Differences between revisions 2 and 79 (spanning 77 versions)
⇤ ← Revision 2 as of 2019-10-30 23:49:54 →
Size: 7423
Editor: TunayDurmaz
Comment: initial draft
← Revision 79 as of 2022-11-28 03:13:21 → ⇥
Size: 11420
Editor: TunayDurmaz
Comment:
Deletions are marked like this. Additions are marked like this.
Line 1: Line 1:
= Under Construction =
Line 7: Line 4:
= CMake =
 1. Dependencies are from Anaconda. CMake runs conda to detect environment location and uses it to find packages.

{{{#!wiki comment
 1. Does not specify all source files, so the files will not be added to IDE project files and will not be available for editing. This makes it inconvenient to use Visual Studio as editor. Need ''add_custom_target ... [SOURCES src1 [src2...]]'' https://cmake.org/cmake/help/v3.15/command/add_custom_target.html
}}}

 1. Make targets can be listed with {{{make help}}}. Some convenience targets:
 {{{
$ make help
The following are some of the valid targets for this Makefile:
... .....
... .....
... PythonFiles
... test-rt
... test-py-compile
... test-verbose-broken
... test-progs
... test-verbose
... .....
... .....
}}}

 1. ''libpython'' can be linked statically or dynamically when python is built. It is important for python extensions to be aware of the type of linking in order to avoid segfaults. (Need a little more details, refs?)

 1. opengl ???

 1. cmake <source-dir> -DENABLE_WARNINGS=OFF

{{{#!wiki comment
 1. Modern cmake, targets as much as possible, interface libs(?), anaconda, find_packages in cmake,...
}}}		 = Binary Distribution =


 !GitHub webhooks are setup to send notifications to blake. Blake forwards those to three build machines. Currently, webhooks are being listened to only on Linux. Linux runs the server that drives the Jenkins jobs.


== Jenkins Setup ==


Jenkins server runs on Linux, Jenkins agents on Linux, Mac and Windows. The server instance manages Jenkins, the agents run the jobs.

 1. On Linux, to start Jenkins, run command:{{{
docker stop jenkins-master

docker rm jenkins-master

docker run -d -u root --name jenkins-master -p 8080:8080 -p 50000:50000 --restart unless-stopped -v /home/eman2/jenkins_home:/var/jenkins_home -e PLUGINS_FORCE_UPGRADE=true -e TRY_UPGRADE_IF_NO_MARKER=true --restart unless-stopped jenkins/jenkins:lts

}}}

 1. Install Java on agents.
 1. Setup passwordless ssh connections from Linux server to agents.
 1. Nodes: http://10.10.11.176:8080/computer/
  1. http://10.10.11.176:8080/computer/linux/configure
    1. name: linux
    1. remoteFS: /home/eman2/linux-1-agent/
    1. numExecutors: 100
    1. host: eman-centos7-01
    1. credentialsId: jenkins-key-eman2
    1. label: eman
    1. envVars
     1. DEPLOY_PATH: /opt/web2py_apps/web2py/applications/cryoem/static/software/
     1. HOME_DIR: /home/eman2
     1. PATH+EXTRA: /home/eman2/miniconda3/bin
  1. http://10.10.11.176:8080/computer/mac/configure
    1. name: mac
    1. remoteFS: /Users/eman/mac-1-agent
    1. numExecutors: 100
    1. host: eman-macmini
    1. credentialsId: jenkins-key-eman
    1. label: eman
    1. envVars
     1. DEPLOY_PATH: /opt/web2py_apps/web2py/applications/cryoem/static/software/
     1. HOME_DIR: /Users/eman/
     1. PATH+EXTRA: /Users/eman/miniconda3/bin
  1. http://10.10.11.176:8080/computer/win/configure
    1. name: win
    1. remoteFS: D:\workspace\win-1-agent
    1. numExecutors: 100
    1. host: BM-WIN-01
    1. credentialsId: jenkins-key-eman
    1. !JavaPath: "D:\Downloads\openjdk-11+28_windows-x64_bin\jdk-11\bin\java.exe"
    1. Prefix Start Agent Command: D: &&
    1. label: eman
    1. envVars
     1. DEPLOY_PATH: /opt/web2py_apps/web2py/applications/cryoem/static/software/
     1. HOME_DIR: D:
     1. PATH+EXTRA: D:\Miniconda3;D:\Miniconda3\Scripts

