Collecting rdkit==2022.3.3 Using cached rdkit-2022.3.3-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (22.7 MB) Requirement already satisfied: numpy in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from rdkit==2022.3.3) (1.21.6) Collecting Pillow Using cached Pillow-9.5.0-cp37-cp37m-manylinux_2_28_x86_64.whl (3.4 MB) Installing collected packages: Pillow, rdkit Successfully installed Pillow-9.5.0 rdkit-2022.3.3 Collecting git+https://github.com/bp-kelley/descriptastorus.git@d552f934757378a61dd1799cdb589a864032cd1b Cloning https://github.com/bp-kelley/descriptastorus.git (to revision d552f934757378a61dd1799cdb589a864032cd1b) to /tmp/pip-req-build-2m4a5s6t Running command git clone --filter=blob:none --quiet https://github.com/bp-kelley/descriptastorus.git /tmp/pip-req-build-2m4a5s6t Running command git rev-parse -q --verify 'sha^d552f934757378a61dd1799cdb589a864032cd1b' Running command git fetch -q https://github.com/bp-kelley/descriptastorus.git d552f934757378a61dd1799cdb589a864032cd1b Running command git checkout -q d552f934757378a61dd1799cdb589a864032cd1b Resolved https://github.com/bp-kelley/descriptastorus.git to commit d552f934757378a61dd1799cdb589a864032cd1b Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pandas_flavor Using cached pandas_flavor-0.6.0-py3-none-any.whl (7.2 kB) Collecting xarray Using cached xarray-0.20.2-py3-none-any.whl (845 kB) Collecting pandas>=0.23 Using cached pandas-1.3.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.3 MB) Requirement already satisfied: numpy>=1.17.3 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from pandas>=0.23->pandas_flavor->descriptastorus==2.3.0.5) (1.21.6) Requirement already satisfied: python-dateutil>=2.7.3 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from pandas>=0.23->pandas_flavor->descriptastorus==2.3.0.5) (2.8.2) Collecting pytz>=2017.3 Using cached pytz-2023.3-py2.py3-none-any.whl (502 kB) Requirement already satisfied: importlib-metadata in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from xarray->pandas_flavor->descriptastorus==2.3.0.5) (6.7.0) Requirement already satisfied: typing-extensions>=3.7 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from xarray->pandas_flavor->descriptastorus==2.3.0.5) (4.6.3) Requirement already satisfied: six>=1.5 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from python-dateutil>=2.7.3->pandas>=0.23->pandas_flavor->descriptastorus==2.3.0.5) (1.16.0) Requirement already satisfied: zipp>=0.5 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from importlib-metadata->xarray->pandas_flavor->descriptastorus==2.3.0.5) (3.15.0) Building wheels for collected packages: descriptastorus Building wheel for descriptastorus (setup.py): started Building wheel for descriptastorus (setup.py): finished with status 'done' Created wheel for descriptastorus: filename=descriptastorus-2.3.0.5-py3-none-any.whl size=60674 sha256=9ce4be2a9e95c18684c59e16afb3ea3760306d849e8f2dd9109d32829c943d83 Stored in directory: /home/simran/.cache/pip/wheels/1b/67/6e/dde6628ee37275be412c809ebe68145aa5c73e5ff6d1063455 Successfully built descriptastorus Installing collected packages: pytz, pandas, xarray, pandas_flavor, descriptastorus Successfully installed descriptastorus-2.3.0.5 pandas-1.3.5 pandas_flavor-0.6.0 pytz-2023.3 xarray-0.20.2 Collecting tqdm==4.62.2 Using cached tqdm-4.62.2-py2.py3-none-any.whl (76 kB) Installing collected packages: tqdm Successfully installed tqdm-4.62.2 Collecting torch==1.9.0 Using cached torch-1.9.0-cp37-cp37m-manylinux1_x86_64.whl (831.4 MB) Requirement already satisfied: typing-extensions in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from torch==1.9.0) (4.6.3) Installing collected packages: torch Successfully installed torch-1.9.0 Collecting scipy==1.7.1 Using cached scipy-1.7.