2024-10¶

October 19, 2024
in system
1 min read

Install AMD chipset driver Windows 11 24H2

How to solve the "AMD system not detected" error when installing AMD chipset driver in Windows 11 24H2.

Install VBS support: Settings > System > Optional features > Add "VBSCRIPT". You should be able to install the driver afterward.

October 7, 2024
in code
1 min read

Convert vector of vector to matrix

Use the stack function.

stack([[1,0,1],[0,0,1]], dims=1) == [ 1 0 1 ; 0 0 1 ]

October 7, 2024
in code
1 min read

IJulia use Python package provided by CondaPkg

Source: stackoverflow

Set the JUPYTER environment variable to CondaPkg.jl-provided jupyter and IJulia.jl will take it to start the kernel.

using CondaPkg
CondaPkg.add("jupyter")
ENV["JUPYTER"] = CondaPkg.which("jupyter")

using Pkg
Pkg.add("IJulia") # if IJulia was not yet installed
Pkg.build("IJulia") # To change the configuration of existing installation

September 16, 2024
in system
1 min read

heredoc: Passing multiple lines of string

Use heredoc to pass the string as-is between two delimiters (e.g. EOF)

cat << "EOF" >> ~/.xprofile
# ~/.xprofile
export GTK_IM_MODULE=ibus
export QT_IM_MODULE=ibus
export XMODIFIERS=@im=ibus
ibus-daemon -drx
EOF

Will append the following lines in ~/.xprofile:

.xprofile

export GTK_IM_MODULE=ibus
export QT_IM_MODULE=ibus
export XMODIFIERS=@im=ibus
ibus-daemon -drx

September 3, 2024
in system
1 min read

Upgrading from ubuntu 22.04 to 24.04

Before upgrade

Backup your data.
Use ppa-purge to remove currently activated PPAs. The unremovable git-lfs gave me headache for several hours.

September 3, 2024
in system
1 min read

Reload nvidia GPU driver

Reload nvidia GPU driver to fix "NVML: Driver/library version mismatch" error without rebooting. Source

April 25, 2024
in DevOps
5 min read

GitLab CICD tips

GitLab CI/CD is a tool built into GitLab for software development for Continuous Integration (CI) and Continuous Delivery/Deployment (CD).

Parallel Matrix build

Test and build in parallel with matrix build in Gitlab CI/CD.

For example,

.gitlab-ci.yml

test:
  image: $IMAGE
  script:
    - echo $MSG
    - python -V
  parallel:
    matrix:
      # First cartesian set of parameters
      - IMAGE: ['python:3.6-alpine', 'python:3.7-alpine']
        MSG: ['Test1', 'Test2']
      # Second cartesian set of parameters

This will create 4 jobs with a combination of a custom message and a specific Python image.

See also the blog post by Michael Friedrich for more parallel matrix build with GitLab CI/CD.

Replace old `only/except` with new `rules` to include or exclude jobs in pipelines

GitLab CI/CD rules reference

Note

Rules cannot be used together with only/except. Otherwise, GitLab will return a key may not be used with rules error.

only run if this is a scheduled pipeline

.gitlab-ci.yml

scheduled-update:
  # only run if this is a scheduled pipeline
  rules:
    - if: $CI_PIPELINE_SOURCE == "schedule"

Run upon push

.gitlab-ci.yml

push-job:
  rules:
    - if: $CI_PIPELINE_SOURCE == "push"

Run upon merge request

.gitlab-ci.yml

merge-request:
  rules:
    - if: $CI_PIPELINE_SOURCE == "merge_request_event"

Run only for the commits in the default branch

.gitlab-ci.yml

# GitLab pages job
pages:
  rules:
    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH

Run only for tags

.gitlab-ci.yml

pages:
  rules:
    - if: $CI_COMMIT_TAG

Choose a specific runner

Use tags to tun jobs in a specific runner e.g., your self-hosted GitLab runner in the workstation.

.gitlab-ci.yml

run-custom:
  tags:
    - myWS
  script:
    - echo "Running in my workstation."

Create a release

Create a release with GitLab CI/CD pipelines with the release-cli docker image:

.gitlab-ci.yml

release_job:
  stage: release
  image: registry.gitlab.com/gitlab-org/release-cli:latest
  rules:
    - if: $CI_COMMIT_TAG                  # Run this job when a tag is created manually
  script:
    - echo "Running the release job."
  release:
    name: "Release $CI_COMMIT_TAG"
    description: "Release created using the release-cli."

Cache Conda Packages

We can cache conda packages by setting CONDA_PKGS_DIRS environment variable inside the project folder (CI_PROJECT_DIR) so that the GitLab runner can cache these dependencies.

.gitlab-ci.yml

image: condaforge/miniforge3:latest

variables:
  CONDA_PKGS_DIRS: "${CI_PROJECT_DIR}/.cache/conda/pkgs"

cache:
  - key:
      files:
        - environment.yml
    paths:
      - .env/
      - .cache/conda/pkgs

before_script:
  - conda env update --prefix ./.env --file environment.yml --prune
  - source activate ./.env

Because GitLab only caches files inside the project folder (CI_PROJECT_DIR)

CONDA_PKGS_DIRS is set to ${CI_PROJECT_DIR}/.cache/conda/pkgs to hold the downloaded compressed packages.
Extracted environment folder is set to ${CI_PROJECT_DIR}/.env using the --prefix option.

