Eli Draizen edraizen
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| # Pablo Gainza Cirauqui 2016 LPDI IBI STI EPFL | |
| # This pymol plugin for Masif just enables the load ply functions. | |
| import os, sys | |
| import math, re | |
| from pymol import cmd, stored | |
| import sys | |
| from pymol import cmd, stored |
edraizen
/ intro-to-jupyter-bme4550.ipynb
Created
September 14, 2020 17:44
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| $sudo /usr/local/bin/singularity build --tmpdir /home/ec2-user/SageMaker/scratch pytorch_1.6.0_ME_0.5_v1.simg Singularity | |
| .... | |
| + git clone https://github.com/NVIDIA/MinkowskiEngine.git | |
| + cd MinkowskiEngine | |
| + git checkout v0.5 | |
| + make clean | |
| + export CXX=/usr/bin/gcc-8 | |
| + python setup.py install --force_cuda --cuda_home=/usr/local/cuda-10.2 | |
| No CUDA runtime is found, using CUDA_HOME='/usr/local/cuda-10.2' | |
| WARNING: Skipping MinkowskiEngine as it is not installed. |
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| # Copyright (c) Chris Choy ([email protected]). | |
| # | |
| # Permission is hereby granted, free of charge, to any person obtaining a copy of | |
| # this software and associated documentation files (the "Software"), to deal in | |
| # the Software without restriction, including without limitation the rights to | |
| # use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies | |
| # of the Software, and to permit persons to whom the Software is furnished to do | |
| # so, subject to the following conditions: | |
| # | |
| # The above copyright notice and this permission notice shall be included in all |
edraizen
/ DistributedDataset.py
Created
September 9, 2021 18:11
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| from torch.utils.data import Dataset as _Dataset | |
| from torch.utils.data import Subset | |
| import h5pyd | |
| class DistributedDataset(_Dataset): | |
| """Read dataset from h5 file. If key specifies a dataset, each row is an | |
| independent sample. If kay specifies a group, each dataset is an independent | |
| sample. |
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| <!DOCTYPE html> | |
| <html> | |
| <head> | |
| <title>Grid</title> | |
| <script src="https://ajax.googleapis.com/ajax/libs/jquery/2.0.0/jquery.min.js"></script> | |
| <script src="https://3Dmol.org/build/3Dmol-min.js"></script> | |
| <style type="text/css"> | |
| .mol-container { | |
| width: 100%; | |
| height: 800px; |
edraizen
/ fixes_for_masif.sh
Last active
October 29, 2021 20:48
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| export MASIF_DIR=/change/me/ | |
| sed -i '/pyparsing/d' $MASIF_DIR/masif_env/lib/python3.7/site-packages/packaging-21.2-py3.7.egg/EGG-INFO/requires.txt | |
| sed -i '/pandas/d' $MASIF_DIR/masif_env/lib/python3.7/site-packages/dask-2021.10.0-py3.7.egg/EGG-INFO/requires.txt | |
| sed -i '/pandas/d' $MASIF_DIR/masif_env/lib/python3.7/site-packages/StrBioInfo-0.9a0.dev1-py3.7.egg/EGG-INFO/requires.txt |
edraizen
/ hsds_jobstore.out
Created
December 21, 2021 04:49
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| #env | grep TOIL | |
| TOIL_WORKDIR=/var/lib/toil | |
| TOIL_S3_HOST=minio.minio-tenant-1.svc.cluster.local | |
| TOIL_AWS_SECRET_NAME=aws-credentials | |
| TOIL_KUBERNETES_HOST_PATH=/media/smb-rivanna/ed4bu/UrfoldServer/urfold_runs/cath_pipeline/h5_restructure/k8/ | |
| TOIL_DOCKER_NAME=molmimic | |
| TOIL_S3_USE_SSL=False | |
| TOIL_KUBERNETES_OWNER=default | |
| TOIL_APPLIANCE_SELF=edraizen/molmimic:0.0.1 | |
| TOIL_S3_PORT=80 |
edraizen
/ hello_world.out
Created
December 22, 2021 20:26
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| /usr/local/lib/python3.8/dist-packages/requests/__init__.py:102: RequestsDependencyWarning: urllib3 (1.26.7) or chardet (2.3.0)/charset_normalizer (2.0.6) doesn't match a supported version! | |
| warnings.warn("urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported " | |
| [2021-12-22T20:20:43+0000] [MainThread] [D] [toil.statsAndLogging] Suppressing the following loggers: {'adal-python', 'botocore', 'kubernetes', 'urllib3', 'docker', 'boto', 'websocket', 'pymesos', 'charset_normalizer', 'bcdocs', 'google', 'oauthlib', 'google_auth_oauthlib', 'dill', 'requests_oauthlib', 'requests', 'boto3'} | |
| [2021-12-22T20:20:43+0000] [MainThread] [D] [toil.batchSystems.contained_executor] Starting executor | |
| [2021-12-22T20:20:43+0000] [MainThread] [D] [toil.batchSystems.contained_executor] Adopting environment: dict_keys(['TOIL_S3_HOST', 'TOIL_S3_PORT', 'TOIL_S3_USE_SSL', 'HS_ENDPOINT', 'HS_USERNAME', 'HS_PASSWORD', 'TOIL_RT_LOGGING_ADDRESS', 'TOIL_RT_LOGGING_LEVEL', 'OMP_NUM_THREADS']) | |
| [2021-12-22T20:20:43+0000] |
edraizen
/ worker_cachingFileStoreError.out
Created
December 29, 2021 22:40
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| INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- | |
| INFO:toil:Running Toil version 5.6.0a1-458a26c04268e57ebace072e1d64b6a087e99e51-dirty on host default-toil-c49a786e-6899-4cc4-ae90-f49e2c9cfaaf-0-j5pbg. | |
| DEBUG:toil:Configuration: {'workflowID': 'be4ac964-d6a0-4efa-84e3-220a4b14a690', 'workflowAttemptNumber': 0, 'jobStore': 's3hsds:us-east-1:/home/ed4bu/hello-world', 'logLevel': 'DEBUG', 'workDir': None, 'noStdOutErr': False, 'stats': False, 'clean': 'always', 'clusterStats': None, 'restart': False, 'batchSystem': 'kubernetes', 'disableAutoDeployment': False, 'maxLocalJobs': 2, 'manualMemArgs': False, 'coalesceStatusCalls': False, 'statePollingWait': None, 'parasolCommand': 'parasol', 'parasolMaxBatches': 10000, 'scale': 1.0, 'mesos_endpoint': '10.42.0.155:5050', 'allocate_mem': False, 'tes_endpoint': 'http://10.42.0.155:8000', 'tes_user': None, 'tes_password': None, 'tes_bearer_token': None, 'kubernetes_host_path': '/media/smb-rivanna/ed4bu/UrfoldServer/urfold_runs/cath_pipeline/h5_restructure/k8/', 'kubernetes_ow |