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Jack Betteridge edited this page Jul 20, 2022 · 1 revision

Previously a script based installation has been used to install Firedrake on ARCHER2, this is no longer recommended and we now encourage you to use Spack. (The old repository is available here)

Spack install Firedrake on ARCHER2

We will work with the in a directory /work/[budget code]/[budget code]/[$USER]/workspace, where [budget code] is replaced by your project code and [$USER] is your username.

Prerequisites

You should familiarise yourself with as much of Spack's functionality as possible. To achieve the same flexibility as we have on desktop installs the Firedrake Spack install leverages a lot of Spack's features. More information about Spack can be found on their website.

Spack

Start in a directory on the WORK filesystem, not HOME as it is not accessible from the compute nodes. You may wish to set SPACK_USER_CONFIG_PATH which defaults to ~/.spack to change where spack looks for user level configuration files. Changing SPACK_USER_CONFIG_PATH isn't necessary if everything is correctly configured within the spack environment.

Environment

We recommend using the GNU toolchain and GCC compilers at version 10.2.0, see additional notes for more info.

The following clones the Spack repo, loads modules to setup the environment and activates Spack.

git clone -c feature.manyFiles=true [email protected]:spack/spack.git

module purge
module load load-epcc-module

# Load programming environment and compiler
module load PrgEnv-gnu/8.1.0
module swap gcc gcc/10.2.0

module swap cray-mpich cray-mpich/8.1.9
module swap cray-dsmml cray-dsmml/0.2.1
module swap cray-libsci cray-libsci/21.08.1.2
module load xpmem
module load cmake/3.21.3
module load cray-python/3.9.4.1

. spack/share/spack/setup-env.sh

If you want to use a different BLAS and LAPACK and Scalapack library you don't need to load cray-libsci and you should run module unload cray-libsci. For instance the AMD optimised CPU libraries (AOCL) could be loaded instead module load aocl/3.1

If you really want to try the other compilers replace the two isolated lines under # Load programming environment and compiler with

module load PrgEnv-aocc/8.1.0
module swap aocc aocc/3.0.0
# or
module load PrgEnv-cray/8.1.0
module swap cce cce/12.0.3

for the AMD or Cray compilers respectively.

