Official documentation below.
For the development documentation of the deployment stack, see
deploy/README.md.
We build Docker images based on Ubuntu 18.04, and the same settings can be used to set Spack up on the desktops:
$ git clone https://github.com/BlueBrain/spack.git
$ mkdir ~/.spack
$ cp spack/sysconfig/ubuntu-18.04/*.yaml ~/.spack
$ sed -e 's/#.*//g' spack/sysconfig/ubuntu-18.04/packages|xargs -r sudo apt-get install
$ spack compiler find
$ . spack/share/spack/setup-env.sh
Now to build software, i.e., MVDTool:
$ git clone git@github.com:BlueBrain/MVDTool.git
$ cd MVDTool
$ spack setup mvdtool@develop
$ cd build
$ ../spconfig.py ..
$ make
Alternatively, to quickly install software based on a local source checkout:
$ git clone git@github.com:BlueBrain/MVDTool.git
$ cd MVDTool
$ spack diy -y --test=root mvdtool@my-custom-version
This version of MVDTool can now be re-used by Spack to build other
software, when ^mvdtool@my-custom-version is appended to the appropriate
spec.
On BB5, clone this repository to get started using Spack. The following commands are a good way to get started:
$ git clone https://github.com/BlueBrain/spack.git
$ . spack/share/spack/setup-env.sh
$ spack spec -I spykfunc|head -n 15
Input spec
--------------------------------
- spykfunc
Concretized
--------------------------------
- spykfunc@0.12.0%gcc@4.8.5 arch=linux-rhel7-x86_64
- ^hdf5@1.10.4%gcc@4.8.5~cxx~debug~fortran+hl~mpi+pic+shared~szip~threadsafe arch=linux-rhel7-x86_64
- ^zlib@1.2.11%gcc@4.8.5+optimize+pic+shared arch=linux-rhel7-x86_64
- ^highfive@1.6%gcc@4.8.5~boost build_type=RelWithDebInfo ~mpi arch=linux-rhel7-x86_64
- ^cmake@3.13.0%gcc@4.8.5~doc+ncurses+openssl+ownlibs~qt arch=linux-rhel7-x86_64
- ^ncurses@6.1%gcc@4.8.5~symlinks~termlib arch=linux-rhel7-x86_64
- ^pkgconf@1.5.4%gcc@4.8.5 arch=linux-rhel7-x86_64
- ^openssl@1.1.1%gcc@4.8.5+systemcerts arch=linux-rhel7-x86_64
- ^perl@5.26.2%gcc@4.8.5+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-rhel7-x86_64
Here we see all the software that would be required to build one program of
the circuit building workflow.
The leading - sign in the output signifies that this particular piece of
software would have to be built from scratch.
To reduce the amount of time spent compiling the same software, we can
configure Spack to use centrally build packages on BB5:
$ mkdir -p ~/.spack
$ ln -s /gpfs/bbp.cscs.ch/apps/hpc/jenkins/config/*.yaml ~/.spack
$ export SPACK_INSTALL_PREFIX=$HOME/software
The configuration thus set up uses the environment variable
SPACK_INSTALL_PREFIX as the installation directory for packages.
With the above setup, any packages installed can be found in ~/software.
Every call to Spack reads this environment variable, temporarily changing
it is a good way to test changes.
