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diff --git a/lib/spack/docs/tutorial_sc16_spack_basics.rst b/lib/spack/docs/tutorial_sc16_spack_basics.rst deleted file mode 100644 index 9511907ceb..0000000000 --- a/lib/spack/docs/tutorial_sc16_spack_basics.rst +++ /dev/null @@ -1,1255 +0,0 @@ -.. _basics-tutorial: - -========================================= -Basic Installation Tutorial -========================================= - -This tutorial will guide you through the process of installing software -using Spack. We will first cover the `spack install` command, focusing on -the power of the spec syntax and the flexibility it gives to users. We -will also cover the `spack find` command for viewing installed packages -and the `spack uninstall` command. Finally, we will touch on how Spack -manages compilers, especially as it relates to using Spack-built -compilers within Spack. We will include full output from all of the -commands demonstrated, although we will frequently call attention to only -small portions of that output (or merely to the fact that it -succeeded). The provided output is all from a cluster running Red Hat -Enterprise Linux. - -.. _basics-tutorial-install: - ----------------- -Installing Spack ----------------- - -Spack works out of the box. Simply clone spack and get going. - -.. code-block:: console - - $ git clone https://github.com/LLNL/spack.git - Initialized empty Git repository in ~/spack/.git/ - remote: Counting objects: 47125, done. - remote: Compressing objects: 100% (68/68), done. - remote: Total 47125 (delta 16), reused 2 (delta 2), pack-reused 47047 - Receiving objects: 100% (47125/47125), 12.02 MiB | 2.11 MiB/s, done. - Resolving deltas: 100% (23044/23044), done. - $ cd spack - -Then add Spack to your path. - -.. code-block:: console - - $ export PATH=~/spack/bin:$PATH - -You're good to go! - ------------------ -What is in Spack? ------------------ - -The ``spack list`` command shows available packages. - -.. code-block:: console - - $ spack list - ==> 1016 packages. - abinit hwloc piranha r-rjava - ack hydra pixman r-rjson - activeharmony hypre pkg-config r-rjsonio - ... - -The ``spack list`` command can also take a query string. Spack -automatically adds wildcards to both ends of the string. For example, -we can view all available python packages. - -.. code-block:: console - - $ spack list py - ==> 129 packages. - py-3to2 py-epydoc py-nestle py-pycparser py-six - py-alabaster py-flake8 py-netcdf py-pydatalog py-sncosmo - py-argcomplete py-funcsigs py-networkx py-pyelftools py-snowballstemmer - ... - -------------------- -Installing Packages -------------------- - -Installing a package with Spack is very simple. To install a piece of -software, simply type ``spack install <package_name>`` - -.. code-block:: console - - $ spack install libelf - ==> Installing libelf - ==> Trying to fetch from ~/spack/var/spack/cache/libelf/libelf-0.8.13.tar.gz - curl: (37) Couldn't open file ~/spack/var/spack/cache/libelf/libelf-0.8.13.tar.gz - ==> Fetching from ~/spack/var/spack/cache/libelf/libelf-0.8.13.tar.gz failed. - ==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.13.tar.gz - ################################################################################################################################################################################# 100.0% - ==> Staging archive: ~/spack/var/spack/stage/libelf-0.8.13-csrt4qxfkhjgn5xg3zjpkir7xdnszl2a/libelf-0.8.13.tar.gz - ==> Created stage in ~/spack/var/spack/stage/libelf-0.8.13-csrt4qxfkhjgn5xg3zjpkir7xdnszl2a - ==> No patches needed for libelf - ==> Building libelf [Package] - ==> Executing phase : 'install' - ==> Successfully installed libelf - Fetch: 1.21s. Build: 8.42s. Total: 9.62s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/libelf-0.8.13-csrt4qxfkhjgn5xg3zjpkir7xdnszl2a - - -Spack's spec syntax is the interface by which we can request specific -configurations of the package. The ``%`` sigil is used to specify -compilers. - -.. code-block:: console - - $ spack install libelf %intel - ==> Installing libelf - ==> Trying to fetch from ~/spack/var/spack/cache/libelf/libelf-0.8.13.tar.gz - ################################################################################################################################################################################# 100.0% - ==> Staging archive: ~/spack/var/spack/stage/libelf-0.8.13-7wgp32xksatkvw2tbssmehw2t5tnxndj/libelf-0.8.13.tar.gz - ==> Created stage in ~/spack/var/spack/stage/libelf-0.8.13-7wgp32xksatkvw2tbssmehw2t5tnxndj - ==> No patches needed for libelf - ==> Building libelf [Package] - ==> Executing phase : 'install' - ==> Successfully installed libelf - Fetch: 0.09s. Build: 50.64s. Total: 50.72s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/intel-16.0.3/libelf-0.8.13-7wgp32xksatkvw2tbssmehw2t5tnxndj - -Note that this installation is located separately from the previous -one. We will discuss this in more detail later, but this is part of what -allows Spack to support arbitrarily versioned software. - -You can check for particular versions before requesting them. We will -use the ``spack versions`` command to see the available versions, and then -install a different version of ``libelf``. - -.. code-block:: console - - $ spack versions libelf - ==> Safe versions (already checksummed): - 0.8.13 - 0.8.12 - ==> Remote versions (not yet checksummed): - 0.8.11 - 0.8.10 - 0.8.9 - 0.8.8 - 0.8.7 - 0.8.6 - 0.8.5 - 0.8.4 - 0.8.3 - 0.8.2 - 0.8.0 - 0.7.0 - 0.6.4 - 0.5.2 - - -The ``@`` sigil is used to specify versions, both of packages and of -compilers. - -.. code-block:: console - - $ spack install libelf @0.8.12 - ==> Installing libelf - ==> Trying to fetch from ~/spack/var/spack/cache/libelf/libelf-0.8.12.tar.gz - curl: (37) Couldn't open file ~/spack/var/spack/cache/libelf/libelf-0.8.12.tar.gz - ==> Fetching from ~/spack/var/spack/cache/libelf/libelf-0.8.12.tar.gz failed. - ==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.12.tar.gz - ################################################################################################################################################################################# 100.0% - ==> Staging archive: ~/spack/var/spack/stage/libelf-0.8.12-ipggckv6i7h44iryzfa4dwdela32a7fy/libelf-0.8.12.tar.gz - ==> Created stage in ~/spack/var/spack/stage/libelf-0.8.12-ipggckv6i7h44iryzfa4dwdela32a7fy - ==> No patches needed for libelf - ==> Building libelf [Package] - ==> Executing phase : 'install' - ==> Successfully installed libelf - Fetch: 1.12s. Build: 7.88s. Total: 9.00s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/libelf-0.8.12-ipggckv6i7h44iryzfa4dwdela32a7fy - - - - $ spack install libelf %intel@15.0.4 - ==> Installing libelf - ==> Trying to fetch from ~/spack/var/spack/cache/libelf/libelf-0.8.13.tar.gz - ################################################################################################################################################################################# 100.0% - ==> Staging archive: ~/spack/var/spack/stage/libelf-0.8.13-w33hrejdyqu2j2gggdswitls2zv6kdsi/libelf-0.8.13.tar.gz - ==> Created stage in ~/spack/var/spack/stage/libelf-0.8.13-w33hrejdyqu2j2gggdswitls2zv6kdsi - ==> No patches needed for libelf - ==> Building libelf [Package] - ==> Executing phase : 'install' - ==> Successfully installed libelf - Fetch: 0.09s. Build: 55.51s. Total: 55.60s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/intel-15.0.4/libelf-0.8.13-w33hrejdyqu2j2gggdswitls2zv6kdsi - - -The spec syntax also includes compiler flags. Spack accepts -``cppflags``, ``cflags``, ``cxxflags``, ``fflags``, ``ldflags``, and -``ldlibs`` parameters. The values of these fields must be quoted on -the command line if they include spaces. These values are injected -into the compile line automatically by the Spack compiler wrappers. - -.. code-block:: console - - $ spack install libelf @0.8.12 cppflags="-O3" - ==> Installing libelf - ==> Trying to fetch from ~/spack/var/spack/cache/libelf/libelf-0.8.12.tar.gz - ################################################################################################################################################################################# 100.0% - ==> Staging archive: ~/spack/var/spack/stage/libelf-0.8.12-vrv2ttbd34xlfoxy4jwt6qsjrcbalmmw/libelf-0.8.12.tar.gz - ==> Created stage in ~/spack/var/spack/stage/libelf-0.8.12-vrv2ttbd34xlfoxy4jwt6qsjrcbalmmw - ==> No patches needed for libelf - ==> Building libelf [Package] - ==> Executing phase : 'install' - ==> Successfully installed libelf - Fetch: 0.04s. Build: 7.95s. Total: 7.99s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/libelf-0.8.12-vrv2ttbd34xlfoxy4jwt6qsjrcbalmmw - - -The ``spack find`` command is used to query installed packages. Note that -some packages appear identical with the default output. The ``-l`` flag -shows the hash of each package, and the ``-f`` flag shows any non-empty -compiler flags of those packages. - -.. code-block:: console - - $ spack find - ==> 5 installed packages. - -- linux-redhat6-x86_64 / gcc@4.4.7 ----------------------------- - libelf@0.8.12 - libelf@0.8.12 - libelf@0.8.13 - - -- linux-redhat6-x86_64 / intel@15.0.4 -------------------------- - libelf@0.8.13 - - -- linux-redhat6-x86_64 / intel@16.0.3 -------------------------- - libelf@0.8.13 - - - - $ spack find -lf - ==> 5 installed packages. - -- linux-redhat6-x86_64 / gcc@4.4.7 ----------------------------- - ipggckv libelf@0.8.12%gcc - - vrv2ttb libelf@0.8.12%gcc cppflags="-O3" - - csrt4qx libelf@0.8.13%gcc - - - -- linux-redhat6-x86_64 / intel@15.0.4 -------------------------- - w33hrej libelf@0.8.13%intel - - - -- linux-redhat6-x86_64 / intel@16.0.3 -------------------------- - 7wgp32x libelf@0.8.13%intel - - -Spack generates a hash for each spec. This hash is a function of the full -provenance of the package, so any change to the spec affects the -hash. Spack uses this value to compare specs and to generate unique -installation directories for every combinatorial version. As we move into -more complicated packages with software dependencies, we can see that -Spack reuses existing packages to satisfy a dependency only when the -existing package's hash matches the desired spec. - -.. code-block:: console - - $ spack install libdwarf - ==> Installing libdwarf - ==> libelf is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/libelf-0.8.13-csrt4qxfkhjgn5xg3zjpkir7xdnszl2a - ==> Can not find version 20160507 in url_list - ==> Trying to fetch from ~/spack/var/spack/cache/libdwarf/libdwarf-20160507.tar.gz - curl: (37) Couldn't open file ~/spack/var/spack/cache/libdwarf/libdwarf-20160507.tar.gz - ==> Fetching from ~/spack/var/spack/cache/libdwarf/libdwarf-20160507.tar.gz failed. - ==> Trying to fetch from http://www.prevanders.net/libdwarf-20160507.tar.gz - ################################################################################################################################################################################# 100.0% - ==> Staging archive: ~/spack/var/spack/stage/libdwarf-20160507-yfx6p3g3rkmqvcqbmtb34o6pln7pqvcz/libdwarf-20160507.tar.gz - ==> Created stage in ~/spack/var/spack/stage/libdwarf-20160507-yfx6p3g3rkmqvcqbmtb34o6pln7pqvcz - ==> No patches needed for libdwarf - ==> Building libdwarf [Package] - ==> Executing phase : 'install' - ==> Successfully installed libdwarf - Fetch: 1.56s. Build: 33.59s. Total: 35.15s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/libdwarf-20160507-yfx6p3g3rkmqvcqbmtb34o6pln7pqvcz - - -Dependencies can be explicitly requested using the ``^`` sigil. Note that -the spec syntax is recursive. Anything we could specify about the -top-level package, we can also specify about a dependency using ``^``. - -.. code-block:: console - - $ spack install libdwarf ^libelf @0.8.12 %intel - ==> Installing libdwarf - ==> Installing libelf - ==> Trying to fetch from ~/spack/var/spack/cache/libelf/libelf-0.8.12.tar.gz - ################################################################################################################################################################################# 100.0% - ==> Staging archive: ~/spack/var/spack/stage/libelf-0.8.12-4blbe3qxqct3ymrfoxxnxysmybvbxay7/libelf-0.8.12.tar.gz - ==> Created stage in ~/spack/var/spack/stage/libelf-0.8.12-4blbe3qxqct3ymrfoxxnxysmybvbxay7 - ==> No patches needed for libelf - ==> Building libelf [Package] - ==> Executing phase : 'install' - ==> Successfully installed libelf - Fetch: 0.04s. Build: 52.16s. Total: 52.19s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/intel-16.0.3/libelf-0.8.12-4blbe3qxqct3ymrfoxxnxysmybvbxay7 - ==> Can not find version 20160507 in url_list - ==> Trying to fetch from ~/spack/var/spack/cache/libdwarf/libdwarf-20160507.tar.gz - ################################################################################################################################################################################# 100.0% - ==> Staging archive: ~/spack/var/spack/stage/libdwarf-20160507-csruprgucaujkfkrcywhwou7nbeis5fo/libdwarf-20160507.tar.gz - ==> Created stage in ~/spack/var/spack/stage/libdwarf-20160507-csruprgucaujkfkrcywhwou7nbeis5fo - ==> No patches needed for libdwarf - ==> Building libdwarf [Package] - ==> Executing phase : 'install' - ==> Successfully installed libdwarf - Fetch: 0.40s. Build: 2m 17.29s. Total: 2m 17.69s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/intel-16.0.3/libdwarf-20160507-csruprgucaujkfkrcywhwou7nbeis5fo - - -Packages can also be referred to from the command line by their package -hash. Using the ``spack find -lf`` command earlier we saw that the hash -of our optimized installation of libelf (``cppflags="-O3"``) began with -``vrv2ttb``. We can now explicitly build with that package without typing -the entire spec, by using the ``/`` sigil to refer to it by hash. As with -other tools like git, you do not need to specify an *entire* hash on the -command line. You can specify just enough digits to identify a hash -uniquely. If a hash prefix is ambiguous (i.e., two or more installed -packages share the prefix) then spack will report an error. - -.. code-block:: console - - $ spack install libdwarf ^/vrv2ttb - ==> Installing libdwarf - ==> libelf is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/libelf-0.8.12-vrv2ttbd34xlfoxy4jwt6qsjrcbalmmw - ==> Can not find version 20160507 in url_list - ==> Trying to fetch from ~/spack/var/spack/cache/libdwarf/libdwarf-20160507.tar.gz - #################################################################################################################################################################################################################################################### 100.0% - ==> Staging archive: ~/spack/var/spack/stage/libdwarf-20160507-dtg3tgnp7htccoly26gduqlrgvnwcp5t/libdwarf-20160507.tar.gz - ==> Created stage in ~/spack/var/spack/stage/libdwarf-20160507-dtg3tgnp7htccoly26gduqlrgvnwcp5t - ==> No patches needed for libdwarf - ==> Building libdwarf [Package] - ==> Executing phase : 'install' - ==> Successfully installed libdwarf - Fetch: 0.96s. Build: 24.03s. Total: 24.99s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/libdwarf-20160507-dtg3tgnp7htccoly26gduqlrgvnwcp5t - - -The ``spack find`` command can also take a ``-d`` flag, which can show -dependency information. Note that each package has a top-level entry, -even if it also appears as a dependency. - -.. code-block:: console - - $ spack find -ldf - ==> 9 installed packages. - -- linux-redhat6-x86_64 / gcc@4.4.7 ----------------------------- - dtg3tgn libdwarf@20160507%gcc - vrv2ttb ^libelf@0.8.12%gcc cppflags="-O3" - - yfx6p3g libdwarf@20160507%gcc - csrt4qx ^libelf@0.8.13%gcc - - ipggckv libelf@0.8.12%gcc - - vrv2ttb libelf@0.8.12%gcc cppflags="-O3" - - csrt4qx libelf@0.8.13%gcc - - - -- linux-redhat6-x86_64 / intel@15.0.4 -------------------------- - w33hrej libelf@0.8.13%intel - - - -- linux-redhat6-x86_64 / intel@16.0.3 -------------------------- - csruprg libdwarf@20160507%intel - 4blbe3q ^libelf@0.8.12%intel - - 4blbe3q libelf@0.8.12%intel - - 7wgp32x libelf@0.8.13%intel - - -As we get to more complex packages, full installs will take too long to -build in the time allotted for this tutorial. Our collaborators at CERN -have been working on binary caching for Spack, which would allow for very -fast installs of previously built packages. We are still working out the -security ramifications of the feature, but it is coming soon. - -For now, we will switch to doing "fake" installs. When supplied with the -``--fake`` flag (primarily used for debugging), Spack computes build -metadata the same way it normally would, but it does not download the -source or run the install script for a pacakge. We can use this to -quickly demonstrate some of the more advanced Spack features in our -limited tutorial time. - -``HDF5`` is an example of a more complicated package, with an MPI -dependency. If we install it "out of the box," it will build with -``openmpi``. - -.. code-block:: console - - $ spack install --fake hdf5 - ==> Installing hdf5 - ==> Installing zlib - ==> Building zlib [Package] - ==> Successfully installed zlib - Fetch: . Build: 0.11s. Total: 0.11s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/zlib-1.2.8-ayc4jq7vxuzge5n444gutvskeytfdruh - ==> Installing openmpi - ==> Installing hwloc - ==> Installing libpciaccess - ==> Installing util-macros - ==> Building util-macros [Package] - ==> Successfully installed util-macros - Fetch: . Build: 0.11s. Total: 0.11s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/util-macros-1.19.0-pc6zhs4cnkmg2cv4et4fizsp6scuvacg - ==> Installing libtool - ==> Installing m4 - ==> Installing libsigsegv - ==> Building libsigsegv [Package] - ==> Successfully installed libsigsegv - Fetch: . Build: 0.11s. Total: 0.11s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/libsigsegv-2.10-q4cok3yber7lhf3jswg6mysg7oi53unh - ==> Building m4 [Package] - ==> Successfully installed m4 - Fetch: . Build: 0.23s. Total: 0.23s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/m4-1.4.17-qijdzvhjyybrtwbqm73vykhmkaqro3je - ==> Building libtool [Package] - ==> Successfully installed libtool - Fetch: . Build: 0.11s. Total: 0.11s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/libtool-2.4.6-rdx5nkfjwlvcanz5il3ys2pe34j4vxx5 - ==> Installing pkg-config - ==> Building pkg-config [Package] - ==> Successfully installed pkg-config - Fetch: . Build: 0.11s. Total: 0.11s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/pkg-config-0.29.1-wpjnlzahdw6ahkrgmqyeugkj2zhv4tui - ==> Building libpciaccess [Package] - ==> Successfully installed libpciaccess - Fetch: . Build: 0.10s. Total: 0.10s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/libpciaccess-0.13.4-m2f6fpm22rpprq2ihkmfx6llf363264m - ==> Building hwloc [Package] - ==> Successfully installed hwloc - Fetch: . Build: 0.23s. Total: 0.23s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/hwloc-1.11.4-xpb6hbl2hsze25cgdgfnoppn6rchhzaz - ==> Building openmpi [Package] - ==> Successfully installed openmpi - Fetch: . Build: 0.35s. Total: 0.35s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openmpi-2.0.1-j4cgoq4furxvr73pq72r2qgywgksw3qn - ==> Building hdf5 [AutotoolsPackage] - ==> Successfully installed hdf5 - Fetch: . Build: 0.61s. Total: 0.61s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/hdf5-1.10.0-patch1-ezvtnox35albuaxqryuondweyjgeo6es - - -Spack packages can also have variants. Boolean variants can be specified -using the ``+`` and ``~`` or ``-`` sigils. There are two sigils for -``False`` to avoid conflicts with shell parsing in different -situations. Variants (boolean or otherwise) can also be specified using -the same syntax as compiler flags. Here we can install HDF5 without MPI -support. - -.. code-block:: console - - $ spack install --fake hdf5~mpi - ==> Installing hdf5 - ==> zlib is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/zlib-1.2.8-ayc4jq7vxuzge5n444gutvskeytfdruh - ==> Building hdf5 [AutotoolsPackage] - ==> Successfully installed hdf5 - Fetch: . Build: 0.22s. Total: 0.22s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/hdf5-1.10.0-patch1-twppaioxqn6lti4grgopnmhwcq3h2rpw - - -We might also want to install HDF5 with a different MPI -implementation. While MPI is not a package itself, packages can depend on -abstract interfaces like MPI. Spack handles these through "virtual -dependencies." A package, such as HDF5, can depend on the MPI -interface. Other packages (``openmpi``, ``mpich``, ``mvapich``, etc.) -provide the MPI interface. Any