Spack Prototype for PSI

2023-04-27 08:06:59 +00:00
parent 8a0d620eb0
commit adb8e3eb09
53 changed files with 91348 additions and 2826 deletions
--- a/env/sles15/ffbidx/spack.yaml
+++ b/env/sles15/ffbidx/spack.yaml
@ -0,0 +1,24 @@
+spack:
+  upstreams:
+    spack-instance-1:
+      install_tree: /afs/psi.ch/sys/spack-rhel7/spack/opt/spack
+  config:
+    build_stage:
+    - /scratch/$user/spack-stage
+    install_tree:
+      root: /data/user/$user/spack-install
+  concretizer:
+    unify: true
+  include:
+  - ../sysconfigs/modules.yaml
+  - ../sysconfigs/compilers.yaml
+  - ../sysconfigs/packages.yaml
+  repos:
+  - ../../../
+  specs:
+  - openblas
+  - ffbidx@main%gcc@12.1.0+python+simple_data_files+simple_data_indexer+test_all cuda_arch=60
+  develop:
+    ffbidx:
+      path: /scratch/$user/spack-dev/fast-feedback-indexer
+      spec: ffbidx@main+python+simple_data_files+simple_data_indexer+test_all cuda_arch=60
--- a/env/sles15/hyquas/spack.lock
+++ b/env/sles15/hyquas/spack.lock
--- a/env/sles15/hyquas/spack.yaml
+++ b/env/sles15/hyquas/spack.yaml
@ -0,0 +1,31 @@
+spack:
+  upstreams:
+    spack-instance-1:
+      install_tree: /afs/psi.ch/sys/spack-rhel7/spack/opt/spack
+  config:
+    build_stage:
+    - /scratch/$user/spack-stage
+    install_tree:
+      root: /data/user/$user/spack-install
+  concretizer:
+    unify: true
+  include:
+  - ../sysconfigs/modules.yaml
+  - ../sysconfigs/compilers.yaml
+  - ../sysconfigs/packages.yaml
+  repos:
+  - ../../../
+  specs:
+  - git-lfs
+  - cmake@3.25.2%gcc@12.1.0
+  - openmpi@4.1.5%gcc schedulers=slurm fabrics=auto +pmi +cxx +cxx_exceptions +cuda
+    +legacylaunchers ^slurm +pmix +hwloc +gtk +readline +restd +mariadb
+  - cuda@11.0.2
+  - hyquas@main%gcc+cuda cuda_arch=70 ~mpi+schedule+use_double+micro_bench+eval_pp~disable_assert
+    backend=mix mat_size=7
+  develop:
+    hyquas:
+      path: /scratch/$user/spack-dev/HyQuas
+      spec: hyquas@main%gcc+cuda cuda_arch=70 ~mpi+schedule+use_double+micro_bench+eval_pp~disable_assert
+        backend=mix mat_size=7
+  view: false
--- a/env/sles15/py-hiqsimulator/spack.lock
+++ b/env/sles15/py-hiqsimulator/spack.lock
--- a/env/sles15/py-hiqsimulator/spack.yaml
+++ b/env/sles15/py-hiqsimulator/spack.yaml
@ -0,0 +1,25 @@
+spack:
+  upstreams:
+    spack-instance-1:
+      install_tree: /afs/psi.ch/sys/spack-rhel7/spack/opt/spack
+  config:
+    build_stage:
+    - /scratch/$user/spack-stage
+    install_tree:
+      root: /data/user/$user/spack-install
+  concretizer:
+    unify: true
+  include:
+  - ../sysconfigs/modules.yaml
+  - ../sysconfigs/compilers.yaml
+  - ../sysconfigs/packages.yaml
+  repos:
+  - ../../../
+  specs:
+  - openmpi@4.1.5%gcc
+  - py-hiqsimulator@develop%gcc
+  develop:
+    py-hiqsimulator:
+      path: /scratch/$user/spack-dev/HiQsimulator
+      spec: py-hiqsimulator@develop%gcc
+  view: false
--- a/env/sles15/py-hiqsimulator/test/run.slurm
+++ b/env/sles15/py-hiqsimulator/test/run.slurm
