Spack | zh - HackMD

--- title: Spack | zh tags: Guide, TWNIA3, TW GA: --- <div style="text-align: right">更新日期：2024/11/10</div> # Spack [TOC] ## 簡介 [Spack](https://spack.io/)是由[LLNL](https://www.llnl.gov/)發展的一個套件管理工具，處理安裝各種HPC領域常用的編譯器、函式庫、科學計算軟體編譯設定與相依性，除了LLNL本身的維護外，亦由世界各大HPC單位組織和廠商支持贊助，目前累計各式軟體、函式庫版本超過6800。國網中心的計算主機系統的用戶來自許多不同領域，執行各式各樣的計算工作，即使是使用相同的軟體，也可能有不同的設定需求，囿於有限的人力資源，無法即時提供完整的軟體安裝協助，因此可依照個人需求選項，自行安裝設定軟體的Spack對HPC用戶就顯得相當實用。 ## 設定使用 ### 安裝與設定 1. 登入主機執行git取得spack [demo_user@lgn302 ~]$ git clone -c feature.manyFiles=true https://github.com/spack/spack.git ``` Cloning into 'spack'... remote: Enumerating objects: 507890, done. remote: Counting objects: 100% (3199/3199), done. remote: Compressing objects: 100% (2008/2008), done. remote: Total 507890 (delta 547), reused 1888 (delta 405), pack-reused 504691 Receiving objects: 100% (507890/507890), 169.26 MiB | 22.69 MiB/s, done. Resolving deltas: 100% (238331/238331), done. Updating files: 100% (11129/11129), done. ``` :::info git於目前目錄建立一個名稱為spack的目錄 ::: 2. 設定spack環境變數 [demo_user@lgn302 ~]$ . ~/spack/share/spack/setup-env.sh 或 [demo_user@lgn302 ~]$ source ~/spack/share/spack/setup-env.sh :::info 此為設定spack相關環境變數，正常情況不會有任何輸出，至此已完成spack設定可以開始利用spack指令搜尋、安裝軟體與library。 ::: 3. 日後更新 [demo_user@lgn302 ~]$ cd spack [demo_user@lgn302 spack]$ git pull :::spoiler 輸出範例 ``` warning: Pulling without specifying how to reconcile divergent branches is discouraged. You can squelch this message by running one of the following commands sometime before your next pull: git config pull.rebase false # merge (the default strategy) git config pull.rebase true # rebase git config pull.ff only # fast-forward only You can replace "git config" with "git config --global" to set a default preference for all repositories. You can also pass --rebase, --no-rebase, or --ff-only on the command line to override the configured default per invocation. remote: Enumerating objects: 4128, done. remote: Counting objects: 100% (2484/2484), done. remote: Compressing objects: 100% (288/288), done. remote: Total 4128 (delta 2186), reused 2371 (delta 2107), pack-reused 1644 Receiving objects: 100% (4128/4128), 2.29 MiB | 30.42 MiB/s, done. Resolving deltas: 100% (2346/2346), completed with 586 local objects. From https://github.com/spack/spack 5f58a4c079..0960f691a1 develop -> origin/develop * [new branch] backports/v0.21.2 -> origin/backports/v0.21.2 * [new branch] bugfix/compiler-flag-propagation -> origin/bugfix/compiler-flag-propagation * [new branch] bugfix/patches-across-repos -> origin/bugfix/patches-across-repos * [new branch] dependabot/github_actions/actions/upload-artifact-4.3.1 -> origin/dependabot/github_actions/actions/upload-artifact-4.3.1 * [new branch] e4s-24.02 -> origin/e4s-24.02 fea922e92e..7b5e468a5b features/read-compilers-from-packages-yaml -> origin/features/read-compilers-from-packages-yaml 