From 8b63023eec285a8c98b2aaf7472cee3794fa3b7d Mon Sep 17 00:00:00 2001
From: Sylvester Joosten <sylvester.joosten@gmail.com>
Date: Tue, 31 Mar 2020 15:53:33 -0500
Subject: [PATCH] Added python-based deploy scripts, and updated Readme.
---
README.md | 35 ++++++++-
deploy.py | 160 ++++++++++++++++++++++++++++++++++++++++++
install/__init__.py | 7 ++
install/launcher.py | 111 +++++++++++++++++++++++++++++
install/modulefile.py | 46 ++++++++++++
install/util.py | 38 ++++++++++
6 files changed, 396 insertions(+), 1 deletion(-)
create mode 100755 deploy.py
create mode 100644 install/__init__.py
create mode 100644 install/launcher.py
create mode 100644 install/modulefile.py
create mode 100644 install/util.py
diff --git a/README.md b/README.md
index 0cd27916b..7e2c714ee 100644
--- a/README.md
+++ b/README.md
@@ -2,7 +2,40 @@ EIC software container
============================================
Installation
------------
+------------
+
+1. Clone the repository and go into the directory
+```bash
+git clone https://eicweb.phy.anl.gov/containers/eic_container.git
+cd eic_container
+```
+
+2. Run the deploy script `deploy.py` to install to your `<PREFIX>` of choice
+ (e.g. $HOME/local/opt/eic_container_1.0.4). By default the
+ modelefile will be installed to `$PREFIX/../../etc/modulefiles`.
+ You can use the `-v` flag to select the version you want to deploy, or omit the
+ flag if you want to install the master build. The recommended stable
+ release version is `v1.0.4`.
+```bash
+./deploy.py -v 1.0.4 <PREFIX>
+```
+
+3. To use the container: load the modulefile, and then use the included apps as if
+ they are native apps on your system!
+```
+module load eic_container
+```
+
+4. (Advanced) If you need to add additional bind directives for the internal singularity container,
+ you can add them with the `-b` flag. Run `./deploy.py -h` to see a list of all
+ supported options.
+
+
+Installation (throug cmake)
+---------------------------
+
+*Use of the cmake-based deploy is deprecated, We recommend to use the `deploy.py` method
+instead.*
1. Checkout the repository and create a build directory
```
diff --git a/deploy.py b/deploy.py
new file mode 100755
index 000000000..0ed318154
--- /dev/null
+++ b/deploy.py
@@ -0,0 +1,160 @@
+#!/usr/bin/env python3
+
+## eic_container: Argonne Universal EIC Container
+
+'''
+Deploy the singularity container built by the CI for this version of the software.
+
+The current version is determined from the currently loaded git branch or tag,
+unless it is explicitly set on the command line.
+
+Authors:
+ - Whitney Armstrong <warmstrong@anl.gov>
+ - Sylvester Joosten <sjoosten@anl.gov>
+'''
+
+import os
+import argparse
+import urllib.request
+from install import make_launcher, make_modulefile
+from install.util import smart_mkdir, project_version, InvalidArgumentError
+
+## Gitlab group and project/program name.
+GROUP_NAME='containers'
+PROJECT_NAME='eic_container'
+PROGRAMS = [('container_dev', '/usr/bin/bash'),
+ 'ddsim',
+ 'geoConverter',
+ 'materialScan',
+ 'geoDisplay',
+ 'geoPluginRun',
+ 'teveDisplay',
+ 'ddeve',
+ 'g4FromXML'
+ 'geoDisplay',
+ 'listcomponents',
+ 'print_materials',
+ 'dumpBfield',
+ 'g4gdmlDisplay',
+ 'geoPluginRun',
+ 'materialBudget',
+ 'pyddg4',
+ 'dumpdetector',
+ 'graphicalScan',
+ 'root',
+ 'root-config',
+ 'rootbrowse',
+ 'rootls',
+ 'mongo',
+ 'mongod',
+ 'mongodump',
+ 'mongoexport',
+ 'mongoimport',
+ 'mongostat']
+
+## URL for the current container (git tag will be filled in by the script)
+CONTAINER_URL = r'https://eicweb.phy.anl.gov/{group}/{project}/-/jobs/artifacts/{version}/raw/build/eic.sif?job=eic_singularity'
+
+CONTAINER_ENV=r'''source /usr/local/bin/thisdd4hep.sh
+ROOT_INCLUDE_PATH=/usr/local/include:/usr/include/eigen3:$ROOT_INCLUDE_PATH
+'''
+
+## Singularity bind directive
+BIND_DIRECTIVE= '-B {0}:{0}'
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser()
+ parser.add_argument(
+ 'prefix',
+ help='Install prefix. This is where the container will be deployed.')
+ parser.add_argument(
+ '-v', '--version',
+ dest='version',
+ default=project_version(),
+ help='(opt.) project version. Default: current git branch/tag.')
+ parser.add_argument(
+ '-f', '--force',
+ action='store_true',
+ help='Force-overwrite already downloaded container',
+ default=False)
+ parser.add_argument(
+ '-b', '--bind-path',
+ dest='bind_paths',
+ action='append',
+ help='(opt.) extra bind paths for singularity.')
