ejpm

ejpm stands for eJANA packet manager helper

The goal of ejpm is to provide easy experience of:

• installing eJANA reconstruction framework and supporting packages
• unify installation for different environments: e.g. various operating systems, docker images, etc.

The secondary goal is to help users with e^JANA plugin development cycle.

Table of contents:

• Motivation
• EJPM installation
• Get ejana installed
• Manage environment
• Troubleshooting
• Manual or devel installation
• Adding a package
  • Adding Git+Cmake package example

Cheat sheet:

Install ejpm:

# install EJPM
sudo python -m pip install ejpm

# OR without sudo: add --user flag and ensure ~/.local/bin is in your PATH
python -m pip install --user -U ejpm

JLab machines with certificate problems - add these flags to the command above:
--trusted-host pypi.python.org --trusted-host files.pythonhosted.org --trusted-host pypi.org
see Troubleshooting chapter for details

Install everything else

# install prerequesties
ejpm req centos ejana         # get list of OS packets required to build jana and deps
sudo yum install ...          # install whatever 'ejpm req' shows

# setup installation dir and existing packets, introspect
ejpm --top-dir=<where-to>     # Directory where packets will be installed
ejpm                          # To see how ejpm is configured
ejpm install ejana --explain  # To see what is to be installed
ejpm set root `$ROOTSYS`      # if you have CERN.ROOT. Or skip this step
ejpm set <packet> <path>      # set other existing packets. Or skip this step!!!

# Build and install the rest
ejpm install ejana            # install ejana and dependencies (like genfit, jana and rave)
ejpm install g4e              # install Geant-4-Eic and dependencies (Geant4, etc)

# Set environment
source<(ejpm env)             # set environment variables
ejpm env csh > your.csh       # if you are still on CSH

# If that worked don't read the next...

Motivation

TL;DR; Major HEP and NP scientific packages are not supported by some major distros and usually are crappy (at least in terms of dependency requirements). Everybody have to reinvent the wheel to include such packages in their software chains and make users' lives easier. And we do.

Longer reading

ejpm is here as there is no standard convention in HEP and NP of how to distribute and install software packages with its dependencies. Some packages (like eigen, xerces, etc.) are usually supported by OS maintainers, while others (Cern ROOT, Geant4, Rave) are usually built by users or other packet managers and could be located anywhere. We also praise "version hell" (e.g. when GenFit doesn't compile with CLHEP from ubuntu repo) and lack of software manpower (e.g. to sufficiently and continuously maintain packages for major distros or even to fix some simple issues on GitHub).

Still we love our users and know they will never install everything on their own so we try to get things easier for them!

At this points ejpm tries to unify experience and make it simple to deploy eJANA for:

• Users on RHEL 7 and CentOS
• Users on Ubutnu (and Windows with WSL)
• Docker and other containers

The experience should be as easy as pointing right configuration and installing everything automatically with just few commands. But also it should provide a possibility to fine control over installed dependencies and help with development.

Design features

• Essentials:

  • ejpm is written in pure python (2 and 3 compatible) with minimum dependencies
  • it is shipped by pip (python official repo), so can be installed with one command on all major platforms
  • CLI (command line interface) - provides users with commands to manipulate packets
  • JSON database stores the current state and packets locations
  • It makes easy to... e.g. switch between known versions, rebuild packets, deploy missing packets, continue after fail, etc.

• Under the hood:

  • Each packet has a single python file that defines how it will be installed and configured
  • Each such file is easy to read and modify by inexperienced users in case they would love to
  • Installation steps written in a style close to Dockerfile (same command names, etc)

Alternatives

Is there something existing? What others do? - Simple bash build scripts quickly get bloated and complex. Dockerfiles and similar stuff are too-tool-related. Build systems like scons or cmake also too centric on compiling something rather than managing packets chains. Full featured package managers and tools like Homebrew are pretty complex to tame (for dealing with just 5 deps).

So ejpm is something more advanced than build scripts, but less cumbersome than real packet managers, it is in pure python, and being focused on our specific problems.

ejpm is not:

1. It is not a real package manager which automatically solves dependency trees
2. ejpm is not a requirment for eJANA. It is not a part of eJANA build system and one can compile and install eJANA without ejpm

Users are pretty much encouraged to change the code and everything is done here to be user-change-friendly

Installation

TL;DR;

sudo pip install --upgrade ejpm    # system level installation
pip install --user --upgrade ejpm  # User level. $HOME/.local/bin should be in $PATH

If you have certificate problems on JLab machines: (more options on certificates):

# System level copy-paste:
sudo python -m pip install --trusted-host pypi.python.org --trusted-host files.pythonhosted.org --trusted-host pypi.org -U ejpm
# User level copy-paste:
python -m pip install --trusted-host pypi.python.org --trusted-host files.pythonhosted.org --trusted-host pypi.org --user -U ejpm

More on this:

• See INSTALLATION TROUBLESHOOTING If you don't have pip or right python version.
• See Jlab root certificate problems and how to solve them
• See Manual or development installation to use this repo directly, develop EJPM or don't want to mess with pip at all?