4d5a4a13a5..233db21d20 gartung-buildcache-check-fix -> origin/gartung-buildcache-check-fix * [new branch] improve-find-in-env -> origin/improve-find-in-env * [new branch] install-status-format -> origin/install-status-format 78680aad1b..02cb7ede49 llnl/radiuss-packages-update-start-over -> origin/llnl/radiuss-packages-update-start-over * [new branch] packages/pythia6-dead-hepforge -> origin/packages/pythia6-dead-hepforge + d21f421e44...f672f7d753 solver-setup-type-annotations -> origin/solver-setup-type-annotations (forced update) * [new branch] task/2024_02_add_conduit_0.9.0_release -> origin/task/2024_02_add_conduit_0.9.0_release * [new tag] develop-2024-01-21 -> develop-2024-01-21 * [new tag] develop-2024-01-28 -> develop-2024-01-28 * [new tag] develop-2024-02-04 -> develop-2024-02-04 Updating 5f58a4c079..0960f691a1 Updating files: 100% (598/598), done. Fast-forward .github/pull_request_template.md | 6 + .github/workflows/audit.yaml | 2 +- .github/workflows/build-containers.yml | 4 +- .github/workflows/ci.yaml | 2 +- ...（略）... ``` :::  ### spack基本指令說明所有的指令都支援使用Tab鍵補齊，包含指令與keyword（package name）都可以。 * list 列出軟體/函式庫。不加任何keyword，則列出全部；keyword可為完整字串或部分字元。如：spack list mpi :::spoiler 範例 ``` [demo_user@lgn302 ~]$ spack list <--列出當時spack所有的package 3dtk parquet-format py-sierrapy 3proxy parsec py-simpervisor 7zip parsimonator py-simpleeval abacus parsplice py-simplegeneric abduco pasta py-simplejson abi-compliance-checker pastix py-simplekml .... parmmg py-shroud zziplib parquet-cpp py-shtab ==> 7616 packages [demo_user@lgn302 ~]$ spack list gcc <--列出包含gcc字眼的package armpl-gcc gcc gcc-runtime gccmakedep gccxml ==> 5 packages [demo_user@lgn302 ~]$ spack list intel <--列出包含intel字眼的package intel intel-mkl intel-oneapi-compilers-classic intel-oneapi-ipp intel-oneapi-vpl py-intel-openmp intel-daal intel-mpi intel-oneapi-dal intel-oneapi-ippcp intel-oneapi-vtune intel-gpu-tools intel-mpi-benchmarks intel-oneapi-dnn intel-oneapi-itac intel-parallel-studio intel-gtpin intel-oneapi-advisor intel-oneapi-dpct intel-oneapi-mkl intel-pin intel-ipp intel-oneapi-ccl intel-oneapi-dpl intel-oneapi-mpi intel-tbb intel-llvm intel-oneapi-compilers intel-oneapi-inspector intel-oneapi-tbb intel-xed ==> 31 packages [demo_user@lgn302 ~]$ spack list mpi <--列出包含mpi字眼的package compiz intel-oneapi-compilers mpich mpiwrapper pnmpi rkt-compiler-lib cray-mpich intel-oneapi-compilers-classic mpifileutils mpix-launch-swift py-dask-mpi spectrum-mpi exempi intel-oneapi-mpi mpilander msmpi py-mpi4jax spiral-package-mpi fujitsu-mpi mpi-bash mpileaks openmpi py-mpi4py sst-dumpi hpcx-mpi mpi-serial mpip pbmpi py-tempita umpire intel-mpi mpi-test-suite mpir perl-params-validationcompiler r-rmpi vampirtrace intel-mpi-benchmarks mpibind mpitrampoline phylobayesmpi rempi wi4mpi ==> 42 packages ``` ::: * info 查詢軟體相關資訊，包含有哪些版本、安裝選項、相依軟體、函式庫、... :::spoiler 