Configuration

  1. Populate $SPACK_USER_CONFIG_PATH/cray/compilers.yaml with the following YAML. Note that this contains most of the available compilers, you only need to configure for the compilers you will use.
$SPACK_USER_CONFIG_PATH/cray/compilers.yaml 
compilers:
- compiler:
    spec: [email protected]
    paths:
      cc: cc
      cxx: CC
      f77: ftn
      fc: ftn
    flags:
      cflags: null
      cxxflags: null
      fflags: null
    operating_system: sles15
    target: any
    modules:
    - PrgEnv-aocc
    - aocc/2.2.0
    environment: {}
    extra_rpaths: []
- compiler:
    spec: [email protected]
    paths:
      cc: cc
      cxx: CC
      f77: ftn
      fc: ftn
    flags:
      cflags: null
      cxxflags: null
      fflags: null
    operating_system: sles15
    target: any
    modules:
    - PrgEnv-aocc
    - aocc/2.2.0.1
    environment: {}
    extra_rpaths: []
- compiler:
    spec: [email protected]
    paths:
      cc: cc
      cxx: CC
      f77: ftn
      fc: ftn
    flags:
      cflags: -Wno-unused-command-line-argument -mllvm -eliminate-similar-expr=false
      cxxflags: -Wno-unused-command-line-argument -mllvm -eliminate-similar-expr=false
      fflags: -Wno-unused-command-line-argument -mllvm -eliminate-similar-expr=false
      ldflags: -Wl,-rpath,/opt/cray/libfabric/1.11.0.4.71/lib64 -L/opt/cray/libfabric/1.11.0.4.71/lib64 -lfabric
    operating_system: sles15
    target: any
    modules:
    - PrgEnv-aocc
    - aocc/3.0.0
    environment: {}
    extra_rpaths: []
- compiler:
    spec: [email protected]
    paths:
      cc: cc
      cxx: CC
      f77: ftn
      fc: ftn
    flags: {}
    operating_system: sles15
    target: any
    modules:
    - PrgEnv-cray
    - cce/11.0.4
    environment: {}
    extra_rpaths: []
- compiler:
    spec: [email protected]
    paths:
      cc: cc
      cxx: CC
      f77: ftn
      fc: ftn
    flags: {}
    operating_system: sles15
    target: any
    modules:
    - PrgEnv-cray
    - cce/12.0.3
    environment: {}
    extra_rpaths: []
- compiler:
    spec: [email protected]
    paths:
      cc: cc
      cxx: CC
      f77: ftn
      fc: ftn
    flags: {}
    operating_system: sles15
    target: any
    modules:
    - PrgEnv-gnu
    - gcc/9.3.0
    environment: {}
    extra_rpaths: []
- compiler:
    spec: [email protected]
    paths:
      cc: cc
      cxx: CC
      f77: ftn
      fc: ftn
    flags: {}
    operating_system: sles15
    target: any
    modules:
    - PrgEnv-gnu
    - gcc/10.2.0
    environment: {}
    extra_rpaths: []
- compiler:
    spec: [email protected]
    paths:
      cc: cc
      cxx: CC
      f77: ftn
      fc: ftn
    flags: {}
    operating_system: sles15
    target: any
    modules:
    - PrgEnv-gnu
    - gcc/10.3.0
    environment: {}
    extra_rpaths: []
- compiler:
    spec: [email protected]
    paths:
      cc: cc
      cxx: CC
      f77: ftn
      fc: ftn
    flags: {}
    operating_system: sles15
    target: any
    modules:
    - PrgEnv-gnu
    - gcc/11.2.0
    environment: {}
    extra_rpaths: []
- compiler:
    spec: [email protected]
    paths:
      cc: cc
      cxx: CC
      f77: ftn
      fc: ftn
    flags: {}
    operating_system: sles15
    target: any
    modules:
    - PrgEnv-amd
    - rocmcc/2.14-nosmp
    environment: {}
    extra_rpaths: []
- compiler:
    spec: [email protected]
    paths:
      cc: cc
      cxx: CC
      f77: ftn
      fc: ftn
    flags: {}
    operating_system: sles15
    target: any
    modules:
    - PrgEnv-amd
    - rocmcc/2.14
    environment: {}
    extra_rpaths: []
  1. Populate $SPACK_USER_CONFIG_PATH/packages.yaml with the following
$SPACK_USER_CONFIG_PATH/packages.yaml 
packages:
  all:
    providers:
      mpi: [cray-mpich]
  cray-mpich:
    externals:
    - spec: [email protected]%[email protected]
      modules:
      - PrgEnv-gnu
      - gcc/10.2.0
      - cray-mpich/8.1.9
    - spec: [email protected]%[email protected]
      # Pretend mpich is version 8.1.6 due to the following bug in spack
      # https://github.com/spack/spack/issues/29459
      # Only with aocc compiler
      modules:
      - PrgEnv-aocc
      - aocc/3.0.0
      - cray-mpich/8.1.9
      prefix: /opt/cray/pe/mpich/8.1.9/ofi/aocc/3.0
    - spec: [email protected]%[email protected]
      modules:
      - PrgEnv-cray
      - cce/12.0.3
      - cray-mpich/8.1.9
    buildable: False
  cray-libsci:
    externals:
      - spec: [email protected]
        modules:
        - cray-libsci/21.04.1.1
      - spec: [email protected]
        modules:
        - cray-libsci/21.08.1.2
        environment:
          append_path:
          - PE_PKGCONFIG_PRODUCTS: PE_MPICH
    buildable: False
  amdblis:
    externals:
    - spec: [email protected]
      modules:
      - aocl/3.1
    buildable: False
  amdfftw:
    externals:
    - spec: [email protected]
      modules:
      - aocl/3.1
    buildable: False
  amdlibflame:
    externals:
    - spec: [email protected]
      modules:
      - aocl/3.1
    buildable: False
  amdlibm:
    externals:
    - spec: [email protected]
      modules:
      - aocl/3.1
    buildable: False
  amdscalapack:
    externals:
    - spec: [email protected]
      modules:
      - aocl/3.1
    buildable: False
  aocl-sparse:
    externals:
    - spec: [email protected]
      modules:
      - aocl/3.1
    buildable: False
  python:
    externals:
      - spec: [email protected]
        modules:
        - cray-python/3.9.4.1
      - spec: [email protected]
        modules:
        - cray-python/3.8.5.0
    buildable: False
  flex:
    externals:
    - spec: [email protected]+lex
      prefix: /usr
  # System texinfo causes issues!
  # texinfo:
  #   externals:
  #   - spec: [email protected]
  #     prefix: /usr
  automake:
    externals:
    - spec: [email protected]
      prefix: /usr
  binutils:
    externals:
    - spec: [email protected]
      prefix: /usr
  bison:
    externals:
    - spec: [email protected]
      prefix: /usr
  libtool:
    externals:
    - spec: [email protected]
      prefix: /usr
  m4:
    externals:
    - spec: [email protected]
      prefix: /usr
  openssh:
    externals:
    - spec: [email protected]
      prefix: /usr
  gawk:
    externals:
    - spec: [email protected]
      prefix: /usr
  pkg-config:
    externals:
    - spec: [email protected]
      prefix: /usr
    buildable: False
  pkgconf:
    externals:
    - spec: [email protected]
      prefix: /usr
    buildable: False
  openssl:
    externals:
    - spec: [email protected]
      prefix: /usr
  groff:
    externals:
    - spec: [email protected]
      prefix: /usr
  autoconf:
    externals:
    - spec: [email protected]
      prefix: /usr
  findutils:
    externals:
    - spec: [email protected]
      prefix: /usr
  git:
    externals:
    - spec: [email protected]~tcltk
      prefix: /usr
  tar:
    externals:
    - spec: [email protected]
      prefix: /usr
  subversion:
    externals:
    - spec: [email protected]
      prefix: /usr
  cmake:
    externals:
    - spec: [email protected]
      prefix: /usr
    - spec: [email protected]
      prefix: /work/y07/shared/utils/core/cmake/3.21.3
  gmake:
    externals:
    - spec: [email protected]
      prefix: /usr
  diffutils:
    externals:
    - spec: [email protected]
      prefix: /usr

