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Updates to Configuration Tutorial for SC18 (#9811)

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* Updates to Configuration Tutorial for SC18

* Suggested rewording
This commit is contained in:
Adam J. Stewart 2018-11-12 00:50:59 -06:00 committed by Greg Becker
parent 71561f9d2b
commit a1676ab012
1 changed files with 243 additions and 177 deletions
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lib/spack/docs/tutorial_configuration.rst
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@ -13,7 +13,7 @@ This tutorial will guide you through various configuration options
that allow you to customize Spack's behavior with respect to
software installation. We will first cover the configuration file
hierarchy. Then, we will cover configuration options for compilers,
focusing on how it can be used to extend Spack's compiler auto-detection.
focusing on how they can be used to extend Spack's compiler auto-detection.
Next, we will cover the packages configuration file, focusing on
how it can be used to override default build options as well as
specify external package installations to use. Finally, we will
@ -36,17 +36,19 @@ Configuration Scopes
Depending on your use case, you may want to provide configuration
settings common to everyone on your team, or you may want to set
default behaviors specific to a single user account. Spack provides
4 configuration *scopes* to handle this customization. These scopes,
six configuration *scopes* to handle this customization. These scopes,
in order of decreasing priority, are:
====================== ==================================
Scope Directory
====================== ==================================
User configurations ``~/.spack``
Project configurations ``$SPACK_ROOT/etc/spack``
System configurations ``/etc/spack``
Default configurations ``$SPACK_ROOT/etc/spack/defaults``
====================== ==================================
============ ===================================================
Scope Directory
============ ===================================================
Command-line N/A
Custom Custom directory, specified with ``--config-scope``
User ``~/.spack/``
Site ``$SPACK_ROOT/etc/spack/``
System ``/etc/spack/``
Defaults ``$SPACK_ROOT/etc/spack/defaults/``
============ ===================================================
Spack's default configuration settings reside in
``$SPACK_ROOT/etc/spack/defaults``. These are useful for reference,
@ -65,24 +67,40 @@ configuration files to the ``~/.spack`` directory. When Spack first
checked for compilers on your system, you may have noticed that it
placed your compiler configuration in this directory.
Configuration settings can also be placed in a custom location,
which is then specified on the command line via ``--config-scope``.
An example use case is managing two sets of configurations, one for
development and another for production preferences.
Settings specified on the command line have precedence over all
other configuration scopes.
^^^^^^^^^^^^^^^^^^^^^^^^
Platform-specific Scopes
^^^^^^^^^^^^^^^^^^^^^^^^
Some facilities manage multiple platforms from a single shared
filesystem. In order to handle this, each of the configuration
file system. In order to handle this, each of the configuration
scopes listed above has two *sub-scopes*: platform-specific and
platform-independent. For example, compiler settings can be stored
in ``compilers.yaml`` configuration files in the following locations:
- ``~/.spack/<platform>/compilers.yaml``
- ``~/.spack/compilers.yaml``
- ``$SPACK_ROOT/etc/spack/<platform>/compilers.yaml``
- ``$SPACK_ROOT/etc/spack/compilers.yaml``
- ``/etc/spack/<platform>/compilers.yaml``
- ``/etc/spack/compilers.yaml``
- ``$SPACK_ROOT/etc/defaults/<platform>/compilers.yaml``
- ``$SPACK_ROOT/etc/defaults/compilers.yaml``
#. ``~/.spack/<platform>/compilers.yaml``
#. ``~/.spack/compilers.yaml``
#. ``$SPACK_ROOT/etc/spack/<platform>/compilers.yaml``
#. ``$SPACK_ROOT/etc/spack/compilers.yaml``
#. ``/etc/spack/<platform>/compilers.yaml``
#. ``/etc/spack/compilers.yaml``
#. ``$SPACK_ROOT/etc/defaults/<platform>/compilers.yaml``
#. ``$SPACK_ROOT/etc/defaults/compilers.yaml``
These files are listed in decreasing order of precedence, so files in
``~/.spack/<platform>`` will override settings in ``~/.spack``.