=== Jenkins Setup on Linux ===
 1. http://10.10.11.176:8080/manage/configure
  1. Labels: main master
  1. Jenkins URL: http://10.10.11.176:8080/
  1. System Admin e-mail address: eman-bot (linux)<eman.github@gmail.com>
  1. SSH Servers
   1. Name: Installer-Server
   1. Hostname: cryoem.bcm.edu
   1. Username: eman-binary-uploader
   1. Remote Directory: /opt/web2py_apps/web2py/applications/cryoem/static/software/

 1. http://10.10.11.176:8080/manage/configureSecurity/
  1. Agents
   1. TCP port for inbound agents
    1. Fixed: 50000
  1. Git Host Key Verification Configuration
   1. Host Key Verification Strategy
    1. Known hosts file

 1. Credentials: http://10.10.11.176:8080/manage/credentials/
  {{{
ID Name
gh-eman-bot eman-bot (gh-eman-
jenkins-key-eman eman (jenkins-key-eman)
jenkins-key-eman2 eman2 (jenkins-key-eman2)
}}}

PATH



== Jenkins Setup ==

 1. Jenkins master needs PATH prepended with $CONDA_PREFIX/bin

== Jenkins Setup ==
 1. Login info: 10.10.11.176:8080/ username: eman2
 1. Jobs
  * multi: Triggers job cryoem-eman2 on agents
  * cryoem-eman2: Test(?) and binary builds
  * eman-dev(?): Triggers new build of eman-dev
  1. http://10.10.11.176:8080/job/build-binary/
  1. http://10.10.11.176:8080/job/build-binary-trigger/
  1. http://10.10.11.176:8080/job/cryoem-eman2-trigger/
  1. http://10.10.11.176:8080/job/cryoem-eman2/
  1. http://10.10.11.176:8080/job/eman-bump-version/
  1. http://10.10.11.176:8080/job/eman-feedstock-building-eman-v2.99/
  1. http://10.10.11.176:8080/job/eman-feedstock-trigger-from-eman-master/
  1. http://10.10.11.176:8080/job/eman-feedstock-update-version/
 1. Settings, Plugins ?
 1. Binary builds require conda-build, constructor
Packaging is done with {{{constructor}}}, a tool for making installers from conda packages.


  1. JenkinsCI: [[https://github.com/cryoem/eman2/blob/master/Jenkinsfile|Jenkinsfile]]
    1. Secrets like ssh keys are stored locally in Jenkins
    1. Some env vars need to be set by agents:
      1. HOME_DIR, DEPLOY_PATH, PATH+EXTRA (to add miniconda to PATH).
      1. PATH+EXTRA is not set on win. (?)
         1. Now, it is set on win, too.
    1. {{{
 Launch method: via SSH
   Advanced:
     Prefix Start Agent Command: "D: && "
}}}
    1. On windows for sh calls in jenkins to work "Git for Windows" might need to be installed.


 1. Binary builds on local build machines.
  1. Manually triggered by including "[ci build]" anywhere in the last commit message. Manually triggered builds on master branch are uploaded as [[https://cryoem.bcm.edu/downloads/view_eman2_version/25|continuous builds]] and builds triggered from any other branch are uploaded to [[https://cryoem.bcm.edu/downloads/view_eman2_version/26|testing area]].
  1. Any branch in the form of "release-" triggers continuous builds without having to include "[ci build]" in the commit message. Once the release branch is ready, release binaries are manually copied from cont. builds folder into the release folder on the server.


