.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
.. _getting_started:
===============
Getting Started
===============
--------------------
System Prerequisites
--------------------
Spack has the following minimum system requirements, which are assumed to
be present on the machine where Spack is run:
.. csv-table:: System prerequisites for Spack
:file: tables/system_prerequisites.csv
:header-rows: 1
These requirements can be easily installed on most modern Linux systems;
on macOS, XCode is required. Spack is designed to run on HPC
platforms like Cray. Not all packages should be expected
to work on all platforms. A build matrix showing which packages are
working on which systems is planned but not yet available.
------------
Installation
------------
Getting Spack is easy. You can clone it from the `github repository
<https://github.com/spack/spack>`_ using this command:
.. code-block:: console
$ git clone https://github.com/spack/spack.git
This will create a directory called ``spack``.
.. _shell-support:
^^^^^^^^^^^^^
Shell support
^^^^^^^^^^^^^
Once you have cloned Spack, we recommend sourcing the appropriate script
for your shell:
.. code-block:: console
# For bash/zsh/sh
$ . spack/share/spack/setup-env.sh
# For tcsh/csh
$ source spack/share/spack/setup-env.csh
# For fish
$ . spack/share/spack/setup-env.fish
That's it! You're ready to use Spack.
Sourcing these files will put the ``spack`` command in your ``PATH``, set
up your ``MODULEPATH`` to use Spack's packages, and add other useful
shell integration for :ref:`certain commands <packaging-shell-support>`,
:ref:`environments <environments>`, and :ref:`modules <modules>`. For
``bash`` and ``zsh``, it also sets up tab completion.
In order to know which directory to add to your ``MODULEPATH``, these scripts
query the ``spack`` command. On shared filesystems, this can be a bit slow,
especially if you log in frequently. If you don't use modules, or want to set
``MODULEPATH`` manually instead, you can set the ``SPACK_SKIP_MODULES``
environment variable to skip this step and speed up sourcing the file.
If you do not want to use Spack's shell support, you can always just run
the ``spack`` command directly from ``spack/bin/spack``.
When the ``spack`` command is executed it searches for an appropriate
Python interpreter to use, which can be explicitly overridden by setting
the ``SPACK_PYTHON`` environment variable. When sourcing the appropriate shell
setup script, ``SPACK_PYTHON`` will be set to the interpreter found at
sourcing time, ensuring future invocations of the ``spack`` command will
continue to use the same consistent python version regardless of changes in
the environment.
^^^^^^^^^^^^^^^^^^^^
Bootstrapping clingo
^^^^^^^^^^^^^^^^^^^^
Spack supports using ``clingo`` as an external solver to compute which software
needs to be installed. The default configuration allows Spack to install
``clingo`` from a public buildcache, created by a Github Action workflow. In this
case the bootstrapping procedure is transparent to the user, except for a
slightly long waiting time on the first concretization of a spec:
.. code-block:: console
$ spack find -b
==> Showing internal bootstrap store at "/home/spack/.spack/bootstrap/store"
==> 0 installed packages
$ time spack solve zlib
==> Best of 2 considered solutions.
==> Optimization Criteria:
Priority Criterion Value
1 deprecated versions used 0
2 version weight 0
3 number of non-default variants (roots) 0
4 multi-valued variants 0
5 preferred providers for roots 0
6 number of non-default variants (non-roots) 0
7 preferred providers (non-roots) 0
8 compiler mismatches 0
9 version badness 0
10 count of non-root multi-valued variants 0
11 non-preferred compilers 0
12 target mismatches 0
13 non-preferred targets 0
zlib@1.2.11%gcc@11.1.0+optimize+pic+shared arch=linux-ubuntu18.04-broadwell
real 0m30,618s
user 0m27,278s
sys 0m1,549s
After this command you'll see that ``clingo`` has been installed for Spack's own use:
.. code-block:: console
$ spack find -b
==> Showing internal bootstrap store at "/home/spack/.spack/bootstrap/store"
==> 2 installed packages
-- linux-rhel5-x86_64 / gcc@9.3.0 -------------------------------
clingo-bootstrap@spack python@3.6
Subsequent calls to the concretizer will then be much faster:
.. code-block:: console
$ time spack solve zlib
[ ... ]
real 0m1,222s
user 0m1,146s
sys 0m0,059s
If for security or for other reasons you don't want to or can't install precompiled
binaries, Spack can fall-back to bootstrap ``clingo`` from source files. To forbid
Spack from retrieving binaries from the bootstrapping buildcache, the following
command must be given:
.. code-block:: console
$ spack bootstrap untrust github-actions
==> "github-actions" is now untrusted and will not be used for bootstrapping
since an "untrusted" way of bootstrapping software will not be considered
by Spack. You can verify the new settings are effective with:
.. code-block:: console
$ spack bootstrap list
Name: github-actions UNTRUSTED
Type: buildcache
Info:
url: https://mirror.spack.io/bootstrap/github-actions/v0.1
homepage: https://github.com/alalazo/spack-bootstrap-mirrors
releases: https://github.com/alalazo/spack-bootstrap-mirrors/releases
Description:
Buildcache generated from a public workflow using Github Actions.
The sha256 checksum of binaries is checked before installation.
Name: spack-install TRUSTED
Type: install
Description:
Specs built from sources by Spack. May take a long time.