of these providers can be requested for -an MPI dependency. For example, we can build HDF5 with MPI support -provided by mpich by specifying a dependency on ``mpich``. Spack also -supports versioning of virtual dependencies. A package can depend on the -MPI interface at version 3, and provider packages specify what version of -the interface *they* provide. The partial spec ``^mpi@3`` can be safisfied -by any of several providers. - -.. code-block:: console - - $ spack install --fake hdf5+mpi ^mpich - ==> Installing hdf5 - ==> mpich is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/mpich-3.2-5jlp2ndnsb67txggraglu47vjmayx5za - ==> zlib is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/zlib-1.2.8-ayc4jq7vxuzge5n444gutvskeytfdruh - ==> Building hdf5 [AutotoolsPackage] - ==> Successfully installed hdf5 - Fetch: . Build: 0.38s. Total: 0.38s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/hdf5-1.10.0-patch1-j36yfw25i6gdd3q4vwlupgkpwic4ua6m - - -We'll do a quick check in on what we have installed so far. - -.. code-block:: console - - $ spack find -ldf - ==> 22 installed packages. - -- linux-redhat6-x86_64 / gcc@4.4.7 ----------------------------- - twppaio hdf5@1.10.0-patch1%gcc - ayc4jq7 ^zlib@1.2.8%gcc - - j36yfw2 hdf5@1.10.0-patch1%gcc - 5jlp2nd ^mpich@3.2%gcc - ayc4jq7 ^zlib@1.2.8%gcc - - ezvtnox hdf5@1.10.0-patch1%gcc - j4cgoq4 ^openmpi@2.0.1%gcc - xpb6hbl ^hwloc@1.11.4%gcc - m2f6fpm ^libpciaccess@0.13.4%gcc - ayc4jq7 ^zlib@1.2.8%gcc - - xpb6hbl hwloc@1.11.4%gcc - m2f6fpm ^libpciaccess@0.13.4%gcc - - dtg3tgn libdwarf@20160507%gcc - vrv2ttb ^libelf@0.8.12%gcc cppflags="-O3" - - yfx6p3g libdwarf@20160507%gcc - csrt4qx ^libelf@0.8.13%gcc - - ipggckv libelf@0.8.12%gcc - - vrv2ttb libelf@0.8.12%gcc cppflags="-O3" - - csrt4qx libelf@0.8.13%gcc - - m2f6fpm libpciaccess@0.13.4%gcc - - q4cok3y libsigsegv@2.10%gcc - - rdx5nkf libtool@2.4.6%gcc - - qijdzvh m4@1.4.17%gcc - q4cok3y ^libsigsegv@2.10%gcc - - 5jlp2nd mpich@3.2%gcc - - j4cgoq4 openmpi@2.0.1%gcc - xpb6hbl ^hwloc@1.11.4%gcc - m2f6fpm ^libpciaccess@0.13.4%gcc - - wpjnlza pkg-config@0.29.1%gcc - - pc6zhs4 util-macros@1.19.0%gcc - - ayc4jq7 zlib@1.2.8%gcc - - - -- linux-redhat6-x86_64 / intel@15.0.4 -------------------------- - w33hrej libelf@0.8.13%intel - - - -- linux-redhat6-x86_64 / intel@16.0.3 -------------------------- - csruprg libdwarf@20160507%intel - 4blbe3q ^libelf@0.8.12%intel - - 4blbe3q libelf@0.8.12%intel - - 7wgp32x libelf@0.8.13%intel - - -Spack models the dependencies of packages as a directed acyclic graph -(DAG). The ``spack find -d`` command shows the tree representation of -that graph. We can also use the ``spack graph`` command to view the entire -DAG as a graph. - -.. code-block:: console - - $ spack graph hdf5+mpi ^mpich - o hdf5 - |\ - o | zlib - / - o mpich - -You may also have noticed that there are some packages shown in the -``spack find -d`` output that we didn't install explicitly. These are -dependencies that were installed implicitly. A few packages installed -implicitly are not shown as dependencies in the ``spack find -d`` -output. These are build dependencies. For example, ``libpciaccess`` is a -dependency of openmpi and requires m4 to build. Spack will build `m4`` as -part of the installation of ``openmpi``, but it does not become a part of -the DAG because it is not linked in at run time. Spack handles build -dependencies differently because of their different (less strict) -consistency requirements. It is entirely possible to have two packages -using different versions of a dependency to build, which obviously cannot -be done with linked dependencies. - -``HDF5`` is more complicated than our basic example of libelf and -libdwarf, but it's still within the realm of software that an experienced -HPC user could reasonably expect to install given a bit of time. Now -let's look at a more complicated package. - -.. code-block:: console - - $ spack install --fake trilinos - ==> Installing trilinos - ==> Installing superlu-dist - ==> openmpi is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openmpi-2.0.1-j4cgoq4furxvr73pq72r2qgywgksw3qn - ==> Installing parmetis - ==> openmpi is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openmpi-2.0.1-j4cgoq4furxvr73pq72r2qgywgksw3qn - ==> Installing cmake - ==> Installing bzip2 - ==> Building bzip2 [Package] - ==> Successfully installed bzip2 - Fetch: . Build: 0.11s. Total: 0.11s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/bzip2-1.0.6-gll2xsahysy7ji5gkmfxwkofdt3mwjhs - ==> expat is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/expat-2.2.0-mg5kwd3kluxdgorj32vzbp7aksg3vqej - ==> Installing ncurses - ==> Building ncurses [Package] - ==> Successfully installed ncurses - Fetch: . Build: 0.11s. Total: 0.11s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/ncurses-6.0-fttg4astvrtq2buey4wq66tnyu7bgj2c - ==> zlib is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/zlib-1.2.8-ayc4jq7vxuzge5n444gutvskeytfdruh - ==> Installing openssl - ==> zlib is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/zlib-1.2.8-ayc4jq7vxuzge5n444gutvskeytfdruh - ==> Building openssl [Package] - ==> Successfully installed openssl - Fetch: . Build: 0.23s. Total: 0.23s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openssl-1.0.2j-kt5xyk2dkho6tzadnqlbnbujmljprylg - ==> Installing libarchive - ==> Installing lzma - ==> Building lzma [Package] - ==> Successfully installed lzma - Fetch: . Build: 0.11s. Total: 0.11s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/lzma-4.32.7-hah2cdo3zbulz6yg5do6dvnfn6en5v5c - ==> Installing nettle - ==> m4 is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/m4-1.4.17-qijdzvhjyybrtwbqm73vykhmkaqro3je - ==> Installing gmp - ==> m4 is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/m4-1.4.17-qijdzvhjyybrtwbqm73vykhmkaqro3je - ==> Building gmp [AutotoolsPackage] - ==> Successfully installed gmp - Fetch: . Build: 0.11s. Total: 0.11s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/gmp-6.1.1-uwn4gfdtq3sywy5uf4f7znrh66oybikf - ==> Building nettle [Package] - ==> Successfully installed nettle - Fetch: . Build: 0.18s. Total: 0.18s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/nettle-3.2-w4ieitifcmrldo4ra7as63apagzf56ja - ==> bzip2 is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/bzip2-1.0.6-gll2xsahysy7ji5gkmfxwkofdt3mwjhs - ==> expat is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/expat-2.2.0-mg5kwd3kluxdgorj32vzbp7aksg3vqej - ==> Installing libxml2 - ==> Installing xz - ==> Building xz [Package] - ==> Successfully installed xz - Fetch: . Build: 0.11s. Total: 0.11s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/xz-5.2.2-bxh6cpyqqozazm5okvjqk23sww3gccnf - ==> zlib is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/zlib-1.2.8-ayc4jq7vxuzge5n444gutvskeytfdruh - ==> Building libxml2 [Package] - ==> Successfully installed