Configuration Tutorial¶
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 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 briefly touch on the config configuration file, which manages more high-level Spack configuration options.
For all of these features we will demonstrate how we build up a full
configuration file. For some we will then demonstrate how the
configuration affects the install command, and for others we will use
the spack spec
command to demonstrate how the configuration
changes have affected Spack's concretization algorithm. The provided
output is all from a server running Ubuntu version 16.04.
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 six configuration scopes to handle this customization. These scopes, in order of decreasing priority, are:
Scope |
Directory |
---|---|
Command-line |
N/A |
Custom |
Custom directory, specified with |
User |
|
Site |
|
System |
|
Defaults |
|
Spack's default configuration settings reside in
$SPACK_ROOT/etc/spack/defaults
. These are useful for reference,
but should never be directly edited. To override these settings,
create new configuration files in any of the higher-priority
configuration scopes.
A particular cluster may have multiple Spack installations associated
with different projects. To provide settings common to all Spack
installations, put your configuration files in /etc/spack
.
To provide settings specific to a particular Spack installation,
you can use the $SPACK_ROOT/etc/spack
directory.
For settings specific to a particular user, you will want to add
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
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
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, the configuration scopes are updated as dictionaries in increasing order of precedence, allowing higher precedence files to override lower. YAML dictionaries use a colon ":" to specify key-value pairs. Spack extends YAML syntax slightly to allow a double-colon "::" to specify a key-value pair. When a double-colon is used to specify a key-value pair, instead of adding that section Spack replaces what was in that section with the new value. For example, a user compilers configuration file as follows:
compilers::
- compiler:
environment: {}
extra_rpaths: []
flags: {}
modules: []
operating_system: ubuntu16.04
paths:
cc: /usr/bin/gcc
cxx: /usr/bin/g++
f77: /usr/bin/gfortran
fc: /usr/bin/gfortran
spec: gcc@5.4.0
target: x86_64
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
were listed in other configuration files.
Compiler Configuration¶
For most tasks, we can use Spack with the compilers auto-detected the
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
control using the compilers configuration file.
We will start by opening the compilers configuration file
$ spack config edit compilers
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: []
flags: {}
modules: []
operating_system: ubuntu16.04
paths:
cc: /usr/bin/clang
cxx: /usr/bin/clang++
f77: null
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: []
flags: {}
modules: []
operating_system: ubuntu16.04
paths:
cc: /usr/bin/gcc
cxx: /usr/bin/g++
f77: /usr/bin/gfortran
fc: /usr/bin/gfortran
spec: gcc@5.4.0
target: x86_64
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.
- 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
Let's talk about the sections of this compiler entry that we've changed.
The biggest change we've made is to the paths
section. This lists
the paths to the compilers to use for each language/specification.
In this case, we point to the clang compiler for C/C++ and the gfortran
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, 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
different compilers, and are primarily useful for configuration files that
will be used across multiple systems.
We can verify that our new compiler works by invoking it now:
$ spack install --no-cache zlib %clang@3.8.0-gfortran
...
This new compiler also works on Fortran codes:
$ spack install --no-cache cfitsio %clang@3.8.0-gfortran -bzip2
...
Compiler Flags¶
Some compilers may require specific compiler flags to work properly in
a particular computing environment. Spack provides configuration
options for setting compiler flags every time a specific compiler is
invoked. These flags become part of the package spec and therefore of
the build provenance. As on the command line, the flags are set
through the implicit build variables cflags
, cxxflags
, cppflags
,
fflags
, ldflags
, and ldlibs
.
Let's open our compilers configuration file again and add a compiler flag.
- 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
We can test this out using the spack spec
command to show how the
spec is concretized.
$ spack spec cfitsio %clang@3.8.0-gfortran
Input spec
--------------------------------
cfitsio%clang@3.8.0-gfortran
Normalized
--------------------------------
cfitsio%clang@3.8.0-gfortran
Concretized
--------------------------------
cfitsio@3.410%clang@3.8.0-gfortran cppflags="-g" +bzip2+shared arch=linux-ubuntu16.04-x86_64
^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.