When bootstrapping from sources, Spack requires a compiler with support
for C++14 (GCC on ``linux``, Apple Clang on ``darwin``) and static C++
standard libraries on ``linux``. Spack will build the required software
on the first request to concretize a spec:
.. code-block:: console
$ spack solve zlib
[+] /usr (external bison-3.0.4-wu5pgjchxzemk5ya2l3ddqug2d7jv6eb)
[+] /usr (external cmake-3.19.4-a4kmcfzxxy45mzku4ipmj5kdiiz5a57b)
[+] /usr (external python-3.6.9-x4fou4iqqlh5ydwddx3pvfcwznfrqztv)
==> Installing re2c-1.2.1-e3x6nxtk3ahgd63ykgy44mpuva6jhtdt
[ ... ]
==> Optimization: [0, 0, 0, 0, 0, 1, 0, 0, 0]
zlib@1.2.11%gcc@10.1.0+optimize+pic+shared arch=linux-ubuntu18.04-broadwell
.. tip::
If you want to speed-up bootstrapping ``clingo`` from sources, you may try to
search for ``cmake`` and ``bison`` on your system:
.. code-block:: console
$ spack external find cmake bison
==> The following specs have been detected on this system and added to /home/spack/.spack/packages.yaml
bison@3.0.4 cmake@3.19.4
"""""""""""""""""""
The Bootstrap Store
"""""""""""""""""""
All the tools Spack needs for its own functioning are installed in a separate store, which lives
under the ``${HOME}/.spack`` directory. The software installed there can be queried with:
.. code-block:: console
$ spack find --bootstrap
==> Showing internal bootstrap store at "/home/spack/.spack/bootstrap/store"
==> 3 installed packages
-- linux-ubuntu18.04-x86_64 / gcc@10.1.0 ------------------------
clingo-bootstrap@spack python@3.6.9 re2c@1.2.1
In case it's needed the bootstrap store can also be cleaned with:
.. code-block:: console
$ spack clean -b
==> Removing software in "/home/spack/.spack/bootstrap/store"
^^^^^^^^^^^^^^^^^^
Check Installation
^^^^^^^^^^^^^^^^^^
With Spack installed, you should be able to run some basic Spack
commands. For example:
.. command-output:: spack spec netcdf-c
In theory, Spack doesn't need any additional installation; just
download and run! But in real life, additional steps are usually
required before Spack can work in a practical sense. Read on...
^^^^^^^^^^^^^^^^^
Clean Environment
^^^^^^^^^^^^^^^^^
Many packages' installs can be broken by changing environment
variables. For example, a package might pick up the wrong build-time
dependencies (most of them not specified) depending on the setting of
``PATH``. ``GCC`` seems to be particularly vulnerable to these issues.
Therefore, it is recommended that Spack users run with a *clean
environment*, especially for ``PATH``. Only software that comes with
the system, or that you know you wish to use with Spack, should be
included. This procedure will avoid many strange build errors.
^^^^^^^^^^^^^^^^^^^^^^^^^^
Optional: Alternate Prefix
^^^^^^^^^^^^^^^^^^^^^^^^^^
You may want to run Spack out of a prefix other than the git repository
you cloned. The ``spack clone`` command provides this
functionality. To install spack in a new directory, simply type:
.. code-block:: console
$ spack clone /my/favorite/prefix
This will install a new spack script in ``/my/favorite/prefix/bin``,
which you can use just like you would the regular spack script. Each
copy of spack installs packages into its own ``$PREFIX/opt``
directory.
.. _compiler-config:
----------------------
Compiler configuration
----------------------
Spack has the ability to build packages with multiple compilers and
compiler versions. Spack searches for compilers on your machine
automatically the first time it is run. It does this by inspecting
your ``PATH``.
.. _cmd-spack-compilers:
^^^^^^^^^^^^^^^^^^^
``spack compilers``
^^^^^^^^^^^^^^^^^^^
You can see which compilers spack has found by running ``spack
compilers`` or ``spack compiler list``:
.. code-block:: console
$ spack compilers
==> Available compilers
-- gcc ---------------------------------------------------------
gcc@4.9.0 gcc@4.8.0 gcc@4.7.0 gcc@4.6.2 gcc@4.4.7
gcc@4.8.2 gcc@4.7.1 gcc@4.6.3 gcc@4.6.1 gcc@4.1.2
-- intel -------------------------------------------------------
intel@15.0.0 intel@14.0.0 intel@13.0.0 intel@12.1.0 intel@10.0
intel@14.0.3 intel@13.1.1 intel@12.1.5 intel@12.0.4 intel@9.1
intel@14.0.2 intel@13.1.0 intel@12.1.3 intel@11.1
intel@14.0.1 intel@13.0.1 intel@12.1.2 intel@10.1
-- clang -------------------------------------------------------
clang@3.4 clang@3.3 clang@3.2 clang@3.1
-- pgi ---------------------------------------------------------
pgi@14.3-0 pgi@13.2-0 pgi@12.1-0 pgi@10.9-0 pgi@8.0-1
pgi@13.10-0 pgi@13.1-1 pgi@11.10-0 pgi@10.2-0 pgi@7.1-3
pgi@13.6-0 pgi@12.8-0 pgi@11.1-0 pgi@9.0-4 pgi@7.0-6
Any of these compilers can be used to build Spack packages. More on
how this is done is in :ref:`sec-specs`.
.. _cmd-spack-compiler-add:
^^^^^^^^^^^^^^^^^^^^^^
``spack compiler add``
^^^^^^^^^^^^^^^^^^^^^^
An alias for ``spack compiler find``.
.. _cmd-spack-compiler-find:
^^^^^^^^^^^^^^^^^^^^^^^
``spack compiler find``
^^^^^^^^^^^^^^^^^^^^^^^
If you do not see a compiler in this list, but you want to use it with
Spack, you can simply run ``spack compiler find`` with the path to
where the compiler is installed. For example:
.. code-block:: console
$ spack compiler find /usr/local/tools/ic-13.0.079
==> Added 1 new compiler to ~/.spack/linux/compilers.yaml
intel@13.0.079
Or you can run ``spack compiler find`` with no arguments to force
auto-detection. This is useful if you do not know where compilers are
installed, but you know that new compilers have been added to your
``PATH``. For example, you might load a module, like this:
.. code-block:: console
$ module load gcc-4.9.0
$ spack compiler find
==> Added 1 new compiler to ~/.spack/linux/compilers.yaml
gcc@4.9.0
This loads the environment module for gcc-4.9.0 to add it to
``PATH``, and then it adds the compiler to Spack.
