Spack has the following minimum requirements, which must be installed before Spack is run:
- Python 2 (2.6 or 2.7) or 3 (3.4 - 3.7)
- A C/C++ compiler
- If using the
These requirements can be easily installed on most modern Linux systems; on Macintosh, XCode is required. Spack is designed to run on HPC platforms like Cray and BlueGene/Q. 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.
Getting Spack is easy. You can clone it from the github repository using this command:
$ git clone https://github.com/spack/spack.git
This will create a directory called
Add Spack to the Shell¶
We’ll assume that the full path to your downloaded Spack directory is
SPACK_ROOT environment variable. Add
to your path and you’re ready to go:
$ export PATH=$SPACK_ROOT/bin:$PATH $ spack install libelf
For a richer experience, use Spack’s shell support:
# For bash/zsh users $ export SPACK_ROOT=/path/to/spack $ . $SPACK_ROOT/share/spack/setup-env.sh # For tcsh or csh users (note you must set SPACK_ROOT) $ setenv SPACK_ROOT /path/to/spack $ source $SPACK_ROOT/share/spack/setup-env.csh
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
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.
With Spack installed, you should be able to run some basic Spack commands. For example:
$ spack spec netcdf Input spec -------------------------------- netcdf Concretized -------------------------------- firstname.lastname@example.orgemail@example.com~dap~hdf4 maxdims=1024 maxvars=8192 +mpi~parallel-netcdf+shared arch=linux-ubuntu16.04-x86_64 ^firstname.lastname@example.orgemail@example.com~cxx~debug~fortran+hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64 ^firstname.lastname@example.orgemail@example.com~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64 ^firstname.lastname@example.orgemail@example.com~cairo~cuda+libxml2+pci+shared arch=linux-ubuntu16.04-x86_64 ^firstname.lastname@example.orgemail@example.com arch=linux-ubuntu16.04-x86_64 ^firstname.lastname@example.orgemail@example.com arch=linux-ubuntu16.04-x86_64 ^firstname.lastname@example.orgemail@example.com patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64 ^firstname.lastname@example.orgemail@example.com arch=linux-ubuntu16.04-x86_64 ^firstname.lastname@example.orgemail@example.com arch=linux-ubuntu16.04-x86_64 ^firstname.lastname@example.orgemail@example.com arch=linux-ubuntu16.04-x86_64 ^firstname.lastname@example.orgemail@example.com~python arch=linux-ubuntu16.04-x86_64 ^firstname.lastname@example.orgemail@example.com arch=linux-ubuntu16.04-x86_64 ^firstname.lastname@example.orgemail@example.com+optimize+pic+shared arch=linux-ubuntu16.04-x86_64 ^firstname.lastname@example.orgemail@example.com patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64 ^firstname.lastname@example.orgemail@example.com arch=linux-ubuntu16.04-x86_64 ^firstname.lastname@example.orgemail@example.com+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64 ^firstname.lastname@example.orgemail@example.com arch=linux-ubuntu16.04-x86_64 ^firstname.lastname@example.orgemail@example.com arch=linux-ubuntu16.04-x86_64 ^firstname.lastname@example.orgemail@example.com~symlinks~termlib arch=linux-ubuntu16.04-x86_64 ^firstname.lastname@example.orgemail@example.com arch=linux-ubuntu16.04-x86_64
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:
$ spack clone /my/favorite/prefix
This will install a new spack script in
which you can use just like you would the regular spack script. Each
copy of spack installs packages into its own
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…
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
You can see which compilers spack has found by running
spack compiler list:
$ spack compilers ==> Available compilers -- gcc --------------------------------------------------------- firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com -- intel ------------------------------------------------------- firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com -- clang ------------------------------------------------------- firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com -- pgi --------------------------------------------------------- firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org
Any of these compilers can be used to build Spack packages. More on how this is done is in Specs & dependencies.
spack compiler add¶
An alias for
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:
$ spack compiler find /usr/local/tools/ic-13.0.079 ==> Added 1 new compiler to ~/.spack/compilers.yaml email@example.com
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:
$ module load gcc-4.9.0 $ spack compiler find ==> Added 1 new compiler to ~/.spack/compilers.yaml firstname.lastname@example.org
This loads the environment module for gcc-4.9.0 to add it to
PATH, and then it adds the compiler to Spack.