@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+ 
+#SBATCH -N 4                                     # 4 nodes are requested
+#SBATCH -t 00:03:00                              # Walltime, 3 minutes
+#SBATCH -n 8                                     # 8 processes are requested
+#SBATCH --ntasks-per-socket=1                    # 1 process per allocated socket
+#SBATCH --hint=compute_bound                     # Use all cores in each socket, one thread per core
+#SBATCH --exclusive                              # node should not be shared with other jobs
+
+mpirun  python3 ./examples/teleport_mpi.py       # Execute program
--- a/env/sles15/stable/spack.lock
+++ b/env/sles15/stable/spack.lock
--- a/env/sles15/stable/spack.yaml
+++ b/env/sles15/stable/spack.yaml
@ -0,0 +1,66 @@
+spack:
+  concretizer:
+    unify: false
+  config:
+    build_stage:
+    - /scratch/spack/spack-stage
+  definitions:
+  - aocc_mpi:
+    - ^cray-mpich
+  - aocc_pckgs:
+    - gromacs@2021.7
+  - cce_mpi:
+    - ^cray-mpich
+  - cce_pckgs:
+    - gromacs@2021.7
+  - gcc_7.5.0_mpi:
+    - ^openmpi@4.1.5
+  - gcc_11.2.0_mpi:
+    - ^cray-mpich
+  - gcc_7.5.0_pckgs:
+    - trilinos@11.14.3 +mpi+cuda cuda_arch=60 ~tpetra
+  - gcc_11.2.0_pckgs:
+    - gams@31.1.1
+    - gromacs@2022.5 +mpi
+    - h5hut@2.0.0rc3 +mpi
+    - lammps@20221222
+    - trilinos@13.4.1 ~fortran
+  - intel_mpi:
+    - ^cray-mpich
+  - intel_pckgs:
+    - gromacs@2021.7
+  - nvhpc_mpi:
+    - ^cray-mpich
+  - nvhpc_pckgs:
+    - quantum-espresso@7.0 +mpi+cuda
+  include:
+  - ../sysconfigs/packages.yaml
+  - ../sysconfigs/compilers.yaml
+  - ../sysconfigs/modules.yaml
+  specs:
+  - matrix:
+    - [$aocc_pckgs]
+    - [$aocc_mpi]
+    - ['%aocc@3.1.0']
+  - matrix:
+    - [$cce_pckgs]
+    - [$cce_mpi]
+    - ['%cce@13.0.0']
+  - matrix:
+    - [$gcc_7.5.0_pckgs]
+    - [$gcc_7.5.0_mpi]
+    - [^openblas]
+    - ['%gcc@7.5.0']
+  - matrix:
+    - [$gcc_11.2.0_pckgs]
+    - [$gcc_11.2.0_mpi]
+    - ['%gcc@11.2.0']
+  - matrix:
+    - [$nvhpc_pckgs]
+    - [$nvhpc_mpi]
+    - ['%nvhpc@20.9']
+  - matrix:
+    - [$intel_pckgs]
+    - [$intel_mpi]
+    - ['%oneapi@2021.2.0']
+  view: false
--- a/env/sles15/sysconfigs/compilers.yaml
+++ b/env/sles15/sysconfigs/compilers.yaml
@ -0,0 +1,111 @@
+compilers:
+  - compiler:
+      environment: {}
+      extra_rpaths: []
+      flags: {}
+      modules:
+        - PrgEnv-cray/8.3.0
+        - cce/13.0.0
+        - libfabric/1.15.2.0
+      operating_system: sles15
+      paths:
+        cc: cc
+        cxx: CC
+        f77: ftn
+        fc: ftn
+      spec: cce@13.0.0
+      target: x86_64
+  - compiler:
+      environment: {}
+      extra_rpaths: []
+      flags: {}
+      modules:
+        - PrgEnv-gnu/8.3.0
+        - gcc/11.2.0
+        - libfabric/1.15.2.0
+      operating_system: sles15
+      paths:
+        cc: cc
+        cxx: CC
+        f77: ftn
+        fc: ftn
+      spec: gcc@11.2.0
+      target: x86_64
+  - compiler:
+      environment: {}