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (28.5 MB) Requirement already satisfied: numpy<1.23.0,>=1.16.5 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from scipy==1.7.1) (1.21.6) Installing collected packages: scipy Successfully installed scipy-1.7.1 Collecting scikit-learn==0.24.2 Using cached scikit_learn-0.24.2-cp37-cp37m-manylinux2010_x86_64.whl (22.3 MB) Collecting joblib>=0.11 Using cached joblib-1.3.1-py3-none-any.whl (301 kB) Requirement already satisfied: scipy>=0.19.1 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from scikit-learn==0.24.2) (1.7.1) Collecting threadpoolctl>=2.0.0 Using cached threadpoolctl-3.1.0-py3-none-any.whl (14 kB) Requirement already satisfied: numpy>=1.13.3 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from scikit-learn==0.24.2) (1.21.6) Installing collected packages: threadpoolctl, joblib, scikit-learn Successfully installed joblib-1.3.1 scikit-learn-0.24.2 threadpoolctl-3.1.0 Collecting git+https://github.com/ersilia-os/bentoml-ersilia.git Cloning https://github.com/ersilia-os/bentoml-ersilia.git to /tmp/pip-req-build-32qeul_z Running command git clone --filter=blob:none --quiet https://github.com/ersilia-os/bentoml-ersilia.git /tmp/pip-req-build-32qeul_z Resolved https://github.com/ersilia-os/bentoml-ersilia.git to commit a0f0040a1198e8f1704f0395e5d9ce328aaecf71 Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Requirement already satisfied: python-json-logger in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from bentoml==0.11.0) (2.0.7) Requirement already satisfied: flask in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from bentoml==0.11.0) (2.2.5) Requirement already satisfied: chardet in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from bentoml==0.11.0) (5.1.0) Requirement already satisfied: sqlalchemy-utils in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from bentoml==0.11.0) (0.41.1) Requirement already satisfied: tabulate in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from bentoml==0.11.0) (0.9.0) Requirement already satisfied: sqlalchemy in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from bentoml==0.11.0) (2.0.16) Requirement already satisfied: protobuf<3.19,>=3.8.0 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from bentoml==0.11.0) (3.18.3) Requirement already satisfied: packaging in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from bentoml==0.11.0) (23.1) Requirement already satisfied: multidict in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from bentoml==0.11.0) (6.0.4) Requirement already satisfied: requests in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from bentoml==0.11.0) (2.31.0) Requirement already satisfied: boto3 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from bentoml==0.11.0) (1.26.158) Requirement already satisfied: alembic in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from bentoml==0.11.0) (1.11.1) Requirement already satisfied: prometheus-client in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from bentoml==0.11.0) (0.17.0) Requirement already satisfied: werkzeug in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from bentoml==0.11.0) (2.2.3) Requirement already satisfied: ruamel.yaml in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from bentoml==0.11.0) (0.17.32) Requirement already satisfied: humanfriendly in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from bentoml==0.11.0) (10.0) Requirement already satisfied: psutil in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from bentoml==0.11.0) (5.9.5) Requirement already satisfied: numpy in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from bentoml==0.11.0) (1.21.6) Requirement