Advanced Compiler Configuration¶
There are three fields of the compiler configuration entry that we 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
useful when a particular module is loaded. Any modules in the
modules
field of the compiler configuration will be loaded as part
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 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_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,
this field can be set by
- compiler:
...
extra_rpaths:
- /apps/intel/ComposerXE2017/compilers_and_libraries_2017.5.239/linux/compiler/lib/intel64_lin
...
The environment
field of the compiler configuration is used for
compilers that require environment variables to be set during build
time. For example, if your Intel compiler suite requires the
INTEL_LICENSE_FILE
environment variable to point to the proper
license server, you can set this in compilers.yaml
as follows:
- compiler:
environment:
set:
INTEL_LICENSE_FILE: 1713@license4
...
In addition to set
, environment
also supports unset
,
prepend-path
, and append-path
.
Configuring Package Preferences¶
Package preferences in Spack are managed through the packages.yaml
configuration file. First, we will look at the default
packages.yaml
file.
$ spack config --scope defaults edit packages
# -------------------------------------------------------------------------
# This file controls default concretization preferences for Spack.
#
# Settings here are versioned with Spack and are intended to provide
# sensible defaults out of the box. Spack maintainers should edit this
# file to keep it current.
#
# Users can override these settings by editing the following files.
#
# Per-spack-instance settings (overrides defaults):
# $SPACK_ROOT/etc/spack/packages.yaml
#
# Per-user settings (overrides default and site settings):
# ~/.spack/packages.yaml
# -------------------------------------------------------------------------
packages:
all:
compiler: [gcc, intel, pgi, clang, xl, nag, fj]
providers:
D: [ldc]
awk: [gawk]
blas: [openblas]
daal: [intel-daal]
elf: [elfutils]
fftw-api: [fftw]
gl: [mesa+opengl, opengl]
glx: [mesa+glx, opengl]
glu: [mesa-glu, openglu]
golang: [gcc]
ipp: [intel-ipp]
java: [jdk, openjdk, ibm-java]
jpeg: [libjpeg-turbo, libjpeg]
lapack: [openblas]
mariadb-client: [mariadb-c-client, mariadb]
mkl: [intel-mkl]
mpe: [mpe2]
mpi: [openmpi, mpich]
mysql-client: [mysql, mariadb-c-client]
ninja: [ninja, ninja-fortran]
ninja-fortran: [ninja-fortran, ninja@kitware]
opencl: [pocl]
openfoam: [openfoam-com, openfoam-org, foam-extend]
pil: [py-pillow]
pkgconfig: [pkgconf, pkg-config]
scalapack: [netlib-scalapack]
szip: [libszip, libaec]
tbb: [intel-tbb]
unwind: [libunwind]
permissions:
read: world
write: user
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.
$ spack spec hdf5
Input spec
--------------------------------
hdf5
Concretized
--------------------------------
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 preferences.
$ spack config edit packages
packages:
all:
compiler: [clang, gcc, intel, pgi, xl, nag]
providers:
mpi: [mpich, openmpi]
Because of the configuration scoping we discussed earlier, this overrides the default settings just for these two items.
$ spack spec hdf5
Input spec
--------------------------------
hdf5
Concretized
--------------------------------
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
Variant Preferences¶
The packages configuration file can also set variant preferences for
package variants. For example, let's change our preferences to build all
packages without shared libraries. We will accomplish this by turning
off the shared
variant on all packages that have one.
packages:
all:
compiler: [clang, gcc, intel, pgi, xl, nag]
providers:
mpi: [mpich, openmpi]
variants: ~shared
We can check the effect of this command with spack spec hdf5
again.
$ spack spec hdf5
Input spec
--------------------------------
hdf5
Concretized
--------------------------------
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
we've seen throughout this tutorial, hdf5 builds with MPI enabled by
default in Spack. If we were working on a project that would routinely
need serial hdf5, that might get annoying quickly, having to type
hdf5~mpi
all the time. Instead, we'll update our preferences for
hdf5.
packages:
all:
compiler: [clang, gcc, intel, pgi, xl, nag]
providers:
mpi: [mpich, openmpi]
variants: ~shared
hdf5:
variants: ~mpi
Now hdf5 will concretize without an MPI dependency by default.
$ spack spec hdf5
Input spec
--------------------------------
hdf5
Concretized
--------------------------------
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 set separately for an individual package.