-----------
YAML Format
-----------
Spack configurations are YAML dictionaries. Every configuration file
begins with a top-level dictionary that tells Spack which
configuration set it modifies. When Spack checks it's configuration,
@ -117,7 +135,7 @@ ensures that no other compilers are used, as the user configuration
scope is the last scope searched and the ``compilers::`` line replaces
all previous configuration files information. If the same
configuration file had a single colon instead of the double colon, it
would add the gcc version 5.4.0 compiler to whatever other compilers
would add the GCC version 5.4.0 compiler to whatever other compilers
were listed in other configuration files.
.. _configs-tutorial-compilers:
@ -127,8 +145,8 @@ Compiler Configuration
----------------------
For most tasks, we can use Spack with the compilers auto-detected the
first time Spack runs on a system. As we discussed in the basic
installation section, we can also tell Spack where compilers are
first time Spack runs on a system. As discussed in the basic
installation tutorial, we can also tell Spack where compilers are
located using the ``spack compiler add`` command. However, in some
circumstances we want even more fine-grained control over the
compilers available. This section will teach you how to exercise that
@ -144,6 +162,19 @@ We will start by opening the compilers configuration file
.. code-block:: yaml
compilers:
- compiler:
environment: {}
extra_rpaths: []
flags: {}
modules: []
operating_system: ubuntu16.04
paths:
cc: /usr/bin/clang-3.7
cxx: /usr/bin/clang++-3.7
f77: null
fc: null
spec: clang@3.7.1-2ubuntu2
target: x86_64
- compiler:
environment: {}
extra_rpaths: []
@ -157,6 +188,19 @@ We will start by opening the compilers configuration file
fc: null
spec: clang@3.8.0-2ubuntu4
target: x86_64
- compiler:
environment: {}
extra_rpaths: []
flags: {}
modules: []
operating_system: ubuntu16.04
paths:
cc: /usr/bin/gcc-4.7
cxx: /usr/bin/g++-4.7
f77: /usr/bin/gfortran-4.7
fc: /usr/bin/gfortran-4.7
spec: gcc@4.7
target: x86_64
- compiler:
environment: {}
extra_rpaths: []
@ -172,27 +216,27 @@ We will start by opening the compilers configuration file
target: x86_64
This specifies one version of the gcc compiler and one version of the
clang compiler with no flang compiler. Now suppose we have a code that
we want to compile with the clang compiler for C/C++ code, but with
This specifies two versions of the GCC compiler and two versions of the
Clang compiler with no Flang compiler. Now suppose we have a code that
we want to compile with the Clang compiler for C/C++ code, but with
gfortran for Fortran components. We can do this by adding another entry
to the ``compilers.yaml`` file.
.. code-block:: yaml
- compiler:
environment: {}
extra_rpaths: []
flags: {}
modules: []
operating_system: ubuntu16.04
paths:
cc: /usr/bin/clang
cxx: /usr/bin/clang++
f77: /usr/bin/gfortran
fc: /usr/bin/gfortran
spec: clang@3.8.0-gfortran
target: x86_64
environment: {}
extra_rpaths: []
flags: {}
modules: []
operating_system: ubuntu16.04
paths:
cc: /usr/bin/clang
cxx: /usr/bin/clang++
f77: /usr/bin/gfortran
fc: /usr/bin/gfortran
spec: clang@3.8.0-gfortran
target: x86_64
Let's talk about the sections of this compiler entry that we've changed.
@ -203,7 +247,7 @@ compiler for both specifications of Fortran. We've also changed the
``spec`` entry for this compiler. The ``spec`` entry is effectively the
name of the compiler for Spack. It consists of a name and a version
number, separated by the ``@`` sigil. The name must be one of the supported
compiler names in Spack (gcc, intel, pgi, xl, xl_r, clang, nag, cce).
compiler names in Spack (gcc, intel, pgi, xl, xl_r, clang, nag, cce, arm).
The version number can be an arbitrary string of alphanumeric characters,
as well as ``-``, ``.``, and ``_``. The ``target`` and ``operating_system``
sections we leave unchanged. These sections specify when Spack can use
@ -214,7 +258,7 @@ We can verify that our new compiler works by invoking it now:
.. code-block:: console
$ spack install zlib %clang@3.8.0-gfortran
$ spack install --no-cache zlib %clang@3.8.0-gfortran
...
@ -222,7 +266,7 @@ This new compiler also works on Fortran codes:
.. code-block:: console
$ spack install cfitsio %clang@3.8.0-gfortran
$ spack install --no-cache cfitsio %clang@3.8.0-gfortran -bzip2
...