already satisfied: docker in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from bentoml==0.11.0) (6.1.3) Requirement already satisfied: cerberus in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from bentoml==0.11.0) (1.3.4) Requirement already satisfied: importlib-resources in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from alembic->bentoml==0.11.0) (5.12.0) Requirement already satisfied: Mako in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from alembic->bentoml==0.11.0) (1.2.4) Requirement already satisfied: typing-extensions>=4 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from alembic->bentoml==0.11.0) (4.6.3) Requirement already satisfied: importlib-metadata in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from alembic->bentoml==0.11.0) (6.7.0) Requirement already satisfied: greenlet!=0.4.17 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from sqlalchemy->bentoml==0.11.0) (2.0.2) Requirement already satisfied: jmespath<2.0.0,>=0.7.1 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from boto3->bentoml==0.11.0) (1.0.1) Requirement already satisfied: s3transfer<0.7.0,>=0.6.0 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from boto3->bentoml==0.11.0) (0.6.1) Requirement already satisfied: botocore<1.30.0,>=1.29.158 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from boto3->bentoml==0.11.0) (1.29.158) Requirement already satisfied: setuptools in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from cerberus->bentoml==0.11.0) (65.6.3) Requirement already satisfied: urllib3>=1.26.0 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from docker->bentoml==0.11.0) (1.26.16) Requirement already satisfied: websocket-client>=0.32.0 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from docker->bentoml==0.11.0) (1.6.0) Requirement already satisfied: certifi>=2017.4.17 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from requests->bentoml==0.11.0) (2022.12.7) Requirement already satisfied: idna<4,>=2.5 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from requests->bentoml==0.11.0) (3.4) Requirement already satisfied: charset-normalizer<4,>=2 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from requests->bentoml==0.11.0) (3.1.0) Requirement already satisfied: Jinja2>=3.0 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from flask->bentoml==0.11.0) (3.1.2) Requirement already satisfied: itsdangerous>=2.0 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from flask->bentoml==0.11.0) (2.1.2) Requirement already satisfied: click>=8.0 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from flask->bentoml==0.11.0) (8.1.3) Requirement already satisfied: MarkupSafe>=2.1.1 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from werkzeug->bentoml==0.11.0) (2.1.3) Requirement already satisfied: ruamel.yaml.clib>=0.2.7 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from ruamel.yaml->bentoml==0.11.0) (0.2.7) Requirement already satisfied: python-dateutil<3.0.0,>=2.1 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from botocore<1.30.0,>=1.29.158->boto3->bentoml==0.11.0) (2.8.2) Requirement already satisfied: zipp>=0.5 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from importlib-metadata->alembic->bentoml==0.11.0) (3.15.0) Requirement already satisfied: six>=1.5 in /home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages (from python-dateutil<3.0.0,>=2.1->botocore<1.30.0,>=1.29.158->boto3->bentoml==0.11.0) (1.16.0) 00:37:15 | DEBUG | Activation done 00:37:15 | DEBUG | Creating environment YAML file 00:37:18 | DEBUG | Storing Conda environment in the local environment database 00:37:18 | DEBUG | Done with the Conda setup 00:37:18 | DEBUG | Using environment eos8451 00:37:18 | DEBUG | Running