+      extra_rpaths: []
+      flags: {}
+      modules:
+        - libfabric/1.15.2.0
+      operating_system: sles15
+      paths:
+        cc: /usr/bin/gcc
+        cxx: /usr/bin/g++
+        f77: /usr/bin/gfortran
+        fc: /usr/bin/gfortran
+      spec: gcc@7.5.0
+      target: x86_64
+  - compiler:
+      environment: {}
+      extra_rpaths: []
+      flags: {}
+      modules:
+        - PrgEnv-nvidia/8.3.0
+        - nvidia/20.9
+        - libfabric/1.15.2.0
+      operating_system: sles15
+      paths:
+        cc: cc
+        cxx: CC
+        f77: ftn
+        fc: ftn
+      spec: nvhpc@20.9
+      target: x86_64
+  - compiler:
+      environment: {}
+      extra_rpaths: []
+      flags: {}
+      modules:
+        - PrgEnv-intel/8.3.0
+        - intel/2021.2.0
+        - libfabric/1.15.2.0
+      operating_system: sles15
+      paths:
+        cc: cc
+        cxx: CC
+        f77: ftn
+        fc: ftn
+      spec: intel@2021.2.0
+      target: x86_64
+  - compiler:
+      environment: {}
+      extra_rpaths: []
+      flags: {}
+      modules:
+        - PrgEnv-intel/8.3.0
+        - intel-oneapi/2021.2.0
+        - libfabric/1.15.2.0
+      operating_system: sles15
+      paths:
+        cc: cc
+        cxx: CC
+        f77: ftn
+        fc: ftn
+      spec: oneapi@2021.2.0
+      target: x86_64
+  - compiler:
+      environment: {}
+      extra_rpaths: []
+      flags: {}
+      modules:
+        - PrgEnv-aocc/8.3.0
+        - aocc/3.1.0
+        - libfabric/1.15.2.0
+      operating_system: sles15
+      paths:
+        cc: cc
+        cxx: CC
+        f77: ftn
+        fc: ftn
+      spec: aocc@3.1.0
+      target: x86_64
--- a/env/sles15/sysconfigs/modules.yaml
+++ b/env/sles15/sysconfigs/modules.yaml
@ -0,0 +1,96 @@
+modules:
+  default:
+    tcl:
+      blacklist_implicits: true
+      all:
+        autoload: direct
+        conflict:
+          - '{name}'
+        environment:
+          set:
+            ${PACKAGE}_INCLUDE_DIR: '{prefix}/include'
+            ${PACKAGE}_LIBRARY_DIR: '{prefix}/lib'
+            ${PACKAGE}_VERSION: '{version}'
+      intel-oneapi-mpi:
+        environment:
+          set:
+            I_MPI_CXX: 'mpiicpc'
+            I_MPI_F77: 'mpiifort'
+            I_MPI_F90: 'mpiifort'
+            I_MPI_FC: 'mpiifort'
+            I_MPI_ICC: 'mpiicc'
+            MPIEXEC: 'mpiexec.hydra'
+            MPIFC: 'mpiifort'
+            MPIFORTRAN: 'mpiifort'
+            MPIRUN: 'mpirun'
+      mpich:
+        environment:
+          set:
+            MPIEXEC: ${prefix}/bin/mpiexec
+            MPIFC: ${prefix}/bin/mpif90
+            MPIFORTRAN: ${prefix}/bin/mpif90
+            MPIRUN: ${prefix}/bin/mpirun
+      openblas:
+        environment:
+          set:
+            BLASLIB: ${prefix}/libopenblas.a
+      openmpi:
+        environment:
+          set:
+            MPIEXEC: ${prefix}/bin/mpiexec
+            MPIFC: ${prefix}/bin/mpif90
+            MPIFORTRAN: ${prefix}/bin/mpif90
