Installation without Network

2. Installation without Network#

If you need to install Firedrake on some HPC without internet access, you can use the source mirror feature of spack. A mirror is a URL that points to a directory, either on the local filesystem or on some server, containing tarballs for all of Spack’s packages.

We assume the local host can access the network (github, etc.). If the login node can access the network, the operations on the local host can be executed on the login node. Generally, HPC uses shared storage, so there is no need to arhive and upload the downloaded packages.

In the following, we will install spack and firedrake in directory $HOME/opt.

Note that the multi-line commands are connected by “&& \” for copy and paste.

Here is a list of web pages on spack and installing firedrake using spack:

  1. spack install:

  2. spack mirror:

  3. firedrake spack:

2.1. Local host#

The following command are run on local host with internet access.

2.1.1. Create installation directory#

mkdir -p $HOME/opt

2.1.2. Clone spack#

cd $HOME/opt && \
git clone -c feature.manyFiles=true https://github.com/lrtfm/spack.git && \
pushd spack && \
git checkout lrtfm/develop && \
popd && \
source $HOME/opt/spack/share/spack/setup-env.sh

Note

Here, we clone spack from https://github.com/lrtfm/spack.git, a fork of spack, and use the branch lrtfm/develop, which have some patchs. You could clone spack from the offical source https://github.com/spack/spack.git.

Note

Add the following command to $HOME/.bashrc to enable the shell support of spack.

source $HOME/opt/spack/share/spack/setup-env.sh

2.1.3. Create mirror for bootstrap#

spack bootstrap mirror --binary-packages $HOME/opt/bootstrap

The output looks like:

==> Adding "clingo-bootstrap@spack+python %gcc target=x86_64" and dependencies to the mirror at /home/xyz/opt/bootstrap/bootstrap_cache

==> Adding "gnupg@2.3: %gcc target=x86_64" and dependencies to the mirror at /home/xyz/opt/bootstrap/bootstrap_cache
==> Adding "patchelf@0.13.1: %gcc target=x86_64" and dependencies to the mirror at /home/xyz/opt/bootstrap/bootstrap_cache
==> Adding "gnuconfig" and dependencies to the mirror at /home/xyz/opt/bootstrap/bootstrap_cache
==> Adding binary packages from "https://github.com/spack/spack-bootstrap-mirrors/releases/download/v0.4/bootstrap-buildcache.tar.gz" to the mirro
r at /home/xyz/opt/bootstrap/bootstrap_cache

To register the mirror on the platform where it's supposed to be used, move "/home/xyz/opt/bootstrap" to its final location and run the following
command(s):

  % spack bootstrap add --trust local-sources <final-path>/metadata/sources
  % spack bootstrap add --trust local-binaries <final-path>/metadata/binaries

2.1.4. Pack spack and bootstrap#

tar -czvf spack.tar.gz spack
tar -czvf bootstrap.tar.gz bootstrap

2.1.5. Clone firedrake-spack#

cd $HOME/opt && \
git clone https://github.com/lrtfm/firedrake-spack.git && \
pushd firedrake-spack && \
git checkout lrtfm/air-gapped-install && \
popd

Note

Here, we clone firedrake-spack from https://github.com/lrtfm/firedrake-spack.git, which have some patchs. You may clone firedrake-spack from the offical source https://github.com/firedrakeproject/firedrake-spack.git.

2.1.6. Pack firedrake-spack#

tar -czvf firedrake-spack.tar.gz firedrake-spack

2.1.7. Add repo to spack#

spack repo add firedrake-spack

Note

This command can be run in an spack env which will be created below

2.1.8. Check the installation of spack#

The command spack info py-firedrake should have the following output

$ spack info py-firedrake
PythonPackage:   py-firedrake

Description:
    Firedrake is an automated system for the portable solution of partial
    differential equations using the finite element method (FEM)

Homepage: https://firedrakeproject.org

Preferred version:
    develop    [git] https://github.com/firedrakeproject/firedrake.git on branch master

Safe versions:
    develop    [git] https://github.com/firedrakeproject/firedrake.git on branch master

Deprecated versions:
    None

Variants:
    Name [Default]               When    Allowed values    Description
    =========================    ====    ==============    ===============================================

    64-bit-indices [off]         --      on, off           Install PETSc using 64bit indices
    build_system [python_pip]    --      python_pip        Build systems supported by the package
    complex [off]                --      on, off           Install Firedrake in complex mode
    minimal-petsc [off]          --      on, off           Build PETSc with minimal packages for Firedrake
    slepc [off]                  --      on, off           Install SLEPc and slepc4py

Build Dependencies:
    eigen            mpi            py-cython  py-h5py        py-mpi4py    py-pip        py-pyadjoint  py-scipy       py-sympy  py-vtk    slepc
    libspatialindex  petsc          py-fiat    py-islpy       py-numpy     py-pkgconfig  py-pyop2      py-setuptools  py-tsfc   py-wheel
    libsupermesh     py-cachetools  py-finat   py-matplotlib  py-petsc4py  py-progress   py-requests   py-slepc4py    py-ufl    python