libxml2 - Fetch: . Build: 0.35s. Total: 0.35s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/libxml2-2.9.4-un323rppyu5qipkegyf7flmymvtmunrx - ==> zlib is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/zlib-1.2.8-ayc4jq7vxuzge5n444gutvskeytfdruh - ==> Installing lz4 - ==> Building lz4 [Package] - ==> Successfully installed lz4 - Fetch: . Build: 0.12s. Total: 0.12s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/lz4-131-ivy2fcaw7ywujx74weebdi5bsm7q4vkc - ==> openssl is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openssl-1.0.2j-kt5xyk2dkho6tzadnqlbnbujmljprylg - ==> xz is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/xz-5.2.2-bxh6cpyqqozazm5okvjqk23sww3gccnf - ==> Installing lzo - ==> Building lzo [AutotoolsPackage] - ==> Successfully installed lzo - Fetch: . Build: 0.11s. Total: 0.11s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/lzo-2.09-dlgnm74ozo6baactkft5oah2jre2ri2i - ==> Building libarchive [Package] - ==> Successfully installed libarchive - Fetch: . Build: 1.35s. Total: 1.35s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/libarchive-3.2.1-biq3kebw7vel7njusill7vv7mjldkqjv - ==> xz is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/xz-5.2.2-bxh6cpyqqozazm5okvjqk23sww3gccnf - ==> Installing curl - ==> zlib is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/zlib-1.2.8-ayc4jq7vxuzge5n444gutvskeytfdruh - ==> openssl is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openssl-1.0.2j-kt5xyk2dkho6tzadnqlbnbujmljprylg - ==> Building curl [Package] - ==> Successfully installed curl - Fetch: . Build: 0.36s. Total: 0.36s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/curl-7.50.3-oze4gqutj4x2isbkcn5ob2bhhxbskod4 - ==> Building cmake [Package] - ==> Successfully installed cmake - Fetch: . Build: 1.64s. Total: 1.64s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/cmake-3.6.1-n2nkknrku6dvuneo3rjumim7axt7n36e - ==> Installing metis - ==> cmake is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/cmake-3.6.1-n2nkknrku6dvuneo3rjumim7axt7n36e - ==> Building metis [Package] - ==> Successfully installed metis - Fetch: . Build: 0.11s. Total: 0.11s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/metis-5.1.0-ithifyl4xvqbn76js23wsb4tjnztrbdv - ==> Building parmetis [Package] - ==> Successfully installed parmetis - Fetch: . Build: 0.62s. Total: 0.62s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/parmetis-4.0.3-rtg6hml5t6acdcnxomn3l5zfiful4d2t - ==> Installing openblas - ==> Building openblas [Package] - ==> Successfully installed openblas - Fetch: . Build: 0.11s. Total: 0.11s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openblas-0.2.19-bwofa7fhff6od5zn56vy3j4eeyupsqgt - ==> metis is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/metis-5.1.0-ithifyl4xvqbn76js23wsb4tjnztrbdv - ==> Building superlu-dist [Package] - ==> Successfully installed superlu-dist - Fetch: . Build: 0.85s. Total: 0.85s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/superlu-dist-5.1.1-25r6jlvkpjnkiuwt2rtbzhk3l3htuxs7 - ==> cmake is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/cmake-3.6.1-n2nkknrku6dvuneo3rjumim7axt7n36e - ==> Installing glm - ==> cmake is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/cmake-3.6.1-n2nkknrku6dvuneo3rjumim7axt7n36e - ==> Building glm [Package] - ==> Successfully installed glm - Fetch: . Build: 0.12s. Total: 0.12s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/glm-0.9.7.1-7a6oho4aerz7vftxd5ur7lywscht2iry - ==> Installing hypre - ==> openmpi is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openmpi-2.0.1-j4cgoq4furxvr73pq72r2qgywgksw3qn - ==> openblas is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openblas-0.2.19-bwofa7fhff6od5zn56vy3j4eeyupsqgt - ==> Building hypre [Package] - ==> Successfully installed hypre - Fetch: . Build: 0.61s. Total: 0.61s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/hypre-2.11.1-lf7hcejiiww5peesh57quda72z67veit - ==> metis is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/metis-5.1.0-ithifyl4xvqbn76js23wsb4tjnztrbdv - ==> Installing netlib-scalapack - ==> openmpi is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openmpi-2.0.1-j4cgoq4furxvr73pq72r2qgywgksw3qn - ==> cmake is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/cmake-3.6.1-n2nkknrku6dvuneo3rjumim7axt7n36e - ==> openblas is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openblas-0.2.19-bwofa7fhff6od5zn56vy3j4eeyupsqgt - ==> Building netlib-scalapack [Package] - ==> Successfully installed netlib-scalapack - Fetch: . Build: 0.61s. Total: 0.61s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/netlib-scalapack-2.0.2-dvcanz2qq4dfcexznbhbmzbxfj43uz4q - ==> Installing suite-sparse - ==> Installing tbb - ==> Building tbb [Package] - ==> Successfully installed tbb - Fetch: . Build: 0.12s. Total: 0.12s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/tbb-4.4.4-zawzkkhrmdonbjpj3a5bb6gkgnqlrjeu - ==> openblas is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openblas-0.2.19-bwofa7fhff6od5zn56vy3j4eeyupsqgt - ==> metis is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/metis-5.1.0-ithifyl4xvqbn76js23wsb4tjnztrbdv - ==> Building suite-sparse [Package] - ==> Successfully installed suite-sparse - Fetch: . Build: 0.49s. Total: 0.49s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/suite-sparse-4.5.3-lvur6hriy2j7xfjwh5punp3exwpynzm6 - ==> openmpi is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openmpi-2.0.1-j4cgoq4furxvr73pq72r2qgywgksw3qn - ==> Installing netcdf - ==> m4 is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/m4-1.4.17-qijdzvhjyybrtwbqm73vykhmkaqro3je - ==> curl is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/curl-7.50.3-oze4gqutj4x2isbkcn5ob2bhhxbskod4 - ==> zlib is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/zlib-1.2.8-ayc4jq7vxuzge5n444gutvskeytfdruh - ==> hdf5 is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/hdf5-1.10.0-patch1-ezvtnox35albuaxqryuondweyjgeo6es - ==> Building netcdf [Package] - ==> Successfully installed netcdf - Fetch: . Build: 0.90s. Total: 0.90s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/netcdf-4.4.1-tcl4zbrmdfrit2cqlaxig6xieu5h552j - ==> Installing mumps - ==> netlib-scalapack is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/netlib-scalapack-2.0.2-dvcanz2qq4dfcexznbhbmzbxfj43uz4q - ==> openmpi is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openmpi-2.0.1-j4cgoq4furxvr73pq72r2qgywgksw3qn - ==> openblas is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openblas-0.2.19-bwofa7fhff6od5zn56vy3j4eeyupsqgt - ==> Building mumps [Package] - ==> Successfully installed mumps - Fetch: . Build: 0.74s. Total: 0.74s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/mumps-5.0.2-kr5r4nnx5tfcacxnk3ii5dsxbe6pu5fy - ==> Installing matio - ==> Building matio [Package] - ==> Successfully installed matio - Fetch: . Build: 0.11s. Total: 