After adding the correct setup, the dependency graph of our software to install has changed significantly:
$ spack spec -I spykfunc|head -n 15
Input spec
--------------------------------
- spykfunc
Concretized
--------------------------------
[+] spykfunc@0.12.0%gcc@6.4.0 arch=linux-rhel7-x86_64
[^] ^hdf5@1.10.4%gcc@6.4.0~cxx~debug~fortran+hl~mpi+pic+shared~szip~threadsafe arch=linux-rhel7-x86_64
[^] ^zlib@1.2.11%gcc@6.4.0+optimize+pic+shared arch=linux-rhel7-x86_64
[^] ^highfive@1.6%gcc@6.4.0~boost build_type=RelWithDebInfo ~mpi arch=linux-rhel7-x86_64
[^] ^jdk@1.8.0_191-b12%gcc@6.4.0 arch=linux-rhel7-x86_64
[^] ^mvdtool@1.4%gcc@6.4.0 build_type=RelWithDebInfo ~mpi~python arch=linux-rhel7-x86_64
[+] ^boost@1.68.0%gcc@6.4.0+atomic+chrono~clanglibcpp cxxstd=default +date_time~debug+exception+filesystem+graph~icu+iostreams+locale+log+math~mpi+multithreaded~numpy patches=2ab6c72d03dec6a4ae20220a9dfd5c8c572c5294252155b85c6874d97c323199 ~pic+program_options~python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave arch=linux-rhel7-x86_64
[+] ^cmake@3.13.0%gcc@6.4.0~doc+ncurses+openssl+ownlibs~qt arch=linux-rhel7-x86_64
[^] ^py-bb5@0.2%gcc@6.4.0 patches=22a56c05830b2e40dffbcbbc70cd2e95c006e13cb4da867f1b7e0d6292ff6618 arch=linux-rhel7-x86_64
This tells us that all required software is either installed in an upstream
database or provided as external packages in the package database ([^]
and [+], respectively).
To see all installed packages available through the central installations directly, use:
$ spack find -lv|&head
==> 265 installed packages
-- linux-rhel7-x86_64 / gcc@6.4.0 -------------------------------
s26d2n5 arrow@0.11.0 build_type=Release +parquet+python
ocjfhxp arrow@0.11.0 build_type=Release +parquet+python
figbvwx autoconf@2.69
py26izr automake@1.13.4
v6f6e33 binutils@2.31.1+gold~libiberty+nls~plugins
j4xbdil bison@3.0.5
o4mvxg2 boost@1.68.0+atomic+chrono~clanglibcpp cxxstd=default +date_time~debug+exception+filesystem+graph~icu+iostreams+locale+log+math~mpi+multithreaded~numpy patches=2ab6c72d03dec6a4ae20220a9dfd5c8c572c5294252155b85c6874d97c323199 ~pic+program_options~python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave
lnnxkhm bzip2@1.0.6+shared
These packages act like locally installed packages, only that you will not
be able to uninstall them.
Spack has access to the full dependency graph of the packages above, and
environments will be set accordingly.
The configuration of upstream package databases can be found in
~/.spack/upsreams.yaml.
Additional packages are installed and available as external software, where
Spack will trim the dependency tree and only consider the external package
without any sub-dependencies.
The information for external packages is stored in
~/.spack/packages.yaml, and can also be printed on the command line:
$ spack config get packages|&grep -C 1 paths:|tail -n 20
--
util-macros:
paths:
util-macros@1.19.1: /gpfs/bbp.cscs.ch/apps/hpc/jenkins/deploy/tools/2018-12-19/linux-rhel7-x86_64/gcc-6.4.0/util-macros-1.19.1-et5doh3u6t
--
valgrind:
paths:
valgrind@3.13.0 +boost~mpi+only64bit+ubsan: /gpfs/bbp.cscs.ch/apps/hpc/jenkins/deploy/tools/2018-12-19/linux-rhel7-x86_64/gcc-6.4.0/valgrind-3.13.0-z5rpvffayd
--
xz:
paths:
xz@5.2: /usr
--
zeromq:
paths:
zeromq@4.2.5 +libsodium: /gpfs/bbp.cscs.ch/apps/hpc/jenkins/deploy/external-libraries/2019-01-04/linux-rhel7-x86_64/gcc-6.4.0/zeromq-4.2.5-qvzt3welbs
--
zlib:
paths:
zlib@1.2.11 +optimize+pic+shared: /gpfs/bbp.cscs.ch/apps/hpc/jenkins/deploy/external-libraries/2019-01-04/linux-rhel7-x86_64/gcc-6.4.0/zlib-1.2.11-w43e56tzqj
Centrally build modules can be made available by sourcing the following script:
$ . /gpfs/bbp.cscs.ch/apps/hpc/jenkins/config/modules.sh
$ module avail|&tail
/gpfs/bbp.cscs.ch/apps/hpc/jenkins/deploy/applications/2018-12-19/modules/tcl/linux-rhel7-x86_64
functionalizer/3.11.0 py-bluepyopt/1.6.56/python2
neurodamus/hippocampus/python3 py-bluepyopt/1.6.56/python3
neurodamus/master/python3 py-efel/3.0.22/python2
neurodamus/plasticity/python3 py-efel/3.0.22/python3
neurodamus/plasticity/python3-knl spykfunc/0.12.0/python3
parquet-converters/0.3 steps/3.3.0/python3/parallel
py-bluepymm/0.6.38/python2 synapsetool/0.3.2/parallel
py-bluepymm/0.6.38/python3 touchdetector/4.3.3
The output above shows the applications category of modules, which are
generated from centrally build packages.