== Linux ==

docker run -d -u root --name jenkins-master -p 8080:8080 -p 50000:50000 --restart unless-stopped -v /home/eman2/jenkins_home:/var/jenkins_home -v /var/run/docker.sock:/var/run/docker.sock -e PLUGINS_FORCE_UPGRADE=true -e TRY_UPGRADE_IF_NO_MARKER=true --restart unless-stopped cryoem/jenkins:dev



== Mac ==

slave clock sync https://blog.shameerc.com/2017/03/quick-tip-fixing-time-drift-issue-on-docker-for-mac docker run --rm --privileged alpine hwclock -s



== Windows ==

OPENGL: https://github.com/conda/conda-recipes/blob/master/qt5/notes.md
Line 42: Line 155:
Feedstocks, conda-smithy, https://anaconda.org/cryoem/
 1. ftgl
 1. fftw-mpi
 1. openmpi
 1. pydusa and pydusa-feedstock
 1. constructor and constructor-feedstock
 1. eman-deps-feedstock, eman-deps-cli
 1. eman-packaging-feedstock


File structure, dependencies ? ABI compat

 1. conda
 1. conda-build
 1. constructor


= Continuous Integration =

 1. !GitHub webhooks
 1. Test source build and conda recipe build (conda-build).
 1. Binary builds on local build machines.
  1. Manually triggered build on master and non-master.
  1. Cron builds.
  1. Release binaries manually copied from cont. builds.

 1. [[https://circleci.com/gh/cryoem/eman2|CircleCI]]: [[https://github.com/cryoem/eman2/blob/master/.circleci/config.yml|.circleci/config.yml]]
 1. [[https://travis-ci.org/cryoem/eman2|TravisCI]]: [[https://github.com/cryoem/eman2/blob/master/.travis.yml|.travis.yml]]
 1. [[https://ci.appveyor.com/|Appveyor]]: [[https://github.com/cryoem/eman2/blob/master/appveyor.yml|appveyor.yml]]
 1. JenkinsCI: [[https://github.com/cryoem/eman2/blob/master/Jenkinsfile|Jenkinsfile]], binary builds


= Jenkins Setup =
 1. Triggers
  1. GitHub webhooks
  1. Cron
  1. Binary build trigger

 1. Jenkins master needs PATH prepended with $CONDA_PREFIX/bin
 1. Jenkins Docker image, docker-coompose or docker stack deploy
Dependencies not available on anaconda or conda-forge are available [[https://anaconda.org/cryoem/|cryoem]]. The binaries are built and uploaded using [[https://conda-forge.org/|conda-forge's]] [[https://github.com/conda-forge/conda-smithy|conda-smithy]]. [[https://github.com/conda-forge/conda-smithy|conda-smithy]] takes care of generating feedstocks, registering them on !GitHub and online CI services and building conda recipes.





EMAN2 is built with `conda-build` using binaries from https://anaconda.org, packaged into an installer with [[https://github.com/cryoem/constructor.git|constructor]] as of '''v2.2'''.

 1. [[https://github.com/conda/conda|conda]] is the package manager.
 1. https://anaconda.org is the online repository of binaries.
 1. [[https://github.com/conda/conda-build|conda-build]] is the tool to build from source.
 1. [[https://github.com/cryoem/constructor.git|constructor]] is the tool to package eman2 and dependency binaries into a single installer file.

EMAN2 is distributed as a single installer which includes all its dependencies.

== Conda ==

Packages that are available on https://anaconda.org can be installed into any conda environment by issuing the command {{{conda install <package>}}}. Conda installs the package along with its dependencies. In order for packages to benefit from this automation, they need to be packaged in a specific way. That can be done with {{{conda-build}}}. {{{conda-build}}} builds packages according to instructions provided in a {{{recipe}}}. A recipe consists of a file with package metadata, {{{meta.yaml}}}, and any other necessary resources like build scripts, ({{{build.sh}}}, {{{bld.bat}}}), patches and so on.