+ parser.add_argument(
+ '-m', '--module-path',
+ dest='module_path',
+ help='(opt.) Root module path where you want to install a modulefile. D: <prefix>/../../etc/modulefiles')
+
+ args = parser.parse_args()
+
+ print('Deploying', PROJECT_NAME, 'version', args.version)
+
+ ## Check if our bind paths are valid
+ bind_directive = ''
+ if args.bind_paths and len(args.bind_paths):
+ print('Singularity bind paths:')
+ for path in args.bind_paths:
+ print(' -', path)
+ if not os.path.exists(path):
+ print('ERROR: path', path, 'does not exist.')
+ raise InvalidArgumentError()
+ bind_directive = ' '.join([BIND_DIRECTIVE.format(path) for path in args.bind_paths])
+
+ ## We want to slightly modify our version specifier: if it leads with a 'v' drop the v
+ ## for everything installed, but ensure we have the leading v as well where needed
+ version = '{}'.format(args.version)
+ vversion = '{}'.format(args.version)
+ if version[0] is 'v':
+ version = version[1:]
+ if vversion[0].isdigit():
+ vversion= 'v{}'.format(args.version)
+
+ ## Create our install prefix if needed and ensure it is writable
+ args.prefix = os.path.abspath(args.prefix)
+ if not args.module_path:
+ args.module_path = '{}/etc/modulefiles'.format(args.prefix)
+ print('Install prefix:', args.prefix)
+ print('Creating install prefix if needed...')
+ bindir = '{}/bin'.format(args.prefix)
+ libdir = '{}/lib'.format(args.prefix)
+ libexecdir = '{}/libexec'.format(args.prefix)
+ root_prefix = os.path.abspath('{}/..'.format(args.prefix))
+ moduledir = '{}/etc/modulefiles/{}'.format(root_prefix, PROJECT_NAME)
+ for dir in [bindir, libdir, libexecdir, moduledir]:
+ print(' -', dir)
+ smart_mkdir(dir)
+
+ ## At this point we know we can write to our desired prefix and that we have a set of
+ ## valid bind paths
+
+ ## Get the container
+ ## We want to slightly modify our version specifier: if it leads with a 'v' drop the v
+ container = '{}/{}.sif.{}'.format(libdir, PROJECT_NAME, version)
+ if not os.path.exists(container) or args.force:
+ url = CONTAINER_URL.format(group=GROUP_NAME, project=PROJECT_NAME, version=vversion)
+ print('Downloading container from:', url)
+ print('Destination:', container)
+ urllib.request.urlretrieve(url, container)
+ else:
+ print('WARNING: Container found at', container)
+ print(' ---> run with -f to force a re-download')
+
+ make_modulefile(PROJECT_NAME, version, moduledir, bindir)
+
+ ## configure the application launchers
+ print('Configuring applications launchers: ')
+ for prog in PROGRAMS:
+ app = prog
+ exe = prog
+ if type(prog) == tuple:
+ app = prog[0]
+ exe = prog[1]
+ make_launcher(app, container, bindir,
+ bind=bind_directive,
+ libexecdir=libexecdir,
+ exe=exe,
+ env=CONTAINER_ENV)
+
+ print('Container deployment successful!')
diff --git a/install/__init__.py b/install/__init__.py
new file mode 100644
index 000000000..7a9953f35
--- /dev/null
+++ b/install/__init__.py
@@ -0,0 +1,7 @@
+#!/usr/bin/env python3
+
+## eic_container: Argonne Universal EIC Container
+
+from install.util import smart_mkdir, project_version
+from install.launcher import make_launcher
+from install.modulefile import make_modulefile
diff --git a/install/launcher.py b/install/launcher.py
new file mode 100644
index 000000000..6ab5f0903
--- /dev/null
+++ b/install/launcher.py
@@ -0,0 +1,111 @@
+#!/usr/bin/env python3
+
+'''
+Generic launcher script to launch applications in this container.
+
+The launcher script fires off an auxilary wrapper script in the container,
+responsible to correctly setup the environment and then launch the application
+of choice.