範例 ``` [demo_user@lgn302 ~]$ spack info intel-oneapi-mpi <--列出intel-oneapi-mpi相關資訊 Package: intel-oneapi-mpi Description: Intel MPI Library is a multifabric message-passing library that implements the open-source MPICH specification. Use the library to create, maintain, and test advanced, complex applications that perform better on high-performance computing (HPC) clusters based on Intel processors. LICENSE INFORMATION: By downloading and using this software, you agree to the terms and conditions of the software license agreements at https://intel.ly/393CijO. Homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/mpi-library.html Preferred version: <--未指定版本時的預設安裝版本 2021.11.0 https://registrationcenter-download.intel.com/akdlm//IRC_NAS/2c45ede0-623c-4c8e-9e09-bed27d70fa33/l_mpi_oneapi_p_2021.11.0.49513_offline.sh Safe versions: 2021.11.0 https://registrationcenter-download.intel.com/akdlm//IRC_NAS/2c45ede0-623c-4c8e-9e09-bed27d70fa33/l_mpi_oneapi_p_2021.11.0.49513_offline.sh 2021.10.0 https://registrationcenter-download.intel.com/akdlm/IRC_NAS/4f5871da-0533-4f62-b563-905edfb2e9b7/l_mpi_oneapi_p_2021.10.0.49374_offline.sh 2021.9.0 https://registrationcenter-download.intel.com/akdlm/IRC_NAS/718d6f8f-2546-4b36-b97b-bc58d5482ebf/l_mpi_oneapi_p_2021.9.0.43482_offline.sh 2021.8.0 https://registrationcenter-download.intel.com/akdlm/irc_nas/19131/l_mpi_oneapi_p_2021.8.0.25329_offline.sh 2021.7.1 https://registrationcenter-download.intel.com/akdlm/irc_nas/19010/l_mpi_oneapi_p_2021.7.1.16815_offline.sh 2021.7.0 https://registrationcenter-download.intel.com/akdlm/irc_nas/18926/l_mpi_oneapi_p_2021.7.0.8711_offline.sh 2021.6.0 https://registrationcenter-download.intel.com/akdlm/irc_nas/18714/l_mpi_oneapi_p_2021.6.0.602_offline.sh 2021.5.1 https://registrationcenter-download.intel.com/akdlm/irc_nas/18471/l_mpi_oneapi_p_2021.5.1.515_offline.sh 2021.5.0 https://registrationcenter-download.intel.com/akdlm/irc_nas/18370/l_mpi_oneapi_p_2021.5.0.495_offline.sh 2021.4.0 https://registrationcenter-download.intel.com/akdlm/irc_nas/18186/l_mpi_oneapi_p_2021.4.0.441_offline.sh 2021.3.0 https://registrationcenter-download.intel.com/akdlm/irc_nas/17947/l_mpi_oneapi_p_2021.3.0.294_offline.sh 2021.2.0 https://registrationcenter-download.intel.com/akdlm/irc_nas/17729/l_mpi_oneapi_p_2021.2.0.215_offline.sh 2021.1.1 https://registrationcenter-download.intel.com/akdlm/irc_nas/17397/l_mpi_oneapi_p_2021.1.1.76_offline.sh Deprecated versions: None Variants: build_system [generic] generic Build systems supported by the package envmods [true] false, true Toggles environment modifications external-libfabric [false] false, true Enable external libfabric dependency generic-names [false] false, true Use generic names, e.g mpicc instead of mpiicc ilp64 [false] false, true Build with ILP64 support Build Dependencies: None Link Dependencies: libfabric Run Dependencies: libfabric Licenses: None ``` ::: * versions 顯示軟體版本，包含safe versions（source chechsum驗證）與未經checksum的版本。 :::spoiler 範例 ``` [demo_user@lgn302 ~]$ spack versions intel-oneapi-mpi ==> Safe versions (already checksummed): 2021.11.0 2021.10.0 2021.9.0 2021.8.0 2021.7.1 2021.7.0 2021.6.0 2021.5.1 2021.5.0 2021.4.0 2021.3.0 2021.2.0 2021.1.1 ==> Remote versions (not yet checksummed): 19131 18926 18471 18186 17729 718d6f8f-2546-4b36-b97b-bc58d5482ebf 2c45ede0-623c-4c8e-9e09-bed27d70fa33 19010 18714 18370 17947 17397 4f5871da-0533-4f62-b563-905edfb2e9b7 ``` ::: * install 安裝spack list所列出的packages，除了最新版本外，亦可指定先前版本、指定編譯器、MPI種類、版本等組合 :::spoiler 範例 ``` [demo_user@lgn302 ~]$ spack install intel-oneapi-mpi ==> Fetching https://mirror.spack.io/bootstrap/github-actions/v0.5/build_cache/linux-centos7-x86_64-gcc-10.2.1-patchelf-0.18.0-afv7arjarb7nzmlh7c5slkfxykybuqce.spec.json ==> Fetching https://mirror.spack.io/bootstrap/github-actions/v0.5/build_cache/linux-centos7-x86_64/gcc-10.2.1/patchelf-0.18.0/linux-centos7-x86_64-gcc-10.2.1-patchelf-0.18.0-afv7arjarb7nzmlh7c5slkfxykybuqce.spack ==> Installing "patchelf@=0.18.0%gcc@=10.2.1 ldflags='-static-libstdc++ -static-libgcc' build_system=autotools arch=linux-centos7-x86_64" from a buildcache ==> Fetching https://mirror.spack.io/bootstrap/github-actions/v0.5/build_cache/linux-centos7-x86_64-gcc-10.2.1-clingo-bootstrap-spack-t4yf34cuvquqp5xd66zybmcfyhwbdlsf.spec.json ==> Fetching https://mirror.spack.io/bootstrap/github-actions/v0.5/build_cache/linux-centos7-x86_64/gcc-10.2.1/clingo-bootstrap-spack/linux-centos7-x86_64-gcc-10.2.1-clingo-bootstrap-spack-t4yf34cuvquqp5xd66zybmcfyhwbdlsf.spack ==> Installing "clingo-bootstrap@=spack%gcc@=10.2.1~docs+ipo+optimized+python+static_libstdcpp build_system=cmake build_type=Release generator=make patches=bebb819,ec99431 arch=linux-centos7-x86_64" from a buildcache ==> Installing gcc-runtime-8.5.0-ifampldlu2tf3ukzkt3yctwksoevqveh [1/2] ==> No binary for gcc-runtime-8.5.0-ifampldlu2tf3ukzkt3yctwksoevqveh found: installing from source ==> No patches needed for gcc-runtime ==> gcc-runtime: Executing phase: 'install' ==> gcc-runtime: Successfully installed gcc-runtime-8.5.0-ifampldlu2tf3ukzkt3yctwksoevqveh Stage: 0.00s. Install: 0.21s. Post-install: 0.04s. Total: 0.27s [+] /home/demo_user/spack/opt/spack/linux-rocky8-skylake_avx512/gcc-8.5.0/gcc-runtime-8.5.0-ifampldlu2tf3ukzkt3yctwksoevqveh ==> Installing intel-oneapi-mpi-2021.11.0-2bmu5dpvks5lutv4ncrp2zncrdqg5hwx [2/2] ==> No binary for intel-oneapi-mpi-2021.11.0-2bmu5dpvks5lutv4ncrp2zncrdqg5hwx found: installing from source ==> Fetching https://registrationcenter-download.intel.com/akdlm//IRC_NAS/2c45ede0-623c-4c8e-9e09-bed27d70fa33/l_mpi_oneapi_p_2021.11.0.49513_offline.sh ==> No patches needed for intel-oneapi-mpi ==> intel-oneapi-mpi: Executing phase: 'install' ==> intel-oneapi-mpi: