Distributed Development, Centralised Delivery - SAGrid Jenkins + CVMFS

Jenkins + CVMFS :
Distributed Development,
Centralised Delivery
Bruce Becker | bbecker@csir.co.za
Coordinator: SAGrid
SANREN, Meraka Institute, CSIR
Stefanus Riekert | RiekertSJPK@ufs.ac.za
HPC Application Engineer
University of the Free State

Bruce Becker: Coordinator, SAGrid | bbecker@csir.co.za | http://www.sagrid.ac.za
Outline
● What users want
● SAGrid VO – a catch-all VO with many applications
● Problem statements:
● Problem 1: ”the usual problem” – maintaining
applications in a distributed computing environment
● Problem 2: ”Another usual problem” - maintaining a
complex application inventory
● General solution : CVMFS + Jenkins
● Some specifics of SAGrid CI platform
● Outlook

SAGrid as a catch-all VO
● The South African National Grid operates a
catch-all VO which all South African researchers
can use to access computing and data
resources.
● SAGrid VO is not a domain-specific VO, so
● several widely-varying uses for the applications
supported by this VO
● Applications requested by users or communities
themselves

What users want
Amazing infrastructure
Some users want highly
varied, modular
application selection
Vertically integrated
Highly specialised
applications
Highly trained supportHighly trained support

What users get sometimes

The problem (1) -
”the usual problem”
● Software distribution was done mostly by hand”:
● Someone from the ops team develops script to install the application
● Apps installed via job submission
● Tags applied via script or by the job itself
● Issues:
● Major overhead of work
● Inconsistent installation procedures between applications and sites
● Bottleneck in porting applications (has to be done by someone in the
VO)
● Duplication of effort, especially in dependencies of applications
● Difficult to manage application lifecycles

The problem (2) -
what about the community ?
● Managing the inventory in a catch-all VO can be complex
when there are many applications
● Prioritising porting requests depends on the knowledge
of the export porting the application
●
Can lead to major delays in porting and deploying applications
● However, a user or community usually has an expert who
knows how to tune, port and configure the application
properly, as well as dependencies
●
Usually, ”they” have to conform to ”us” - learn grid tools and
terminology, etc

Problem (3) :
Changes to the playing field
● New middleware stacks
● New architectures – GPGPU, ARM

Questions to answer
● How do we lower the barrier to entry to the grid or
cloud infrastructure ?
● How can the application expert prove to the resource
provider that the application will actually run on the
execution environment of the site ?
● How can we manage the lifecycle of applications
across multiple versions, architectures, configurations ?
● How can we ensure that once applications are
”certified”, they are actually available on as many sites
as possible ?

General Solution:
Jenkins + CVMFS
● The issues outlined are ”typical” in a large
software project
● Usually solved by judicious use of Continuous
Integration system
● Once applications have been ”ported”, put them
into a trusted repository
● Previously – built RPMs, but required site-
admin intervention
● One-time configuration with CVMFS

First, some changes
● Distribute the effort, centralise the tools
● Move repository from ”closed” SVN repo
– https://ops.sagrid.ac.za/trac/svn/repo
● to git
– https://github.com/SAGridOps/SoftwareInstallation
● Don't have to give write access to a single repo, instead
accept pull requests
● Take advantage of all the Github infrastructure
● Expand possible contributors to those ”outside” the
infrastructure
● Recognise individuals' contribution

Recognise individuals...

Decentralise the team

Collaborate with code

Let the robots do the work
● Define what we want to deploy – let the experts
take care of how to deploy
● DevOps paradigm – same review/tag/release
mechanisms on operations code as we have for
scientific applications
● Teach a marketable skill
● Allow specialisation
● Enable remote management of complex services
● Ensure that published methodology is adopted
methodology

Quality Control and feedback
● Ensure that
requested
applications are
included in the repo
● Provide testing and
QA infrastructure
● Self-serve to users

The CI environment
● Jenkins is extremely flexible... can do almost anything
● AuthN/AuthZ
● Currently using Github Oauth
● Take advantage of future Identity Federation
● We wanted to simulate different execution
environments
● Already in production
● Planned for future
● Track and re-use depedendencies

Matrix-based builds
● Independent different builds and build statuses for
different configurations:
● Application name
● Version
● OS
● Architecture
● … can add specific tuning configurations...
● We can see exactly what's broken where – build
more resilient integration code.