@ -243,19 +287,19 @@ Let's open our compilers configuration file again and add a compiler flag.
.. code-block:: yaml
- compiler:
environment: {}
extra_rpaths: []
flags:
cppflags: -g
modules: []
operating_system: ubuntu16.04
paths:
cc: /usr/bin/clang
cxx: /usr/bin/clang++
f77: /usr/bin/gfortran
fc: /usr/bin/gfortran
spec: clang@3.8.0-gfortran
target: x86_64
environment: {}
extra_rpaths: []
flags:
cppflags: -g
modules: []
operating_system: ubuntu16.04
paths:
cc: /usr/bin/clang
cxx: /usr/bin/clang++
f77: /usr/bin/gfortran
fc: /usr/bin/gfortran
spec: clang@3.8.0-gfortran
target: x86_64
We can test this out using the ``spack spec`` command to show how the
@ -278,14 +322,14 @@ spec is concretized.
^bzip2@1.0.6%clang@3.8.0-gfortran cppflags="-g" +shared arch=linux-ubuntu16.04-x86_64
We can see that "cppflags=-g" has been added to every node in the DAG.
We can see that ``cppflags="-g"`` has been added to every node in the DAG.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Advanced Compiler Configuration
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
There are three fields of the compiler configuration entry that we
have not talked about yet.
have not yet talked about.
The ``modules`` field of the compiler is used primarily on Cray systems,
but can be useful on any system that has compilers that are only
@ -295,12 +339,12 @@ of the build environment for packages using that compiler.
The ``extra_rpaths`` field of the compiler configuration is used for
compilers that do not rpath all of their dependencies by
default. Since compilers are generally installed externally to Spack,
default. Since compilers are often installed externally to Spack,
Spack is unable to manage compiler dependencies and enforce
rpath usage. This can lead to packages not finding link dependencies
imposed by the compiler properly. For compilers that impose link
dependencies on the resulting executables that are not rpath'ed into
the executable automatically, the ``extra_rpath`` field of the compiler
the executable automatically, the ``extra_rpaths`` field of the compiler
configuration tells Spack which dependencies to rpath into every
executable created by that compiler. The executables will then be able
to find the link dependencies imposed by the compiler. As an example,
@ -330,6 +374,9 @@ license server, you can set this in ``compilers.yaml`` as follows:
...
In addition to ``set``, ``environment`` also supports ``unset``,
``prepend-path``, and ``append-path``.
.. _configs-tutorial-package-prefs:
-------------------------------
@ -351,8 +398,8 @@ configuration file. First, we will look at the default
This sets the default preferences for compilers and for providers of
virtual packages. To illustrate how this works, suppose we want to
change the preferences to prefer the clang compiler and to prefer
mpich over openmpi. Currently, we prefer gcc and openmpi
change the preferences to prefer the Clang compiler and to prefer
MPICH over OpenMPI. Currently, we prefer GCC and OpenMPI.
.. code-block:: console
@ -361,20 +408,27 @@ mpich over openmpi. Currently, we prefer gcc and openmpi
--------------------------------
hdf5
Normalized
--------------------------------
hdf5
^zlib@1.1.2:
Concretized
--------------------------------
hdf5@1.10.1%gcc@5.4.0+cxx~debug+fortran+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
^openmpi@3.0.0%gcc@5.4.0~cuda fabrics= ~java schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
^hwloc@1.11.7%gcc@5.4.0~cuda+libxml2~pci arch=linux-ubuntu16.04-x86_64
^libxml2@2.9.4%gcc@5.4.0~python arch=linux-ubuntu16.04-x86_64
^pkg-config@0.29.2%gcc@5.4.0+internal_glib arch=linux-ubuntu16.04-x86_64
^xz@5.2.3%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
^zlib@1.2.11%gcc@5.4.0+pic+shared arch=linux-ubuntu16.04-x86_64
hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
^openmpi@3.1.3%gcc@5.4.0~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
^hwloc@1.11.9%gcc@5.4.0~cairo~cuda+libxml2+pci+shared arch=linux-ubuntu16.04-x86_64
^libpciaccess@0.13.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
^util-macros@1.19.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
^libxml2@2.9.8%gcc@5.4.0~python arch=linux-ubuntu16.04-x86_64
^xz@5.2.4%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
^numactl@2.0.11%gcc@5.4.0 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64
^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
Now we will open the packages configuration file and update our
@ -404,16 +458,23 @@ overrides the default settings just for these two items.