+            MPIRUN: ${prefix}/bin/mpirun
+      root:
+        environment:
+          set:
+            ROOTSYS: ${prefix}
+      cuda:
+        environment:
+          prepend_path:
+            ${PACKAGE}_PATH: '{prefix}'
+            LIBRARY_PATH: '{prefix}/lib64/stubs'
+            LIBRARY_PATH: '{prefix}/targets/x86_64-linux/lib/stubs'
+          set:
+            ${PACKAGE}_DIR: '{prefix}'
+            ${PACKAGE}_INCLUDE_DIR: '{prefix}/include'
+            ${PACKAGE}_LIBRARY_DIR: '{prefix}/lib'
+            ${PACKAGE}_PATH: '{prefix}'
+            ${PACKAGE}_VERSION: '{version}'
+      hdf5~mpi:
+        environment:
+          set:
+            ${PACKAGE}_DIR: '{prefix}'
+            ${PACKAGE}_HOME: '{prefix}'
+            ${PACKAGE}_INCLUDE_DIR: '{prefix}/include'
+            ${PACKAGE}_LIBRARY_DIR: '{prefix}/lib'
+            ${PACKAGE}_LIBRARY_DIR: '{prefix}/lib64'
+            ${PACKAGE}_PREFIX: '{prefix}'
+            ${PACKAGE}_ROOT: '{prefix}'
+            ${PACKAGE}_VERSION: '{version}'
+  prefix_inspections:
+    '':
+      - CMAKE_PREFIX_PATH
+    bin:
+      - PATH
+    include:
+      - C_INCLUDE_PATH
+      - CPLUS_INCLUDE_PATH
+    lib:
+      - LIBRARY_PATH
+      - LD_LIBRARY_PATH
+    lib/pkgconfig:
+      - PKG_CONFIG_PATH
+    lib64:
+      - LIBRARY_PATH
+      - LD_LIBRARY_PATH
+    lib64/pkgconfig:
+      - PKG_CONFIG_PATH
+    man:
+      - MANPATH
+    share/aclocal:
+      - ACLOCAL_PATH
+    share/man:
+      - MANPATH
+    share/pkgconfig:
+      - PKG_CONFIG_PATH
--- a/env/sles15/sysconfigs/packages.yaml
+++ b/env/sles15/sysconfigs/packages.yaml
@ -0,0 +1,281 @@
+---
+packages:
+  '%aocc':
+    require: '%aocc'
+  '%cce':
+    require: '%cce'
+  '%clang':
+    require: '%clang'
+  '%gcc':
+    require: '%gcc@7.5.0'
+  '%nvhpc':
+    require: '%nvhpc'
+  '%oneapi':
+    require: '%oneapi'
+  all:
+    providers:
+      blas: [ cray-libsci ]
+      mpi: [ cray-mpich ]
+      pkgconfig: [ pkg-config ]
+    target:
+      - zen
+  autoconf:
+    buildable: false
+    externals:
+      - prefix: /usr
+        spec: autoconf@2.69
+  automake:
+    buildable: false
+    externals:
+      - prefix: /usr
+        spec: automake@1.15.1
+  berkeley-db:
+    require: '%gcc@7.5.0'
+  binutils:
+    buildable: false
+    externals:
+      - prefix: /usr
+        spec: binutils@2.37.20211103
+  bison:
+    buildable: false
+    externals:
+      - prefix: /usr
+        spec: bison@3.0.4
+  boost:
+    require: '%gcc@7.5.0'
+  ca-certificates-mozilla:
+    require: '%gcc@7.5.0'
+  cairo:
+    require: '%gcc@7.5.0'
+  cmake:
+    externals:
+    - spec: cmake@3.17.0
+      prefix: /usr
+    require: 
+    - one_of: [
+        "cmake@3.17.0",
+        "cmake@3.25.2%gcc@7.5.0"
+    ]
+  coreutils:
+    buildable: false
+    externals:
+      - prefix: /usr
+        spec: coreutils@8.32
+  cray-libsci:
+    externals:
+      - modules:
+          - cray-libsci/21.08.1.2
+        spec: cray-libsci@21.08.1.2