.. note::
By default, spack does not fill in the ``modules:`` field in the
``compilers.yaml`` file. If you are using a compiler from a
module, then you should add this field manually.
See the section on :ref:`compilers-requiring-modules`.
.. _cmd-spack-compiler-info:
^^^^^^^^^^^^^^^^^^^^^^^
``spack compiler info``
^^^^^^^^^^^^^^^^^^^^^^^
If you want to see specifics on a particular compiler, you can run
``spack compiler info`` on it:
.. code-block:: console
$ spack compiler info intel@15
intel@15.0.0:
paths:
cc = /usr/local/bin/icc-15.0.090
cxx = /usr/local/bin/icpc-15.0.090
f77 = /usr/local/bin/ifort-15.0.090
fc = /usr/local/bin/ifort-15.0.090
modules = []
operating_system = centos6
...
This shows which C, C++, and Fortran compilers were detected by Spack.
Notice also that we didn't have to be too specific about the
version. We just said ``intel@15``, and information about the only
matching Intel compiler was displayed.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Manual compiler configuration
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
If auto-detection fails, you can manually configure a compiler by
editing your ``~/.spack/<platform>/compilers.yaml`` file. You can do this by running
``spack config edit compilers``, which will open the file in your ``$EDITOR``.
Each compiler configuration in the file looks like this:
.. code-block:: yaml
compilers:
- compiler:
modules: []
operating_system: centos6
paths:
cc: /usr/local/bin/icc-15.0.024-beta
cxx: /usr/local/bin/icpc-15.0.024-beta
f77: /usr/local/bin/ifort-15.0.024-beta
fc: /usr/local/bin/ifort-15.0.024-beta
spec: intel@15.0.0
For compilers that do not support Fortran (like ``clang``), put
``None`` for ``f77`` and ``fc``:
.. code-block:: yaml
compilers:
- compiler:
modules: []
operating_system: centos6
paths:
cc: /usr/bin/clang
cxx: /usr/bin/clang++
f77: None
fc: None
spec: clang@3.3svn
Once you save the file, the configured compilers will show up in the
list displayed by ``spack compilers``.
You can also add compiler flags to manually configured compilers. These
flags should be specified in the ``flags`` section of the compiler
specification. The valid flags are ``cflags``, ``cxxflags``, ``fflags``,
``cppflags``, ``ldflags``, and ``ldlibs``. For example:
.. code-block:: yaml
compilers:
- compiler:
modules: []
operating_system: centos6
paths:
cc: /usr/bin/gcc
cxx: /usr/bin/g++
f77: /usr/bin/gfortran
fc: /usr/bin/gfortran
flags:
cflags: -O3 -fPIC
cxxflags: -O3 -fPIC
cppflags: -O3 -fPIC
spec: gcc@4.7.2
These flags will be treated by spack as if they were entered from
the command line each time this compiler is used. The compiler wrappers
then inject those flags into the compiler command. Compiler flags
entered from the command line will be discussed in more detail in the
following section.
^^^^^^^^^^^^^^^^^^^^^^^
Build Your Own Compiler
^^^^^^^^^^^^^^^^^^^^^^^
If you are particular about which compiler/version you use, you might
wish to have Spack build it for you. For example:
.. code-block:: console
$ spack install gcc@4.9.3
Once that has finished, you will need to add it to your
``compilers.yaml`` file. You can then set Spack to use it by default
by adding the following to your ``packages.yaml`` file:
.. code-block:: yaml
packages:
all:
compiler: [gcc@4.9.3]
.. _compilers-requiring-modules:
^^^^^^^^^^^^^^^^^^^^^^^^^^^
Compilers Requiring Modules
^^^^^^^^^^^^^^^^^^^^^^^^^^^
Many installed compilers will work regardless of the environment they
are called with. However, some installed compilers require
``$LD_LIBRARY_PATH`` or other environment variables to be set in order
to run; this is typical for Intel and other proprietary compilers.
In such a case, you should tell Spack which module(s) to load in order
to run the chosen compiler (If the compiler does not come with a
module file, you might consider making one by hand). Spack will load
this module into the environment ONLY when the compiler is run, and
NOT in general for a package's ``install()`` method. See, for
example, this ``compilers.yaml`` file:
.. code-block:: yaml
compilers:
- compiler:
modules: [other/comp/gcc-5.3-sp3]
operating_system: SuSE11
paths:
cc: /usr/local/other/SLES11.3/gcc/5.3.0/bin/gcc
cxx: /usr/local/other/SLES11.3/gcc/5.3.0/bin/g++
f77: /usr/local/other/SLES11.3/gcc/5.3.0/bin/gfortran
fc: /usr/local/other/SLES11.3/gcc/5.3.0/bin/gfortran
spec: gcc@5.3.0
Some compilers require special environment settings to be loaded not just
to run, but also to execute the code they build, breaking packages that
need to execute code they just compiled. If it's not possible or
practical to use a better compiler, you'll need to ensure that
environment settings are preserved for compilers like this (i.e., you'll
need to load the module or source the compiler's shell script).
By default, Spack tries to ensure that builds are reproducible by
cleaning the environment before building. If this interferes with your
compiler settings, you CAN use ``spack install --dirty`` as a workaround.
Note that this MAY interfere with package builds.
.. _licensed-compilers:
^^^^^^^^^^^^^^^^^^
Licensed Compilers
^^^^^^^^^^^^^^^^^^
Some proprietary compilers require licensing to use. If you need to
use a licensed compiler (eg, PGI), the process is similar to a mix of
build your own, plus modules:
#. Create a Spack package (if it doesn't exist already) to install
your compiler. Follow instructions on installing :ref:`license`.
#. Once the compiler is installed, you should be able to test it by
using Spack to load the module it just created, and running simple
builds (eg: ``cc helloWorld.c && ./a.out``)
#. Add the newly-installed compiler to ``compilers.yaml`` as shown
above.