== Recipes, Feedstocks and anaconda.org channel: cryoem ==

Most of EMAN2 dependencies can be found on anaconda's channels, {{{defaults}}} and {{{conda-forge}}}. A few that do not exist or need to be customized have been built and uploaded to channel [[https://anaconda.org/cryoem/dashboard|cryoem]]. The recipes are hosted in separate repositories on [[https://github.com/cryoem/|GitHub]]. Every recipe repository follows the feedstock approach of [[http://conda-forge.github.io/|conda-forge]]. See [[https://github.com/cryoem?utf8=%E2%9C%93&q=-feedstock&type=&language=|here]] for a complete list.



== Feedstocks ==
 * https://github.com/cryoem/eman-deps-feedstock
 * https://github.com/cryoem/pydusa-feedstock
 * https://github.com/cryoem/eman-feedstock

=== General instructions ===
 1. Existing feedstocks
 1. Files to edit: recipe/, conda-build.yaml, conda-forge.yaml
 1. conda create -n smithy conda-smithy -c conda-forge
 1. conda-smithy rerender
 1. More info in conda-smithy/README.md, conda smithy -h, conda-forge.org/docs
 1. New feedstocks
 1. conda-smithy/README.md, conda smithy -h

=== Conda-smithy Workflow ===

Conda smithy uses tokens to authenticate with !GitHub.
 {{{#!highlight yaml
# conda-forge.yml

channels:
  sources: [cryoem, defaults, conda-forge]
  targets:
  - [cryoem, main]

github:
  user_or_org: cryoem
  repo_name: <package>-feedstock

provider:
  linux: circle
  osx: travis
  win: appveyor

azure:
  build_id: blank
}}}

 {{{#!highlight yaml
# recipe/conda_build_config.yaml

channel_sources:
- cryoem, defaults,conda-forge
channel_targets:
- cryoem dev

}}}

Conda-smithy commands:
 {{{#!highlight bash
conda create -n smithy conda-smithy
conda activate smithy
conda smithy init <recipe_directory>
conda smithy register-github <feedstock_directory> --organization cryoem
conda smithy register-ci --organization cryoem --without-azure --without-drone
conda smithy rerender --no-check-uptodate
}}}







= Build System Notes =


== CMake ==

 1. ''libpython'' can be linked statically or dynamically when python is built. It is important for python extensions to be aware of the type of linking in order to avoid segfaults. This can be accomplished by querying Py_ENABLE_SHARED.

 {{{#!highlight bash
python -c "import sysconfig; print(sysconfig.get_config_var('Py_ENABLE_SHARED'))"
}}}

 In EMAN, it is done in [[https://github.com/cryoem/eman2/blob/master/cmake/FindPython.cmake#L29-L73|cmake/FindPython.cmake]]

 1. OpenGL detection when Anaconda's compilers are used is done using a [[https://github.com/cryoem/eman2/blob/master/recipe/cross-linux.cmake|cmake toolchain file]].

 1. glext.h file needed for OpenGL related module compilation is already present on Linux and Mac. On Windows, it is manually copied once into C:\Program Files\Microsoft SDKs\Windows\v6.0A\Include\gl. On Appveyor it is downloaded as part of env setup every time a test is run.



==== Jenkins Docker ====
Line 84: Line 267:
 1. plugins
 1. config, jcasc, config.xml, users.xml, jobs/*.xml?, gpg encrypt
 1. Agent nodes setup, agent nodes auto-start		  1. Agent nodes setup
Line 88: Line 269:
  1. Master only
  1. Master and agent per machine
  1. Single master and OS agents


== Linux ==
 1. systemctl

docker run -d -u root -p 8080:8080 -p 50000:50000 --restart unless-stopped -v /home/eman2/jenkins_home:/var/jenkins_home -v /var/run/docker.sock:/var/run/docker.sock jenkins/jenkins:lts &

docker run -d -u root --name jenkins-master -p 8080:8080 -p 50000:50000 --restart unless-stopped -v /home/eman2/jenkins_home:/var/jenkins_home -v /var/run/docker.sock:/var/run/docker.sock -e PLUGINS_FORCE_UPGRADE=true -e TRY_UPGRADE_IF_NO_MARKER=true --restart unless-stopped cryoem/jenkins:dev

cron:

