copying torch_scatter/scatter.py -> build/lib.linux-x86_64-3.7/torch_scatter
copying torch_scatter/utils.py -> build/lib.linux-x86_64-3.7/torch_scatter
copying torch_scatter/__init__.py -> build/lib.linux-x86_64-3.7/torch_scatter
copying torch_scatter/segment_csr.py -> build/lib.linux-x86_64-3.7/torch_scatter
copying torch_scatter/placeholder.py -> build/lib.linux-x86_64-3.7/torch_scatter
creating build/lib.linux-x86_64-3.7/torch_scatter/composite
copying torch_scatter/composite/logsumexp.py -> build/lib.linux-x86_64-3.7/torch_scatter/composite
copying torch_scatter/composite/std.py -> build/lib.linux-x86_64-3.7/torch_scatter/composite
copying torch_scatter/composite/__init__.py -> build/lib.linux-x86_64-3.7/torch_scatter/composite
copying torch_scatter/composite/softmax.py -> build/lib.linux-x86_64-3.7/torch_scatter/composite
running egg_info
writing torch_scatter.egg-info/PKG-INFO
writing dependency_links to torch_scatter.egg-info/dependency_links.txt
writing requirements to torch_scatter.egg-info/requires.txt
writing top-level names to torch_scatter.egg-info/top_level.txt
reading manifest file 'torch_scatter.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*' found under directory 'test'
writing manifest file 'torch_scatter.egg-info/SOURCES.txt'
running build_ext
building 'torch_scatter._segment_coo_cpu' extension
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/csrc
creating build/temp.linux-x86_64-3.7/csrc/cpu
gcc -pthread -B /home/dhruv/miniconda3/envs/confgf/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DWITH_PYTHON -Icsrc -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/TH -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/THC -I/home/dhruv/miniconda3/envs/confgf/include/python3.7m -c csrc/segment_coo.cpp -o build/temp.linux-x86_64-3.7/csrc/segment_coo.o -O3 -Wno-sign-compare -DAT_PARALLEL_OPENMP -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=_segment_coo_cpu -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/dhruv/miniconda3/envs/confgf/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DWITH_PYTHON -Icsrc -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/TH -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/THC -I/home/dhruv/miniconda3/envs/confgf/include/python3.7m -c csrc/cpu/segment_coo_cpu.cpp -o build/temp.linux-x86_64-3.7/csrc/cpu/segment_coo_cpu.o -O3 -Wno-sign-compare -DAT_PARALLEL_OPENMP -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=_segment_coo_cpu -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
g++ -pthread -shared -B /home/dhruv/miniconda3/envs/confgf/compiler_compat -L/home/dhruv/miniconda3/envs/confgf/lib -Wl,-rpath=/home/dhruv/miniconda3/envs/confgf/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/csrc/segment_coo.o build/temp.linux-x86_64-3.7/csrc/cpu/segment_coo_cpu.o -L/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/lib -lc10 -ltorch -ltorch_cpu -ltorch_python -o build/lib.linux-x86_64-3.7/torch_scatter/_segment_coo_cpu.so -s
building 'torch_scatter._segment_coo_cuda' extension
creating build/temp.linux-x86_64-3.7/csrc/cuda
gcc -pthread -B /home/dhruv/miniconda3/envs/confgf/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DWITH_PYTHON -DWITH_CUDA -Icsrc -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/TH -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/THC -I/usr/local/cuda/include -I/home/dhruv/miniconda3/envs/confgf/include/python3.7m -c csrc/segment_coo.cpp -o build/temp.linux-x86_64-3.7/csrc/segment_coo.o -O3 -Wno-sign-compare -DAT_PARALLEL_OPENMP -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=_segment_coo_cuda -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/dhruv/miniconda3/envs/confgf/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DWITH_PYTHON -DWITH_CUDA -Icsrc -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/TH -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/THC -I/usr/local/cuda/include -I/home/dhruv/miniconda3/envs/confgf/include/python3.7m -c csrc/cpu/segment_coo_cpu.cpp -o build/temp.linux-x86_64-3.7/csrc/cpu/segment_coo_cpu.o -O3 -Wno-sign-compare -DAT_PARALLEL_OPENMP -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=_segment_coo_cuda -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