.. _mixed-toolchains:
^^^^^^^^^^^^^^^^
Mixed Toolchains
^^^^^^^^^^^^^^^^
Modern compilers typically come with related compilers for C, C++ and
Fortran bundled together. When possible, results are best if the same
compiler is used for all languages.
In some cases, this is not possible. For example, starting with macOS El
Capitan (10.11), many packages no longer build with GCC, but XCode
provides no Fortran compilers. The user is therefore forced to use a
mixed toolchain: XCode-provided Clang for C/C++ and GNU ``gfortran`` for
Fortran.
#. You need to make sure that Xcode is installed. Run the following command:
.. code-block:: console
$ xcode-select --install
If the Xcode command-line tools are already installed, you will see an
error message:
.. code-block:: none
xcode-select: error: command line tools are already installed, use "Software Update" to install updates
#. For most packages, the Xcode command-line tools are sufficient. However,
some packages like ``qt`` require the full Xcode suite. You can check
to see which you have installed by running:
.. code-block:: console
$ xcode-select -p
If the output is:
.. code-block:: none
/Applications/Xcode.app/Contents/Developer
you already have the full Xcode suite installed. If the output is:
.. code-block:: none
/Library/Developer/CommandLineTools
you only have the command-line tools installed. The full Xcode suite can
be installed through the App Store. Make sure you launch the Xcode
application and accept the license agreement before using Spack.
It may ask you to install additional components. Alternatively, the license
can be accepted through the command line:
.. code-block:: console
$ sudo xcodebuild -license accept
Note: the flag is ``-license``, not ``--license``.
#. Run ``spack compiler find`` to locate Clang.
#. There are different ways to get ``gfortran`` on macOS. For example, you can
install GCC with Spack (``spack install gcc``) or with Homebrew
(``brew install gcc``).
#. The only thing left to do is to edit ``~/.spack/darwin/compilers.yaml`` to provide
the path to ``gfortran``:
.. code-block:: yaml
compilers:
- compiler:
...
paths:
cc: /usr/bin/clang
cxx: /usr/bin/clang++
f77: /path/to/bin/gfortran
fc: /path/to/bin/gfortran
spec: apple-clang@11.0.0
If you used Spack to install GCC, you can get the installation prefix by
``spack location -i gcc`` (this will only work if you have a single version
of GCC installed). Whereas for Homebrew, GCC is installed in
``/usr/local/Cellar/gcc/x.y.z``.
^^^^^^^^^^^^^^^^^^^^^
Compiler Verification
^^^^^^^^^^^^^^^^^^^^^
You can verify that your compilers are configured properly by installing a
simple package. For example:
.. code-block:: console
$ spack install zlib%gcc@5.3.0
.. _vendor-specific-compiler-configuration:
--------------------------------------
Vendor-Specific Compiler Configuration
--------------------------------------
With Spack, things usually "just work" with GCC. Not so for other
compilers. This section provides details on how to get specific
compilers working.
^^^^^^^^^^^^^^^
Intel Compilers
^^^^^^^^^^^^^^^
Intel compilers are unusual because a single Intel compiler version
can emulate multiple GCC versions. In order to provide this
functionality, the Intel compiler needs GCC to be installed.
Therefore, the following steps are necessary to successfully use Intel
compilers:
#. Install a version of GCC that implements the desired language
features (``spack install gcc``).
#. Tell the Intel compiler how to find that desired GCC. This may be
done in one of two ways:
"By default, the compiler determines which version of ``gcc`` or ``g++``
you have installed from the ``PATH`` environment variable.
If you want use a version of ``gcc`` or ``g++`` other than the default
version on your system, you need to use either the ``-gcc-name``
or ``-gxx-name`` compiler option to specify the path to the version of
``gcc`` or ``g++`` that you want to use."
-- `Intel Reference Guide <https://software.intel.com/en-us/node/522750>`_
Intel compilers may therefore be configured in one of two ways with
Spack: using modules, or using compiler flags.
""""""""""""""""""""""""""
Configuration with Modules
""""""""""""""""""""""""""
One can control which GCC is seen by the Intel compiler with modules.
A module must be loaded both for the Intel Compiler (so it will run)
and GCC (so the compiler can find the intended GCC). The following
configuration in ``compilers.yaml`` illustrates this technique:
.. code-block:: yaml
compilers:
- compiler:
modules: [gcc-4.9.3, intel-15.0.24]
operating_system: centos7
paths:
cc: /opt/intel-15.0.24/bin/icc-15.0.24-beta
cxx: /opt/intel-15.0.24/bin/icpc-15.0.24-beta
f77: /opt/intel-15.0.24/bin/ifort-15.0.24-beta
fc: /opt/intel-15.0.24/bin/ifort-15.0.24-beta
spec: intel@15.0.24.4.9.3
.. note::
The version number on the Intel compiler is a combination of
the "native" Intel version number and the GNU compiler it is
targeting.
""""""""""""""""""""""""""
Command Line Configuration
""""""""""""""""""""""""""
One can also control which GCC is seen by the Intel compiler by adding
flags to the ``icc`` command:
#. Identify the location of the compiler you just installed:
.. code-block:: console
$ spack location --install-dir gcc
~/spack/opt/spack/linux-centos7-x86_64/gcc-4.9.3-iy4rw...