0 0 * * * bash /home/eman2/workspace/cronjobs/cleanup_harddisk.sh

$ cat Desktop/docker.txt docker run -p 8080:8080 -p 50000:50000 jenkins/jenkins:lts docker run -p 8080:8080 -p 50000:50000 --restart unless-stopped jenkins/jenkins:lts docker run -p 8080:8080 -p 50000:50000 --restart unless-stopped -v /home/eman2/jenkins_home:/var/jenkins_home jenkins/jenkins:lts docker run -p 8080:8080 -p 50000:50000 --restart unless-stopped -v /var/jenkins_home:/home/eman2/jenkins_home jenkins/jenkins:lts

# Working docker run -u root -p 8080:8080 -p 50000:50000 --restart unless-stopped -v /home/eman2/jenkins_home:/var/jenkins_home jenkins/jenkins:lts docker run -u root -p 8080:8080 -p 50000:50000 --restart unless-stopped -v /home/eman2/jenkins_home:/var/jenkins_home jenkins

docker run -d -u root -p 8080:8080 -p 50000:50000 --restart unless-stopped -v /home/eman2/jenkins_home:/var/jenkins_home -v /var/run/docker.sock:/var/run/docker.sock jenkins/jenkins:lts

sudo docker run -it -v /var/jenkins_home:/home/eman2/jenkins_home jenkins

startup: right-click ???


== Mac ==
 1. plist

docker run -d --name jenkins-master -p 8080:8080 -p 50000:50000 -v /Users/eman/workspace/jenkins_home:/var/jenkins_home --restart unless-stopped jenkins/jenkins:lts

Auto startup: plist https://imega.club/2015/06/01/autostart-slave-jenkins-mac/ /Users/eman/Library/LaunchAgents

slave clock sync https://blog.shameerc.com/2017/03/quick-tip-fixing-time-drift-issue-on-docker-for-mac docker run --rm --privileged alpine hwclock -s

client 0 free swap space

$ cat Desktop/docker.txt docker run -p 8080:8080 -v /Users/eman/workspace/jenkins_home:/var/jenkins_home jenkins docker run -it -p 8080:8080 -v /Users/eman/workspace/jenkins_home:/var/jenkins_home --restart unless-stopped jenkins

# Working docker run -it -p 8080:8080 -v /Users/eman/workspace/jenkins_home:/var/jenkins_home --restart unless-stopped jenkins/jenkins:lts

# Blue Ocean docker run \

 . -u root \ --rm \ -d \ -p 8080:8080 \ -v jenkins-data:/var/jenkins_home \ -v /var/run/docker.sock:/var/run/docker.sock \ jenkinsci/blueocean

# Latest docker run -d --name jenkins-master -p 8080:8080 -p 50000:50000 -v /Users/eman/workspace/jenkins_home:/var/jenkins_home --restart unless-stopped jenkins/jenkins:lts

FROM jenkins/jenkins:lts COPY plugins.txt /usr/share/jenkins/ref/plugins.txt RUN /usr/local/bin/install-plugins.sh < /usr/share/jenkins/ref/plugins.txt

plugins.txt: ace-editor:latest bouncycastle-api:latest branch-api:latest chef-identity:latest

Settings: tokens slaves


== Windows ==
Move jenkins_home http://tech.nitoyon.com/en/blog/2014/02/25/jenkins-home-win/

Run as service: Open Task Manager(Ctrl+Shift+Esc), New task, Browse to agent.jnlp and run as admin does this work? This is when starting via Web Launcher doesn't work.

currently, task scheduler works need to have miniconda pn path, set it during miniconda installation, but do not(?) register python.

While installing miniconda register python and add to PATH. Then, conda init in cmd (git init cmd.exe) and git windows (git init bash). And, maybe restart???

