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EasyBuild

Fred Hutch Researchers

What they want:

  1. reliable systems and hardware
  2. reliable software

Reliable Systems & Hardware

Out of scope (call us)

What about software?

  • current versions built consistently and quickly
  • software and version accounting for all jobs
  • reliable citation sources and re-producibility

How do we do it?

./configure; make; sudo make install

Download tarball, check required packages, install them, build, re-check required packages, make test, make install, build modulefile.

Then repeat:

  • for the next package
  • exactly for new versions of this package

Reliable Software

EasyBuild: building software with ease

Features

  • multiple versions and builds of many software packages
  • automated package dependency system
  • re-producible software package builds
  • automated environment modules managment
  • curated toolchains

EasyBuild Benefits

  • 1058 Software Packages (6600+ package versions)
  • 54 toolchains
  • 150+ contributors
  • 87% of our existing software stack out of the box

EasyBuild Understanding

  • Terms & Components
  • Building software
  • Fred Hutch Implementation
  • Community and Collaboration

EasyBuild Terms

  • environment modules ($ module load R)
  • easyconfigs (build recipe)
  • toolchains GCC, Intel, Clang/LLVM, etc. + libs

Environment Modules

Environment Module Overview

  • sets and unsets environment variables
  • avoids conflicts between software packages
  • provides dependency resolution
  • provides administrative hooks

Use Environment Modules...

  • simple, end user-driven, scriptable
  • administrative hooks
  • greatly simplifies tangled, gnarly environments
  • use Lmod if you can

... with EasyBuild!

  • automated modulefile creation
  • managment of module hierarchy
  • don't write modules, just use them

Module Dependency Example

Module List

Shell Env Example

Module List

Easyconfigs

Easyconfigs

Easyconfigs...

  • are text files (python)
  • define a software package + version + toolchain
  • can define extentions/modules/libraries
  • can define options and environment variables

Easyconfig Example

!python
name = 'git'
version = '2.8.0'
homepage = 'http://git-scm.com/'
description = """Git is a free and open source distributed version control system designed
to handle everything from small to very large projects with speed and efficiency."""
toolchain = {'name': 'foss', 'version': '2016a'}
sources = ['v%(version)s.tar.gz']
source_urls = ['https://github.com/git/git/archive']
dependencies = [
('cURL', '7.47.0'),
('expat', '2.1.0'),
('gettext', '0.19.7'),
('Perl', '5.22.1', '-bare'),
]

Toolchains

What are toolchains?

  • are defined in easyconfig files
  • are a collection of compilers and support libraries
  • provide consistent builds for module stacks
  • aid in re-producibility
  • are a great place for optimization fan-out

Toolchain example

GCCcore/4.9.3
binutils/2.2.5-GCCcore-4.9.3
GCC/4.9.3-2.25
numactl/2.0.11-GCC-4.9.3-2.25
hwloc/1.11.2-GCC-4.9.2-2.25
OpenMPI/1.10.2-GCC-4.9.3-2.25
OpenBLAS/0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0
gompi/2016a
FFTW/3.3.4-gompi-2016a
ScaLAPACK/2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0

Toolchains and performance

rbench on R-3.3.0:

  • 179 secs R compiled on Ubuntu 14.04
  • 83 secs (54% faster) EasyBuild foss-2016a R
  • 91 secs (49% faster) EasyBuild intel-2016a R
  • 86 secs (52% faster) Microsoft R (yes, on linux)

Re-producibility

  • easyconfig is package, version, toolchain
  • toolchain is compiler, base libraries
  • environment is complex, Modules and Easybuild manage it
  • easyconfigs will build and run the same for everyone
  • and everywhere (new OS, toolchain, etc.)

EasyBuilding Software

Prerequisites

  • Python
  • Environment Modules

Bootstrapping EasyBuild

!bash
$ curl -O https://raw.github.../bootstrap_eb.py
$ python bootstrap_eb.py $EASYBUILD_PREFIX
$ module use $EASYBUILD_PREFIX/modules/all
$ module load EasyBuild

build something

Let's build something

EasyBuild @FredHutch

Fred Hutch goals

  • centralized, shared packages
  • non-root, multiple, individual builders in a group
  • fast release of new versions
  • "fat" R with up-to-date libraries optimized

Executive decisions

Toolchains:

  • foss-n: Free Open Source Software - GCC, OpenBLAS, ScaLAPACK
  • intel-n: Intel C & Fortran, Intel Math Kernel Libraries

Deployment:

  • universal read-only NFS export
  • common EasyBuild hierarchy

Engineering Decisions

  • NFS mounted /app on all systems (nfs ro)
  • EasyBuild PREFIX owned by POSIX group
  • EASYBUILD ENV VARS to support group building
  • EasyBuild is easy-built; everything in /app
  • EasyBuilds done on a build host (nfs rw)

EasyBuild @FredHutch Metrics

  • 218/757 software packages/versions built (add pkg list)
  • 86% built in 4 months
  • 87% of our old software stack re-built
  • 4 SysAdmins independently building consistent packages

FredHutch Software

Python, HDF5, R, Perl, netCDF, SAMtools, BWA, SRA-Toolkit, R Bioconductor, MUSCLE, GATK, fastqc, Cufflinks, Bowtie, BEAST, WHAM,TopHat, svtoolkit, STAR, SPLITREAD, samblaster, RSEM, Rosetta, Queue, PyMOL, ngsShort, mrsFAST, MEME, matplotlib, lumpy, GROMACS, ClustalW2, bioperl, biopython, BEDTools, BEDOps, bcl2fastq, bcftools, bamUtils, BamTools

What's the catch?

  • adapting existing easyconfigs can be easy
  • writing new easyconfigs is less easy
  • existing community accepts all easyconfigs
  • proliferation of package matrix
  • hard to know where to start

FredHutch Next Step Goals

  • reduce EasyBuild ramp-up time
  • build EB life-sciences community
  • provide new versions quickly/publicly
  • share tools and code
  • reduce complexity of writing new easyconfigs

Next Step Details

  • provide 200+ life sciences packages in an hour
  • help implement expanded toolchains/package clusters
  • publish easyconfigs upstream
  • publish life-sciences github repo
  • published detailed implementation example
  • take ownership of R easyconfig
  • implement EasyBuild in container (docker/LXD)

Contact

If you have any questions:

bmcgough@fredhutch.org

https://fredhutch.github.io/easybuild-life-sciences/EasyBuild_Presentation.html