Build System Notes

CMake

1. Dependency binaries are pulled from Anaconda. CMake uses conda environment location to find packages.

2. Make targets can be listed with make help. Some convenience targets are:

   $ 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
   ... .....
   ... .....

3. 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

4. OpenGL detection when Anaconda's compilers are used is done using a cmake toolchain file.
5. 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.
6. Compiler warnings are turned off by default and can be turned on by setting ENABLE_WARNINGS=ON

      1 cmake <source-dir> -DENABLE_WARNINGS=ON
   

7. Setting compiler and linker options by include_directories, add_definitions that have global affects are avoided and target-focused design employing modern cmake concepts like interface libraries are used as much as possible.

Anaconda

Dependencies not available on anaconda or conda-forge are available on our channel 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. Some of the packages available on cryoem.

1. Not available on anaconda: ftgl and pydusa.
2. Forked and customized: openmpi (compiled with --disable-dlopen) and fftw-mpi (fftw compiled with mpi support).
3. Meta-package for EMAN dependencies: eman-deps. eman-deps depends on eman-deps-cli and gui packages, pyqt and pyopengl.
4. Meta-package for build machine setup: eman-packaging. Depends on conda, conda-build and forked constructor. It is used when setting up build machine environments. Forked constructor contains some customizations for eman. These are applied as patches in constructor-feedstock.

Conda-smithy Workflow

Conda smithy uses tokens to authenticate with GitHub and online CI services.

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

Under Construction

Continuous Integration

1. GitHub webhooks

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

4. CircleCI: .circleci/config.yml

5. TravisCI: .travis.yml

6. Appveyor: appveyor.yml

7. JenkinsCI: Jenkinsfile, binary builds

Docker Images

1. CentOS 6
2. Jenkins
3. CircleCI

Jenkins Setup

1. Triggers

   1. GitHub webhooks

   2. Cron
   3. Binary build trigger
2. Jenkins master needs PATH prepended with $CONDA_PREFIX/bin
3. Jenkins Docker image, docker-coompose or docker stack deploy
4. docker-compose.yml at home dir in build machines

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

6. plugins
7. config, jcasc, config.xml, users.xml, jobs/*.xml?, gpg encrypt
8. Agent nodes setup, agent nodes auto-start
9. Server and agent per machine vs single server and os agents
   1. Master only
   2. Master and agent per machine
   3. 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

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

Distribution

Binaries on cryoem.bcm.edu

EMAN2 on anaconda.org

EMAN2 Docker images