+  cray-mpich:
+    buildable: false
+    externals:
+      - modules:
+          - cray-mpich/8.1.12
+        spec: cray-mpich@8.1.12 ~wrappers
+  ctffind:
+    require: '%gcc@7.5.0'
+  cuda:
+    externals:
+      - prefix: /opt/nvidia/hpc_sdk/Linux_x86_64/20.9/cuda
+        spec: cuda@11.0.0%nvhpc@20.9
+  curl:
+    buildable: false
+    externals:
+      - prefix: /usr
+        spec: curl@7.66.0+gssapi+ldap+nghttp2
+  diffutils:
+    buildable: false
+    externals:
+      - prefix: /usr
+        spec: diffutils@3.6
+  expat:
+    require: '%gcc@7.5.0'
+  fftw:
+    buildable: false
+    externals:
+      - modules:
+          - cray-fftw/3.3.8.13
+        spec: fftw@3.3.8.13
+  findutils:
+    buildable: false
+    externals:
+      - prefix: /usr
+        spec: findutils@4.8.0
+  flex:
+    buildable: false
+    externals:
+      - prefix: /usr
+        spec: flex@2.6.4+lex
+  fltk:
+    require: '%gcc@7.5.0'
+  fontconfig:
+    require: '%gcc@7.5.0'
+  gams:
+    buildable: false
+    externals:
+      - prefix: /opt/psi/Tools/GAMS/31.1.1/gams31.1_linux_x64_64_sfx
+        spec: gams@31.1.1%gcc
+  gawk:
+    buildable: false
+    externals:
+      - prefix: /usr
+        spec: gawk@4.2.1
+  gdbm:
+    require: '%gcc@7.5.0'
+  gettext:
+    require: '%gcc@7.5.0'
+  git:
+    buildable: false
+    externals:
+      - prefix: /usr
+        spec: git@2.35.3~tcltk
+  gmake:
+    buildable: false
+    externals:
+      - prefix: /usr
+        spec: gmake@4.2.1
+  groff:
+    buildable: false
+    externals:
+      - prefix: /usr
+        spec: groff@1.22.3
+  hdf5:
+    externals:
+      - modules:
+          - cray-hdf5-parallel/1.12.0.7
+        spec: hdf5@1.12.0.7+mpi
+      - prefix: /opt/cray/pe/hdf5-parallel/1.12.0.7/nvidia/20.7
+        spec: hdf5@1.12.0.7%nvhpc+mpi
+      - modules:
+          - cray-hdf5/1.12.0.7
+        spec: hdf5@1.12.0.7~mpi
+  libbsd:
+    require: '%gcc@7.5.0'
+  libevent:
+    require: '%gcc@7.5.0'
+  libfabric:
+    buildable: false
+    externals:
+      - prefix: /opt/cray/libfabric/1.15.2.0
+        spec: libfabric@1.15.2.0
+  libiconv:
+    require: '%gcc@7.5.0'
+  libidn2:
+    require: '%gcc@7.5.0'
+  libmd:
+    require: '%gcc@7.5.0'
+  libpciaccess:
+    require: '%gcc@7.5.0'
+  libsigsegv:
+    require: '%gcc@7.5.0'
+  libtool:
+    buildable: false
+    externals:
+      - prefix: /usr
+        spec: libtool@2.4.6
+  libxml2:
+    require: '%gcc@7.5.0'
+  llvm:
+    buildable: false
+    externals:
+      - prefix: /opt/AMD/aocc-compiler-3.1.0
+        spec: llvm@15.0.3
+  m4:
+    buildable: false
+    externals:
+      - prefix: /usr
+        spec: m4@1.4.18
+  ncurses:
+    require: '%gcc@7.5.0'
+  netcdf-c:
+    buildable: false
+    externals:
+      - modules:
+          - cray-parallel-netcdf/1.12.1.7
+        spec: netcdf-c@4.0.1 +mpi
+  netcdf-fortran:
+    buildable: false
+    externals:
+      - modules:
+          - cray-parallel-netcdf/1.12.1.7
+        spec: netcdf-fortran@4.0.1