command: python pack.py 00:37:18 | DEBUG | Run commandlines on eos8451 00:37:18 | DEBUG | python pack.py 00:37:19 | DEBUG | Activating base environment 00:37:19 | DEBUG | Current working directory: /home/simran/eos/dest/eos8451 00:37:19 | DEBUG | Running bash /tmp/ersilia-k4g5aiyd/script.sh > /tmp/ersilia-zjs1g0bj/command_outputs.log 2>&1 00:37:22 | DEBUG | # conda environments: # base /home/simran/miniconda3 eos2lm8 /home/simran/miniconda3/envs/eos2lm8 eos5smc /home/simran/miniconda3/envs/eos5smc eos78ao /home/simran/miniconda3/envs/eos78ao eos7w6n /home/simran/miniconda3/envs/eos7w6n eos8451 * /home/simran/miniconda3/envs/eos8451 eos8fth /home/simran/miniconda3/envs/eos8fth eosbase-bentoml-0.11.0-py37 /home/simran/miniconda3/envs/eosbase-bentoml-0.11.0-py37 eosbase-bentoml-0.11.0-py38 /home/simran/miniconda3/envs/eosbase-bentoml-0.11.0-py38 ersilia /home/simran/miniconda3/envs/ersilia redial /home/simran/miniconda3/envs/redial redial-2020 /home/simran/miniconda3/envs/redial-2020 sa-score /home/simran/miniconda3/envs/sa-score [2023-07-27 00:37:22,421] INFO - BentoService bundle 'eos8451:20230727003721_65067C' saved to: /home/simran/bentoml/repository/eos8451/20230727003721_65067C 00:37:22 | DEBUG | Activation done 00:37:22 | DEBUG | Previous command successfully run inside eos8451 conda environment 00:37:22 | DEBUG | Now trying to establish symlinks 00:37:22 | DEBUG | BentoML location is /home/simran/bentoml/repository/eos8451/20230727003721_65067C 00:37:22 | DEBUG | Ersilia Bento location is /home/simran/eos/repository/eos8451/20230727003721_65067C 00:37:22 | DEBUG | Building symlinks between /home/simran/eos/repository/eos8451/20230727003721_65067C and /home/simran/bentoml/repository/eos8451/20230727003721_65067C 00:37:22 | DEBUG | Creating model symlink bundle artifacts > dest 00:37:22 | DEBUG | Creating model_install_commands.sh symlink dest <> bundle 00:37:22 | INFO | Could not create symbolic link from /home/simran/eos/dest/eos8451/data.h5 to /home/simran/eos/isaura/lake/eos8451_public.h5 00:37:22 | DEBUG | Run file found in framework: /home/simran/eos/repository/eos8451/20230727003721_65067C/eos8451/artifacts/framework/run.sh 00:37:22 | DEBUG | Run commandlines on eos8451 00:37:22 | DEBUG | which python > /tmp/ersilia-3r3auimm/tmp.txt 00:37:23 | DEBUG | Activating base environment 00:37:23 | DEBUG | Current working directory: /home/simran 00:37:23 | DEBUG | Running bash /tmp/ersilia-brq454cu/script.sh > /tmp/ersilia-6_miybg3/command_outputs.log 2>&1 00:37:24 | DEBUG | # conda environments: # base /home/simran/miniconda3 eos2lm8 /home/simran/miniconda3/envs/eos2lm8 eos5smc /home/simran/miniconda3/envs/eos5smc eos78ao /home/simran/miniconda3/envs/eos78ao eos7w6n /home/simran/miniconda3/envs/eos7w6n eos8451 * /home/simran/miniconda3/envs/eos8451 eos8fth /home/simran/miniconda3/envs/eos8fth eosbase-bentoml-0.11.0-py37 /home/simran/miniconda3/envs/eosbase-bentoml-0.11.0-py37 eosbase-bentoml-0.11.0-py38 /home/simran/miniconda3/envs/eosbase-bentoml-0.11.0-py38 ersilia /home/simran/miniconda3/envs/ersilia redial /home/simran/miniconda3/envs/redial redial-2020 /home/simran/miniconda3/envs/redial-2020 sa-score /home/simran/miniconda3/envs/sa-score 00:37:24 | DEBUG | Activation done 00:37:24 | DEBUG | Python executable: /home/simran/miniconda3/envs/eos8451/bin/python 00:37:24 | DEBUG | Conda is needed Packing model: 121.75694155693054s 50%|██████████████████████████████████████████▌ | 4/8 [02:10<03:18, 49.70s/it]00:37:24 | DEBUG | Checking if model needs to be integrated to a tool Checking if model needs to be integrated to a tool: 0.0018868446350097656s 62%|█████████████████████████████████████████████████████▏ | 5/8 [02:10<02:29, 49.70s/it]00:37:24 | DEBUG | Getting model card of eos8451 