Firedrake

Installation

  1. Clone the repo:

    git clone https://github.com/firedrakeproject/firedrake-spack.git
# or
git clone [email protected]:firedrakeproject/firedrake-spack.git

  2. Add the repository to spack spack repo add <repo directory>

  3. Create an spack environment spack env create -d ./firedrake

  4. Activate that environment spack env activate -p ./firedrake

  5. To avoid a bunch of errors add a whole bunch of packages to the development package list:

    spack develop py-firedrake@develop
spack develop libsupermesh@develop
spack develop petsc@develop
spack develop chaco@petsc
spack develop py-fiat@develop
spack develop py-finat@develop
spack develop py-islpy@develop
spack develop py-petsc4py@develop
spack develop py-pyadjoint@develop
spack develop py-pyop2@develop
spack develop py-coffee@develop
spack develop py-loopy@develop
spack develop py-cgen@develop

spack develop py-codepy@develop
spack develop py-genpy@develop
spack develop py-tsfc@develop
spack develop py-ufl@develop

  6. To work around the fact that /home is not accessible from compute nodes the location of the firedrake repo needs to be set inside $SPACK_ENV/spack.yaml:

    spack:
  repos:
  - /work/[budget code]/[budget code]/[$USER]/workspace/firedrake-spack

    Where the path should point to the repo cloned in step 1.

  7. Then custom configure the packages inside $SPACK_ENV/spack.yaml:

    spack:
  include:
  - packages.yaml

  8. And create $SPACK_ENV/packages.yaml with contents:

    packages:
  all:
    compiler: [[email protected]]
    providers:
      mpi: [cray-mpich]
      blas: [cray-libsci]
      lapack: [cray-libsci]
      scalapack: [cray-libsci]
  netlib-scalapack:
    externals:
      # Pretend cray-libsci is netlib-scalapack
      - spec: [email protected]
        modules:
        - cray-libsci/21.08.1.2
    buildable: False
  py-numpy:
    externals:
    - spec: [email protected]
      modules:
      - cray-libsci/21.08.1.2
      - cray-python/3.9.4.1
      prefix: /opt/cray/pe/python/3.9.4.1/
    buildable: False
  py-scipy:
    externals:
    - spec: [email protected]
      modules:
      - cray-libsci/21.08.1.2
      - cray-python/3.9.4.1
      prefix: /opt/cray/pe/python/3.9.4.1/
    buildable: False

    If using AMD or Cray compilers replace the compiler above ([[email protected]]) with [[email protected]] or [[email protected]].