BUG: miniconda3 conda-build=3.17.8 adds vc14 even if python2 is requested in build reqs


= Distribution =

== Binaries on cryoem.bcm.edu ==

== EMAN2 on anaconda.org ==

== EMAN2 Docker images ==

{{{#!wiki comment
= Build System Components =

digraph build_system_components {
    a [label = "Source code"]
    //=== CMake and Anaconda ===

    b [label = "Binaries"]
    //=== Test and CI ===
    d [label = "Test"]

    c [label = "Distribute"]
    c1 [label = "Package with Constructor"]
    c2 [label = "Conda recipe"]
    c3 [label = "Docker Image"]

    a -> b [ label = "CMake" ]
    b -> c
    b -> d -> c

    c -> c1
    c -> c2
    c -> c3

}


{{attachment:build_system_components.png}}
}}}
==== Docker ====
Docker images and helper scripts are at --(https://github.com/cryoem/docker-images )-- https://github.com/cryoem/build-scripts.

Command to run docker with GUI support, CentOS7: {{{
xhost + local:root

docker run -it -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY=unix$DISPLAY cryoem/eman-nvidia-cuda8-centos7

# When done with eman
xhost - local:root
}}}

:FIXME: Runs as root on Linux. `chown` doesn't work, the resulting installer has root ownership.

Contents

  1. Binary Distribution
    1. Jenkins Setup
      1. Jenkins Setup on Linux
    2. Jenkins Setup
    3. Jenkins Setup
    4. Linux
    5. Mac
    6. Windows
  2. Anaconda
    1. Conda
    2. Recipes, Feedstocks and anaconda.org channel: cryoem
    3. Feedstocks
      1. General instructions
      2. Conda-smithy Workflow
  3. Build System Notes
    1. CMake
        1. Jenkins Docker
        2. Docker

Binary Distribution

  • GitHub webhooks are setup to send notifications to blake. Blake forwards those to three build machines. Currently, webhooks are being listened to only on Linux. Linux runs the server that drives the Jenkins jobs.

Jenkins Setup

Jenkins server runs on Linux, Jenkins agents on Linux, Mac and Windows. The server instance manages Jenkins, the agents run the jobs.

  1. On Linux, to start Jenkins, run command:

    docker stop jenkins-master

docker rm jenkins-master

docker run -d -u root --name jenkins-master -p 8080:8080 -p 50000:50000 --restart unless-stopped -v /home/eman2/jenkins_home:/var/jenkins_home -e PLUGINS_FORCE_UPGRADE=true -e TRY_UPGRADE_IF_NO_MARKER=true --restart unless-stopped jenkins/jenkins:lts
  2. Install Java on agents.
  3. Setup passwordless ssh connections from Linux server to agents.

  4. Nodes: http://10.10.11.176:8080/computer/

    1. http://10.10.11.176:8080/computer/linux/configure

      1. name: linux
      2. remoteFS: /home/eman2/linux-1-agent/
      3. numExecutors: 100
      4. host: eman-centos7-01
      5. credentialsId: jenkins-key-eman2
      6. label: eman
      7. envVars
        1. DEPLOY_PATH: /opt/web2py_apps/web2py/applications/cryoem/static/software/
        2. HOME_DIR: /home/eman2
        3. PATH+EXTRA: /home/eman2/miniconda3/bin

    2. http://10.10.11.176:8080/computer/mac/configure

      1. name: mac
      2. remoteFS: /Users/eman/mac-1-agent
      3. numExecutors: 100
      4. host: eman-macmini
      5. credentialsId: jenkins-key-eman
      6. label: eman
      7. envVars
        1. DEPLOY_PATH: /opt/web2py_apps/web2py/applications/cryoem/static/software/
        2. HOME_DIR: /Users/eman/
        3. PATH+EXTRA: /Users/eman/miniconda3/bin

    3. http://10.10.11.176:8080/computer/win/configure

      1. name: win
      2. remoteFS: D:\workspace\win-1-agent
      3. numExecutors: 100
      4. host: BM-WIN-01
      5. credentialsId: jenkins-key-eman