Successfully installed intel-oneapi-mpi-2021.11.0-2bmu5dpvks5lutv4ncrp2zncrdqg5hwx Stage: 11.71s. Install: 17.10s. Post-install: 1.47s. Total: 30.31s [+] /home/demo_user/spack/opt/spack/linux-rocky8-skylake_avx512/gcc-8.5.0/intel-oneapi-mpi-2021.11.0-2bmu5dpvks5lutv4ncrp2zncrdqg5hwx ``` ``` [demo_user@lgn302 ~]$ spack install intel-oneapi-mpi@2021.10.0 <--指定版本 [+] /home/demo_user/spack/opt/spack/linux-rocky8-skylake_avx512/gcc-8.5.0/gcc-runtime-8.5.0-ifampldlu2tf3ukzkt3yctwksoevqveh ==> Installing intel-oneapi-mpi-2021.10.0-oz7nkbp427zs4agas6huuiyloafbmcq2 [2/2] ==> No binary for intel-oneapi-mpi-2021.10.0-oz7nkbp427zs4agas6huuiyloafbmcq2 found: installing from source ==> Fetching https://registrationcenter-download.intel.com/akdlm/IRC_NAS/4f5871da-0533-4f62-b563-905edfb2e9b7/l_mpi_oneapi_p_2021.10.0.49374_offline.sh ==> No patches needed for intel-oneapi-mpi ==> intel-oneapi-mpi: Executing phase: 'install' ==> intel-oneapi-mpi: Successfully installed intel-oneapi-mpi-2021.10.0-oz7nkbp427zs4agas6huuiyloafbmcq2 Stage: 13.32s. Install: 15.99s. Post-install: 1.43s. Total: 30.77s [+] /home/demo_user/spack/opt/spack/linux-rocky8-skylake_avx512/gcc-8.5.0/intel-oneapi-mpi-2021.10.0-oz7nkbp427zs4agas6huuiyloafbmcq2 ``` ::: * find 列出已透過spack安裝的package :::spoiler 範例 ``` [spiraea7@lgn302 ~]$ spack find -- linux-rocky8-skylake_avx512 / gcc@8.5.0 ---------------------- gcc-runtime@8.5.0 intel-oneapi-mpi@2021.10.0 intel-oneapi-mpi@2021.11.0 ==> 3 installed packages ``` ::: * uninstall 移除已安裝的package，若有不同的版本，須指定版本。 :::spoiler 範例 ``` [demo_user@lgn302 ~]$ spack uninstall intel-oneapi-mpi@2021.10.0 -- linux-rocky8-skylake_avx512 / gcc@8.5.0 ---------------------- oz7nkbp intel-oneapi-mpi@2021.10.0 ==> 1 packages will be uninstalled. Do you want to proceed? [y/N] y ==> Successfully uninstalled intel-oneapi-mpi@2021.10.0%gcc@8.5.0+envmods~external-libfabric~generic-names~ilp64 build_system=generic arch=linux-rocky8-skylake_avx512/oz7nkbp ``` ``` [demo_user@lgn302 ~]$ spack uninstall intel-oneapi-mpi -- linux-rocky8-skylake_avx512 / gcc@8.5.0 ---------------------- 2bmu5dp intel-oneapi-mpi@2021.11.0 ==> 1 packages will be uninstalled. Do you want to proceed? [y/N] y ==> Successfully uninstalled intel-oneapi-mpi@2021.11.0%gcc@8.5.0+envmods~external-libfabric~generic-names~ilp64 build_system=generic arch=linux-rocky8-skylake_avx512/2bmu5dp ``` ::: * compiler add/find 搜尋並加入PATH中可用的編譯器 info 列出編譯器路徑、module、OS等相關資訊 list 等同 compilers，列出可用的編譯器 :::spoiler 範例 ``` [demo_user@lgn302 ~]$ spack compiler list ==> Available compilers -- dpcpp rocky8-x86_64 ------------------------------------------ dpcpp@2024.0.2 -- gcc rocky8-x86_64 -------------------------------------------- gcc@8.5.0 -- intel rocky8-x86_64 ------------------------------------------ intel@2021.11.1 -- oneapi rocky8-x86_64 ----------------------------------------- oneapi@2024.0.2 ``` ``` [demo_user@lgn302 ~]$ spack compiler info oneapi@2024.0.2 oneapi@2024.0.2: paths: cc = /opt/ohpc/Taiwania3/pkg/intel/2024/oneapi/compiler/2024.0/bin/icx cxx = /opt/ohpc/Taiwania3/pkg/intel/2024/oneapi/compiler/2024.0/bin/icpx f77 = /opt/ohpc/Taiwania3/pkg/intel/2024/oneapi/compiler/2024.0/bin/ifx fc = /opt/ohpc/Taiwania3/pkg/intel/2024/oneapi/compiler/2024.0/bin/ifx modules = [] operating system = rocky8 ``` ``` [demo_user@lgn302 ~]$ ml gcc [demo_user@lgn302 ~]$ spack compiler find ==> Added 1 new compiler to /home/demo_user/.spack/linux/compilers.yaml gcc@13.2.0 ==> Compilers are defined in the following files: /home/demo_user/.spack/linux/compilers.yaml [demo_user@lgn302 ~]$ spack compiler info gcc@13.2.0 gcc@13.2.0: paths: cc = /opt/ohpc/Taiwania3/Intel/pkg/gcc/13.2.0/bin/gcc cxx = /opt/ohpc/Taiwania3/Intel/pkg/gcc/13.2.0/bin/g++ f77 = /opt/ohpc/Taiwania3/Intel/pkg/gcc/13.2.0/bin/gfortran fc = /opt/ohpc/Taiwania3/Intel/pkg/gcc/13.2.0/bin/gfortran modules = [] operating system = rocky8 ``` ::: * compilers 等同compiler list，列出可用編譯器。 :::spoiler 範例 ``` [demo_user@lgn302 ~]$ spack compilers ==> Available compilers -- dpcpp rocky8-x86_64 ------------------------------------------ dpcpp@2024.0.2 -- gcc rocky8-x86_64 -------------------------------------------- gcc@8.5.0 gcc@13.2.0 -- intel rocky8-x86_64 ------------------------------------------ intel@2021.11.1 -- oneapi rocky8-x86_64 ----------------------------------------- oneapi@2024.0.2 ``` ::: ### 安裝軟體以安裝gcc 13.1.0為例 * @：指定版本，如gcc@13.1.0 * %：指定編譯器，如 %gcc@8.5.0 * +、-、~：啟用或關閉選項(布林值屬性的選項)，其值如true/false、enable/disable的參數選項 * name=<value>：非布林屬性的選項，如build_type=Release * ^：相依套件的spec ``` [demo_user@lgn302 ~]$ spack install gcc @13.1.0%gcc@8.5.0 build_type=Release +graphite [+] /usr (external diffutils-3.6-rlm3yakysnl6owva6nnkin3gmrez57zg) [+] /usr (external gawk-4.2.1-atcivfoublwnzdqb57jljwdnncgv6upj) ...（略） ==> Installing gcc-13.1.0-cdw4nvh6mbehmg4h77kbs62e2mwtjv7y [24/24] ==> No binary for gcc-13.1.0-cdw4nvh6mbehmg4h77kbs62e2mwtjv7y found: installing from source ==> Fetching https://mirror.spack.io/_source-cache/archive/61/61d684f0aa5e76ac6585ad8898a2427aade8979ed5e7f85492286c4dfc13ee86.tar.xz ==> Ran patch() for gcc ==> gcc: Executing phase: 'autoreconf' ==> gcc: Executing phase: 'configure' ==> gcc: Executing phase: 'build' ==> gcc: Executing phase: 'install' ==> gcc: Successfully installed gcc-13.1.0-cdw4nvh6mbehmg4h77kbs62e2mwtjv7y Stage: 12.20s. Autoreconf: 0.00s. Configure: 3.27s. Build: 18m 7.01s. Install: 7.10s. Post-install: 1.76s. Total: 18m 31.53s [+] /home/demo_user/spack/opt/spack/linux-rocky8-skylake_avx512/gcc-8.5.0/gcc-13.1.0-cdw4nvh6mbehmg4h77kbs62e2mwtjv7y ``` ### 如何使用既有的編譯器與函式庫透過Spaack安裝軟體待補 ## 參考連結 * [Spack文件](https://spack.readthedocs.io/en/latest/) * [Spack support of HPC applications](https://developer.amd.com/spack/)