00:37:24 | DEBUG | Trying to get metadata from: /home/simran/eos/dest/eos8451 00:37:24 | DEBUG | Card saved at /home/simran/eos/dest/eos8451/card.json 00:37:24 | DEBUG | Saving slug grover-esol Getting model card: 0.5638346672058105s 75%|███████████████████████████████████████████████████████████████▊ | 6/8 [02:10<00:47, 23.51s/it]00:37:24 | DEBUG | Checking that autoservice works 00:37:24 | DEBUG | Setting AutoService for eos8451 00:37:24 | DEBUG | No service class provided, deciding automatically 00:37:24 | DEBUG | No service class file exists in /home/simran/eos/repository/eos8451/20230727003721_65067C/service_class.txt 00:37:24 | DEBUG | Setting virtual environment at /home/simran/eos/dest/eos8451 00:37:25 | DEBUG | Service class: conda 00:37:25 | DEBUG | Getting APIs from list file [] 00:37:25 | DEBUG | Getting APIs from Bento 00:37:25 | DEBUG | Getting info from BentoML and storing in /tmp/ersilia-yehpvf21/info.json 00:37:27 | DEBUG | Info {'name': 'eos8451', 'version': '20230727003721_65067C', 'created_at': '2023-07-27T07:37:22.299639Z', 'env': {'conda_env': 'name: bentoml-default-conda-env\nchannels:\n- defaults\ndependencies: []\n', 'python_version': '3.7.16', 'docker_base_image': 'bentoml/model-server:0.11.0-py37', 'pip_packages': ['bentoml==0.11.0']}, 'artifacts': [{'name': 'model', 'artifact_type': 'Artifact', 'metadata': {}}], 'apis': [{'name': 'run', 'input_type': 'JsonInput', 'docs': "BentoService inference API 'run', input: 'JsonInput', output: 'DefaultOutput'", 'output_config': {'cors': '*'}, 'output_type': 'DefaultOutput', 'mb_max_latency': 10000, 'mb_max_batch_size': 2000, 'batch': True}]} Checking that autoservice works: 2.768505573272705s 88%|██████████████████████████████████████████████████████████████████████████▍ | 7/8 [02:13<00:17, 17.81s/it]00:37:27 | DEBUG | Initializing model for inferring its structure 00:37:27 | DEBUG | No status file exists 00:37:27 | DEBUG | Is fetched: False 00:37:27 | DEBUG | Schema not yet available 00:37:27 | DEBUG | Setting AutoService for eos8451 00:37:27 | DEBUG | No service class provided, deciding automatically 00:37:27 | DEBUG | Service class file exists in folder /home/simran/eos/repository/eos8451/20230727003721_65067C/service_class.txt 00:37:27 | DEBUG | Service class: conda 00:37:27 | DEBUG | Model successfully initialized in sniffer 00:37:27 | DEBUG | No built-in example available. Generating a test one. 00:37:28 | DEBUG | Reading card from eos8451 00:37:28 | DEBUG | Reading shape from eos8451 00:37:28 | DEBUG | Input Shape: Single 00:37:28 | DEBUG | Input type is: compound 00:37:28 | DEBUG | Input shape is: Single 00:37:28 | DEBUG | Importing module: .types.compound 00:37:28 | DEBUG | Checking RDKIT and other requirements necessary for compound inputs 00:37:28 | DEBUG | InputShapeSingle shape: Single 00:37:28 | DEBUG | Inputs sampled: 2 00:37:28 | DEBUG | Sniffing model 00:37:28 | DEBUG | Getting model size 00:37:28 | DEBUG | Mode size is 30.81281089782715 MB 00:37:28 | DEBUG | Serving model 00:37:28 | DEBUG | Cleaning processes before serving 00:37:28 | DEBUG | /home/simran/eos/tmp/eos5smc.pid 00:37:28 | DEBUG | Cleaning [5072] processes 00:37:28 | DEBUG | Cleaning temp dir 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-m9y_htgs 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-ih198oco 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-6_miybg3 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-todok99r 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-qc86q3y3 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-zs_ls6y8 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-zl1h1h5m 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-zjs1g0bj 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-rnxiw2sk 