      6. JavaPath: "D:\Downloads\openjdk-11+28_windows-x64_bin\jdk-11\bin\java.exe"

      7. Prefix Start Agent Command: D: &&

      8. label: eman
      9. envVars
        1. DEPLOY_PATH: /opt/web2py_apps/web2py/applications/cryoem/static/software/
        2. HOME_DIR: D:
        3. PATH+EXTRA: D:\Miniconda3;D:\Miniconda3\Scripts

Jenkins Setup on Linux

  1. http://10.10.11.176:8080/manage/configure

    1. Labels: main master

    2. Jenkins URL: http://10.10.11.176:8080/

    3. System Admin e-mail address: eman-bot (linux)<eman.github@gmail.com>

    4. SSH Servers
      1. Name: Installer-Server
      2. Hostname: cryoem.bcm.edu
      3. Username: eman-binary-uploader
      4. Remote Directory: /opt/web2py_apps/web2py/applications/cryoem/static/software/

  2. http://10.10.11.176:8080/manage/configureSecurity/

    1. Agents
      1. TCP port for inbound agents
        1. Fixed: 50000
    2. Git Host Key Verification Configuration
      1. Host Key Verification Strategy
        1. Known hosts file

  3. Credentials: http://10.10.11.176:8080/manage/credentials/ 

    • ID                  Name
gh-eman-bot         eman-bot (gh-eman-
jenkins-key-eman    eman (jenkins-key-eman)
jenkins-key-eman2   eman2 (jenkins-key-eman2)

PATH

Jenkins Setup

  1. Jenkins master needs PATH prepended with $CONDA_PREFIX/bin

Jenkins Setup

  1. Login info: 10.10.11.176:8080/ username: eman2
  2. Jobs
  3. Settings, Plugins ?
  4. Binary builds require conda-build, constructor

Packaging is done with constructor, a tool for making installers from conda packages.

  1. JenkinsCI: Jenkinsfile

    1. Secrets like ssh keys are stored locally in Jenkins
    2. Some env vars need to be set by agents:
      1. HOME_DIR, DEPLOY_PATH, PATH+EXTRA (to add miniconda to PATH).
      2. PATH+EXTRA is not set on win. (?)
        1. Now, it is set on win, too. 
    3.  Launch method: via SSH
   Advanced:
     Prefix Start Agent Command: "D: && "
    4. On windows for sh calls in jenkins to work "Git for Windows" might need to be installed.
  1. Binary builds on local build machines.

    1. Manually triggered by including "[ci build]" anywhere in the last commit message. Manually triggered builds on master branch are uploaded as continuous builds and builds triggered from any other branch are uploaded to testing area.

    2. Any branch in the form of "release-" triggers continuous builds without having to include "[ci build]" in the commit message. Once the release branch is ready, release binaries are manually copied from cont. builds folder into the release folder on the server.

Linux

docker run -d -u root --name jenkins-master -p 8080:8080 -p 50000:50000 --restart unless-stopped -v /home/eman2/jenkins_home:/var/jenkins_home -v /var/run/docker.sock:/var/run/docker.sock -e PLUGINS_FORCE_UPGRADE=true -e TRY_UPGRADE_IF_NO_MARKER=true --restart unless-stopped cryoem/jenkins:dev

Mac

slave clock sync https://blog.shameerc.com/2017/03/quick-tip-fixing-time-drift-issue-on-docker-for-mac docker run --rm --privileged alpine hwclock -s

Windows

OPENGL: https://github.com/conda/conda-recipes/blob/master/qt5/notes.md

Anaconda

Dependencies not available on anaconda or conda-forge are available cryoem. The binaries are built and uploaded using conda-forge's conda-smithy. conda-smithy takes care of generating feedstocks, registering them on GitHub and online CI services and building conda recipes.

EMAN2 is built with conda-build using binaries from https://anaconda.org, packaged into an installer with constructor as of v2.2.

  1. conda is the package manager.