#. Set up ``compilers.yaml``, for example:
.. code-block:: yaml
compilers:
- compiler:
modules: [intel-15.0.24]
operating_system: centos7
paths:
cc: /opt/intel-15.0.24/bin/icc-15.0.24-beta
cxx: /opt/intel-15.0.24/bin/icpc-15.0.24-beta
f77: /opt/intel-15.0.24/bin/ifort-15.0.24-beta
fc: /opt/intel-15.0.24/bin/ifort-15.0.24-beta
flags:
cflags: -gcc-name ~/spack/opt/spack/linux-centos7-x86_64/gcc-4.9.3-iy4rw.../bin/gcc
cxxflags: -gxx-name ~/spack/opt/spack/linux-centos7-x86_64/gcc-4.9.3-iy4rw.../bin/g++
fflags: -gcc-name ~/spack/opt/spack/linux-centos7-x86_64/gcc-4.9.3-iy4rw.../bin/gcc
spec: intel@15.0.24.4.9.3
^^^
PGI
^^^
PGI comes with two sets of compilers for C++ and Fortran,
distinguishable by their names. "Old" compilers:
.. code-block:: yaml
cc: /soft/pgi/15.10/linux86-64/15.10/bin/pgcc
cxx: /soft/pgi/15.10/linux86-64/15.10/bin/pgCC
f77: /soft/pgi/15.10/linux86-64/15.10/bin/pgf77
fc: /soft/pgi/15.10/linux86-64/15.10/bin/pgf90
"New" compilers:
.. code-block:: yaml
cc: /soft/pgi/15.10/linux86-64/15.10/bin/pgcc
cxx: /soft/pgi/15.10/linux86-64/15.10/bin/pgc++
f77: /soft/pgi/15.10/linux86-64/15.10/bin/pgfortran
fc: /soft/pgi/15.10/linux86-64/15.10/bin/pgfortran
Older installations of PGI contains just the old compilers; whereas
newer installations contain the old and the new. The new compiler is
considered preferable, as some packages
(``hdf``) will not build with the old compiler.
When auto-detecting a PGI compiler, there are cases where Spack will
find the old compilers, when you really want it to find the new
compilers. It is best to check this ``compilers.yaml``; and if the old
compilers are being used, change ``pgf77`` and ``pgf90`` to
``pgfortran``.
Other issues:
* There are reports that some packages will not build with PGI,
including ``libpciaccess`` and ``openssl``. A workaround is to
build these packages with another compiler and then use them as
dependencies for PGI-build packages. For example:
.. code-block:: console
$ spack install openmpi%pgi ^libpciaccess%gcc
* PGI requires a license to use; see :ref:`licensed-compilers` for more
information on installation.
.. note::
It is believed the problem with HDF 4 is that everything is
compiled with the ``F77`` compiler, but at some point some Fortran
90 code slipped in there. So compilers that can handle both FORTRAN
77 and Fortran 90 (``gfortran``, ``pgfortran``, etc) are fine. But
compilers specific to one or the other (``pgf77``, ``pgf90``) won't
work.
^^^
NAG
^^^
The Numerical Algorithms Group provides a licensed Fortran compiler. Like Clang,
this requires you to set up a :ref:`mixed-toolchains`. It is recommended to use
GCC for your C/C++ compilers.
The NAG Fortran compilers are a bit more strict than other compilers, and many
packages will fail to install with error messages like:
.. code-block:: none
Error: mpi_comm_spawn_multiple_f90.f90: Argument 3 to MPI_COMM_SPAWN_MULTIPLE has data type DOUBLE PRECISION in reference from MPI_COMM_SPAWN_MULTIPLEN and CHARACTER in reference from MPI_COMM_SPAWN_MULTIPLEA
In order to convince the NAG compiler not to be too picky about calling conventions,
you can use ``FFLAGS=-mismatch`` and ``FCFLAGS=-mismatch``. This can be done through
the command line:
.. code-block:: console
$ spack install openmpi fflags="-mismatch"
Or it can be set permanently in your ``compilers.yaml``:
.. code-block:: yaml
- compiler:
modules: []
operating_system: centos6
paths:
cc: /soft/spack/opt/spack/linux-x86_64/gcc-5.3.0/gcc-6.1.0-q2zosj3igepi3pjnqt74bwazmptr5gpj/bin/gcc
cxx: /soft/spack/opt/spack/linux-x86_64/gcc-5.3.0/gcc-6.1.0-q2zosj3igepi3pjnqt74bwazmptr5gpj/bin/g++
f77: /soft/spack/opt/spack/linux-x86_64/gcc-4.4.7/nag-6.1-jt3h5hwt5myezgqguhfsan52zcskqene/bin/nagfor
fc: /soft/spack/opt/spack/linux-x86_64/gcc-4.4.7/nag-6.1-jt3h5hwt5myezgqguhfsan52zcskqene/bin/nagfor
flags:
fflags: -mismatch
spec: nag@6.1
---------------
System Packages
---------------
Once compilers are configured, one needs to determine which
pre-installed system packages, if any, to use in builds. This is
configured in the file ``~/.spack/packages.yaml``. For example, to use
an OpenMPI installed in /opt/local, one would use:
.. code-block:: yaml
packages:
openmpi:
externals:
- spec: openmpi@1.10.1
prefix: /opt/local
buildable: False
In general, Spack is easier to use and more reliable if it builds all of
its own dependencies. However, there are several packages for which one
commonly needs to use system versions:
^^^
MPI
^^^
On supercomputers, sysadmins have already built MPI versions that take
into account the specifics of that computer's hardware. Unless you
know how they were built and can choose the correct Spack variants,
you are unlikely to get a working MPI from Spack. Instead, use an
appropriate pre-installed MPI.
If you choose a pre-installed MPI, you should consider using the
pre-installed compiler used to build that MPI; see above on
``compilers.yaml``.
^^^^^^^
OpenSSL
^^^^^^^
The ``openssl`` package underlies much of modern security in a modern
OS; an attacker can easily "pwn" any computer on which they can modify SSL.
Therefore, any ``openssl`` used on a system should be created in a
"trusted environment" --- for example, that of the OS vendor.
OpenSSL is also updated by the OS vendor from time to time, in
response to security problems discovered in the wider community. It
is in everyone's best interest to use any newly updated versions as
soon as they come out. Modern Linux installations have standard
procedures for security updates without user involvement.
Spack running at user-level is not a trusted environment, nor do Spack
users generally keep up-to-date on the latest security holes in SSL. For
these reasons, a Spack-installed OpenSSL should likely not be trusted.