Typical workflow
Testingmatrix
Defines relevant
tests in Jenkins
Writes code to
pass required tests
Dev/Stage env.Application
developer
Infrastructure
expert
Reads description
of execution environment tests
Promote a build
to CVMFS

Dependency management
simple case
● Common problem with applications :
need a specific version of a
compiler
● Compiling the compiler can itself be
tricky...
● Jenkins tests the full dependency
chain necessary

Real-world application
● GADGET –
astrophysics
hydrodynamic
simulations
● Many (levels of)
dependencies

Public Application Dashboard

Authenticated view

Generic build script
# GADGET requires HDF5 FFTW2 ZLIB and
openmpi
module add ci
module add fftw/2.1.5
module add hdf5
module add openmpi
module add gsl
# GADGET requires HDF5 FFTW2 ZLIB and
openmpi
module add ci
module add fftw/2.1.5
module add hdf5
module add openmpi
module add gsl
rm rf $FFTW_DIR
tar xvfz /repo/$SITE/$OS/$ARCH/fftw/$FFTW_VERSION/build.tar.gz C /
rm rf $HDF5_DIR
tar xvfz /repo/$SITE/$OS/$ARCH/hdf5/$HDF5_VERSION/build.tar.gz C /
rm rf $OPENMPI_DIR
tar xvfz /repo/$SITE/$OS/$ARCH/openmpi/$OPENMPI_VERSION/build.tar.gz C /
rm rf $GSL_DIR
tar xvfz /repo/$SITE/$OS/$ARCH/gsl/$GSL_VERSION/build.tar.gz C /
rm rf $FFTW_DIR
tar xvfz /repo/$SITE/$OS/$ARCH/fftw/$FFTW_VERSION/build.tar.gz C /
rm rf $HDF5_DIR
tar xvfz /repo/$SITE/$OS/$ARCH/hdf5/$HDF5_VERSION/build.tar.gz C /
rm rf $OPENMPI_DIR
tar xvfz /repo/$SITE/$OS/$ARCH/openmpi/$OPENMPI_VERSION/build.tar.gz C /
rm rf $GSL_DIR
tar xvfz /repo/$SITE/$OS/$ARCH/gsl/$GSL_VERSION/build.tar.gz C /
Set up the
environment
Clean build, retrieve
dependency artifacts

Generic build script
make install DESTDIR=$WORKSPACE/build
mkdir p $REPO_DIR
rm rf $REPO_DIR/*
tar cvzf $REPO_DIR/build.tar.gz C
$WORKSPACE/build apprepo
make install DESTDIR=$WORKSPACE/build
mkdir p $REPO_DIR
rm rf $REPO_DIR/*
tar cvzf $REPO_DIR/build.tar.gz C
$WORKSPACE/build apprepo
Actually build...
Create the artifact
cat <<MODULE_FILE
#%Module1.0
## $NAME modulefile
##
proc ModulesHelp { } {
    puts stderr "       This module does nothing but alert the user"
    puts stderr "       that the [moduleinfo name] module is not available"
}
preqreq("gsl","fftw/2.1.5","hdf5")
modulewhatis   "$NAME $VERSION."
setenv       GSL_VERSION       $VERSION
setenv       GSL_DIR           /apprepo/$::env(SITE)/$::env(OS)/$::env(ARCH)/$NAME/$VERSION
prependpath LD_LIBRARY_PATH   $::env(GSL_DIR)/lib
MODULE_FILE
) > modules/$VERSION
cat <<MODULE_FILE
#%Module1.0
## $NAME modulefile
##
proc ModulesHelp { } {
    puts stderr "       This module does nothing but alert the user"
    puts stderr "       that the [moduleinfo name] module is not available"
}
preqreq("gsl","fftw/2.1.5","hdf5")
modulewhatis   "$NAME $VERSION."
setenv       GSL_VERSION       $VERSION
setenv       GSL_DIR           /apprepo/$::env(SITE)/$::env(OS)/$::env(ARCH)/$NAME/$VERSION
prependpath LD_LIBRARY_PATH   $::env(GSL_DIR)/lib
MODULE_FILE
) > modules/$VERSION
Create the modulefile

So, it works ! … almost
Next steps
● We have an open, collaborative, low-barrier platform for researchers
to bring applications to the grid
● Small technical tasks :
● Implement promoted builds mechanism to populate sagrid.ac.za CVMFS repo
● Implement SAML AuthN, integrate IdF
● Probes to check that CVMFS is mounted on sites (?)
● Operating in ”stealth mode” at the moment – not advertising, but open
to anyone who is interested to collect feedback
● Addressing specific user communities to test drive the system:
● Machine learning astro applications (rapid prototyping)
● Bioinformatics application suites (complex ecosystem)
● Present next phase of the project in November in Cape Town – move
to production

Distributed Development, Centralised Delivery - SAGrid Jenkins + CVMFS

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