  2. https://anaconda.org is the online repository of binaries.

  3. conda-build is the tool to build from source.

  4. constructor is the tool to package eman2 and dependency binaries into a single installer file.

EMAN2 is distributed as a single installer which includes all its dependencies.

Conda

Packages that are available on https://anaconda.org can be installed into any conda environment by issuing the command conda install <package>. Conda installs the package along with its dependencies. In order for packages to benefit from this automation, they need to be packaged in a specific way. That can be done with conda-build. conda-build builds packages according to instructions provided in a recipe. A recipe consists of a file with package metadata, meta.yaml, and any other necessary resources like build scripts, (build.sh, bld.bat), patches and so on.

Recipes, Feedstocks and anaconda.org channel: cryoem

Most of EMAN2 dependencies can be found on anaconda's channels, defaults and conda-forge. A few that do not exist or need to be customized have been built and uploaded to channel cryoem. The recipes are hosted in separate repositories on GitHub. Every recipe repository follows the feedstock approach of conda-forge. See here for a complete list.

Feedstocks

General instructions

  1. Existing feedstocks
  2. Files to edit: recipe/, conda-build.yaml, conda-forge.yaml
  3. conda create -n smithy conda-smithy -c conda-forge
  4. conda-smithy rerender
  5. More info in conda-smithy/README.md, conda smithy -h, conda-forge.org/docs
  6. New feedstocks
  7. conda-smithy/README.md, conda smithy -h

Conda-smithy Workflow

Conda smithy uses tokens to authenticate with GitHub. 

  •    1 # conda-forge.yml
   2 
   3 channels:
   4   sources: [cryoem, defaults, conda-forge]
   5   targets:
   6   - [cryoem, main]
   7 
   8 github:
   9   user_or_org: cryoem
  10   repo_name: <package>-feedstock
  11 
  12 provider:
  13   linux: circle
  14   osx: travis
  15   win: appveyor
  16 
  17 azure:
  18   build_id: blank

       1 # recipe/conda_build_config.yaml
   2 
   3 channel_sources:
   4 - cryoem, defaults,conda-forge
   5 channel_targets:
   6 - cryoem dev

Conda-smithy commands: 

  •    1 conda create -n smithy conda-smithy
   2 conda activate smithy
   3 conda smithy init <recipe_directory>
   4 conda smithy register-github <feedstock_directory> --organization cryoem
   5 conda smithy register-ci --organization cryoem --without-azure --without-drone
   6 conda smithy rerender --no-check-uptodate

Build System Notes

CMake

  1. libpython can be linked statically or dynamically when python is built. It is important for python extensions to be aware of the type of linking in order to avoid segfaults. This can be accomplished by querying Py_ENABLE_SHARED. 

       1 python -c "import sysconfig; print(sysconfig.get_config_var('Py_ENABLE_SHARED'))"

    In EMAN, it is done in cmake/FindPython.cmake

  2. OpenGL detection when Anaconda's compilers are used is done using a cmake toolchain file.

  3. glext.h file needed for OpenGL related module compilation is already present on Linux and Mac. On Windows, it is manually copied once into C:\Program Files\Microsoft SDKs\Windows\v6.0A\Include\gl. On Appveyor it is downloaded as part of env setup every time a test is run.

Jenkins Docker

  1. docker-compose.yml at home dir in build machines

  2. TZ: https://stackoverflow.com/a/46384925

  3. Agent nodes setup
  4. Server and agent per machine vs single server and os agents

Docker

Docker images and helper scripts are at https://github.com/cryoem/docker-images https://github.com/cryoem/build-scripts.

Command to run docker with GUI support, CentOS7: 

xhost + local:root

docker run -it -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY=unix$DISPLAY cryoem/eman-nvidia-cuda8-centos7

# When done with eman
xhost - local:root

:FIXME: Runs as root on Linux. chown doesn't work, the resulting installer has root ownership.

EMAN2/BuildSystem (last edited 2022-12-12 03:42:44 by TunayDurmaz)