9.6 KiB
9.6 KiB
The PSI Spack Deployment
How to use on Merlin systems (Merlin6/Merlin7)
module load spack
# If you want to use the unstable software stack do:
spack env activate -p unstable
Install your own software
# Check if your package is already implemented in Spack
# You can also use the following website: https://packages.spack.io/
[stable] user@login001:~> spack list $pkg_name # e.g opal
# Check the package variants you want to set e.g +cuda +openmp ^openmpi ...
[stable] user@login001:~> spack info $pkg_name # e.g opal
# Add your package to the environment
[stable] user@login001:~> spack add $pkg_name@version +variant1 ^dep1@version1
# If you want to install from local source clone your source under
# /afs/psi.ch/sys/spack/user/$USER/spack-environment/$pkg_name
# and tell Spack you want to use it using:
[stable] user@login001:~> spack develop $pkg_name@version # Skip this if you don't want to develop from local source
# Check the whole dependency tree of your spec and
# if you don't need to set more variants
[stable] user@login001:~> spack concretize
# Install your packages
[stable] user@login001:~> spack install # -v for verbose
# Load your package
[stable] user@login001:~> spack load $pkg_name@version +variant1 ^dep1@version1
# Submit your script
[stable] user@login001:~> sbatch batch.script
Switching between environments
There are two environment available to users; stable and unstable.
The first one is loaded by default when loading the module.
If you want to switch between the two and use different software stack you can use the following command:
spack env activate -p unstable # or stable
Managing your environments
When adding the following command you actually add a package to your own software stack;
[stable] user@login001:~> spack add $pkg_name@version +variant1 ^dep1@version1
You can check which package will be concretized and are in your environment using;
[unstable] user@login001:~> spack find
==> In environment unstable
==> 1 root specs
- visit ~adios2+vtkm+gui
==> Included specs
-- no arch / gcc ------------------------------------------------
gromacs%gcc
-- no arch / gcc@12.3.0 -----------------------------------------
cp2k@2024.1%gcc@12.3.0 opal@master%gcc@12.3.0 py-alphafold@2.3.2%gcc@12.3.0
cp2k@2024.1%gcc@12.3.0 py-alphafold@2.3.2%gcc@12.3.0 quantum-espresso@7.3.1%gcc@12.3.0
-- no arch / oneapi@2024.1.0 ------------------------------------
gromacs@2024.1%oneapi@2024.1.0
==> Installed packages
-- linux-rhel7-x86_64 / gcc@4.8.5 -------------------------------
autoconf@2.72 curl@8.7.1 gdbm@1.23 libffi@3.4.6 mpfr@4.2.1 pkg-config@0.29.2 readline@8.2
autoconf@2.72 diffutils@3.10 gettext@0.19.8.1 libidn2@2.3.7 mpfr@4.2.1 pkg-config@0.29.2 sqlite@3.43.2
autoconf-archive@2023.02.20 diffutils@3.10 gettext@0.19.8.1 libmd@1.0.4 ncurses@6.5 py-fypp@3.1 texinfo@7.0.3
autoconf-archive@2023.02.20 expat@2.6.2 git@2.42.0 libpciaccess@0.17 ncurses@6.5 py-fypp@3.1 util-linux-uuid@2.36.2
automake@1.16.5 findutils@4.9.0 glibc@2.17 libsigsegv@2.14 nghttp2@1.57.0 py-pip@23.1.2 util-macros@1.19.3
automake@1.16.5 findutils@4.9.0 glibc@2.17 libsigsegv@2.14 ninja@1.11.1 py-setuptools@59.4.0 xz@5.4.6
berkeley-db@18.1.40 flex@2.6.3 gmake@4.4.1 libtool@2.4.7 numactl@2.0.14 py-wheel@0.41.2 zlib-ng@2.1.6
berkeley-db@18.1.40 gawk@5.3.0 gmake@4.4.1 libunistring@1.2 nvhpc@24.3 python@3.8.18 zlib-ng@2.1.6
binutils@2.42 gawk@5.3.0 gmp@6.2.1 libxcrypt@4.4.35 openssh@9.7p1 python@3.9.18 zstd@1.5.6
binutils@2.42 gcc@12.3.0 gmp@6.2.1 libxml2@2.10.3 openssl@3.3.0 python@3.11.7 zstd@1.5.6
binutils@2.42 gcc@12.3.0 krb5@1.20.1 m4@1.4.19 openssl@3.3.0 python-venv@1.0
bison@3.8.2 gcc-runtime@4.8.5 libbsd@0.12.1 m4@1.4.19 pcre2@10.43 python-venv@1.0
bzip2@1.0.8 gcc-runtime@4.8.5 libedit@3.1-20230828 mpc@1.3.1 perl@5.38.0 re2c@2.2
bzip2@1.0.8 gdbm@1.23 libevent@2.1.12 mpc@1.3.1 perl@5.38.0 readline@8.2
-- linux-rhel7-x86_64 / gcc@12.3.0 ------------------------------
