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Install Your Scientific Software Stack Easily with Spack

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Install Your Scientific Software Stack Easily with Spack Install your scientific software stack easily with Spack Les mardis du developpement´ technologique Florent Pruvost (SED) Outline 1. Context 2. Features overview 3. In practice 4. Some feedback Florent Pruvost (SED) – Install your scientific software stack easily with Spack 2 1 Context Florent Pruvost (SED) – Install your scientific software stack easily with Spack 3 A scientific software stack • modular, several languages, different build systems Application Linear Algebra Optimized Kernels Graph Processing Runtime Systems Paradigms Miscellaneous • difficulty to be an expert in all the chain Florent Pruvost (SED) – Install your scientific software stack easily with Spack 4 An example: Aerosol • a finite elements library developed by the Inria teams Cagire and Cardamom Aerosol PaMPA PaStiX HDF5 XML2 PT-SCOTCH StarPU BLAS/LAPACK MPI CUDA Florent Pruvost (SED) – Install your scientific software stack easily with Spack 5 Constraints • R&D ) develop prototypes - test many different builds • computing/data intensive application ) HPC environment - different machines, OSes, environments - remote connection, not administrator • performances ) highly tuned installation - well chosen components - specific build options • reproducibility - control the environment - characterize what influence the build Florent Pruvost (SED) – Install your scientific software stack easily with Spack 6 Wish list • a simple process to install a default version • a flexible way to choose build variants - choose compiler, software versions - enable components, e.g. MPI : yes/no - build options, e.g. --enable-debug • be able to install it on a remote machine (supercomputer) - no root permissions - no internet access (not necessarily) • be able to reproduce experiments - not destructive installation - control the environment and thirdparty libraries Florent Pruvost (SED) – Install your scientific software stack easily with Spack 7 Traditional tools: binary package managers • dpkg (APT), RPM, pacman, etc • designed to manage a single stack • install one version of each package in a single prefix (/usr) - root permission required • seamless upgrades to a stable, well tested stack Florent Pruvost (SED) – Install your scientific software stack easily with Spack 8 Traditional tools: port systems • BSD Ports, portage, Macports, Homebrew, Gentoo, etc • minimal support for builds parameterized by compilers, dependency versions Florent Pruvost (SED) – Install your scientific software stack easily with Spack 9 Traditional tools: virtual machines and Linux containers • Docker, etc • containers allow users to build environments for different applications • does not solve the build problem (someone has to build the image) • performance, security, and upgrade issues prevent widespread HPC deployment Florent Pruvost (SED) – Install your scientific software stack easily with Spack 10 Tools designed for scientific applications a short list to focus on: Nix/Guix, Easybuild, Spack • Common features: - build from sources - own directory structure - hash parametrized by versions, dependencies, etc - no need to be root to install packages - usefull available packages: MPI, BLAS/LAPACK, FFTW, etc • Differences: - robustness VS. flexibility - maturity - languages and technical details Florent Pruvost (SED) – Install your scientific software stack easily with Spack 11 Nix/Guix: functional languages (Guile) • pros: - very precise dependency tracking - cryptographic hashes determine the exact build and run-time dependencies - safe upgrade - nice for reproducibility • cons: - administrator rights required to install Nix/Guix - limited to opensource softwares: no Intel, CUDA - deal with combinatorial builds? - multi-compiler and version support? - virtual dependency? - syntax for parametrization? Florent Pruvost (SED) – Install your scientific software stack easily with Spack 12 Easybuild: Python • pros: - designed for installation on HPC systems - support for proprietary software like Intel and CUDA - can reuse what is already installed, cf. dummy toolchain • cons: - cannot deal with combinatorial builds - requires a file per configuration of a stack - limited command line interface Florent Pruvost (SED) – Install your scientific software stack easily with Spack 13 Spack: Python 2 • pros: - deals with combinatorial builds - a couple of packages = thousands of builds available - nice command line syntax to tune the stack parameters - can reuse what is already installed, cf. config. files - no need to be root - no need to have internet access if tarballs are available locally • cons: - Spack is currently alpha software (young project) - package parameters changed a lot - new nice features = re-write packages - all parameters