Link Dependencies:
    eigen  libspatialindex  libsupermesh  mpi  petsc  python  slepc

Run Dependencies:
    eigen            petsc          py-finat       py-mpi4py    py-pip        py-pyop2         py-scipy       py-tsfc  slepc
    libspatialindex  py-cachetools  py-h5py        py-nbval     py-pkgconfig  py-pytest        py-setuptools  py-ufl
    libsupermesh     py-cython      py-islpy       py-numpy     py-progress   py-pytest-xdist  py-slepc4py    py-vtk
    mpi              py-fiat        py-matplotlib  py-petsc4py  py-pyadjoint  py-requests      py-sympy       python

Now, the contents of $HOME/opt should looks like this:

$ ls -lha
total 214M
drwxrwxr-x  4 z2yang z2yang  112 Oct 30 15:17 .
drwxrwxr-x  3 z2yang z2yang   47 Oct 30 15:02 ..
drwxrwxr-x  5 z2yang z2yang  204 Oct 30 15:16 firedrake-spack
-rw-rw-r--  1 z2yang z2yang 211K Oct 30 15:17 firedrake-spack.tar.gz
drwxrwxr-x 10 z2yang z2yang 4.0K Oct 30 15:17 spack
-rw-rw-r--  1 z2yang z2yang 214M Oct 30 15:15 spack.tar.gz

2.2. Remote host#

The following operations are execuated on compute nodes without internet access.

  1. Installation commands should be run in compute nodes (Is this true?). In HPCs using slurm, you can use srun to start an interactive terminal:

    srun -p xahctest --pty --export=ALL -N 1 -n 64 --exclusive /bin/bash

    or use salloc first and then login to the nodes by using ssh:

    salloc -p xahctest -N 1 -n 4

  2. You should add slurm as external package of spack on system using slurm to submit jobs:

    spack external find slurm

  1. Requirements on compiler:

    1. As compilling openblas@0.3.12 using gcc@7.3.1 will result in error, we use gcc@9.4.0. Because Amazon Linux GCC 7.3.1 has the patch gcc-bug-87467, spack change the conflict rule for openblas when it is compiled by gcc@7 in spack-pr-3443. However, GCC 7.3.1 on some hosts do not have this patch, which will result in error.

    2. The current version of petsc in firedrakeproject will break when using some compilers: https://lists.mcs.anl.gov/pipermail/petsc-users/2023-April/048482.html. Patch has been added to branch lrtfm/air-gapped-install of firedrake-spack.

2.2.1. Install spack#

  1. Create installation directory

    mkdir -p $HOME/opt

  2. Upload files

    Upload firedrake-spack.gz, spack.tar.gz, and bootstrap.tar.gz to directory $HOME/opt on the server.

  3. Unpack the files and install spack

    cd $HOME/opt && \
tar -zxf spack.tar.gz && \
tar -zxf bootstrap.tar.gz && \
source $HOME/opt/spack/share/spack/setup-env.sh && \
spack bootstrap add --trust local-sources $HOME/opt/bootstrap/metadata/sources && \
spack bootstrap add --trust local-binaries $HOME/opt/bootstrap/metadata/binaries

    Note

    Add the following command to the file $HOME/.bashrc to add shell support for spack.

    source $HOME/opt/spack/share/spack/setup-env.sh

    Tip

    On some workstations, the content of the /tmp directory may not have execution permissions. You need to change the spack build directory as follows.

    mkdir -p $HOME/.spack && \
cat > $HOME/.spack/config.yaml <<EOF
config:
  build_stage:
    - \$user_cache_path/stage
EOF

  4. Install the firedrake-spack repo

    cd $HOME/opt && \
tar -zxf firedrake-spack.tar.gz && \
spack repo add firedrake-spack       # Can be run after the creation of the env

2.2.2. Create spack env firedrake#

  1. Create spack env

    FIREDRAKE_ENV_NAME=firedrake-complex-int64 && \
spack env create -d $FIREDRAKE_ENV_NAME && \
spack env activate -p $FIREDRAKE_ENV_NAME && \
spack -e $SPACK_ENV config add concretizer:unify:true

  2. Add packages to the env

    You can add or delete some packages here. We will take the complex+int64 version as an example.

    spack add python py-firedrake@develop%gcc +64-bit-indices+complex ^mpich ^openblas \
    ^petsc+mumps+scalapack+int64+complex+libyaml+parmmg+mmg ^llvm@12.0.1 \
    ^hypre+complex+int64+superlu-dist && \
spack add py-pygmsh py-meshio py-tqdm py-pyyaml