Get ejana installed

(or crash course to ejpm)

TL;DR; example for CentOS/RHEL7

ejpm req centos ejana         # get list of OS packets required to build jana and deps
sudo yum install ...          # install watever 'ejpm req' shows
ejpm --top-dir=<where-to>     # Directory where packets will be installed
ejpm set root `$ROOTSYS`      # if you have CERN.ROOT. Or skip this step
ejpm install ejana --missing  # install ejana and dependencies (like genfit, jana and rave)
source<(ejpm env)             # set environment variables

Step by step explained instruction:

1. Install (or check) required packages form OS:

   ejpm req ubuntu         # for all packets that ejpm knows
   ejpm req centos ejana   # for ejana and its dependencies only
   

   At this point only 'ubuntu' and 'centos' are known words for req command. Put:

   • ubuntu for debian family
   • centos for RHEL and CentOS systems.

   In future macOS and more detailed os-versions will be supported

2. Set top-dir. This is where all missing packets will be installed.

   ejpm --top-dir=<where-to-install-all>
   

3. You may have CERN.ROOT installed (req. version >= 6.14.00). Run this:

   ejpm set root `$ROOTSYS` 
   

   You may set paths for other installed dependencies combining:

   ejpm install ejana --missing --explain    # to see missing dependencies
   ejpm set <name> <path>                    # to set dependency path
   ejpm set jana <path to jana2 install>     # JANA2 as an example
   

   Or you may skip this step and just get everything installed by ejpm

4. Then you can install ejpm and all missing dependencies:

   ejpm install ejana
   

5. Set right environment variables (right in the next section)

Environment

TL;DR; Just source it like:

source <(ejpm env)      
# or
source ~/.local/share/ejpm/env.sh    # .csh for CSH/TCSH
ejpm env                             # To generate env & regenerate env files 

EJPM_DATA_PATH - sets the path where the configuration db.json and env.sh, env.csh are located

longer reading:

1. Dynamically source output of ejpm env command (recommended)

   source <(ejpm env)                # works on bash
   

2. Save output of ejpm env command to a file (can be useful)

    ejpm env sh  > your-file.sh       # get environment for bash or compatible shells
    ejpm env csh > your-file.csh      # get environment for CSH/TCSH
   

3. Use ejpm generated env.sh and env.csh files (lazy and convenient)

   $HOME/.local/share/ejpm/env.sh    # bash and compatible
   $HOME/.local/share/ejpm/env.csh   # for CSH/TCSH
   

   (!) The files are regenerated each time ejpm changes something. If you change db.json by yourself, ejpm doesn't track it automatically, so call ejpm env to regenerate these 2 files

Where EJPM data is stored:

There are standard directories for users data for each operating system. EJPM use them to store db.json and generated environment files (EJPM doesnt use the files by itself).

For linux it is XDG_DATA_HOME*:

~/.local/share/ejpm/env.sh      # sh version
~/.local/share/ejpm/env.csh     # csh version
~/.local/share/ejpm/db.json     # open it, edit it, love it

* - XDG is the standard POSIX paths to store applications data, configs, etc.

EJPM_DATA_PATH - You can control where ejpm stores data by setting EJPM_DATA_PATH environment variable.

INSTALLATION TROUBLESHOOTING

But... there is no pip:
Install it!

sudo easy_install pip       # system level
easy_install pip --user     # user level

For JLab lvl1&2 machines, there is a python installations that have pip :

/apps/python/     # All pythons there have pip and etc
/apps/anaconda/   # Moreover, there is anaconda (python with all major math/physics libs) 

But there is no 'pip' command?
If easy_install installed something, but pip command is not found after, do:

1. If --user flag was used, make sure ~/.local/bin is in your $PATH variable
2. you can fallback to python -m pip instead of using pip command:

   python -m pip install --user --upgrade ejpm
   

But... there is no easy_install!
Install it!

sudo yum install python-setuptools python-setuptools-devel   # centos and RHEL/CentOS 
sudo apt-get install python-setuptools                       # Ubuntu and Debian
# Gentoo. I should not write this for its users, right?

For python3 it is easy_install3 and python3-setuptools

I dont have sudo privileges!

Add "--user" flag both for pip and easy_install for this. Read SO here

JLab certificate problems

If you get errors like:

Retrying (...) after connection broken by 'SSLError(SSLError(1, u'[SSL: CERTIFICATE_VERIFY_FAILED]...

The problem is that pip is trustworthy enough to use secure connection to get packages. And JLab is helpful enough to put its root level certificates in the middle.