--------------------------------
hdf5
Normalized
--------------------------------
hdf5
^zlib@1.1.2:
Concretized
--------------------------------
hdf5@1.10.1%clang@3.8.0-2ubuntu4+cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
^mpich@3.2%clang@3.8.0-2ubuntu4 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
^zlib@1.2.11%clang@3.8.0-2ubuntu4+pic+shared arch=linux-ubuntu16.04-x86_64
hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
^mpich@3.2.1%clang@3.8.0-2ubuntu4 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
^findutils@4.6.0%clang@3.8.0-2ubuntu4 patches=84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e,bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2 arch=linux-ubuntu16.04-x86_64
^autoconf@2.69%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^m4@1.4.18%clang@3.8.0-2ubuntu4 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
^libsigsegv@2.11%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^perl@5.26.2%clang@3.8.0-2ubuntu4+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
^gdbm@1.14.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^readline@7.0%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^ncurses@6.1%clang@3.8.0-2ubuntu4~symlinks~termlib arch=linux-ubuntu16.04-x86_64
^pkgconf@1.4.2%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^automake@1.16.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^libtool@2.4.6%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^texinfo@6.5%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
^^^^^^^^^^^^^^^^^^^
@ -444,16 +505,23 @@ We can check the effect of this command with ``spack spec hdf5`` again.
--------------------------------
hdf5
Normalized
--------------------------------
hdf5
^zlib@1.1.2:
Concretized
--------------------------------
hdf5@1.10.1%clang@3.8.0-2ubuntu4+cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
^mpich@3.2%clang@3.8.0-2ubuntu4 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
^zlib@1.2.11%clang@3.8.0-2ubuntu4+pic~shared arch=linux-ubuntu16.04-x86_64
hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
^mpich@3.2.1%clang@3.8.0-2ubuntu4 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
^findutils@4.6.0%clang@3.8.0-2ubuntu4 patches=84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e,bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2 arch=linux-ubuntu16.04-x86_64
^autoconf@2.69%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^m4@1.4.18%clang@3.8.0-2ubuntu4 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
^libsigsegv@2.11%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^perl@5.26.2%clang@3.8.0-2ubuntu4+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac ~shared+threads arch=linux-ubuntu16.04-x86_64
^gdbm@1.14.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^readline@7.0%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^ncurses@6.1%clang@3.8.0-2ubuntu4~symlinks~termlib arch=linux-ubuntu16.04-x86_64
^pkgconf@1.4.2%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^automake@1.16.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^libtool@2.4.6%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^texinfo@6.5%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
So far we have only made global changes to the package preferences. As
@ -484,15 +552,10 @@ Now hdf5 will concretize without an MPI dependency by default.
--------------------------------
hdf5
Normalized
--------------------------------
hdf5
^zlib@1.1.2:
Concretized
--------------------------------
hdf5@1.10.1%clang@3.8.0-2ubuntu4+cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
^zlib@1.2.11%clang@3.8.0-2ubuntu4+pic~shared arch=linux-ubuntu16.04-x86_64
hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
In general, every attribute that we can set for all packages we can
@ -533,14 +596,9 @@ okay.
--------------------------------
hdf5
Normalized
--------------------------------
hdf5
^zlib@1.1.2:
Concretized
--------------------------------
hdf5@1.10.1%gcc@5.4.0~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
@ -555,14 +613,9 @@ preference of clang. If we explicitly specify clang:
--------------------------------
hdf5%clang
Normalized
--------------------------------
hdf5%clang
^zlib@1.1.2:
Concretized
--------------------------------
hdf5@1.10.1%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
@ -597,14 +650,9 @@ Now Spack will be forced to choose the external zlib.
--------------------------------
hdf5%clang
Normalized
--------------------------------
hdf5%clang
^zlib@1.1.2:
Concretized
--------------------------------
hdf5@1.10.1%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
@ -642,31 +690,32 @@ build with an alternate MPI implementation.