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 Compilers Requiring Modules.
spack compiler info¶
If you want to see specifics on a particular compiler, you can run
spack compiler info on it:
$ spack compiler info intel@15 email@example.com: 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
~/.spack/compilers.yaml file. You can do this by running
spack config edit compilers, which will open the file in your
Each compiler configuration in the file looks like this:
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: firstname.lastname@example.org:
For compilers that do not support Fortran (like
compilers: - compiler: modules:  operating_system: centos6 paths: cc: /usr/bin/clang cxx: /usr/bin/clang++ f77: None fc: None spec: email@example.com
Once you save the file, the configured compilers will show up in the
list displayed by
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
ldlibs. For example:
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: firstname.lastname@example.org
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:
$ spack install email@example.com
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: all: compiler: [firstname.lastname@example.org]
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
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: email@example.com
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.
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 Licensed software.
- 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
cc helloWorld.c && ./a.out)
- Add the newly-installed compiler to
compilers.yamlas shown above.
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
You need to make sure that Xcode is installed. Run the following command:
$ xcode-select --install
If the Xcode command-line tools are already installed, you will see an error message:
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
qtrequire the full Xcode suite. You can check to see which you have installed by running:
$ xcode-select -p
If the output is:
you already have the full Xcode suite installed. If the output is:
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:
$ sudo xcodebuild -license accept
Note: the flag is
spack compiler findto locate Clang.
There are different ways to get
gfortranon 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/compilers.yamlto provide the path to
compilers: darwin-x86_64: firstname.lastname@example.org: cc: /usr/bin/clang cxx: /usr/bin/clang++ f77: /path/to/bin/gfortran fc: /path/to/bin/gfortran
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
You can verify that your compilers are configured properly by installing a simple package. For example:
$ spack install email@example.com
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 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
g++you have installed from the
If you want use a version of
g++other than the default version on your system, you need to use either the
-gxx-namecompiler option to specify the path to the version of
g++that you want to use.”
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
compilers.yaml illustrates this technique:
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: firstname.lastname@example.org
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
Identify the location of the compiler you just installed:
$ spack location --install-dir gcc ~/spack/opt/spack/linux-centos7-x86_64/gcc-4.9.3-iy4rw...
compilers.yaml, for example:
compilers: - compiler: modules: [intel-15.0.24] operating_system: centos7 paths: cc: /opt/intel-15.0.24/bin/icc-15.0.24-beta cflags: -gcc-name ~/spack/opt/spack/linux-centos7-x86_64/gcc-4.9.3-iy4rw.../bin/gcc cxx: /opt/intel-15.0.24/bin/icpc-15.0.24-beta cxxflags: -gxx-name ~/spack/opt/spack/linux-centos7-x86_64/gcc-4.9.3-iy4rw.../bin/g++ f77: /opt/intel-15.0.24/bin/ifort-15.0.24-beta fc: /opt/intel-15.0.24/bin/ifort-15.0.24-beta fflags: -gcc-name ~/spack/opt/spack/linux-centos7-x86_64/gcc-4.9.3-iy4rw.../bin/gcc spec: email@example.com
PGI comes with two sets of compilers for C++ and Fortran, distinguishable by their names. “Old” compilers:
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
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
There are reports that some packages will not build with PGI, including
openssl. A workaround is to build these packages with another compiler and then use them as dependencies for PGI-build packages. For example:
$ spack install openmpi%pgi ^libpciaccess%gcc
PGI requires a license to use; see Licensed Compilers for more information on installation.
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 (
pgfortran, etc) are fine. But
compilers specific to one or the other (
The Numerical Algorithms Group provides a licensed Fortran compiler. Like Clang, this requires you to set up a 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:
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
FCFLAGS=-mismatch. This can be done through
the command line:
$ spack install openmpi fflags="-mismatch"
Or it can be set permanently in your
- 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: firstname.lastname@example.org
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:
packages: openmpi: paths: email@example.com: /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 two packages for which one commonly needs to use system versions:
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
openssl package underlies much of modern security in a modern
OS; an attacker can easily “pwn” any computer on which they can modify SSL.