1. The easiest solution is to declare PiPy sites as trusted:

   python -m pip install --trusted-host pypi.python.org --trusted-host files.pythonhosted.org --trusted-host pypi.org ejpm
   

2. Or to permanently add those sites as trusted in pip.config

   [global]
   trusted-host=
       pypi.python.org
       pypi.org
       files.pythonhosted.org
   

   (The link where to find pip.config on your system)
3. You may want to be a hero and kill the dragon. The quest is to take JLab certs. Then Convert them to pem. Then add certs to pip. Then check it really works on JLab machines. And bring the dragon's head back (i.e. please, add the exact instruction to this file)

Manual or development installation:

TL;DR; Get EJPM, install requirements, ready:

git clone https://gitlab.com/eic/ejpm.git
pip install -r ejpm/requirements.txt

# OR clone and add ejpm/bin to your PATH
export PATH=`pwd`/ejpm/bin:$PATH

requirments:

Click and appdirs are the only requirements. If you have pip do:

pip install --upgrade click appdirs

If for some reason you don't have pip, you don't know python well enough and don't want to mess with it, pips, shmips and doh... Just download and add to PYTHONPATH: this 'click' folder and some folder with appdirs.py

Adding a package

Each packet is represented by a single python file - a recipe which has instructions of how to get and build the package. Usually it provides:

• download/clone command
• build command
• setup of environment variables
• system dependencies (which can be installed by OS packet managers: yum, apt)

For simplicity (at this point) all recipes are located in a folder inside this repo: ejpm/recipes.

Adding Git-CMake package

The most of packages served now by ejpm use git to get source code and cmake to build the package. As git + cmake became a 'standard' there is a basic recipe class which makes adding new git+cmake packets straight forward.

As a dive-in example of adding packets, lets look on how to add such packet using Genfit as a copy-paste example.

ejpm/recipes/genfit.py

1. Set packet name and where to clone from

One should change 3 lines:

class GenfitRecipe(GitCmakeRecipe):
    def __init__(self):
        """Installs Genfit track fitting framework"""
        
        # This name is used in ejpm commands like 'ejpm install genfit'
        super(GenfitRecipe, self).__init__('genfit')
    
        # The branch or tag to be cloned (-b flag)
        self.config['branch'] = 'master'

        # Repo address
        self.config['repo_address'] = 'https://github.com/GenFit/GenFit'   

Basically that is enough to build the package and one can test:

ejpm install yourpacket

2. Set environment variables

This is a done in gen_env function. By using this function ejpm generates environments for csh/tcsh, bash and python*. So 3 commands to be used in this function:

• Set(name, value) - equals export name=value in bash
• Append(name, value) - equals export name=$name:value in bash
• Prepend(name, value) - equals export name=value:$name in bash

@staticmethod
def gen_env(data):
    path = data['install_path']   # data => installation information 

    yield Set('GENFIT_HOME', path)

    # add bin to PATH
    yield Prepend('PATH', os.path.join(path, 'bin'))
   
    # add lib to LD_LIBRARY_PATH
    yield Append('LD_LIBRARY_PATH', os.path.join(path, 'lib'))

One can test gen_env with:

ejpm env

* - if other python packages use ejpm programmatically to build something

3. System requirments

If packet has some dependencies that can be installed by OS packet managers such as apt, one can add them to os_dependencies array.

os_dependencies = {
    'required': {
        'ubuntu': "libboost-dev libeigen3-dev",
        'centos': "boost-devel eigen3-devel"
    },
    'optional': {
        'ubuntu': "",
        'centos': ""
    },
}

(!) don't remove any sections from the map, leave them blank

To test it one can run:

ejpm req ubuntu
ejpm req centos

Adding a custom package

Compared to the previous example, several more functions should be added:

• setup - configures the package
• step_clone, step_build, step_install - execute commands to perform the step

1. Setup

Setup should provide all values, that are going to be used later in 'step_xxx' functions. Usually it is just 3 things:

def setup(self):
    #
    # use_common_dirs_scheme() sets standard package variables:
    # source_path  = {app_path}/src/{branch}          # Where the sources for the current version are located
    # build_path   = {app_path}/build/{branch}        # Where sources are built. Kind of temporary dir
    # install_path = {app_path}/root-{branch}         # Where the binary installation is
    self.use_common_dirs_scheme()

    # Git download link. Clone with shallow copy
    self.clone_command = "git clone --depth 1 -b {branch} {repo_address} {source_path}".format(**self.config)

    # make command:
    self.build_command = './configure && make -j{build_threads} install'.format(**self.config)

2. Step functions

3 docker alike functions that helps to execute stuff:

• run(command) - executes the console command
• workdir(dir) - changes the working directory
• env(name, value) - sets an environment variable

run(self.clone_command)         # Execute git clone command
workdir(self.source_path)       # Go to our build directory
run('./bootstrap')              # This command required to run by rave once...
env('RAVEPATH', self.install_path)