--------------------------------
hdf5%clang+mpi
Normalized
--------------------------------
hdf5%clang+mpi
^mpi
^zlib@1.1.2:
Concretized
--------------------------------
hdf5@1.10.1%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
^openmpi@3.0.0%clang@3.8.0-2ubuntu4~cuda fabrics=verbs ~java schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
^hwloc@1.11.8%clang@3.8.0-2ubuntu4~cuda+libxml2+pci arch=linux-ubuntu16.04-x86_64
hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
^openmpi@3.1.3%clang@3.8.0-2ubuntu4~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
^hwloc@1.11.9%clang@3.8.0-2ubuntu4~cairo~cuda+libxml2+pci~shared arch=linux-ubuntu16.04-x86_64
^libpciaccess@0.13.5%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^libtool@2.4.6%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^m4@1.4.18%clang@3.8.0-2ubuntu4 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00 +sigsegv arch=linux-ubuntu16.04-x86_64
^m4@1.4.18%clang@3.8.0-2ubuntu4 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
^libsigsegv@2.11%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^pkg-config@0.29.2%clang@3.8.0-2ubuntu4+internal_glib arch=linux-ubuntu16.04-x86_64
^pkgconf@1.4.2%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^util-macros@1.19.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^libxml2@2.9.4%clang@3.8.0-2ubuntu4~python arch=linux-ubuntu16.04-x86_64
^xz@5.2.3%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^zlib@1.2.8%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
^libxml2@2.9.8%clang@3.8.0-2ubuntu4~python arch=linux-ubuntu16.04-x86_64
^xz@5.2.4%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
^numactl@2.0.11%clang@3.8.0-2ubuntu4 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64
^autoconf@2.69%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^perl@5.26.2%clang@3.8.0-2ubuntu4+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac ~shared+threads arch=linux-ubuntu16.04-x86_64
^gdbm@1.14.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^readline@7.0%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
^ncurses@6.1%clang@3.8.0-2ubuntu4~symlinks~termlib arch=linux-ubuntu16.04-x86_64
^automake@1.16.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
We have only expressed a preference for mpich over other MPI
implementations, and Spack will happily build with one we haven't
forbid it from using. We could resolve this by requesting
forbid it from building. We could resolve this by requesting
``hdf5%clang+mpi^mpich`` explicitly, or we can configure Spack not to
use any other MPI implementation. Since we're focused on
configurations here and the former can get tedious, we'll need to
@ -697,10 +746,17 @@ again.
buildable: False
intel-mpi:
buildable: False
spectrum-mpi:
buildable: False
intel-parallel-studio:
buildable: False
spectrum-mpi:
buildable: False
mpilander:
buildable: False
charm:
buildable: False
charmpp:
buildable: False
Now that we have configured Spack not to build any of the possible
providers for MPI we can try again.
@ -712,17 +768,11 @@ providers for MPI we can try again.
--------------------------------
hdf5%clang
Normalized
--------------------------------
hdf5%clang
^mpi
^zlib@1.1.2:
Concretized
--------------------------------
hdf5@1.10.1%clang@3.8.0-2ubuntu4+cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
^mpich@3.2%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
^zlib@1.2.8%gcc@5.4.0+pic+shared arch=linux-ubuntu16.04-x86_64
^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
By configuring most of our package preferences in ``packages.yaml``,
@ -732,6 +782,31 @@ preferences, we can specify version preferences as well. Anything
that you can specify on the command line can be specified in
``packages.yaml`` with the exact same spec syntax.
^^^^^^^^^^^^^^^^^^^^^^^^
Installation Permissions
^^^^^^^^^^^^^^^^^^^^^^^^
The ``packages.yaml`` file also controls the default permissions
to use when installing a package. You'll notice that by default,
the installation prefix will be world readable but only user writable.
Let's say we need to install ``converge``, a licensed software package.
Since a specific research group, ``fluid_dynamics``, pays for this
license, we want to ensure that only members of this group can access
the software. We can do this like so:
.. code-block:: yaml
packages:
converge:
permissions:
read: group
group: fluid_dynamics
Now, only members of the ``fluid_dynamics`` group can use any
``converge`` installations.
.. warning::
Make sure to delete or move the ``packages.yaml`` you have been
@ -762,8 +837,8 @@ As you can see, many of the directories Spack uses can be customized.
For example, you can tell Spack to install packages to a prefix
outside of the ``$SPACK_ROOT`` hierarchy. Module files can be
written to a central location if you are using multiple Spack
instances. If you have a fast scratch filesystem, you can run builds
from this filesystem with the following ``config.yaml``:
instances. If you have a fast scratch file system, you can run builds
from this file system with the following ``config.yaml``:
.. code-block:: yaml
@ -788,39 +863,31 @@ into the build.
