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mbl's Introduction

Hi there ๐Ÿ‘‹

I'm Tan Tao-Lin (in eastern name order), currently a PhD student in Physics @ National Tsing Hua University, Taiwan.

  • ๐Ÿ”ญ Iโ€™m currently working on Tensor Network algorithms, and their applications on quantum computing & condensed matter physics.

Experience

  • 2020/07 - 2021/07 ย  ๐Ÿ“ Data Scientist, Phison Electronics Corp.
  • 2019/07 - 2020/06 ย  ๐Ÿ“ Junior Data Engineer, Commerce Connector GmbH, Asia Limited

Education

  • 2021/07 - present ย  ๐ŸŽ“ PhD, Department of Physics, National Tsing Hua University
  • 2015 - 2018 ย  ๐ŸŽ“ M.Sc., Institute of Physics, National Chiao Tung University
  • 2011 - 2015 ย  ๐ŸŽ“ B.Sc., Department of Physics, National Chung Hsing University

mbl's People

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mbl's Issues

Bug: (AccessDenied) when calling the ListObjectsV2 operation

Describe the problem

When calling mlflow client to list the artifacts in runs, an error arises and says Access Denied.

Code to reproduce the issue

from mlflow.tracking.client import MlflowClient

client = MlflowClient(tracking_uri="my_uri")

run = client.search_runs(
    experiment_ids="the_id",
    filter_string="some_condition_string",
    run_view_type=ViewType.ACTIVE_ONLY,
)

artifacts = client.list_artifacts(run.info.run_id)

Error Log

An error occurred (AccessDenied) when calling the ListObjectsV2 operation.

What Happened?

Turns out MLFLOW_S3_ENDPOINT_URL pointing to the minio server needs to be set both on server and client side. MLflow doesn't do that part for you.

Reference

mlflow/mlflow#1813

Refactor: extract highest energy bound with tsdrg variant

Reverse the spectrum with an overall constant -1 doesn't seem to help for extracting the highest energy, results didn't converge to a stable region, although the reason requires further thoughts.

In turn, it's better to use a tsdrg variant, which reserve highest energies as each fusing step, and so there is no need to reverse the Hamiltonian with any overall const. We can just feed in the MPO into this tsdrg variant.

Reference

tanlin2013/tnpy@8c36865

Feature: support for Slurm custer

Feature: compute energy bounds

To find the proper energy window looking for level statistic, it's essential to rescale the energy spectrum with respect to its upper and lower energy bounds in prior.

Dependency Dashboard

This issue lists Renovate updates and detected dependencies. Read the Dependency Dashboard docs to learn more.

Rate-Limited

These updates are currently rate-limited. Click on a checkbox below to force their creation now.

  • chore(deps): update dependency bandit to v1.7.5
  • chore(deps): update dependency flake8-pyproject to v1.2.3
  • chore(deps): update dependency safety to v2.3.5
  • fix(deps): update dependency awswrangler to v2.20.1
  • fix(deps): update dependency pandas to v1.5.3
  • chore(deps): update dependency black to v23.10.0
  • chore(deps): update dependency cruft to v2.15.0
  • chore(deps): update dependency flake8-bugbear to v23.9.16
  • chore(deps): update dependency ipython to v8.16.1
  • chore(deps): update dependency mypy to v1.6.1
  • chore(deps): update dependency nbsphinx to ^0.9.0
  • chore(deps): update dependency pymysql to v1.1.0
  • chore(deps): update dependency pytest to v7.4.2
  • chore(deps): update dependency pytest-cov to v4.1.0
  • chore(deps): update dependency pytest-mock to v3.12.0
  • chore(deps): update dependency vulture to v2.10
  • fix(deps): update dependency constructs to v10.3.0
  • fix(deps): update dependency mlflow to v2.7.1
  • fix(deps): update dependency modin to ^0.24.0
  • fix(deps): update dependency numpy to v1.26.1
  • fix(deps): update dependency orjson to v3.9.9
  • fix(deps): update dependency pandera to ^0.17.0
  • fix(deps): update dependency plotly to v5.17.0
  • fix(deps): update dependency ray to v2.7.1
  • fix(deps): update dependency streamlit to v1.27.2
  • fix(deps): update dependency tqdm to v4.66.1
  • fix(deps): update python
  • chore(deps): update actions/checkout action to v4
  • chore(deps): update actions/setup-node action to v3
  • chore(deps): update dependency @types/node to v18
  • chore(deps): update dependency commitizen to v3
  • chore(deps): update dependency moto to v4
  • chore(deps): update dependency pre-commit to v3
  • chore(deps): update dependency sphinx to v7
  • chore(deps): update dependency sphinx-book-theme to v1
  • chore(deps): update dependency ts-node to v10
  • chore(deps): update dependency typescript to v5
  • chore(deps): update docker/build-push-action action to v5
  • chore(deps): update docker/login-action action to v3
  • chore(deps): update docker/metadata-action action to v5
  • chore(deps): update docker/setup-buildx-action action to v3
  • chore(deps): update docker/setup-qemu-action action to v3
  • chore(deps): update jest monorepo to v29 (major) (@types/jest, jest, ts-jest)
  • fix(deps): update dependency awswrangler to v3
  • fix(deps): update dependency pandas to v2
  • ๐Ÿ” Create all rate-limited PRs at once ๐Ÿ”

Open

These updates have all been created already. Click a checkbox below to force a retry/rebase of any.

