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Managing HPC Software Complexity with Spack Full-day Tutorial 1st Workshop on NSF and DOE High Performance Computing Tools July 10, 2019 The most recent version of these slides can be found at: https://spack.readthedocs.io/en/latest/tutorial.html Eugene, Oregon LLNL-PRES-806064 This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344. github.com/spack/spack Lawrence Livermore National Security, LLC Tutorial Materials Materials: Download the latest version of slides and handouts at: bit.ly/spack-tutorial Slides and hands-on scripts are in the “Tutorial” Section of the docs. § Spack GitHub repository: http://github.com/spack/spack § Spack Documentation: http://spack.readthedocs.io Tweet at us! @spackpm 2 LLNL-PRES-806064 github.com/spack/spack Tutorial Presenters Todd Gamblin Greg Becker 3 LLNL-PRES-806064 github.com/spack/spack Software complexity in HPC is growing glm suite-sparse yaml-cpp metis cmake ncurses parmetis pkgconf nalu hwloc libxml2 xz bzip2 openssl boost trilinos superlu openblas netlib-scalapack mumps openmpi zlib netcdf hdf5 matio m4 libsigsegv parallel-netcdf Nalu: Generalized Unstructured Massively Parallel Low Mach Flow 4 LLNL-PRES-806064 github.com/spack/spack Software complexity in HPC is growing adol-c automake autoconf perl glm suite-sparse yaml-cpp metis cmake ncurses gmp libtool parmetis pkgconf m4 libsigsegv nalu hwloc libxml2 xz bzip2 openssl p4est pkgconf boost hwloc libxml2 trilinos superlu openblas xz netlib-scalapack netcdf-cxx netcdf mumps openmpi zlib netcdf hdf5 nanoflann matio m4 libsigsegv parallel-netcdf matio hdf5 Nalu: Generalized Unstructured Massively Parallel Low Mach Flow sundials glm netlib-scalapack mumps openmpi trilinos hypre openblas gdbm superlu-dist parmetis sqlite readline zlib petsc python dealii slepc ncurses arpack-ng openssl metis cmake gmsh oce suite-sparse tetgen intel-tbb netgen bzip2 assimp boost gsl muparser dealii: C++ Finite Element Library 5 LLNL-PRES-806064 github.com/spack/spack Software complexity in HPC is growing r-randomforest glm suite-sparse yaml-cpp r-labeling metis cmake ncurses parmetis pkgconf nalu r-lazyeval r-munsell hwloc libxml2 xz r-colorspace bzip2 openssl r-rcolorbrewer boost r-viridislite trilinos superlu openblas r-dichromat netlib-scalapack r-scales mumps r-tibble r-assertthat openmpi zlib netcdf hdf5 r-rlang r-gtable matio m4 libsigsegv parallel-netcdf r-ggplot2 r-plyr r-reshape2 r-rcpp r-modelmetrics Nalu: Generalized Unstructured Massively Parallel Low Mach Flow freetype bzip2 gperf r-r6 r-minqa fontconfig r-caret r-nloptr r-digest cairo libxml2 r-rcppeigen pixman r-lme4 harfbuzz libpng r-praise r-testthat pango adol-c automake sed xz gobject-introspection autoconf perl glib gettext r-mgcv r-crayon tar gmp libtool m4 libsigsegv libffi r-nlme p4est pkgconf libtiff hwloc libxml2 r-pbkrtest help2man xz r-mass zlib r-car r-foreach r-iterators flex netcdf-cxx netcdf r-sparsem curl r python ncurses nanoflann pkgconf openssl readline matio r-quantreg r-matrixmodels pcre hdf5 jdk libjpeg-turbo r-matrix cmake sundials r-lattice icu4c sqlite font-util r-adabag r-glmnet glm tk tcl nasm libxau gdbm xproto netlib-scalapack r-cubist r-mlbench libxdmcp openmpi xextproto mumps r-magrittr perl libpthread-stubs trilinos xtrans r-data-table libxcb util-macros hypre r-stringr xcb-proto r-xgboost libx11 inputproto r-rminer r-e1071 r-class r-codetools openblas kbproto gdbm bison r-kknn r-igraph r-irlba r-stringi r-rpart automake superlu-dist parmetis sqlite autoconf readline r-nnet zlib r-pkgconfig petsc gmp libtool m4 libsigsegv python dealii slepc ncurses arpack-ng openssl r-mda cmake metis r-kernlab gmsh oce suite-sparse r-strucchange r-zoo tetgen r-sandwich intel-tbb r-party netgen r-survival bzip2 r-multcomp r-th-data assimp r-plotrix boost r-coin r-mvtnorm r-modeltools gsl r-pls muparser dealii: C++ Finite Element Library R Miner: R Data Mining Library 6 LLNL-PRES-806064 github.com/spack/spack The complexity of the exascale ecosystem threatens productivity. 