One last setting that may be of interest to many users is the ability
to customize the parallelism of Spack builds. By default, Spack
installs all packages in parallel with the number of jobs equal to the
number of cores on the node. For example, on a node with 36 cores,
number of cores on the node. For example, on a node with 16 cores,
this will look like:
.. code-block:: console
$ spack install --verbose zlib
$ spack install --no-cache --verbose zlib
==> Installing zlib
==> Using cached archive: ~/spack/var/spack/cache/zlib/zlib-1.2.11.tar.gz
==> Staging archive: ~/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/zlib-1.2.11.tar.gz
==> Created stage in ~/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
==> Using cached archive: /home/user/spack/var/spack/cache/zlib/zlib-1.2.11.tar.gz
==> Staging archive: /home/user/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/zlib-1.2.11.tar.gz
==> Created stage in /home/user/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
==> No patches needed for zlib
==> Building zlib [Package]
==> Executing phase: 'install'
==> './configure' '--prefix=~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb'
Checking for shared library support...
Building shared library libz.so.1.2.11 with ~/spack/lib/spack/env/gcc/gcc.
Checking for size_t... Yes.
Checking for off64_t... Yes.
Checking for fseeko... Yes.
Checking for strerror... Yes.
Checking for unistd.h... Yes.
Checking for stdarg.h... Yes.
Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf().
Checking for vsnprintf() in stdio.h... Yes.
Checking for return value of vsnprintf()... Yes.
Checking for attribute(visibility) support... Yes.
==> 'make' '-j36'
==> './configure' '--prefix=/home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb'
...
==> 'make' '-j36' 'install'
==> 'make' '-j16'
...
==> 'make' '-j16' 'install'
...
==> Successfully installed zlib
Fetch: 0.00s. Build: 1.03s. Total: 1.03s.
[+] /home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
As you can see, we are building with all 36 cores on the node. If you are
As you can see, we are building with all 16 cores on the node. If you are
on a shared login node, this can slow down the system for other users. If
you have a strict ulimit or restriction on the number of available licenses,
you may not be able to build at all with this many cores. On nodes with 64+
@ -837,33 +904,32 @@ If we uninstall and reinstall zlib, we see that it now uses only 4 cores:
.. code-block:: console
$ spack install -v zlib
$ spack install --no-cache --verbose zlib
==> Installing zlib
==> Using cached archive: ~/spack/var/spack/cache/zlib/zlib-1.2.11.tar.gz
==> Staging archive: ~/spack/var/spack/stage/zlib-1.2.11-ezuwp4pa52e75v6iweawzwymmf4ahxxn/zlib-1.2.11.tar.gz
==> Created stage in ~/spack/var/spack/stage/zlib-1.2.11-ezuwp4pa52e75v6iweawzwymmf4ahxxn
==> Using cached archive: /home/user/spack/var/spack/cache/zlib/zlib-1.2.11.tar.gz
==> Staging archive: /home/user/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/zlib-1.2.11.tar.gz
==> Created stage in /home/user/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
==> No patches needed for zlib
==> Building zlib [Package]
==> Executing phase: 'install'
==> './configure' '--prefix=~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/zlib-1.2.11-ezuwp4pa52e75v6iweawzwymmf4ahxxn'
Checking for shared library support...
Building shared library libz.so.1.2.11 with ~/spack/lib/spack/env/gcc/gcc.
Checking for size_t... Yes.
Checking for off64_t... Yes.
Checking for fseeko... Yes.
Checking for strerror... Yes.
Checking for unistd.h... Yes.
Checking for stdarg.h... Yes.
Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf().
Checking for vsnprintf() in stdio.h... Yes.
Checking for return value of vsnprintf()... Yes.
Checking for attribute(visibility) support... Yes.
==> './configure' '--prefix=/home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb'
...
==> 'make' '-j4'
...
==> 'make' '-j4' 'install'
...
==> Successfully installed zlib
Fetch: 0.00s. Build: 1.03s. Total: 1.03s.
[+] /home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
Obviously, if you want to build everything in serial for whatever reason,
you would set ``build_jobs`` to 1.
--------
Examples
--------
For examples of how other sites configure Spack, see
https://github.com/spack/spack-configs. If you use Spack at your site
and want to share your config files, feel free to submit a pull request!