As long as the system-provided SSL works, you can use it instead. One
can check if it works by trying to download an ``https://``. For
example:
.. code-block:: console
$ curl -O https://github.com/ImageMagick/ImageMagick/archive/7.0.2-7.tar.gz
To tell Spack to use the system-supplied OpenSSL, first determine what
version you have:
.. code-block:: console
$ openssl version
OpenSSL 1.0.2g 1 Mar 2016
Then add the following to ``~/.spack/packages.yaml``:
.. code-block:: yaml
packages:
openssl:
externals:
- spec: openssl@1.0.2g
prefix: /usr
buildable: False
^^^^^^^^^^^^^
BLAS / LAPACK
^^^^^^^^^^^^^
The recommended way to use system-supplied BLAS / LAPACK packages is
to add the following to ``packages.yaml``:
.. code-block:: yaml
packages:
netlib-lapack:
externals:
- spec: netlib-lapack@3.6.1
prefix: /usr
buildable: False
all:
providers:
blas: [netlib-lapack]
lapack: [netlib-lapack]
.. note::
Above we pretend that the system-provided BLAS / LAPACK is ``netlib-lapack``
only because it is the only BLAS / LAPACK provider which use standard names
for libraries (as opposed to, for example, ``libopenblas.so``).
Although we specify external package in ``/usr``, Spack is smart enough not
to add ``/usr/lib`` to RPATHs, where it could cause unrelated system
libraries to be used instead of their Spack equivalents. ``usr/bin`` will be
present in PATH, however it will have lower precedence compared to paths
from other dependencies. This ensures that binaries in Spack dependencies
are preferred over system binaries.
^^^
Git
^^^
Some Spack packages use ``git`` to download, which might not work on
some computers. For example, the following error was
encountered on a Macintosh during ``spack install julia@master``:
.. code-block:: console
==> Cloning git repository:
https://github.com/JuliaLang/julia.git
on branch master
Cloning into 'julia'...
fatal: unable to access 'https://github.com/JuliaLang/julia.git/':
SSL certificate problem: unable to get local issuer certificate
This problem is related to OpenSSL, and in some cases might be solved
by installing a new version of ``git`` and ``openssl``:
#. Run ``spack install git``
#. Add the output of ``spack module tcl loads git`` to your ``.bashrc``.
If this doesn't work, it is also possible to disable checking of SSL
certificates by using:
.. code-block:: console
$ spack --insecure install
Using ``--insecure`` makes Spack disable SSL checking when fetching
from websites and from git.
.. warning::
This workaround should be used ONLY as a last resort! Without SSL
certificate verification, spack and git will download from sites you
wouldn't normally trust. The code you download and run may then be
compromised! While this is not a major issue for archives that will
be checksummed, it is especially problematic when downloading from
name Git branches or tags, which relies entirely on trusting a
certificate for security (no verification).
-----------------------
Utilities Configuration
-----------------------
Although Spack does not need installation *per se*, it does rely on
other packages to be available on its host system. If those packages
are out of date or missing, then Spack will not work. Sometimes, an
appeal to the system's package manager can fix such problems. If not,
the solution is have Spack install the required packages, and then
have Spack use them.
For example, if ``curl`` doesn't work, one could use the following steps
to provide Spack a working ``curl``:
.. code-block:: console
$ spack install curl
$ spack load curl
or alternately:
.. code-block:: console
$ spack module tcl loads curl >>~/.bashrc
or if environment modules don't work:
.. code-block:: console
$ export PATH=`spack location --install-dir curl`/bin:$PATH
External commands are used by Spack in two places: within core Spack,
and in the package recipes. The bootstrapping procedure for these two
cases is somewhat different, and is treated separately below.
^^^^^^^^^^^^^^^^^^^^
Core Spack Utilities
^^^^^^^^^^^^^^^^^^^^
Core Spack uses the following packages, mainly to download and unpack
source code: ``curl``, ``env``, ``git``, ``go``, ``hg``, ``svn``,
``tar``, ``unzip``, ``patch``
As long as the user's environment is set up to successfully run these
programs from outside of Spack, they should work inside of Spack as
well. They can generally be activated as in the ``curl`` example above;
or some systems might already have an appropriate hand-built
environment module that may be loaded. Either way works.
A few notes on specific programs in this list:
""""""""""""""""""""""""""
cURL, git, Mercurial, etc.
""""""""""""""""""""""""""
Spack depends on cURL to download tarballs, the format that most
Spack-installed packages come in. Your system's cURL should always be
able to download unencrypted ``http://``. However, the cURL on some
systems has problems with SSL-enabled ``https://`` URLs, due to
outdated / insecure versions of OpenSSL on those systems. This will
prevent Spack from installing any software requiring ``https://``
until a new cURL has been installed, using the technique above.
.. warning::
remember that if you install ``curl`` via Spack that it may rely on a
user-space OpenSSL that is not upgraded regularly. It may fall out of
date faster than your system OpenSSL.
Some packages use source code control systems as their download method:
``git``, ``hg``, ``svn`` and occasionally ``go``. If you had to install
a new ``curl``, then chances are the system-supplied version of these
other programs will also not work, because they also rely on OpenSSL.
Once ``curl`` has been installed, you can similarly install the others.
^^^^^^^^^^^^^^^^^
Package Utilities
^^^^^^^^^^^^^^^^^
Spack may also encounter bootstrapping problems inside a package's
``install()`` method. In this case, Spack will normally be running
inside a *sanitized build environment*. This includes all of the
package's dependencies, but none of the environment Spack inherited
from the user: if you load a module or modify ``$PATH`` before
launching Spack, it will have no effect.
In this case, you will likely need to use the ``--dirty`` flag when
running ``spack install``, causing Spack to **not** sanitize the build
environment. You are now responsible for making sure that environment
does not do strange things to Spack or its installs.