5+ target architectures/platforms 15+ applications x 80+ software packages x Xeon Power KNL NVIDIA ARM Laptops? Up to 7 compilers 10+ Programming MoDels 2-3 versions of each package x Intel GCC Clang XL x OpenMPI MPICH MVAPICH OpenMP CUDA x PGI Cray NAG OpenACC Dharma Legion RAJA Kokkos + external DepenDencies = up to 1,260,000 combinations! § Every application has its own stack of dependencies. § Developers, users, and facilities dedicate (many) FTEs to building & porting. § Often trade reuse and usability for performance. We must make it easier to rely on others’ software! 7 LLNL-PRES-806064 github.com/spack/spack What is the “production” environment for HPC? § Someone’s home directory? § LLNL? LANL? Sandia? ANL? LBL? TACC? — Environments at large-scale sites are very different. § Which MPI implementation? § Which compiler? § Which dependencies? § Which versions of dependencies? — Many applications require specific dependency versions. Real answer: there isn’t a single production environment or a standard way to build. Reusing someone else’s software is HARD. 8 LLNL-PRES-806064 github.com/spack/spack Spack is a flexible package manager for HPC § How to install Spack: $ git clone https://github.com/spack/spack $ . spack/share/spack/setup-env.sh § How to install a package: $ spack install hdf5 § HDF5 and its dependencies are installed within the Spack directory. § Unlike typical package managers, Spack can also install Get Spack! many variants of the same build. — Different compilers http://github.com/spack/spack — Different MPI implementations — Different build options @spackpm 9 LLNL-PRES-806064 github.com/spack/spack Who can use Spack? People who want to use or distribute software for HPC! 1. End Users of HPC Software — Install and run HPC applications and tools 2. HPC Application Teams — Manage third-party dependency libraries 3. Package Developers — People who want to package their own software for distribution 4. User support teams at HPC Centers — People who deploy software for users at large HPC sites 10 LLNL-PRES-806064 github.com/spack/spack Spack is used worldwide! Over 3,200 software packages Over 1,100 monthly active users (on docs site) Over 400 contributors from labs, academia, industry Plot shows sessions on spack.readthedocs.io for one month 11 LLNL-PRES-806064 github.com/spack/spack Active Users on the spack.readthedocs.io 12 LLNL-PRES-806064 github.com/spack/spack GitHub Stars: Spack and some other popular HPC projects Stars over time Stars per day (same data, 60-day window) 13 LLNL-PRES-806064 github.com/spack/spack Spack is being used on many of the top HPC systems § At HPC sites for software stack+ modules Summit (ORNL) — Reduced Summit deploy time from 2 weeks to 12 hrs. Sierra (LLNL) — EPFL deploys its software stack with Jenkins + Spack — NERSC, LLNL, ANL, other US DOE sites — SJTU in China § Within ECP as part of their software release process Cori (NERSC) — ECP-wide software distribution — SDK workflows SuperMUC-NG (LRZ) § Within High Energy Physics (HEP) community — HEP (Fermi, CERN) have contributed many features to support their workflow 富岳 Fugaku, formerly Post-K § Many others (RIKEN) 14 LLNL-PRES-806064 github.com/spack/spack Contributions to Spack continue to grow! § In November 2015, LLNL provided most of the contributions to Spack § Since then, we’ve gone from 300 to over 3,200 packages § Most packages are from external contributors! § Many contributions in core, as well. § We are committed to sustaining Spack’s open source ecosystem! 