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-35b2q2u0 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-d9r68npd 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-3j8ugrh9 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-k4g5aiyd 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-j2oa7bm0 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-4t0tmm2i 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-zzymadn_ 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-3r3auimm 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-zzeiar0g 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-nulhfh2b 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-wlyc3bgu 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-9vxsvdey 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-zac5mrlp 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-zj7t46ib 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-_h9wuerl 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-t_5xw7mm 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-l4kavntz 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-5glrz5g5 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-yehpvf21 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-koxrsid_ 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-brq454cu 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-bkiqtyhj 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-jdkpuq1n 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-_zrl33uk 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-r11s_94j 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-t21gt2mt 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-qpk80x9w 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-ws90digp 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-2r8xivz9 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-eda2txtd 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-zyn6z5by 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-d26vbs7n 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-tqtvur_r 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-b924bshi 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-79q9kn88 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-6jm54ybo 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-9dmi1v8z 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-hqpodn3i 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-enjwcg7s 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-2l9llp3w 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-0egf8xz6 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-csqthpe6 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-2h5ddj1l 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-5204e6vm 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-oc451_y2 00:37:28 | DEBUG | Flushing temporary directory /tmp/ersilia-gfeos_4u 00:37:28 | DEBUG | Cleaning temp dir 00:37:28 | DEBUG | Silencing docker containers if necessary 00:37:29 | DEBUG | Trying to serve model with BentoML locally 00:37:29 | WARNING | Port None was already in use. Using 49599 instead 00:37:29 | DEBUG | Free port: 49599 00:37:29 | DEBUG | Writing on /tmp/ersilia-4ziy7hlr/serve.sh 00:37:29 | DEBUG | #!/bin/bash 00:37:29 | DEBUG | bentoml serve eos8451:20230727003721_65067C --port 49599 &> /tmp/ersilia-4ziy7hlr/serve.log & 00:37:29 | DEBUG | _pid=$! 