Detected dependencies

docker-compose
docker-compose.yml
mlflow-tracker/aws/sftp/docker-compose.yml
mlflow-tracker/minio/docker-compose.yml
  • minio/minio sha256:beb5fd646b298e0e732c186215926d5ebf8cb0d2ff573bba17b4c4b22ec90ade
  • minio/mc sha256:c734ae7fd20606d4b2c0cf9ef25f22e5f4185406363b9260e7c16f6fe527cfd7
  • mysql/mysql-server sha256:02b97ea35a7057064d04392ade1aef1f0f018b051881986f4910f5088ae7e688
dockerfile
Dockerfile
  • python 3.9.15
mlflow-tracker/aws/Dockerfile
  • python 3.9
mlflow-tracker/minio/mlflow/Dockerfile
  • python 3.9-slim-buster
mlflow-tracker/minio/nginx/Dockerfile
  • nginx 1.17.6
github-actions
.github/workflows/aws-cdk.yml
  • actions/checkout v3
  • docker/setup-qemu-action v1
  • docker/setup-buildx-action v1
  • actions/setup-node v2
.github/workflows/build.yml
  • docker/setup-qemu-action v2
  • docker/setup-buildx-action v2
  • docker/metadata-action v4
  • docker/login-action v2
  • docker/build-push-action v3
.github/workflows/codeql-analysis.yml
  • actions/checkout v3
  • github/codeql-action v2
  • github/codeql-action v2
  • github/codeql-action v2
.github/workflows/doc.yml
  • actions/checkout v3
  • actions/setup-python v4
  • peaceiris/actions-gh-pages v3
.github/workflows/job-deploy.yml
  • actions/checkout v3
  • burnett01/rsync-deployments 5.2
  • actions/checkout v3
  • burnett01/rsync-deployments 5.2
.github/workflows/lint.yml
  • actions/checkout v3
  • actions/cache v3
  • actions/setup-python v4
.github/workflows/release.yml
  • docker/setup-qemu-action v2
  • docker/setup-buildx-action v2
  • docker/metadata-action v4
  • docker/login-action v2
  • docker/build-push-action v3
  • actions/checkout v3
.github/workflows/service-deploy.yml
  • actions/checkout v3
  • burnett01/rsync-deployments 5.2
.github/workflows/test.yml
  • actions/checkout v3
  • codecov/codecov-action v3
npm
mlflow-tracker/aws/package.json
  • aws-cdk-lib 2.22.0
  • constructs ^10.0.0
  • source-map-support ^0.5.16
  • @types/jest ^26.0.10
  • @types/node 10.17.27
  • jest ^26.4.2
  • ts-jest ^26.2.0
  • aws-cdk 2.22.0
  • ts-node ^9.0.0
  • typescript ~3.9.7
pip_requirements
mlflow-tracker/aws/requirements.txt
  • mlflow ==1.25.1
  • pymysql ==1.0.2
  • pysftp ==0.2.9
  • boto3 ~=1.23.0
mlflow-tracker/minio/mlflow/requirements.txt
  • cryptography ==37.0.2
  • boto3 ==1.24.10
  • mlflow ==1.26.1
  • pymysql ==1.0.2
  • protobuf ==3.20.1
poetry
pyproject.toml
  • python >=3.9.15,<3.11
  • tqdm ^4.63.0
  • numpy ^1.22
  • pandas ^1.5.0
  • pandera ^0.13.4
  • awswrangler ^2.20.0
  • tnpy 0.1.1a3
  • mlflow ^2.1.1
  • ray ^2.0.0
  • modin ^0.17.0
  • streamlit ^1.19.0
  • orjson ^3.8.7
  • plotly ^5.13.1
  • pandas-profiling ^3.6.6
  • pre-commit ^2.19.0
  • commitizen ^2.35.0
  • vulture ^2.4
  • bandit ^1.7.4
  • safety ^2.3.4
  • isort ^5.11.0
  • flake8-bugbear ^23.1.14
  • Flake8-pyproject ^1.2.2
  • black ^23.1.0
  • mypy ^1.0.0
  • ipython ^8.5.0
  • pytest ^7.1.2
  • pytest-cov ^4.0.0
  • pytest-mock ^3.9.0
  • pep8-naming ^0.13.0
  • cruft ^2.12.0
  • moto ^3.1.12
  • sphinx ^4.5.0
  • sphinx-book-theme ^0.3.2
  • nbsphinx ^0.8.8
  • m2r2 ^0.3.2
  • pandoc ^2.3

  • Check this box to trigger a request for Renovate to run again on this repository

Feature: mlflow tags

Background

MLflow offers automatic tracking to the code version, but that requires one to execute the program through MLflow Project.

Should we

  • Implement the code versioning tags manually, or
  • Use MLflow Project instead

Pros & Cons

  1. MLflow Project can trigger runs in docker environment, but it's not clear in the documentation how one can elaborate features in docker-compose to here, e.g. network mode, docker volume, shm size, etc.
  2. MLflow Project support multistep workflows, apart from current candidate Apache Airflow.
  3. This means we have to install MLflow at system level.
  4. An alternative way is to set MLflow Project environment as system environment, but actually it runs in docker already. But, though in this way we can track git version automatically, docker version is still required to be retrieved manually.

Reference

  1. https://mlflow.org/docs/latest/tracking.html#concepts
  2. https://mlflow.org/docs/latest/projects.html#building-multistep-workflows

Test: add unit test for mlflow, ray and datawrangler

A lots of panics have appeared in mlflow, ray and datawrangler associated block.

For aws-data-wrangler, moto may help for test.

EDITED

  • Since this project is data-oriented, we still run the test against the real one in Athena table, without using moto
  • Gap ratio parameter should be tested with the mock data generated from poisson and wigner-dyson distribution
  • Absolute offset wasn't correctly constructed
  • level_id should be re-generated if in total_sz-constrained mode
  • Filter out unexpected negative energy gap after taking diff

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