Another way to get Spack to use its own version of something is to add
that something to a package that needs it. For example:
.. code-block:: python
depends_on('binutils', type='build')
This is considered best practice for some common build dependencies,
such as ``autotools`` (if the ``autoreconf`` command is needed) and
``cmake`` --- ``cmake`` especially, because different packages require
a different version of CMake.
""""""""
binutils
""""""""
.. https://groups.google.com/forum/#!topic/spack/i_7l_kEEveI
Sometimes, strange error messages can happen while building a package.
For example, ``ld`` might crash. Or one receives a message like:
.. code-block:: console
ld: final link failed: Nonrepresentable section on output
or:
.. code-block:: console
ld: .../_fftpackmodule.o: unrecognized relocation (0x2a) in section `.text'
These problems are often caused by an outdated ``binutils`` on your
system. Unlike CMake or Autotools, adding ``depends_on('binutils')`` to
every package is not considered a best practice because every package
written in C/C++/Fortran would need it. A potential workaround is to
load a recent ``binutils`` into your environment and use the ``--dirty``
flag.
-----------
GPG Signing
-----------
.. _cmd-spack-gpg:
^^^^^^^^^^^^^
``spack gpg``
^^^^^^^^^^^^^
Spack has support for signing and verifying packages using GPG keys. A
separate keyring is used for Spack, so any keys available in the user's home
directory are not used.
^^^^^^^^^^^^^^^^^^
``spack gpg init``
^^^^^^^^^^^^^^^^^^
When Spack is first installed, its keyring is empty. Keys stored in
:file:`var/spack/gpg` are the default keys for a Spack installation. These
keys may be imported by running ``spack gpg init``. This will import the
default keys into the keyring as trusted keys.
^^^^^^^^^^^^^
Trusting keys
^^^^^^^^^^^^^
Additional keys may be added to the keyring using
``spack gpg trust <keyfile>``. Once a key is trusted, packages signed by the
owner of they key may be installed.
^^^^^^^^^^^^^
Creating keys
^^^^^^^^^^^^^
You may also create your own key so that you may sign your own packages using
``spack gpg create <name> <email>``. By default, the key has no expiration,
but it may be set with the ``--expires <date>`` flag (see the ``gnupg2``
documentation for accepted date formats). It is also recommended to add a
comment as to the use of the key using the ``--comment <comment>`` flag. The
public half of the key can also be exported for sharing with others so that
they may use packages you have signed using the ``--export <keyfile>`` flag.
Secret keys may also be later exported using the
``spack gpg export <location> [<key>...]`` command.
.. note::
Key creation speed
The creation of a new GPG key requires generating a lot of random numbers.
Depending on the entropy produced on your system, the entire process may
take a long time (*even appearing to hang*). Virtual machines and cloud
instances are particularly likely to display this behavior.
To speed it up you may install tools like ``rngd``, which is
usually available as a package in the host OS. On e.g. an
Ubuntu machine you need to give the following commands:
.. code-block:: console
$ sudo apt-get install rng-tools
$ sudo rngd -r /dev/urandom
before generating the keys.
Another alternative is ``haveged``, which can be installed on
RHEL/CentOS machines as follows:
.. code-block:: console
$ sudo yum install haveged
$ sudo chkconfig haveged on
`This Digital Ocean tutorial
<https://www.digitalocean.com/community/tutorials/how-to-setup-additional-entropy-for-cloud-servers-using-haveged>`_
provides a good overview of sources of randomness.
Here is an example of creating a key. Note that we provide a name for the key first
(which we can use to reference the key later) and an email address:
.. code-block:: console
$ spack gpg create dinosaur dinosaur@thedinosaurthings.com
If you want to export the key as you create it:
.. code-block:: console
$ spack gpg create --export key.pub dinosaur dinosaur@thedinosaurthings.com
Or the private key:
.. code-block:: console
$ spack gpg create --export-secret key.priv dinosaur dinosaur@thedinosaurthings.com
You can include both ``--export`` and ``--export-secret``, each with
an output file of choice, to export both.
^^^^^^^^^^^^
Listing keys
^^^^^^^^^^^^
In order to list the keys available in the keyring, the
``spack gpg list`` command will list trusted keys with the ``--trusted`` flag
and keys available for signing using ``--signing``. If you would like to
remove keys from your keyring, ``spack gpg untrust <keyid>``. Key IDs can be
email addresses, names, or (best) fingerprints. Here is an example of listing
the key that we just created:
.. code-block:: console
gpgconf: socketdir is '/run/user/1000/gnupg'
/home/spackuser/spack/opt/spack/gpg/pubring.kbx
----------------------------------------------------------
pub rsa4096 2021-03-25 [SC]
60D2685DAB647AD4DB54125961E09BB6F2A0ADCB
uid [ultimate] dinosaur (GPG created for Spack) <dinosaur@thedinosaurthings.com>
Note that the name "dinosaur" can be seen under the uid, which is the unique
id. We might need this reference if we want to export or otherwise reference the key.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Signing and Verifying Packages
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
In order to sign a package, ``spack gpg sign <file>`` should be used. By
default, the signature will be written to ``<file>.asc``, but that may be
changed by using the ``--output <file>`` flag. If there is only one signing
key available, it will be used, but if there is more than one, the key to use
must be specified using the ``--key <keyid>`` flag. The ``--clearsign`` flag
may also be used to create a signed file which contains the contents, but it
is not recommended. Signed packages may be verified by using
``spack gpg verify <file>``.
^^^^^^^^^^^^^^
Exporting Keys
^^^^^^^^^^^^^^
You likely might want to export a public key, and that looks like this. Let's
use the previous example and ask spack to export the key with uid "dinosaur."
We will provide an output location (typically a `*.pub` file) and the name of
the key.
.. code-block:: console
$ spack gpg export dinosaur.pub dinosaur
You can then look at the created file, `dinosaur.pub`, to see the exported key.