00:37:29 | DEBUG | echo "$_pid" > /tmp/ersilia-4ziy7hlr/serve.pid 00:37:29 | DEBUG | Run command function available 00:37:30 | DEBUG | Running on conda environment eos8451 00:37:30 | DEBUG | Run commandlines on eos8451 00:37:30 | DEBUG | bash /tmp/ersilia-4ziy7hlr/serve.sh 00:37:30 | DEBUG | Activating base environment 00:37:30 | DEBUG | Current working directory: /home/simran 00:37:30 | DEBUG | Running bash /tmp/ersilia-abk1ndq3/script.sh > /tmp/ersilia-p9gyhg44/command_outputs.log 2>&1 00:37:31 | DEBUG | # conda environments: # base /home/simran/miniconda3 eos2lm8 /home/simran/miniconda3/envs/eos2lm8 eos5smc /home/simran/miniconda3/envs/eos5smc eos78ao /home/simran/miniconda3/envs/eos78ao eos7w6n /home/simran/miniconda3/envs/eos7w6n eos8451 * /home/simran/miniconda3/envs/eos8451 eos8fth /home/simran/miniconda3/envs/eos8fth eosbase-bentoml-0.11.0-py37 /home/simran/miniconda3/envs/eosbase-bentoml-0.11.0-py37 eosbase-bentoml-0.11.0-py38 /home/simran/miniconda3/envs/eosbase-bentoml-0.11.0-py38 ersilia /home/simran/miniconda3/envs/ersilia redial /home/simran/miniconda3/envs/redial redial-2020 /home/simran/miniconda3/envs/redial-2020 sa-score /home/simran/miniconda3/envs/sa-score 00:37:31 | DEBUG | Activation done 00:37:31 | DEBUG | Process id: 6891 00:37:31 | DEBUG | Trying to wake up. Iteration: 0 00:37:31 | DEBUG | Timeout: 1000 Sleep time: 1 00:37:31 | DEBUG | Temporary file available: /tmp/ersilia-4ziy7hlr/serve.log 00:37:31 | DEBUG | No error strings found in temporary file 00:37:31 | DEBUG | Waiting for server 00:37:32 | DEBUG | Trying to wake up. Iteration: 1 00:37:32 | DEBUG | Timeout: 1000 Sleep time: 1 00:37:32 | DEBUG | Temporary file available: /tmp/ersilia-4ziy7hlr/serve.log 00:37:32 | DEBUG | No error strings found in temporary file 00:37:32 | DEBUG | Server logging done 00:37:33 | DEBUG | Trying to wake up. Iteration: 2 00:37:33 | DEBUG | Timeout: 1000 Sleep time: 1 00:37:33 | DEBUG | Temporary file available: /tmp/ersilia-4ziy7hlr/serve.log 00:37:33 | DEBUG | No error strings found in temporary file 00:37:33 | DEBUG | Server logging done 00:37:34 | DEBUG | Trying to wake up. Iteration: 3 00:37:34 | DEBUG | Timeout: 1000 Sleep time: 1 00:37:34 | DEBUG | Temporary file available: /tmp/ersilia-4ziy7hlr/serve.log 00:37:34 | DEBUG | No error strings found in temporary file 00:37:34 | DEBUG | Server is ready. Trying to get URL 00:37:34 | DEBUG | URL found: http://127.0.0.1:49599 00:37:34 | DEBUG | Iterating over APIs 00:37:34 | DEBUG | Running API: run 00:37:34 | DEBUG | ['CC1C2C(CC3(C=CC(=O)C(=C3C2OC1=O)C)C)O', 'C1=CN=CC=C1C(=O)NN'] 00:37:34 | DEBUG | API: run 00:37:34 | DEBUG | MODEL ID: eos8451 00:37:34 | DEBUG | SERVICE URL: http://127.0.0.1:49599 00:37:34 | DEBUG | Reading card from eos8451 00:37:34 | DEBUG | Reading shape from eos8451 00:37:34 | DEBUG | Input Shape: Single 00:37:34 | DEBUG | Input type is: compound 00:37:34 | DEBUG | Input shape is: Single 00:37:34 | DEBUG | Importing module: .types.compound 00:37:34 | DEBUG | Checking RDKIT and other requirements necessary for compound inputs 00:37:34 | DEBUG | InputShapeSingle shape: Single 00:37:34 | DEBUG | API eos8451:run initialized at URL http://127.0.0.1:49599 00:37:34 | DEBUG | Schema not yet available 00:37:34 | INFO | No empty output available 00:37:34 | DEBUG | Meta: None 00:37:34 | DEBUG | Posting to run 00:37:34 | DEBUG | Batch size 100 00:37:34 | DEBUG | Schema not yet available 00:37:38 | DEBUG | Status code: 500 00:37:38 | ERROR | Status Code: 500 00:37:38 | WARNING | Batch prediction didn't seem to work. Doing predictions one by one... 00:37:41 | DEBUG | Status code: 500 00:37:41 | ERROR | Status Code: 500 00:37:44 | DEBUG | Status code: 500 00:37:44 | ERROR | Status Code: 500 00:37:44 | DEBUG | Schema not yet available 00:37:44 | DEBUG | Done with unique posting 00:37:44 | DEBUG | Metadata needs to be calculated 00:37:44 | ERROR | Meta not available, run some adapations first and it will be inferred atomatically 00:37:44 | DEBUG | [{'input': {'key': 'LUHMMHZLDLBAKX-UHFFFAOYSA-N', 'input': 'CC1C2C(CC3(C=CC(=O)C(=C3C2OC1=O)C)C)O', 'text': 