15 LLNL-PRES-806064 github.com/spack/spack Spack v0.12.1 is the latest release § New features: 1. Spack environments (covered today) 2. spack.yaml and spack.lock files for tracking dependencies (covered today) 3. Custom configurations via command line (covered today) 4. Better support for linking Python packages into view directories (pip in views) 5. Support for uploading build logs to CDash 6. Packages have more control over compiler flags via flag handlers 7. Better support for module file generation 8. Better support for Intel compilers, Intel MPI, etc. 9. Many performance improvements, improved startup time § Spack is now permissively licensed under Apache-2.0 or MIT — previously LGPL § Over 2,900 packages (800 added since last year) — This is from November; over 3,200 in latest develop branch 16 LLNL-PRES-806064 github.com/spack/spack Related Work Spack is not the first tool to automate builds — Inspired by copious prior work 1. “Functional” Package Managers — Nix https://nixos.org/ — GNU Guix https://www.gnu.org/s/guix/ 2. Build-from-source Package Managers — Homebrew http://brew.sh — MacPorts https://www.macports.org Other tools in the HPC Space: § Easybuild http://hpcugent.github.io/easybuild/ — An installation tool for HPC — Focused on HPC system administrators – different package model from Spack — Relies on a fixed software stack – harder to tweak recipes for experimentation § Conda https://conda.io — Very popular binary package manager for data science — Not targeted at HPC; generally unoptimized binaries 17 LLNL-PRES-806064 github.com/spack/spack What’s on the road map? § Spack Stacks: better support for facility deployment — Extension of environments to better support facility workflows — Ability to easily specify full facility software stack and module configuration — Build all of it at once with a single command! § Better CI Support — GitLab Integration with environments § Architecture-specific binaries — Better provenance for builds — Better support for matching optimized binary packages to machines § Better concretization — Spack’s dependency resolution can hit snags — We need better support to enable features above More on the Spack Road Map tomorrow Morning! 18 LLNL-PRES-806064 github.com/spack/spack Tutorial Overview (times are estimates) 1. For everyone: Welcome & Overview 9:15 - 9:30 2. For everyone: Basics of Building and Linking 9:30 - 9:45 3.
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  • With Yocto/Openembedded

    With Yocto/Openembedded

    PORTING NEW CODE TO RISC-V WITH YOCTO/OPENEMBEDDED Martin Maas ([email protected]) 1st RISC-V Workshop, January 15, 2015 Monterey, CA WHY WE NEED A LINUX DISTRIBUTION • To build an application for RISC-V, you need to: – Download and build the RISC-V toolchain + Linux – Download, patch and build application + dependencies – Create an image and run it in QEMU or on hardware • Problems with this approach: – Error-prone: Easy to corrupt FS or get a step wrong – Reproducibility: Others can’t easily reuse your work – Rigidity: If a dependency changes, need to do it all over • We need a Linux distribution! – Automatic build process with dependency tracking – Ability to distribute binary packages and SDKs 2 RISCV-POKY: A PORT OF THE YOCTO PROJECT • We ported the Yocto Project – Official Linux Foundation Workgroup, supported by a large number of industry partners – Part I: Collection of hundreds of recipes (scripts that describe how to build packages for different platforms), shared with OpenEmbedded project – Part II: Bitbake, a parallel build system that takes recipes and fetches, patches, cross-compiles and produces packages (RPM/DEB), images, SDKs, etc. • Focus on build process and customizability 3 GETTING STARTED WITH RISCV-POKY • Let’s build a full Linux system including the GCC toolchain, Linux, QEMU + a large set of packages (including bash, ssh, python, perl, apt, wget,…) • Step I: Clone riscv-poky: git clone [email protected]:ucb-bar/riscv-poky.git • Step II: Set up the build system: source oe-init-build-env • Step III: Build an image (may