  9. Add Firedrake to the spec for the environment

    spack add py-firedrake@develop \
    %[email protected] \
    ^[email protected] \
    ^[email protected]%[email protected] \
    ^[email protected] \
    ^firedrake.petsc@develop+fftw \
        cflags=\"-O3 -march=native -mtune=native\" \
        cxxflags=\"-O3 -march=native -mtune=native\" \
        fflags=\"-O3 -march=native -mtune=native -ffree-line-length-512\"

  10. Concretize (and log) spack concretize -f 2>&1 | tee $SPACK_ENV/conc.log

    • Splitting the concretize and install steps into 2 distinct parts allows you to review what is being installed before the lengthy installation process begins.

  11. Install (and log) spack install --fail-fast 2>&1 | tee $SPACK_ENV/spack-firedrake-install.log

Testing

Testing must be run on a compute node. An interactive session can be started using

srun --nodes=1 --exclusive --time=00:20:00 \
               --partition=standard --qos=short --reservation=shortqos \
               --account=[budget code] --pty /bin/bash

Alternatively submit a jobscript, see additional notes.

  1. Test you can import Firedrake by running python -c "from firedrake import *"
    • If this fails, before trying anything else, deactivate the environment with spack env deactivate and reactivate with spack env activate -p ./firedrake (as above) and try running python -c "from firedrake import *" again. This appears to be a shortcoming of spack.
  2. Run the basic functionality tests: 
    cd $SPACK_ENV/py-firedrake
pytest tests/regression/ -m "not parallel" -k "poisson_strong or stokes_mini or dg_advection"
    • When running the environment on the compute nodes the variable $HOME needs to be set to something like /work/_projectcode_/_projectcode_/_username_ or /tmp as many dependencies expect to find configuration in $HOME.
    • We don't run parallel tests due to an issue with the current parallel pytest hook, this is in the process of being fixed.
  3. Run the full test suite: 
    cd $SPACK_ENV/src/firedrake
pytest tests -m "not parallel"

Interoperability with pip

If you pip install a Python package on ARCHER2 with or without the Spack environment active, it will get installed as a user, and as such be located in the $HOME directory. This is an issue since the $HOME directory is not mounted on the compute nodes.

The obvious solution to this is not to use pip to install the package and instead attempt to add it to the environment. If the PyPI package is named foo, the corresponding Spack package is likely called py-foo. Spack's builtin repository can be searched by executing spack list foo or spack list py-foo.

If the package is not present the correct solution is to create one and upstream it into Spack's builtin package repository. There are instructions in Spack's documentation on how to do this.

Additional notes:

This page is based off installation notes available here. These notes contain more details of bugs you may encounter and how to build with other compilers.

Example jobscript:

#!/bin/bash
#SBATCH -p standard
#SBATCH -A [budget code]
#SBATCH -J spack
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --qos=standard
#SBATCH -t 0:10:00

myScript="run.sh"

module purge
module load load-epcc-module

module load PrgEnv-gnu/8.1.0
module swap gcc gcc/10.2.0

module swap cray-mpich cray-mpich/8.1.9
module swap cray-dsmml cray-dsmml/0.2.1
module swap cray-libsci cray-libsci/21.08.1.2
module load xpmem
module load cmake/3.21.3
module load cray-python/3.9.4.1

export HOME=/work/[budget code]/[budget code]/[$USER]
source /work/[budget code]/[budget code]/[$USER]/workspace/spack/share/spack/setup-env.sh
spack env activate /work/[budget code]/[budget code]/[$USER]/workspace/firedrake

./${myScript}
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