/usr/local/cuda/bin/nvcc -DWITH_PYTHON -DWITH_CUDA -Icsrc -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/TH -I/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/THC -I/usr/local/cuda/include -I/home/dhruv/miniconda3/envs/confgf/include/python3.7m -c csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/) -o build/temp.linux-x86_64-3.7/csrc/cuda/segment_coo_cuda.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options '-fPIC' -O3 --expt-relaxed-constexpr -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=_segment_coo_cuda -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_61,code=sm_61 -std=c++14
/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning #68-D: integer conversion resulted in a change of sign
/home/dhruv/miniconda3/envs/confgf/lib/python3.7/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning #68-D: integer conversion resulted in a change of sign
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(217): error: no instance of overloaded function "at::Tensor::div_" matches the argument list
argument types are: (at::Tensor, const char [6])
object type is: at::Tensor
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(70): error: no instance of overloaded function "__ldg" matches the argument list
argument types are: (c10::BFloat16 *)
detected during instantiation of "void segment_coo_arg_kernel(const scalar_t *, at::cuda::detail::TensorInfo<int64_t, int>, scalar_t *, int64_t *, size_t, size_t) [with scalar_t=c10::BFloat16]"
(217): here
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(146): error: no instance of overloaded function "__ldg" matches the argument list
argument types are: (c10::BFloat16 *)
detected during instantiation of "void segment_coo_arg_broadcast_kernel(const scalar_t *, at::cuda::detail::TensorInfo<int64_t, int>, scalar_t *, int64_t *, size_t, size_t, size_t) [with scalar_t=c10::BFloat16]"
(217): here
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(299): error: no instance of overloaded function "__ldg" matches the argument list
argument types are: (const c10::BFloat16 *)
detected during instantiation of "void gather_coo_kernel(const scalar_t *, at::cuda::detail::TensorInfo<int64_t, int>, scalar_t *, size_t, size_t) [with scalar_t=c10::BFloat16]"
(368): here
csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)(321): error: no instance of overloaded function "__ldg" matches the argument list
argument types are: (const c10::BFloat16 *)
detected during instantiation of "void gather_coo_broadcast_kernel(const scalar_t *, at::cuda::detail::TensorInfo<int64_t, int>, scalar_t *, size_t, size_t, size_t) [with scalar_t=c10::BFloat16]"
(368): here
58 errors detected in the compilation of "csrc/cuda/[segment_coo_cuda.cu](http://segment_coo_cuda.cu/)".
error: command '/usr/local/cuda/bin/nvcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /home/dhruv/miniconda3/envs/confgf/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-uny9vo1m/torch-scatter_9fc63357621946e09c129266a2493a1f/setup.py'"'"'; __file__='"'"'/tmp/pip-install-uny9vo1m/torch-scatter_9fc63357621946e09c129266a2493a1f/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-2zf8xclq/install-record.txt --single-version-externally-managed --compile --install-headers /home/dhruv/miniconda3/envs/confgf/include/python3.7m/torch-scatter Check the logs for full command output.
failed
CondaEnvException: Pip failed
How to generate the 3D SDF from the output?
Hello,
Congrats on this work. It is quite interesting.
I have some doubts on it. May you help me?
I was able to run the pre-trained models (checkpoints). A pickle is generated, but how to use this pickle to generate the SDF file for the particular molecule?
I noticed that a 2D molecule is generated in this pickle...How to include the conformers -- like an SDF -- so I can use the output 3D molecule?
Cheers,
Alex
There is not summary file in GEOM's QM9 archive.
ConfGF/confgf/dataset/dataset.py
Line 185 in 38aeb6c
Hi,
When I accessed to the webpage of Havard to look for dataset. I saw 2 QM9 files, including qm9_crude.msgpack.tar.gz and
qm9_featurized.msgpack.tar.gz. But none of them have the summary file.
Can you give me the link to the exact GEOM's QM9. I cannot find the archive of dataset aligned with your code.
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