!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 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. Server login info: 10.10.11.176:8080/ username: eman2 3. Install Java on agents. 4. Setup passwordless ssh connections from Linux server to agents. 5. Binary builds require conda-build and constructor. Packaging is done with

constructor

, a tool for making installers from conda packages. 6. Nodes: http://10.10.11.176:8080/computer/

7. http://10.10.11.176:8080/computer/linux/configure
  8. name: linux
  9. remoteFS: /home/eman2/linux-1-agent/
  10. numExecutors: 100
  11. host: eman-centos7-01
  12. credentialsId: jenkins-key-eman2
  13. label: eman
  14. envVars
   15. DEPLOY_PATH: /opt/web2py_apps/web2py/applications/cryoem/static/software/
   16. HOME_DIR: /home/eman2
   17. PATH+EXTRA: /home/eman2/miniconda3/bin

18. http://10.10.11.176:8080/computer/mac/configure
  19. name: mac
  20. remoteFS: /Users/eman/mac-1-agent
  21. numExecutors: 100
  22. host: eman-macmini
  23. credentialsId: jenkins-key-eman
  24. label: eman
  25. envVars
   26. DEPLOY_PATH: /opt/web2py_apps/web2py/applications/cryoem/static/software/
   27. HOME_DIR: /Users/eman/
   28. PATH+EXTRA: /Users/eman/miniconda3/bin

29. http://10.10.11.176:8080/computer/win/configure
  30. name: win
  31. remoteFS: D:\workspace\win-1-agent
  32. numExecutors: 100
  33. host: BM-WIN-01
  34. credentialsId: jenkins-key-eman
  35. !JavaPath: "D:\Downloads\openjdk-11+28_windows-x64_bin\jdk-11\bin\java.exe"
  36. Prefix Start Agent Command: "D: &&"
  37. label: eman
  38. envVars
   39. DEPLOY_PATH: /opt/web2py_apps/web2py/applications/cryoem/static/software/
   40. HOME_DIR: D:
   41. PATH+EXTRA: D:\Miniconda3;D:\Miniconda3\Scripts
  42. On Windows for sh calls in jenkins to work "Git for Windows" might need to be installed.

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

44. Labels: main master
45. Jenkins URL: http://10.10.11.176:8080/
46. System Admin e-mail address: eman-bot (linux)<eman.github@gmail.com>
47. SSH Servers
 48.  Name: Installer-Server
 49.  Hostname: cryoem.bcm.edu
 50.  Username: eman-binary-uploader
 51.  Remote Directory: /opt/web2py_apps/web2py/applications/cryoem/static/software/

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

53. Agents
 54. TCP port for inbound agents
  55. Fixed: 50000
56. Git Host Key Verification Configuration
 57. Host Key Verification Strategy
  58. Known hosts file

59. 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)

60. Jobs

61. http://10.10.11.176:8080/job/cryoem-eman2-trigger/: Triggers job cryoem-eman2 on agents
62. http://10.10.11.176:8080/job/cryoem-eman2/: Test(?) and binary builds
  * eman-dev(?): Triggers new build of eman-dev
63. http://10.10.11.176:8080/job/eman-bump-version/
64. http://10.10.11.176:8080/job/eman-feedstock-update-version/
65. http://10.10.11.176:8080/job/eman-feedstock-trigger-from-eman-master/
66. http://10.10.11.176:8080/job/build-binary/
67. http://10.10.11.176:8080/job/build-binary-trigger/
68. http://10.10.11.176:8080/job/eman-feedstock-building-eman-v2.99/

69. JenkinsCI: Jenkinsfile

 70. Secrets like ssh keys are stored locally in Jenkins
 71. 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]].
 72. 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.

#!wiki comment

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


Not sure if this is true
 73. Jenkins master needs PATH prepended with $CONDA_PREFIX/bin

Dependencies not available on anaconda or conda-forge are available on 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.

74. conda is the package manager. 75. https://anaconda.org is the online repository of binaries. 76. conda-build is the tool to build from source. 77. 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.

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.

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.

• https://github.com/cryoem/eman-deps-feedstock
• https://github.com/cryoem/pydusa-feedstock
• https://github.com/cryoem/eman-feedstock

78. Existing feedstocks 79. Files to edit: recipe/, conda-build.yaml, conda-forge.yaml 80. conda create -n smithy conda-smithy -c conda-forge 81. conda-smithy rerender 82. More info in conda-smithy/README.md, conda smithy -h, conda-forge.org/docs 83. New feedstocks 84. conda-smithy/README.md, conda smithy -h

Conda smithy uses tokens to authenticate with !GitHub.

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

85. 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 cmake/FindPython.cmake

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

87. 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.

{#!wiki comment

=== 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: <code>
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

:: Runs as root on Linux. `chown` doesn't work, the resulting installer has root ownership. </code>}