External Packages¶
The packages configuration file also controls when Spack will build against an externally installed package. On these systems we have a pre-installed zlib.
packages:
all:
compiler: [clang, gcc, intel, pgi, xl, nag]
providers:
mpi: [mpich, openmpi]
variants: ~shared
hdf5:
variants: ~mpi
zlib:
paths:
zlib@1.2.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64: /usr
Here, we've told Spack that zlib 1.2.8 is installed on our system. We've also told it the installation prefix where zlib can be found. We don't know exactly which variants it was built with, but that's okay.
$ spack spec hdf5
Input spec
--------------------------------
hdf5
Concretized
--------------------------------
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
You'll notice that Spack is now using the external zlib installation, but the compiler used to build zlib is now overriding our compiler preference of clang. If we explicitly specify clang:
$ spack spec hdf5 %clang
Input spec
--------------------------------
hdf5%clang
Concretized
--------------------------------
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
Spack concretizes to both hdf5 and zlib being built with clang. This has a side-effect of rebuilding zlib. If we want to force Spack to use the system zlib, we have two choices. We can either specify it on the command line, or we can tell Spack that it's not allowed to build its own zlib. We'll go with the latter.
packages:
all:
compiler: [clang, gcc, intel, pgi, xl, nag]
providers:
mpi: [mpich, openmpi]
variants: ~shared
hdf5:
variants: ~mpi
zlib:
paths:
zlib@1.2.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64: /usr
buildable: False
Now Spack will be forced to choose the external zlib.
$ spack spec hdf5 %clang
Input spec
--------------------------------
hdf5%clang
Concretized
--------------------------------
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
This gets slightly more complicated with virtual dependencies. Suppose we don't want to build our own MPI, but we now want a parallel version of hdf5? Well, fortunately we have mpich installed on these systems.
packages:
all:
compiler: [clang, gcc, intel, pgi, xl, nag]
providers:
mpi: [mpich, openmpi]
variants: ~shared
hdf5:
variants: ~mpi
zlib:
paths:
zlib@1.2.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64: /usr
buildable: False
mpich:
paths:
mpich@3.2%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64: /usr
buildable: False
If we concretize hdf5+mpi
with this configuration file, we will just
build with an alternate MPI implementation.
$ spack spec hdf5 %clang +mpi
Input spec
--------------------------------
hdf5%clang+mpi
Concretized
--------------------------------
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,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
^libsigsegv@2.11%clang@3.8.0-2ubuntu4 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@2.9.8%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 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
modify our packages.yaml
file again.
While we're at it, we can configure hdf5 to build with MPI by default again.
packages:
all:
compiler: [clang, gcc, intel, pgi, xl, nag]
providers:
mpi: [mpich, openmpi]
variants: ~shared
zlib:
paths:
zlib@1.2.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64: /usr
buildable: False
mpich:
paths:
mpich@3.2%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64: /usr
buildable: False
openmpi:
buildable: False
mvapich2:
buildable: False
intel-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.
$ spack spec hdf5 %clang
Input spec
--------------------------------
hdf5%clang
Concretized
--------------------------------
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+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
By configuring most of our package preferences in packages.yaml
,
we can cut down on the amount of work we need to do when specifying
a spec on the command line. In addition to compiler and variant
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:
packages:
converge:
permissions:
read: group
group: fluid_dynamics
Now, only members of the fluid_dynamics
group can use any
converge
installations.
警告
Make sure to delete or move the packages.yaml
you have been
editing up to this point. Otherwise, it will change the hashes
of your packages, leading to differences in the output of later
tutorial sections.
High-level Config¶
In addition to compiler and package settings, Spack allows customization
of several high-level settings. These settings are stored in the generic
config.yaml
configuration file. You can see the default settings by
running:
$ spack config --scope defaults edit config
# -------------------------------------------------------------------------
# This is the default spack configuration file.
#
# Settings here are versioned with Spack and are intended to provide
# sensible defaults out of the box. Spack maintainers should edit this
# file to keep it current.
#
# Users can override these settings by editing the following files.
#
# Per-spack-instance settings (overrides defaults):
# $SPACK_ROOT/etc/spack/config.yaml
#
# Per-user settings (overrides default and site settings):
# ~/.spack/config.yaml
# -------------------------------------------------------------------------
config:
# This is the path to the root of the Spack install tree.
# You can use $spack here to refer to the root of the spack instance.
install_tree: $spack/opt/spack
# Locations where templates should be found
template_dirs:
- $spack/share/spack/templates
# Default directory layout
install_path_scheme: "${ARCHITECTURE}/${COMPILERNAME}-${COMPILERVER}/${PACKAGE}-${VERSION}-${HASH}"
# Locations where different types of modules should be installed.
module_roots:
tcl: $spack/share/spack/modules
lmod: $spack/share/spack/lmod
dotkit: $spack/share/spack/dotkit
# Temporary locations Spack can try to use for builds.
#
# Spack will use the first one it finds that exists and is writable.
# You can use $tempdir to refer to the system default temp directory
# (as returned by tempfile.gettempdir()).
#
# A value of $spack/var/spack/stage indicates that Spack should run
# builds directly inside its install directory without staging them in
# temporary space.
#
# The build stage can be purged with `spack clean --stage`.
build_stage:
- $tempdir
- $spack/var/spack/stage
# Cache directory for already downloaded source tarballs and archived
# repositories. This can be purged with `spack clean --downloads`.
source_cache: $spack/var/spack/cache
# Cache directory for miscellaneous files, like the package index.
# This can be purged with `spack clean --misc-cache`
misc_cache: ~/.spack/cache
# If this is false, tools like curl that use SSL will not verify
# certifiates. (e.g., curl will use use the -k option)
verify_ssl: true
# If set to true, Spack will attempt to build any compiler on the spec
# that is not already available. If set to False, Spack will only use
# compilers already configured in compilers.yaml
install_missing_compilers: False
# If set to true, Spack will always check checksums after downloading
# archives. If false, Spack skips the checksum step.
checksum: true
# If set to true, `spack install` and friends will NOT clean
# potentially harmful variables from the build environment. Use wisely.
dirty: false
# The language the build environment will use. This will produce English
# compiler messages by default, so the log parser can highlight errors.
# If set to C, it will use English (see man locale).
# If set to the empty string (''), it will use the language from the
# user's environment.
build_language: C
# When set to true, concurrent instances of Spack will use locks to
# avoid modifying the install tree, database file, etc. If false, Spack
# will disable all locking, but you must NOT run concurrent instances
# of Spack. For filesystems that don't support locking, you should set
# this to false and run one Spack at a time, but otherwise we recommend
# enabling locks.
locks: true
# The default number of jobs to use when running `make` in parallel.
# If set to 4, for example, `spack install` will run `make -j4`.
# If not set, all available cores are used by default.
# build_jobs: 4
# If set to true, Spack will use ccache to cache C compiles.
ccache: false
# How long to wait to lock the Spack installation database. This lock is used
# when Spack needs to manage its own package metadata and all operations are
# expected to complete within the default time limit. The timeout should
# therefore generally be left untouched.
db_lock_timeout: 120
# How long to wait when attempting to modify a package (e.g. to install it).
# This value should typically be 'null' (never time out) unless the Spack
# instance only ever has a single user at a time, and only if the user
# anticipates that a significant delay indicates that the lock attempt will
# never succeed.
package_lock_timeout: null
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 $SPACK_ROOT
hierarchy. Module files can be
written to a central location if you are using multiple Spack
instances. If you have a fast scratch file system, you can run builds
from this file system with the following config.yaml
:
config:
build_stage:
- /scratch/$user
On systems with compilers that absolutely require environment variables
like LD_LIBRARY_PATH
, it is possible to prevent Spack from cleaning
the build environment with the dirty
setting:
config:
dirty: true
However, this is strongly discouraged, as it can pull unwanted libraries 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 16 cores, this will look like:
$ spack install --no-cache --verbose --overwrite zlib
==> Installing zlib
==> 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=/home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb'
...
==> '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 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+
cores, you may not see a significant speedup of the build anyway. To limit
the number of cores our build uses, set build_jobs
like so:
config:
build_jobs: 2
If we uninstall and reinstall zlib, we see that it now uses only 4 cores:
$ spack install --no-cache --verbose --overwrite zlib
==> Installing zlib
==> 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=/home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb'
...
==> 'make' '-j2'
...
==> 'make' '-j2' '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!