that affect a build are not controlled internally (external compilers and libraries) = all builds are not safe Florent Pruvost (SED) – Install your scientific software stack easily with Spack 14 2 Features overview Florent Pruvost (SED) – Install your scientific software stack easily with Spack 15 Overview • object-oriented Python 2 • Unix systems - Windows is not an OS for HPC • ∼ 500 available packages • opensource, opencommunity (github - pull request) - Feb 10, 2013 - Today - mainly developed by T. Gamblin and friends from LLNL - 95 contributors, 154 forks - 1 release every 6 months Florent Pruvost (SED) – Install your scientific software stack easily with Spack 16 Overview Florent Pruvost (SED) – Install your scientific software stack easily with Spack 16 Handles combinatorial software complexity • each unique dependency graph is a unique configuration • each configuration installed in a unique directory • hash of DAG is appended to prefix • installed packages automatically find dependencies - Spack embeds RPATHs in binaries (compiler wrappers) - no need to use modules or set LD LIBRARY PATH - things work the way you built them Florent Pruvost (SED) – Install your scientific software stack easily with Spack 17 Provides a spec syntax to describe customized DAG configurations • each expression is a spec for a particular configuration - each clause adds a constraint to the spec - constraints are optional – specify only what you need - customize install on the command line! • syntax abstracts details in the common case - makes parameterization by version, compiler, and options easy when necessary Florent Pruvost (SED) – Install your scientific software stack easily with Spack 18 Spack Specs can constrain versions of dependencies • Spack ensures one configuration of each library per DAG - consistency - user does not need to know DAG structure; only the dependency names • Spack can ensure that builds use the same compiler, or you can mix - working on ensuring ABI compatibility when compilers are mixed Florent Pruvost (SED) – Install your scientific software stack easily with Spack 19 Spack handles API-incompatibility • mpi is a virtual dependency • install the same package built with two different MPI implementations: • let Spack choose MPI version, as long as it provides MPI-2 interface: Florent Pruvost (SED) – Install your scientific software stack easily with Spack 20 Spack packages are simple Python scripts Florent Pruvost (SED) – Install your scientific software stack easily with Spack 21 Dependencies may be optional • versions can be tarballs or VCS repositories (git, svn, hg) • the user can define named variants: • and use them to install: $ spack install hwloc +cuda $ spack install hwloc -cuda • dependencies may be optional according to other conditions: - e.g. gcc dependency on mpc from 4.5 on: Florent Pruvost (SED) – Install your scientific software stack easily with Spack 22 Concretization fills in missing configuration details when the user is not explicit Florent Pruvost (SED) – Install your scientific software stack easily with Spack 23 Default behaviours is configurable • configure your preferred: - compilers, versions, depends on, variants • directly in the package, e.g. prefers Python 2.7.11 • or for specific machine/environment, edit ∼/.spack/packages.yaml Florent Pruvost (SED) – Install your scientific software stack easily with Spack 24 Spack builds in isolated environment • forking build process isolates environment for each build • compiler wrappers add include, lib, and RPATH flags - ensure that dependencies are found automatically Florent Pruvost (SED) – Install your scientific software stack easily with Spack 25 3 In practice Florent Pruvost (SED) – Install your scientific software stack easily with Spack 26 Setup • entry point on github: https://github.com/LLNL/spack • read the doc, at least Getting started: http://spack.readthedocs.io/en/latest/index.html $ sudo apt install python $ git clone https://github.com/LLNL/spack.git $ . spack/share/spack/setup-env.sh $ spack install gcc Florent Pruvost (SED) – Install your scientific software stack easily with Spack 27 Check compilers • check compilers found automatically $ spack compiler list • information about a compiler $ spack compiler info gcc Florent Pruvost (SED) – Install your scientific software stack easily with Spack 28 Configure compilers • add compilers installed in some exotic paths $ spack compiler find /home/jdoe/intel/bin • remove non desired compilers $ spack compiler rm clang • compiler configuration can be edited by hand $ vi ~/.spack/compilers.yaml Florent Pruvost (SED) – Install your scientific software stack easily with Spack 29 Install • list available packages $ spack list • information about a package $ spack info hwloc • check the concrete stack to be installed $ spack spec hwloc • install a package $ spack install [-v] hwloc
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