0.11s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/matio-1.5.2-4zrozucookychlvc4q53omp2zyfk2bed - ==> Installing boost - ==> bzip2 is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/bzip2-1.0.6-gll2xsahysy7ji5gkmfxwkofdt3mwjhs - ==> zlib is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/zlib-1.2.8-ayc4jq7vxuzge5n444gutvskeytfdruh - ==> Building boost [Package] - ==> Successfully installed boost - Fetch: . Build: 0.35s. Total: 0.35s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/boost-1.62.0-je7eqvzt74kezwhh55y5lwt5dy6pnali - ==> parmetis is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/parmetis-4.0.3-rtg6hml5t6acdcnxomn3l5zfiful4d2t - ==> openblas is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openblas-0.2.19-bwofa7fhff6od5zn56vy3j4eeyupsqgt - ==> hdf5 is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/hdf5-1.10.0-patch1-ezvtnox35albuaxqryuondweyjgeo6es - ==> Building trilinos [Package] - ==> Successfully installed trilinos - Fetch: . Build: 2.63s. Total: 2.63s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/trilinos-12.8.1-uvd6dfd7x4uyvck4awo3r3frudihn4ar - - -Now we're starting to see the power of Spack. Trilinos has 11 top level -dependecies, many of which have dependencies of their own. Installing -more complex packages can take days or weeks even for an experienced -user. Although we've done a fake installation for the tutorial, a real -installation of trilinos using Spack takes about 3 hours (depending on -the system), but only 20 seconds of programmer time. - -Spack manages constistency of the entire DAG. Every MPI dependency will -be satisfied by the same configuration of MPI, etc. If we install -``trilinos`` again specifying a dependency on our previous HDF5 built -with ``mpich``: - -.. code-block:: console - - $ spack install --fake trilinos ^hdf5+mpi ^mpich - ==> Installing trilinos - ==> Installing superlu-dist - ==> mpich is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/mpich-3.2-5jlp2ndnsb67txggraglu47vjmayx5za - ==> metis is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/metis-5.1.0-ithifyl4xvqbn76js23wsb4tjnztrbdv - ==> Installing parmetis - ==> mpich is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/mpich-3.2-5jlp2ndnsb67txggraglu47vjmayx5za - ==> metis is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/metis-5.1.0-ithifyl4xvqbn76js23wsb4tjnztrbdv - ==> cmake is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/cmake-3.6.1-n2nkknrku6dvuneo3rjumim7axt7n36e - ==> Building parmetis [Package] - ==> Successfully installed parmetis - Fetch: . Build: 0.38s. Total: 0.38s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/parmetis-4.0.3-43kbtni6p5y446c6qdkybq4htj7ot4zn - ==> openblas is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openblas-0.2.19-bwofa7fhff6od5zn56vy3j4eeyupsqgt - ==> Building superlu-dist [Package] - ==> Successfully installed superlu-dist - Fetch: . Build: 0.61s. Total: 0.61s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/superlu-dist-5.1.1-46uuupehmonx5jicc6xnegnud2n5jqyl - ==> cmake is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/cmake-3.6.1-n2nkknrku6dvuneo3rjumim7axt7n36e - ==> glm is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/glm-0.9.7.1-7a6oho4aerz7vftxd5ur7lywscht2iry - ==> Installing hypre - ==> mpich is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/mpich-3.2-5jlp2ndnsb67txggraglu47vjmayx5za - ==> openblas is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openblas-0.2.19-bwofa7fhff6od5zn56vy3j4eeyupsqgt - ==> Building hypre [Package] - ==> Successfully installed hypre - Fetch: . Build: 0.37s. Total: 0.37s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/hypre-2.11.1-6ajnyymoivs5apajd7thjisae36jv4lz - ==> metis is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/metis-5.1.0-ithifyl4xvqbn76js23wsb4tjnztrbdv - ==> Installing netlib-scalapack - ==> mpich is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/mpich-3.2-5jlp2ndnsb67txggraglu47vjmayx5za - ==> cmake is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/cmake-3.6.1-n2nkknrku6dvuneo3rjumim7axt7n36e - ==> openblas is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openblas-0.2.19-bwofa7fhff6od5zn56vy3j4eeyupsqgt - ==> Building netlib-scalapack [Package] - ==> Successfully installed netlib-scalapack - Fetch: . Build: 0.37s. Total: 0.37s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/netlib-scalapack-2.0.2-dayeep27omm26wksd3iqvbu3gezc2eoh - ==> suite-sparse is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/suite-sparse-4.5.3-lvur6hriy2j7xfjwh5punp3exwpynzm6 - ==> Installing netcdf - ==> m4 is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/m4-1.4.17-qijdzvhjyybrtwbqm73vykhmkaqro3je - ==> curl is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/curl-7.50.3-oze4gqutj4x2isbkcn5ob2bhhxbskod4 - ==> zlib is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/zlib-1.2.8-ayc4jq7vxuzge5n444gutvskeytfdruh - ==> hdf5 is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/hdf5-1.10.0-patch1-j36yfw25i6gdd3q4vwlupgkpwic4ua6m - ==> Building netcdf [Package] - ==> Successfully installed netcdf - Fetch: . Build: 0.67s. Total: 0.67s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/netcdf-4.4.1-gfemi4jk4qltvp33xhtpkam7dozbqvhq - ==> Installing mumps - ==> mpich is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/mpich-3.2-5jlp2ndnsb67txggraglu47vjmayx5za - ==> netlib-scalapack is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/netlib-scalapack-2.0.2-dayeep27omm26wksd3iqvbu3gezc2eoh - ==> openblas is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openblas-0.2.19-bwofa7fhff6od5zn56vy3j4eeyupsqgt - ==> Building mumps [Package] - ==> Successfully installed mumps - Fetch: . Build: 0.49s. Total: 0.49s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/mumps-5.0.2-w7t5pl3jhhwitfiyer63zj6zv7idkt3m - ==> mpich is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/mpich-3.2-5jlp2ndnsb67txggraglu47vjmayx5za - ==> matio is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/matio-1.5.2-4zrozucookychlvc4q53omp2zyfk2bed - ==> boost is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/boost-1.62.0-je7eqvzt74kezwhh55y5lwt5dy6pnali - ==> parmetis is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/parmetis-4.0.3-43kbtni6p5y446c6qdkybq4htj7ot4zn - ==> openblas is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/openblas-0.2.19-bwofa7fhff6od5zn56vy3j4eeyupsqgt - ==> hdf5 is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/hdf5-1.10.0-patch1-j36yfw25i6gdd3q4vwlupgkpwic4ua6m - ==> Building trilinos [Package] - ==> Successfully installed trilinos - Fetch: . Build: 2.42s. Total: 2.42s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/trilinos-12.8.1-ffwrpxnq7lhiw2abxn2u7ffr4jjsdwep - -We see that every package in the trilinos DAG that depends on MPI now -uses ``mpich``. - -.. code-block:: console - - $ spack find -d trilinos - ==> 2 installed packages. - -- linux-redhat6-x86_64 / gcc@4.4.7 ----------------------------- - trilinos@12.8.1 - ^boost@1.62.0 - ^bzip2@1.0.6 - ^zlib@1.2.8 - ^glm@0.9.7.1 - ^hdf5@1.10.0-patch1 - ^mpich@3.2 - ^hypre@2.11.1 - ^openblas@0.2.19 - ^matio@1.5.2 - ^metis@5.1.0 - ^mumps@5.0.2 - ^netlib-scalapack@2.0.2 - ^netcdf@4.4.1 - ^curl@7.50.3 - ^openssl@1.0.2j - ^parmetis@4.0.3 - ^suite-sparse@4.5.3 - ^tbb@4.4.4 - ^superlu-dist@5.1.1 - - trilinos@12.8.1 - ^boost@1.62.0 - ^bzip2@1.0.6 - ^zlib@1.2.8 - ^glm@0.9.7.1 - ^hdf5@1.10.0-patch1 - ^openmpi@2.0.1 - ^hwloc@1.11.4 - ^libpciaccess@0.13.4 - ^hypre@2.11.1 - ^openblas@0.2.19 - ^matio@1.5.2 - ^metis@5.1.0 - ^mumps@5.0.2 - ^netlib-scalapack@2.0.2 - ^netcdf@4.4.1 - ^curl@7.50.3 - ^openssl@1.0.2j - ^parmetis@4.0.3 - ^suite-sparse@4.5.3 - ^tbb@4.4.4 - ^superlu-dist@5.1.1 - - -As we discussed before, the ``spack find -d`` command shows the -dependency information as a tree. While that is often sufficient, many -complicated packages, including trilinos, have dependencies that -cannot be fully represented as a tree. Again, the ``spack graph`` -command shows the full DAG of the dependency information. - -.. code-block:: console - - $ spack graph trilinos - o trilinos - |\ - | |\ - | | |\ - | | | |\ - | | | | |\ - | | | | | |\ - | | | | | | |\ - | o | | | | | | netcdf - | |\ \ \ \ \ \ \ - | | |\ \ \ \ \ \ \ - | | | o | | | | | | curl - | | |/| | | | | | | - | |/| | | | | | | | - | | | o | | | | | | openssl - | | |/ / / / / / / - | |/| | | | | | | - | | o | | | | | | hdf5 - | |/| | | | | | | - | | |/ / / / / / - | o | | | | | | zlib - | / / / / / / - o | | | | | | swig - o | | | | | | pcre - / / / / / / - o | | | | | mpi - / / / / / - o | | | | matio - / / / / - o | | | lapack - / / / - o | | glm - / / - o | boost - / - o blas - - -You can control how the output is displayed with a number of options. - -The ASCII output from ``spack graph`` can be difficult to parse for -complicated packages. The output can be changed to the ``graphviz`` -``.dot`` format using the `--dot` flag. - -.. code-block:: console - - $ spack graph --dot trilinos | dot -Tpdf trilinos_graph.pdf - -.. _basics-tutorial-uninstall: - ---------------------- -Uninstalling Packages ---------------------- - -Earlier we installed many configurations each of libelf and -libdwarf. Now we will go through and uninstall some of those packages -that we didn't really need. - -.. code-block:: console - - $ spack find -d libdwarf - ==> 3 installed packages. - -- linux-redhat6-x86_64 / gcc@4.4.7 ----------------------------- - libdwarf@20160507 - ^libelf@0.8.12 - - libdwarf@20160507 - ^libelf@0.8.13 - - - -- linux-redhat6-x86_64 / intel@16.0.3 -------------------------- - libdwarf@20160507 - ^libelf@0.8.12 - - $ spack find libelf - ==> 6 installed packages. - -- linux-redhat6-x86_64 / gcc@4.4.7 ----------------------------- - libelf@0.8.12 libelf@0.8.12 libelf@0.8.13 - - -- linux-redhat6-x86_64 / intel@15.0.4 -------------------------- - libelf@0.8.13 - - -- linux-redhat6-x86_64 / intel@16.0.3 -------------------------- - libelf@0.8.12 libelf@0.8.13 - - -We can uninstall packages by spec using the same syntax as install. - -.. code-block:: console - - $ spack uninstall libelf%intel@15.0.4 - ==> The following packages will be uninstalled : - - -- linux-redhat6-x86_64 / intel@15.0.4 -------------------------- - w33hrej libelf@0.8.13%intel - - - ==> Do you want to proceed ? [y/n] - y - ==> Successfully uninstalled libelf@0.8.13%intel@15.0.4 arch=linux-redhat6-x86_64-w33hrej - - - - $ spack find -lf libelf - ==> 5 installed packages. - -- linux-redhat6-x86_64 / gcc@4.4.7 ----------------------------- - ipggckv libelf@0.8.12%gcc - - vrv2ttb libelf@0.8.12%gcc cppflags="-O3" - - csrt4qx libelf@0.8.13%gcc - - - -- linux-redhat6-x86_64 / intel@16.0.3 -------------------------- - 4blbe3q libelf@0.8.12%intel - - 7wgp32x libelf@0.8.13%intel - - -We can uninstall packages by referring only to their hash. - - -We can use either ``-f`` (force) or ``-d`` (remove dependents as well) to -remove packages that are required by another installed package. - -.. code-block:: console - - $ spack uninstall /4blb - ==> Error: Will not uninstall libelf@0.8.12%intel@16.0.3-4blbe3q - - The following packages depend on it: - -- linux-redhat6-x86_64 / intel@16.0.3 -------------------------- - csruprg libdwarf@20160507%intel - - - ==> Error: You can use spack uninstall --dependents to uninstall these dependencies as well - $ spack uninstall -d /4blb - ==> The following packages will be uninstalled : - - -- linux-redhat6-x86_64 / intel@16.0.3 -------------------------- - csruprg libdwarf@20160507%intel - - 4blbe3q libelf@0.8.12%intel - - - ==> Do you want to proceed ? [y/n] - y - ==> Successfully uninstalled libdwarf@20160507%intel@16.0.3 arch=linux-redhat6-x86_64-csruprg - ==> Successfully uninstalled libelf@0.8.12%intel@16.0.3 arch=linux-redhat6-x86_64-4blbe3q - - -Spack will not uninstall packages that are not sufficiently -specified. The ``-a`` (all) flag can be used to uninstall multiple -packages at once. - -.. code-block:: console - - $ spack uninstall trilinos - ==> Error: trilinos matches multiple packages: - - -- linux-redhat6-x86_64 / gcc@4.4.7 ----------------------------- - ffwrpxn trilinos@12.8.1%gcc+boost~debug+hdf5+hypre+metis+mumps~python+shared+suite-sparse+superlu-dist - - uvd6dfd trilinos@12.8.1%gcc+boost~debug+hdf5+hypre+metis+mumps~python+shared+suite-sparse+superlu-dist - - - ==> Error: You can either: - a) Use a more specific spec, or - b) use spack uninstall -a to uninstall ALL matching specs. - - - - $ spack uninstall /ffwr - ==> The following packages will be uninstalled : - - -- linux-redhat6-x86_64 / gcc@4.4.7 ----------------------------- - ffwrpxn trilinos@12.8.1%gcc+boost~debug+hdf5+hypre+metis+mumps~python+shared+suite-sparse+superlu-dist - - - ==> Do you want to proceed ? [y/n] - y - ==> Successfully uninstalled trilinos@12.8.1%gcc@4.4.7+boost~debug+hdf5+hypre+metis+mumps~python+shared+suite-sparse+superlu-dist arch=linux-redhat6-x86_64-ffwrpxn - ------------------------------ -Advanced ``spack find`` Usage ------------------------------ - -We will go over some additional uses for the `spack find` command not -already covered in the :ref:`basics-tutorial-install` and -:ref:`basics-tutorial-uninstall` sections. - -The ``spack find`` command can accept what we call "anonymous specs." -These are expressions in spec syntax that do not contain a package -name. For example, `spack find %intel` will return every package built -with the intel compiler, and ``spack find cppflags="-O3"`` will -return every package which was built with ``cppflags="-O3"``. - -.. code-block:: console - - $ spack find %intel - ==> 1 installed packages. - -- linux-redhat6-x86_64 / intel@16.0.3 -------------------------- - libelf@0.8.13 - - - - $ spack find cppflags="-O3" - ==> 1 installed packages. - -- linux-redhat6-x86_64 / gcc@4.4.7 ----------------------------- - libelf@0.8.12 - - -The ``find`` command can also show which packages were installed -explicitly (rather than pulled in as a dependency) using the ``-e`` -flag. The ``-E`` flag shows implicit installs only. The ``find`` command can -also show the path to which a spack package was installed using the ``-p`` -command. - -.. code-block:: console - - $ spack find -pe - ==> 10 installed packages. - -- linux-redhat6-x86_64 / gcc@4.4.7 ----------------------------- - hdf5@1.10.0-patch1 ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/hdf5-1.10.0-patch1-twppaioxqn6lti4grgopnmhwcq3h2rpw - hdf5@1.10.0-patch1 ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/hdf5-1.10.0-patch1-j36yfw25i6gdd3q4vwlupgkpwic4ua6m - hdf5@1.10.0-patch1 ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/hdf5-1.10.0-patch1-ezvtnox35albuaxqryuondweyjgeo6es - libdwarf@20160507 ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/libdwarf-20160507-dtg3tgnp7htccoly26gduqlrgvnwcp5t - libdwarf@20160507 ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/libdwarf-20160507-yfx6p3g3rkmqvcqbmtb34o6pln7pqvcz - libelf@0.8.12 ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/libelf-0.8.12-ipggckv6i7h44iryzfa4dwdela32a7fy - libelf@0.8.12 ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/libelf-0.8.12-vrv2ttbd34xlfoxy4jwt6qsjrcbalmmw - libelf@0.8.13 ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/libelf-0.8.13-csrt4qxfkhjgn5xg3zjpkir7xdnszl2a - trilinos@12.8.1 ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/trilinos-12.8.1-uvd6dfd7x4uyvck4awo3r3frudihn4ar - - -- linux-redhat6-x86_64 / intel@16.0.3 -------------------------- - libelf@0.8.13 ~/spack/opt/spack/linux-redhat6-x86_64/intel-16.0.3/libelf-0.8.13-7wgp32xksatkvw2tbssmehw2t5tnxndj - - ---------------------- -Customizing Compilers ---------------------- - - -Spack manages a list of available compilers on the system, detected -automatically from from the user's ``PATH`` variable. The ``spack -compilers`` command is an alias for the command ``spack compiler list``. - -.. code-block:: console - - $ spack compilers - ==> Available compilers - -- gcc ---------------------------------------------------------- - gcc@4.4.7 - - -- intel -------------------------------------------------------- - intel@16.0.3 intel@15.0.1 intel@14.0.0 intel@12.1.3 intel@10.0 - intel@16.0.2 intel@15.0.0 intel@13.1.1 intel@12.1.2 intel@9.1 - intel@16.0.1 intel@14.0.4 intel@13.1.0 intel@12.1.0 - intel@16.0.0 intel@14.0.3 intel@13.0.1 intel@12.0.4 - intel@15.0.4 intel@14.0.2 intel@13.0.0 intel@11.1 - intel@15.0.3 intel@14.0.1 intel@12.1.5 intel@10.1 - - -- pgi ---------------------------------------------------------- - pgi@16.5-0 pgi@15.7-0 pgi@14.7-0 pgi@13.2-0 pgi@11.10-0 pgi@9.0-4 - pgi@16.3-0 pgi@15.5-0 pgi@14.3-0 pgi@13.1-1 pgi@11.1-0 pgi@8.0-1 - pgi@16.1-0 pgi@15.1-0 pgi@13.10-0 pgi@12.8-0 pgi@10.9-0 pgi@7.1-3 - pgi@15.10-0 pgi@14.10-0 pgi@13.6-0 pgi@12.1-0 pgi@10.2-0 pgi@7.0-6 - -The compilers are maintained in a YAML file that can be hand-edited -for special cases. Spack also has tools to add compilers, and -compilers built with Spack can be added to the configuration. - -.. code-block:: console - - $ spack install --fake gcc@6.1.0 - ==> Installing gcc - ==> gmp is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/gmp-6.1.1-uwn4gfdtq3sywy5uf4f7znrh66oybikf - ==> Installing isl - ==> gmp is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/gmp-6.1.1-uwn4gfdtq3sywy5uf4f7znrh66oybikf - ==> Building isl [Package] - ==> Successfully installed isl - Fetch: . Build: 0.19s. Total: 0.19s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/isl-0.14-hs2w7mjjjaakkmbbv5yvfqf7yyzhorl6 - ==> Installing mpc - ==> gmp is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/gmp-6.1.1-uwn4gfdtq3sywy5uf4f7znrh66oybikf - ==> Installing mpfr - ==> gmp is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/gmp-6.1.1-uwn4gfdtq3sywy5uf4f7znrh66oybikf - ==> Building mpfr [Package] - ==> Successfully installed mpfr - Fetch: . Build: 0.17s. Total: 0.17s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/mpfr-3.1.4-7kt5ij437khredfq4bvnyu22t3fmtfvt - ==> Building mpc [Package] - ==> Successfully installed mpc - Fetch: . Build: 0.28s. Total: 0.28s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/mpc-1.0.3-g5taq6lt3zuy5l2jtggi5lctxnl4la5u - ==> Installing binutils - ==> m4 is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/m4-1.4.17-qijdzvhjyybrtwbqm73vykhmkaqro3je - ==> Installing bison - ==> m4 is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/m4-1.4.17-qijdzvhjyybrtwbqm73vykhmkaqro3je - ==> Building bison [Package] - ==> Successfully installed bison - Fetch: . Build: 0.12s. Total: 0.12s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/bison-3.0.4-hkhfysfvq5l6rsns67g2htmkpxauvnwa - ==> Installing flex - ==> m4 is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/m4-1.4.17-qijdzvhjyybrtwbqm73vykhmkaqro3je - ==> bison is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/bison-3.0.4-hkhfysfvq5l6rsns67g2htmkpxauvnwa - ==> Building flex [Package] - ==> Successfully installed flex - Fetch: . Build: 0.11s. Total: 0.11s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/flex-2.6.0-qd6d73rdfrozdrsdpimvl4tj7d5ps7qg - ==> Building binutils [Package] - ==> Successfully installed binutils - Fetch: . Build: 0.11s. Total: 0.11s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/binutils-2.27-iq2hry3gvaxszmwwbnll7njgdgaek56o - ==> mpfr is already installed in ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/mpfr-3.1.4-7kt5ij437khredfq4bvnyu22t3fmtfvt - ==> Building gcc [Package] - ==> Successfully installed gcc - Fetch: . Build: 0.66s. Total: 0.66s. - [+] ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/gcc-6.1.0-j5576zbsot2ydljlthjzhsirsesnogvh - - - - $ spack find -p gcc - ==> 1 installed packages. - -- linux-redhat6-x86_64 / gcc@4.4.7 ----------------------------- - gcc@6.1.0 ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/gcc-6.1.0-j5576zbsot2ydljlthjzhsirsesnogvh - - -If we had done a "real" install of gcc, we could add it to our -configuration now using the `spack compiler add` command, but we would -also be waiting for it to install. If we run the command now, it will -return no new compilers. - -.. code-block:: console - - $ spack compiler add ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/gcc-6.1.0-j5576zbsot2ydljlthjzhsirsesnogvh/bin - ==> Found no new compilers - -If we had done a real install, the output would have been as follows: - -.. code-block:: console - - $ spack compiler add ~/spack/opt/spack/linux-redhat6-x86_64/gcc-4.4.7/gcc-6.1.0-j5576zbsot2ydljlthjzhsirsesnogvh/bin - ==> Added 1 new compiler to ~/.spack/linux/compilers.yaml - gcc@6.1.0 |