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
$ 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:
$ openssl version OpenSSL 1.0.2g 1 Mar 2016
Then add the following to
packages: openssl: paths: firstname.lastname@example.org: /usr buildable: False
BLAS / LAPACK¶
The recommended way to use system-supplied BLAS / LAPACK packages is
to add the following to
packages: netlib-lapack: paths: email@example.com: /usr buildable: False all: providers: blas: [netlib-lapack] lapack: [netlib-lapack]
Above we pretend that the system-provided BLAS / LAPACK is
only because it is the only BLAS / LAPACK provider which use standard names
for libraries (as opposed to, for example,
Although we specify external package in
/usr, Spack is smart enough not
/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.
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:
==> 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
spack install git
- Add the output of
spack module tcl loads gitto your
If this doesn’t work, it is also possible to disable checking of SSL certificates by using:
$ spack --insecure install
--insecure makes Spack disable SSL checking when fetching
from websites and from git.
This workaround should be used ONLY as a last resort! Wihout 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).
certificate for security (no verification).
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
$ spack install curl $ spack load curl
$ spack module tcl loads curl >>~/.bashrc
or if environment modules don’t work:
$ 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, and to load generated environment modules:
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.
If you find that you are missing some of these programs,
build some of them for you with
spack bootstrap. Currently supported
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
until a new cURL has been installed, using the technique above.
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:
svn and occasionally
go. If you had to install
curl, then chances are the system-supplied version of these
other programs will also not work, because they also rely on OpenSSL.
curl has been installed, you can similarly install the others.
In order to use Spack’s generated module files, you must have
lmod. The simplest way
to get the latest version of either of these tools is installing
it as part of Spack’s bootstrap procedure:
$ spack bootstrap
At the moment
spack bootstrap is only able to install
Extending its capabilities to prefer
lmod where possible is in the roadmap,
and likely to happen before the next release.
Alternatively, on many Linux distributions, you can install a pre-built binary from the vendor’s repository. On Fedora/RHEL/CentOS, for example, this can be done with the command:
$ yum install environment-modules
Once you have the tool installed and available in your path, you can source Spack’s setup file:
$ source share/spack/setup-env.sh
This activates shell support and makes commands like
spack load available for use.
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
launching Spack, it will have no effect.
In this case, you will likely need to use the
--dirty flag when
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:
This is considered best practice for some common build dependencies,
autotools (if the
autoreconf command is needed) and
cmake especially, because different packages require
a different version of CMake.
Sometimes, strange error messages can happen while building a package.
ld might crash. Or one receives a message like:
ld: final link failed: Nonrepresentable section on output
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
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
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
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.
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.
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
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.
- 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:
$ 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:
$ sudo yum install haveged $ sudo chkconfig haveged on
This Digital Ocean tutorial provides a good overview of sources of randomness.
In order to list the keys available in the keyring, the
spack gpg list command will list trusted keys with the
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.
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
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>.
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:
$ spack install zlib target=ivybridge
You can also use the operating system to build against the back-end:
$ 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:
$ spack install zlib target=sandybridge
And the front-end operating system is:
$ 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 :
- 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:
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 Compiler configuration.
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
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
Here’s an example of an external configuration for cray modules:
packages: mpich: modules: firstname.lastname@example.orgemail@example.com arch=cray_xc-haswell-CNL10: cray-mpich firstname.lastname@example.orgemail@example.com arch=cray_xc-haswell-CNL10: 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.
For Cray-provided packages, it is best to use
modules: instead of
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
packages: mpich: modules: firstname.lastname@example.orgemail@example.com arch=cray_xc-CNL10-ivybridge: cray-mpich firstname.lastname@example.orgemail@example.com arch=cray_xc-SuSE11-ivybridge: cray-mpich buildable: False netcdf: modules: firstname.lastname@example.orgemail@example.com arch=cray_xc-CNL10-ivybridge: cray-netcdf firstname.lastname@example.orgemail@example.com arch=cray_xc-CNL10-ivybridge: cray-netcdf buildable: False hdf5: modules: firstname.lastname@example.orgemail@example.com arch=cray_xc-CNL10-ivybridge: cray-hdf5 firstname.lastname@example.orgemail@example.com arch=cray_xc-CNL10-ivybridge: cray-hdf5 buildable: False all: compiler: [firstname.lastname@example.org, email@example.com] 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 188.8.131.52. 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 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
will cause Spack to treat a linux container on a Cray system as a base