+
+Authors:
+ - Whitney Armstrong <warmstrong@anl.gov>
+ - Sylvester Joosten <sjoosten@anl.gov>
+'''
+
+import os
+
+## generic launcher bash script to launch the application
+_LAUNCHER='''#!/usr/bin/env bash
+
+## Boilerplate to make pipes work
+piped_args=
+if [ -p /dev/stdin ]; then
+ # If we want to read the input line by line
+ while IFS= read line; do
+ if [ -z "$piped_args" ]; then
+ piped_args="${{line}}"
+ else
+ piped_args="${{piped_args}}\n${{line}}"
+ fi
+ done
+fi
+
+## Fire off the application wrapper
+if [ ${{piped_args}} ] ; then
+ echo -e ${{piped_args}} | singularity exec {bind} {container} {wrapper} $@
+else
+ singularity exec {bind} {container} {wrapper} $@
+fi
+'''
+
+## Wrapper script called from within the container that loads the propper environment and
+## to then actually call our app
+_WRAPPER='''#!/usr/bin/env bash
+
+## setup container environment
+{env}
+
+## Boilerplate to make pipes work
+piped_args=
+if [ -p /dev/stdin ]; then
+ # If we want to read the input line by line
+ while IFS= read line; do
+ if [ -z "$piped_args" ]; then
+ piped_args="${{line}}"
+ else
+ piped_args="${{piped_args}}\n${{line}}"
+ fi
+ done
+fi
+
+## Launch the exe
+if [ ${{piped_args}} ] ; then
+ echo -e ${{piped_args}} | {exe} $@
+else
+ {exe} $@
+fi
+'''
+
+def _write_script(path, content):
+ print(' - creating', path)
+ with open(path, 'w') as file:
+ file.write(content)
+ os.system('chmod +x {}'.format(path))
+
+def make_launcher(app, container, bindir,
+ bind='', libexecdir=None, exe=None, env=''):
+ '''Configure and install a launcher/wrapper pair.
+
+ Arguments:
+ - app: our application
+ - container: absolute path to container
+ - bindir: absolute launcher install path
+ Optional:
+ - bind: singularity bind directives
+ - libexecdir: absolute wrapper install path.
+ Default is bindir.
+ - exe: executable to be associated with app.
+ Default is app.
+ - env: environment directives to be added to the wrapper.
+ Multiline string. Default is nothing
+ '''
+ ## assume bindir and libexecdir exist, are absolute, and are writable
+ if libexecdir is None:
+ libexecdir = bindir
+
+ ## actual exe we want to run, default: same as app
+ exe=app
+
+ ## paths
+ launcher_path = '{}/{}'.format(bindir, app)
+ wrapper_path = '{}/{}_wrap'.format(libexecdir, app)
+
+ ## scripts --> use absolute path for wrapper path inside launcher
+ launcher = _LAUNCHER.format(container=container,
+ bind=bind,
+ wrapper=wrapper_path)
+ wrapper = _WRAPPER.format(env=env, exe=exe)
+
+ ## write our scripts
+ _write_script(launcher_path, launcher)
+ _write_script(wrapper_path, wrapper)
diff --git a/install/modulefile.py b/install/modulefile.py
new file mode 100644
index 000000000..0c222bf96
--- /dev/null
+++ b/install/modulefile.py
@@ -0,0 +1,46 @@
+#!/usr/bin/env python3
+
+## eic_container: Argonne Universal EIC Container
+
+'''
+Install modulefile for this container.
+
+Authors:
+ - Whitney Armstrong <warmstrong@anl.gov>
+ - Sylvester Joosten <sjoosten@anl.gov>
+'''
+
+import os
+
+## Generic module file
+_MODULEFILE='''#%Module1.0#####################################################################
+##
+## for {name} {version}
+##
+proc ModulesHelp {{ }} {{
+ puts stderr "This module sets up the environment for the {name} container"
+}}
+module-whatis "{name} {version}"
+
+# For Tcl script use only
+set version 4.1.4
+
+prepend-path PATH {bindir}
+'''
+
+def make_modulefile(project, version, moduledir, bindir):
+ '''Configure and install a modulefile for this project.
+
+ Arguments:
+ - project: project name
+ - version: project version
+ - moduledir: root modulefile directory
+ - bindir: where executables for this project are located
+ '''
+
+ ## create our modulefile
+ content = _MODULEFILE.format(name=project, version=version, bindir=bindir)
+ fname = '{}/{}'.format(moduledir, version)
+ print(' - creating', fname)
+ with open(fname, 'w') as file:
+ file.write(content)
diff --git a/install/util.py b/install/util.py
new file mode 100644
index 000000000..47cb594a6
--- /dev/null
+++ b/install/util.py
@@ -0,0 +1,38 @@
+#!/usr/bin/env python3
+
+## eic_container: Argonne Universal EIC Container
+
+'''
+Utility functions for this container
+
+Authors:
+ - Whitney Armstrong <warmstrong@anl.gov>
+ - Sylvester Joosten <sjoosten@anl.gov>
+'''
+
+import os
+
+class InvalidArgumentError(Exception):
+ pass
+
+def smart_mkdir(dir):
+ '''functions as mkdir -p, with a write-check.
+
+ Raises an exception if the directory is not writeable.
+ '''
+ if not os.path.exists(dir):
+ try:
+ os.makedirs(dir)
+ except Exception as e:
+ print('ERROR: unable to create directory', dir)
+ raise e
+ if not os.access(dir, os.W_OK):
+ print('ERROR: We do not have the write privileges to', dir)
+ raise InvalidArgumentError()
+
+def project_version():
+ '''Return the project version based on the current git branch/tag.'''
+ ## Shell command to get the current git version
+ git_version_cmd = 'git symbolic-ref -q --short HEAD || git describe --tags --exact-match'
+ ## Strip will remove the leading \n character
+ return os.popen(git_version_cmd).read().strip()
--
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