Conda will create the runtime environment according to environment.yml. The environment folder will be created (if not present) or cached. The option --prune means conda will remove unnecessary packages for subsequent caching.

Git Operations in GitLab CI/CD

Using SSH keys

Warning

Currently the private key cannot be masked and base64 encoding/decoding is needed.

You can use a pair of SSH keys to access a git repository
- The private key would be a CI/CD project variable
- The public key would be a deploy key

You also need additional steps to setup a SSH client in the pipeline.

before_script:
   # apt-get applies to Debian-based images. Change the package manager if needed.
  - 'which ssh-agent || ( apt-get update -qy && apt-get install openssh-client -qqy )'
  - 'which git || ( apt-get update -qy && apt-get install git -qqy )'
  - eval `ssh-agent -s`
  - echo "${SSH_PRIVATE_KEY}" | tr -d '\r' | ssh-add - > /dev/null # add ssh key
  - '[[ -f /.dockerenv ]] && echo -e "Host *\n\tStrictHostKeyChecking no\n\n" > ~/.ssh/config'

And replace the default HTTP-based git origin with the SSH one.

script:
  - git remote rm origin && git remote add origin git@gitlab.com:$CI_PROJECT_PATH.git

Using a personal access token (PAT)

Compared to SSH, using a personal access token (PAT) with write repo right might be simpler. In the following example, the PAT is stored as a masked CI/CD variable GIT_PUSH_TOKEN.

script:
  - bash update.sh
  - |
    if [ -n $(git status --porcelain) ]; then
        echo "Committing updates"
        git config --global user.name "${GITLAB_USER_NAME}"
        git config --global user.email "${GITLAB_USER_EMAIL}"
        git add .
        git commit -m "Automated update: $(date '+%Y-%m-%d-%H-%M-%S')"
        git push "https://${GITLAB_USER_NAME}:${GIT_PUSH_TOKEN}@${CI_REPOSITORY_URL#*@}"
        exit;
    else
        echo "no change, nothing to commit"
    fi

For a MR pipeline, GitLab provides git push options for merge request settings.

script:
  - bash update.sh
  - |
    if [ -n $(git status --porcelain) ]; then
        echo "Committing updates"
        NEW_BR=auto-update-$(date '+%Y-%m-%d-%H-%M-%S')
        git config --global user.name "${GITLAB_USER_NAME}"
        git config --global user.email "${GITLAB_USER_EMAIL}"
        git checkout -b ${NEW_BR}
        git add .
        git commit -m "${NEW_BR}"
        git push "https://${GITLAB_USER_NAME}:${GIT_PUSH_TOKEN}@${CI_REPOSITORY_URL#*@}" \
            -o merge_request.create \
            -o merge_request.target="${CI_DEFAULT_BRANCH}" \
            -o merge_request.merge_when_pipeline_succeeds \
            -o merge_request.remove_source_branch \
            -o merge_request.title="${NEW_BR}" \
            -o merge_request.label="automated update" \
            -o merge_request.assign="${GITLAB_USER_NAME}"
        exit;
    else
        echo "no change, nothing to commit"
    fi

Synchronize GitLab repo to GitHub

Assuming you have two identical repositories on GitLab and GitHub each (you can do this by importing one's repo to the other), the following steps show how to mirror GitLab repositories to GitHub with deploy SSH keys.

On the GitLab side

In the GitLab repo, go to Settings/Repository/Mirroring repositories and set Git repository URL as ssh://git@github.com/<namespace>/<repo>.git. e.g. ssh://git@github.com/sosiristseng/docker-python-julia.git

Warning

The GitHub button gives git@github.com:<namespace>/<repo>.git as the repo URL, one should change it to ssh://git@github.com/<namespace>/<repo>.git for GitLab to access the repository.

Set Mirror direction to push.
Set Authentication method to SSH public key. Optionally you can click Detect host keys.
(Optionally) check "Keep divergent refs" to prevent force pushes and/or "Mirror only protected branches" for a cleaner GitHub mirror.
Click Mirror repository.
Copy the SSH public key (the middle button) and go to the GitHub mirror repo.

On the GitHub side

In the Github mirror repository, go to Settings/Deploy keys and add deploy key.

Paste the SSH public key copied from the GitLab source. Give it a title, allow write access, click add key to finish this step, and viola.

April 25, 2024
in DevOps
1 min read

Status check for a multi-stage workflow

If you run a multi-stage workflow with status checks in branch protection rules, you might found that skipped jobs are treated as "passed". That is, if you have a workflow with a chain of dependent jobs A -> B -> C. When B fails and C is skipped, it still counts as passed when checking job C.¹ Thus, auto-merging may merge broken code.

April 24, 2024
in DevOps
1 min read

Dynamic parallel matrix

Job matrix creates multiple job runs that are based on the combinations of the variables. Sometimes we want a dynamic number of matrix jobs, which requires a JSON array as an output. Here we use json and glob modules in Python to generate that JSON list.¹²