+  ninja:
+    require: '%gcc@7.5.0'
+  openblas:
+    require: '%gcc@7.5.0'
+  opengl:
+    externals:
+      - prefix: /usr
+        spec: opengl@1.7.0
+  openmpi:
+    externals:
+      - prefix: /opt/nvidia/hpc_sdk/Linux_x86_64/20.9/comm_libs/openmpi4/openmpi-4.0.5
+        spec: openmpi@4.0.5%nvhpc@20.9
+    require: 
+    - one_of: [
+        "openmpi@4.1.5%gcc@7.5.0 schedulers=slurm fabrics=auto +pmi +cxx +cxx_exceptions +cuda +legacylaunchers",
+        "openmpi@4.0.5%nvhpc@20.9"
+    ]
+  openssh:
+    buildable: false
+    externals:
+      - prefix: /usr
+        spec: openssh@8.4p1
+  openssl:
+    buildable: false
+    externals:
+      - prefix: /usr
+        spec: openssl@1.1.1d
+  perl:
+    require: '%gcc@7.5.0'
+  pkg-config:
+    buildable: false
+    externals:
+      - prefix: /usr
+        spec: pkg-config@0.29.2
+  pkgconf:
+    require: '%gcc@7.5.0'
+  py-fypp:
+    require: '%gcc@7.5.0'
+  python:
+    require: '%gcc@7.5.0'
+  readline:
+    require: '%gcc@7.5.0'
+  slurm:
+    require: '+pmix +hwloc +gtk +readline +restd +mariadb ^cups'
+  sqlite:
+    require: '%gcc@7.5.0'
+  tar:
+    buildable: false
+    externals:
+      - prefix: /usr
+        spec: tar@1.34
+  texinfo:
+    buildable: false
+    externals:
+      - prefix: /usr
+        spec: texinfo@6.5
+  unuran:
+    require: '%gcc@7.5.0'
+  util-linux-uuid:
+    require: '%gcc@7.5.0'
+  util-macros:
+    require: '%gcc@7.5.0'
+  valgrind:
+    buildable: false
+    externals:
+      - modules:
+          - valgrind4hpc/2.12.8
+        spec: valgrind@2.12.8
+  xpmem:
+    buildable: false
+    externals:
+      - modules:
+          - xpmem/2.4.4-2.3_9.1__gff0e1d9.shasta
+        spec: xpmem@2.4.4
+  xxhash:
+    require: '%gcc@7.5.0'
+  zlib:
+    require: '%gcc@7.5.0'
+  zstd:
+    require: '%gcc@7.5.0'
--- a/env/sles15/unstable/spack.yaml
+++ b/env/sles15/unstable/spack.yaml
@ -0,0 +1,52 @@
+spack:
+  concretizer:
+    unify: when_possible
+  config:
+    build_stage:
+    - /scratch/spack/spack-stage
+  definitions:
+  - aocc_mpi:
+    - ^cray-mpich
+  - aocc_pckgs:
+    - gromacs@2022.5
+  - cce_mpi:
+    - ^cray-mpich
+  - cce_pckgs:
+    - gromacs@2022.5
+  - gcc_11.2.0_mpi:
+    - ^cray-mpich
+  - gcc_11.2.0_pckgs:
+    - gromacs@2023 +mpi +cuda
+    - h5hut +mpi
+    - lammps
+    - trilinos ~fortran
+  - intel_mpi:
+    - ^cray-mpich
+  - intel_pckgs:
+    - gromacs@2022.5
+  - nvhpc_mpi:
+    - ^cray-mpich
+  - nvhpc_pckgs:
+    - quantum-espresso +mpi+cuda hdf5=parallel
+  include:
+  - ../sysconfigs/packages.yaml
+  - ../sysconfigs/compilers.yaml
+  - ../sysconfigs/modules.yaml
+  specs:
+  - matrix:
+    - [$aocc_pckgs]
+    - [$aocc_mpi]
+    - ['%aocc@3.1.0']
+  - matrix:
+    - [$cce_pckgs]
+    - [$cce_mpi]
+    - ['%cce@13.0.0']
+  - matrix:
+    - [$gcc_11.2.0_pckgs]
+    - [$gcc_11.2.0_mpi]
+    - ['%gcc@11.2.0']
+  - matrix:
+    - [$nvhpc_pckgs]
+    - [$nvhpc_mpi]
+    - ['%nvhpc@20.9']
+  view: false