abseil-cpp@20240116.2 libogg@1.3.5 py-beniget@0.3.0 py-ml-collections@0.1.0 py-tabulate@0.8.9
amrex@18.07 libpng@1.6.39 py-biopython@1.79 py-networkx@2.7.1 py-tensorboard@2.11.2
aria2@1.37.0 libssh2@1.11.0 py-bottleneck@1.3.2 py-numexpr@2.8.4 py-tensorboard-data-server@0.6.1
boost@1.85.0 libtheora@1.1.1 py-cachetools@5.2.0 py-numpy@1.17.5 py-tensorboard-plugin-wit@1.8.1
boost@1.85.0 libxc@6.2.2 py-certifi@2023.7.22 py-numpy@1.21.6 py-tensorflow@2.11.0
c-ares@1.27.0 libxsmm@1.17 py-charset-normalizer@3.3.0 py-oauthlib@3.2.2 py-termcolor@1.1.0
cmake@3.27.9 libyaml@0.2.5 py-chex@0.0.7 py-opt-einsum@3.3.0 py-tomli@2.0.1
cp2k@2024.1 llvm@16.0.6 py-contextlib2@21.6.0 py-packaging@23.1 py-toolz@0.12.0
cp2k@2024.1 lua@5.3.6 py-cython@0.29.36 py-pandas@1.3.4 py-typing-extensions@4.8.0
cuda@12.4.0 lz4@1.9.4 py-decorator@5.1.1 py-pdbfixer@1.7 py-urllib3@1.26.12
fftw@3.3.10 mesa-glu@9.0.2 py-dm-haiku@0.0.9 py-pip@23.0 py-websocket-client@1.6.3
fftw@3.3.10 mesa18@18.3.6 py-dm-tree@0.1.6 py-pip@23.1.2 py-werkzeug@2.0.2
freetype@2.10.2 metis@5.1.0 py-docker@5.0.3 py-ply@3.11 py-wheel@0.37.1
gcc-runtime@12.3.0 mithra@2.0 py-etils@0.9.0 py-poetry-core@1.8.1 py-wheel@0.41.2
gcc-runtime@12.3.0 netlib-scalapack@2.2.0 py-flatbuffers@23.5.26 py-protobuf@3.19.4 py-wrapt@1.15.0
gettext@0.19.8.1 opal@master py-flit-core@3.9.0 py-pyasn1@0.4.8 py-zipp@3.17.0
gl2ps@1.4.2 openblas@0.3.25 py-gast@0.4.0 py-pyasn1-modules@0.2.8 python@3.8.18
googletest@1.12.1 openblas@0.3.26 py-google-auth@2.27.0 py-pybind11@2.12.0 python@3.11.7
gsl@2.7.1 openblas@0.3.26 py-google-auth-oauthlib@0.4.6 py-pytest-runner@6.0.0 python-venv@1.0
h5hut@2.0.0rc6 openjdk@11.0.20.1_1 py-google-pasta@0.2.0 py-python-dateutil@2.8.2 python-venv@1.0
hdf5@1.12.3 openmm@7.5.1 py-grpcio@1.60.1 py-pythran@0.9.11 quantum-espresso@7.3.1
hdf5@1.14.3 openmpi@4.1.6 py-h5py@3.11.0 py-pytz@2023.3 re2@2023-09-01
hdf5@1.14.3 openmpi@4.1.6 py-idna@3.4 py-pyyaml@6.0 rust-bootstrap@1.78.0
hh-suite@3.3.0 osmesa@11.2.0 py-immutabledict@2.2.1 py-requests@2.31.0 slurm@23-11-0-1
hmmer@3.4 parmetis@4.0.3 py-importlib-resources@5.12.0 py-requests-oauthlib@1.3.1 swig@4.1.1
hwloc@2.9.1 pcre@8.45 py-jax@0.3.25 py-rsa@4.9 trilinos@13.4.0
jsoncpp@1.9.5 perl-data-dumper@2.173 py-jaxlib@0.3.25 py-scipy@1.7.0 unzip@6.0
kalign@3.4.0 protobuf@3.19.4 py-jmp@0.0.2 py-setuptools@57.4.0 zip@3.0
libgcrypt@1.10.3 py-absl-py@1.0.0 py-libclang@16.0.0 py-setuptools@69.2.0
libgpg-error@1.49 py-alphafold@2.3.2 py-mako@1.2.4 py-setuptools@69.2.0
libint@2.6.0 py-alphafold@2.3.2 py-markdown@3.3.4 py-setuptools-scm@8.0.4
libjpeg@9f py-astunparse@1.6.3 py-markupsafe@2.1.3 py-six@1.16.0
-- linux-rhel7-x86_64 / oneapi@2024.1.0 -------------------------
gromacs@2024.1 hwloc@2.9.1 intel-oneapi-mkl@2024.0.0 intel-oneapi-runtime@2024.1.0 intel-tbb@2021.9.0 openmpi@4.1.6 slurm@23-11-0-1
==> 257 installed packages
The root spec is the specs that are personal to you and that will be concretized and installed.
The installed packages are either packages that were previously installed by admins or packages that you already installed but that are not root.
If you want to remove this package from your personal env, you can use the following command:
[stable] user@login001:~> spack rm $pkg_name@version +variant1 ^dep1@version1
or
[stable] user@login001:~> spack config edit
spack:
...
specs:
-- - visit~adios2+gui+vtkm ^harfbuzz%gcc@12.3.0
++ []
...
and remove it manually from the spec list.
How to use on other systems
Install Spack
user@supersystem:~> cd /scratch/$USER
user@supersystem:~> git clone -c feature.manyFiles=true https://github.com/spack/spack.git
user@supersystem:~> . spack/share/spack/setup-env.sh
# Add PSI specific recipes
user@supersystem:~> git clone https://gitlab.psi.ch/lsm-hpce/alps/spack-psi.git
user@supersystem:~> spack repo add $PWD/spack-psi
user@supersystem:~> spack install $pkg_name # -v for verbose