'CC1C2C(CC3(C=CC(=O)C(=C3C2OC1=O)C)C)O'}, 'output': None}, {'input': {'key': 'QRXWMOHMRWLFEY-UHFFFAOYSA-N', 'input': 'C1=CN=CC=C1C(=O)NN', 'text': 'C1=CN=CC=C1C(=O)NN'}, 'output': None}] 00:37:48 | ERROR | Ersilia exception class: EmptyOutputError Detailed error: Model API eos8451:run did not produce an outputWARNING:root:No normalization for BCUT2D_MWHI WARNING:root:No normalization for BCUT2D_MWLOW WARNING:root:No normalization for BCUT2D_CHGHI WARNING:root:No normalization for BCUT2D_CHGLO WARNING:root:No normalization for BCUT2D_LOGPHI WARNING:root:No normalization for BCUT2D_LOGPLOW WARNING:root:No normalization for BCUT2D_MRHI WARNING:root:No normalization for BCUT2D_MRLOW [WARNING] Horovod cannot be imported; multi-GPU training is unsupported 0%| | 0/3 [00:00 avg_preds, test_smiles = make_predictions(args, train_args) File "/home/simran/eos/repository/eos8451/20230727003721_65067C/eos8451/artifacts/framework/code/task/predict.py", line 96, in make_predictions scaler, features_scaler = load_scalars(path) File "/home/simran/eos/repository/eos8451/20230727003721_65067C/eos8451/artifacts/framework/code/grover/util/utils.py", line 736, in load_scalars state = torch.load(path, map_location=lambda storage, loc: storage) File "/home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages/torch/serialization.py", line 594, in load with _open_file_like(f, 'rb') as opened_file: File "/home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages/torch/serialization.py", line 230, in _open_file_like return _open_file(name_or_buffer, mode) File "/home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages/torch/serialization.py", line 211, in __init__ super(_open_file, self).__init__(open(name, mode)) FileNotFoundError: [Errno 2] No such file or directory: '/home/simran/eos/repository/eos8451/20230727003721_65067C/eos8451/artifacts/framework/finetune/esol/fold_0/model_0/model.pt' Hints: - Visit the fetch troubleshooting site 🚨🚨🚨 Something went wrong with Ersilia 🚨🚨🚨 Error message: Ersilia exception class: EmptyOutputError Detailed error: Model API eos8451:run did not produce an outputWARNING:root:No normalization for BCUT2D_MWHI WARNING:root:No normalization for BCUT2D_MWLOW WARNING:root:No normalization for BCUT2D_CHGHI WARNING:root:No normalization for BCUT2D_CHGLO WARNING:root:No normalization for BCUT2D_LOGPHI WARNING:root:No normalization for BCUT2D_LOGPLOW WARNING:root:No normalization for BCUT2D_MRHI WARNING:root:No normalization for BCUT2D_MRLOW [WARNING] Horovod cannot be imported; multi-GPU training is unsupported 0%| | 0/3 [00:00 avg_preds, test_smiles = make_predictions(args, train_args) File "/home/simran/eos/repository/eos8451/20230727003721_65067C/eos8451/artifacts/framework/code/task/predict.py", line 96, in make_predictions scaler, features_scaler = load_scalars(path) File "/home/simran/eos/repository/eos8451/20230727003721_65067C/eos8451/artifacts/framework/code/grover/util/utils.py", line 736, in load_scalars state = torch.load(path, map_location=lambda storage, loc: storage) File "/home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages/torch/serialization.py", line 594, in load with _open_file_like(f, 'rb') as opened_file: File "/home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages/torch/serialization.py", line 230, in _open_file_like return _open_file(name_or_buffer, mode) File "/home/simran/miniconda3/envs/eos8451/lib/python3.7/site-packages/torch/serialization.py", line 211, in __init__ super(_open_file, self).__init__(open(name, mode)) FileNotFoundError: [Errno 2] No such file or directory: '/home/simran/eos/repository/eos8451/20230727003721_65067C/eos8451/artifacts/framework/finetune/esol/fold_0/model_0/model.pt' Hints: - Visit the fetch troubleshooting site