To update the version of any of these modules, edit the corresponding YAML
configuration:
$ vim spack/deploy/packages/bbp-packages.yaml
If there are dependencies used in a broader scope/by several software
packages, consider adding them to one of the following steps in the
deployment chain (all found in spack/deploy/packages):
parallel-librariesfor everything using MPI or highly performantserial-libraries,python-packagesfor general purpose librariesexternal-librariesfor packages that are seldomly changed and for which the dependency graph may be truncated by Spack (e.g., Spark, Python) - mainly dependencies for building
Commit the changes and file a pull request on Github. Jenkins will build the additional software required, with all output available in a separate directory:
$ ls /gpfs/bbp.cscs.ch/apps/hpc/jenkins/pulls/165
config deploy mirror spack
Software packages and modules should be updated upon pull request merge and
a nightly basis.
The config directory contains the same configuration files as the regular
deployment and can be used instead.
Spack is a multi-platform package manager that builds and installs multiple versions and configurations of software. It works on Linux, macOS, and many supercomputers. Spack is non-destructive: installing a new version of a package does not break existing installations, so many configurations of the same package can coexist.
Spack offers a simple "spec" syntax that allows users to specify versions and configuration options. Package files are written in pure Python, and specs allow package authors to write a single script for many different builds of the same package. With Spack, you can build your software all the ways you want to.
See the Feature Overview for examples and highlights.
To install spack and your first package, make sure you have Python. Then:
$ git clone https://github.com/spack/spack.git
$ cd spack/bin
$ ./spack install libelf
Full documentation for Spack is the first place to look.
Try the Spack Tutorial, to learn how to use spack, write packages, or deploy packages for users at your site.
See also:
- Technical paper and slides on Spack's design and implementation.
- Short presentation from the Getting Scientific Software Installed BOF session at Supercomputing 2015.
Spack is an open source project. Questions, discussion, and contributions are welcome. Contributions can be anything from new packages to bugfixes, or even new core features.
If you are interested in contributing to spack, join the mailing list. We're using Google Groups for this:
Spack has a Slack channel where you can chat about all things Spack:
Sign up here to get an invitation mailed to you.
You can follow @spackpm on Twitter for
updates. Also, feel free to @mention us in in questions or comments
about your own experience with Spack.
Contributing to Spack is relatively easy. Just send us a
pull request.
When you send your request, make develop the destination branch on the
Spack repository.
Your PR must pass Spack's unit tests and documentation tests, and must be PEP 8 compliant. We enforce these guidelines with Travis CI. To run these tests locally, and for helpful tips on git, see our Contribution Guide.
Spack uses a rough approximation of the
Git Flow
branching model. The develop branch contains the latest
contributions, and master is always tagged and points to the latest
stable release.
Many thanks go to Spack's contributors.
Spack was created by Todd Gamblin, tgamblin@llnl.gov.
If you are referencing Spack in a publication, please cite the following paper:
- Todd Gamblin, Matthew P. LeGendre, Michael R. Collette, Gregory L. Lee, Adam Moody, Bronis R. de Supinski, and W. Scott Futral. The Spack Package Manager: Bringing Order to HPC Software Chaos. In Supercomputing 2015 (SC’15), Austin, Texas, November 15-20 2015. LLNL-CONF-669890.
Spack is distributed under the terms of both the MIT license and the Apache License (Version 2.0). Users may choose either license, at their option.
All new contributions must be made under both the MIT and Apache-2.0 licenses.
See LICENSE-MIT, LICENSE-APACHE, COPYRIGHT, and NOTICE for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
LLNL-CODE-647188