  1. Run spack concretize

    spack concretize -f 2>&1 | tee $SPACK_ENV/spack-firedrake-concretize.log

  2. Check the directory $SPACK_ENV

    $ ls -la $SPACK_ENV
total 620
drwxrwxr-x 3 z2yang z2yang    118 Oct 30 16:01 .
drwxrwxr-x 5 z2yang z2yang    147 Oct 30 15:33 ..
drwxrwxr-x 4 z2yang z2yang     89 Oct 30 16:01 .spack-env
-rw-rw-r-- 1 z2yang z2yang  54343 Oct 30 16:01 spack-firedrake-concretize.log
-rw-rw-r-- 1 z2yang z2yang 572917 Oct 30 16:01 spack.lock
-rw-rw-r-- 1 z2yang z2yang    457 Oct 30 16:01 spack.yaml

    We will need the spack.lock file to create mirror in local host.

2.2.3. Create mirror on local host#

The following commands run on local host.

We will create a firedrake env on local host by using the file spack.lock. And then create mirror for the env. After that, we upload the mirror to remote host.

  1. Download spack.lock from remote host to directory $HOME/opt on local host.

  2. Create mirror (May take 10 mins)

    cd $HOME/opt && \
spack env create -d firedrake-mirror-env spack.lock && \
spack env activate -p ./firedrake-mirror-env && \
time spack mirror create -a -d spack-firedrake-mirror 2>&1 | tee creat-mirror.logs

    The above command should have the following output:

    ==> Summary for mirror in file:///home/z2yang/z2yang/local/opt/spack-firedrake-mirror
==> Archive stats:
    0    already present
    244  added
    0    failed to fetch.

real    10m56.048s
user    1m1.559s
sys     0m13.604s

    If there are some fails failed to fetch, you can clean the cache first and then create the mirror

    spack clean -ds && \
time spack mirror create -a -d spack-firedrake-mirror 2>&1 | tee creat-mirror.logs

  3. Pack the mirror

    tar -czvf spack-firedrake-mirror.tar.gz spack-firedrake-mirror

2.2.4. Add mirror#

The following commands run on remote host

  1. Upload mirror

    Upload spack-firedrake-mirror.tar.gz to directory $HOME/opt on the remote host.

  2. Unpack the mirrors

    cd $HOME/opt && \
tar -xzvf spack-firedrake-mirror.tar.gz

  3. Add the mirror to spack

    cat > $HOME/.spack/mirrors.yaml <<EOF
mirrors:
  local_filesystem: file://$HOME/opt/spack-firedrake-mirror
EOF

  4. Check the mirror.

    The output of spack mirror lsit should looks like:

    $ spack mirror list
local_filesystem    file://<your-home-path>/opt/spack-firedrake-mirror
spack-public        https://mirror.spack.io

2.2.5. Install Firedrake#

  1. Run spack develop to avoid some errors

    spack develop py-firedrake@develop && \
spack develop libsupermesh@develop && \
spack develop petsc@develop && \
spack develop slepc@develop && \
spack develop py-fiat@develop && \
spack develop py-finat@develop && \
spack develop py-islpy@develop && \
spack develop py-petsc4py@develop && \
spack develop py-slepc4py@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

    Note

    The int32 version needs the following command:

    spack develop chaco@petsc

  2. Install

    Run the following command to install (It will take 1-2 hours for the first time depending on the system). It may be failed. Good Luck!

    spack concretize -f 2>&1 | tee $SPACK_ENV/spack-firedrake-develop.log && \
time spack install --fail-fast --show-log-on-error \
    --log-file $SPACK_ENV/spack-firedrake-install.log --log-format cdash

    The last lines of the output:

    [+] /home/z2yang/z2yang/server2/opt/spack/opt/spack/linux-ubuntu22.04-cascadelake/gcc-11.3.0/py-firedrake-develop-il3tmyuhh37rnaww3u2yxhxcqawp3hh6
==> Updating view at /home/z2yang/z2yang/server2/opt/firedrake-complex-int64/.spack-env/view

real    184m44.242s
user    836m56.348s
sys     97m42.901s

  3. Deactivate the env

    despacktivate

    Feel free to ignore the following warnings

    $ despacktivate
==> Warning: Skipping reversal of unreversable operation<class 'spack.util.environment.UnsetEnv'> PETSC_ARCH
==> Warning: Skipping reversal of unreversable operation<class 'spack.util.environment.UnsetEnv'> PETSC_ARCH
==> Warning: Skipping reversal of unreversable operation<class 'spack.util.environment.UnsetEnv'> PETSC_ARCH
==> Warning: Skipping reversal of unreversable operation<class 'spack.util.environment.UnsetEnv'> PETSC_ARCH

2.2.6. Usage#

  1. Activate the env

    cd $HOME/opt && \
spack env activate -p $FIREDRAKE_ENV_NAME

  2. Test

    cd $SPACK_ENV/py-firedrake && \
pytest tests/regression/ -k "poisson_strong or stokes_mini or dg_advection"
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