If you want to include the private key, then just add `--secret`:
.. code-block:: console
$ spack gpg export --secret dinosaur.priv dinosaur
This will write the private key to the file `dinosaur.priv`.
.. warning::
You should be very careful about exporting private keys. You likely would
only want to do this in the context of moving your spack installation to
a different server, and wanting to preserve keys for a buildcache. If you
are unsure about exporting, you can ask your local system administrator
or for help on an issue or the Spack slack.
.. _cray-support:
-------------
Spack on Cray
-------------
Spack differs slightly when used on a Cray system. The architecture spec
can differentiate between the front-end and back-end processor and operating system.
For example, on Edison at NERSC, the back-end target processor
is "Ivy Bridge", so you can specify to use the back-end this way:
.. code-block:: console
$ spack install zlib target=ivybridge
You can also use the operating system to build against the back-end:
.. code-block:: console
$ spack install zlib os=CNL10
Notice that the name includes both the operating system name and the major
version number concatenated together.
Alternatively, if you want to build something for the front-end,
you can specify the front-end target processor. The processor for a login node
on Edison is "Sandy bridge" so we specify on the command line like so:
.. code-block:: console
$ spack install zlib target=sandybridge
And the front-end operating system is:
.. code-block:: console
$ spack install zlib os=SuSE11
^^^^^^^^^^^^^^^^^^^^^^^
Cray compiler detection
^^^^^^^^^^^^^^^^^^^^^^^
Spack can detect compilers using two methods. For the front-end, we treat
everything the same. The difference lies in back-end compiler detection.
Back-end compiler detection is made via the Tcl module avail command.
Once it detects the compiler it writes the appropriate PrgEnv and compiler
module name to compilers.yaml and sets the paths to each compiler with Cray\'s
compiler wrapper names (i.e. cc, CC, ftn). During build time, Spack will load
the correct PrgEnv and compiler module and will call appropriate wrapper.
The compilers.yaml config file will also differ. There is a
modules section that is filled with the compiler's Programming Environment
and module name. On other systems, this field is empty []:
.. code-block:: yaml
- compiler:
modules:
- PrgEnv-intel
- intel/15.0.109
As mentioned earlier, the compiler paths will look different on a Cray system.
Since most compilers are invoked using cc, CC and ftn, the paths for each
compiler are replaced with their respective Cray compiler wrapper names:
.. code-block:: yaml
paths:
cc: cc
cxx: CC
f77: ftn
fc: ftn
As opposed to an explicit path to the compiler executable. This allows Spack
to call the Cray compiler wrappers during build time.
For more on compiler configuration, check out :ref:`compiler-config`.
Spack sets the default Cray link type to dynamic, to better match other
other platforms. Individual packages can enable static linking (which is the
default outside of Spack on cray systems) using the ``-static`` flag.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Setting defaults and using Cray modules
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
If you want to use default compilers for each PrgEnv and also be able
to load cray external modules, you will need to set up a ``packages.yaml``.
Here's an example of an external configuration for cray modules:
.. code-block:: yaml
packages:
mpich:
externals:
- spec: "mpich@7.3.1%gcc@5.2.0 arch=cray_xc-haswell-CNL10"
modules:
- cray-mpich
- spec: "mpich@7.3.1%intel@16.0.0.109 arch=cray_xc-haswell-CNL10"
modules:
- cray-mpich
all:
providers:
mpi: [mpich]
This tells Spack that for whatever package that depends on mpi, load the
cray-mpich module into the environment. You can then be able to use whatever
environment variables, libraries, etc, that are brought into the environment
via module load.
.. note::
For Cray-provided packages, it is best to use ``modules:`` instead of ``prefix:``
in ``packages.yaml``, because the Cray Programming Environment heavily relies on
modules (e.g., loading the ``cray-mpich`` module adds MPI libraries to the
compiler wrapper link line).
You can set the default compiler that Spack can use for each compiler type.
If you want to use the Cray defaults, then set them under ``all:`` in packages.yaml.
In the compiler field, set the compiler specs in your order of preference.
Whenever you build with that compiler type, Spack will concretize to that version.
Here is an example of a full packages.yaml used at NERSC
.. code-block:: yaml
packages:
mpich:
externals:
- spec: "mpich@7.3.1%gcc@5.2.0 arch=cray_xc-CNL10-ivybridge"
modules:
- cray-mpich
- spec: "mpich@7.3.1%intel@16.0.0.109 arch=cray_xc-SuSE11-ivybridge"
modules:
- cray-mpich
buildable: False
netcdf:
externals:
- spec: "netcdf@4.3.3.1%gcc@5.2.0 arch=cray_xc-CNL10-ivybridge"
modules:
- cray-netcdf
- spec: "netcdf@4.3.3.1%intel@16.0.0.109 arch=cray_xc-CNL10-ivybridge"
modules:
- cray-netcdf
buildable: False
hdf5:
externals:
- spec: "hdf5@1.8.14%gcc@5.2.0 arch=cray_xc-CNL10-ivybridge"
modules:
- cray-hdf5
- spec: "hdf5@1.8.14%intel@16.0.0.109 arch=cray_xc-CNL10-ivybridge"
modules:
- cray-hdf5
buildable: False
all:
compiler: [gcc@5.2.0, intel@16.0.0.109]
providers:
mpi: [mpich]
Here we tell spack that whenever we want to build with gcc use version 5.2.0 or
if we want to build with intel compilers, use version 16.0.0.109. We add a spec
for each compiler type for each cray modules. This ensures that for each
compiler on our system we can use that external module.
For more on external packages check out the section :ref:`sec-external-packages`.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Using Linux containers on Cray machines
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Spack uses environment variables particular to the Cray programming
environment to determine which systems are Cray platforms. These
environment variables may be propagated into containers that are not
using the Cray programming environment.
To ensure that Spack does not autodetect the Cray programming
environment, unset the environment variable ``MODULEPATH``. This
will cause Spack to treat a linux container on a Cray system as a base
linux distro.
