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diff --git a/lib/spack/docs/tutorial_basics.rst b/lib/spack/docs/tutorial_basics.rst deleted file mode 100644 index 9a6a2074b3..0000000000 --- a/lib/spack/docs/tutorial_basics.rst +++ /dev/null @@ -1,1736 +0,0 @@ -.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other - Spack Project Developers. See the top-level COPYRIGHT file for details. - - SPDX-License-Identifier: (Apache-2.0 OR MIT) - -.. _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 an AWS -instance running Ubuntu 16.04 - -.. _basics-tutorial-install: - ----------------- -Installing Spack ----------------- - -Spack works out of the box. Simply clone spack and get going. We will -clone Spack and immediately checkout the most recent release, v0.12. - -.. code-block:: console - - $ git clone https://github.com/spack/spack - git clone https://github.com/spack/spack - Cloning into 'spack'... - remote: Enumerating objects: 68, done. - remote: Counting objects: 100% (68/68), done. - remote: Compressing objects: 100% (56/56), done. - remote: Total 135389 (delta 40), reused 16 (delta 9), pack-reused 135321 - Receiving objects: 100% (135389/135389), 47.31 MiB | 1.01 MiB/s, done. - Resolving deltas: 100% (64414/64414), done. - Checking connectivity... done. - $ cd spack - $ git checkout releases/v0.12 - Branch releases/v0.12 set up to track remote branch releases/v0.12 from origin. - Switched to a new branch 'releases/v0.12' - -Next add Spack to your path. Spack has some nice command line -integration tools, so instead of simply appending to your ``PATH`` -variable, source the spack setup script. Then add Spack to your path. - -.. code-block:: console - - $ . share/spack/setup-env.sh - -You're good to go! - ------------------ -What is in Spack? ------------------ - -The ``spack list`` command shows available packages. - -.. code-block:: console - - $ spack list - ==> 2907 packages. - abinit libgpuarray py-espresso r-mlrmbo - abyss libgridxc py-espressopp r-mmwrweek - accfft libgtextutils py-et-xmlfile r-mnormt - ... - -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- - ==> 479 packages. - lumpy-sv py-funcsigs py-numpydoc py-utililib - perl-file-copy-recursive py-functools32 py-olefile py-pywavelets - py-3to2 py-future py-ont-fast5-api py-pyyaml - ... - -------------------- -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 zlib - ==> Installing zlib - ==> Searching for binary cache of zlib - ==> Warning: No Spack mirrors are currently configured - ==> No binary for zlib found: installing from source - ==> Fetching http://zlib.net/fossils/zlib-1.2.11.tar.gz - ######################################################################## 100.0% - ==> Staging archive: /home/spack1/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/zlib-1.2.11.tar.gz - ==> Created stage in /home/spack1/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - ==> No patches needed for zlib - ==> Building zlib [Package] - ==> Executing phase: 'install' - ==> Successfully installed zlib - Fetch: 3.27s. Build: 2.18s. Total: 5.44s. - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - -Spack can install software either from source or from a binary -cache. Packages in the binary cache are signed with GPG for -security. For the tutorial we have prepared a binary cache so you -don't have to wait on slow compilation from source. To be able to -install from the binary cache, we will need to configure Spack with -the location of the binary cache and trust the GPG key that the binary -cache was signed with. - -.. code-block:: console - - $ spack mirror add tutorial /mirror - $ spack gpg trust /mirror/public.key - gpg: keybox '/home/spack1/spack/opt/spack/gpg/pubring.kbx' created - gpg: /home/spack1/spack/opt/spack/gpg/trustdb.gpg: trustdb created - gpg: key 3B7C69B2: public key "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" imported - gpg: Total number processed: 1 - gpg: imported: 1 - -You'll learn more about configuring Spack later in the tutorial, but -for now you will be able to install the rest of the packages in the -tutorial from a binary cache using the same ``spack install`` -command. By default this will install the binary cached version if it -exists and fall back on installing from source. - -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 zlib %clang - ==> Installing zlib - ==> Searching for binary cache of zlib - ==> Finding buildcaches in /mirror/build_cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64-gcc-7.2.0-texinfo-6.5-cuqnfgfhhmudqp5f7upmld6ax7pratzw.spec.yaml - ######################################################################## 100.0% - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64-gcc-4.7-zlib-1.2.11-bq2wtdxakpjytk2tjr7qu23i4py2fi2r.spec.yaml - ######################################################################## 100.0% - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-dyninst-9.3.2-bu6s2jzievsjkwtcnrtimc5b625j5omf.spec.yaml - ######################################################################## 100.0% - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64-gcc-7.2.0-openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4.spec.yaml - ... - ==> Installing zlib from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.11/linux-ubuntu16.04-x86_64-clang-3.8.0-2ubuntu4-zlib-1.2.11-4pt75q7qq6lygf3hgnona4lyc2uwedul.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:08:01 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed zlib from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.11-4pt75q7qq6lygf3hgnona4lyc2uwedul - -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 ``zlib``. - -.. code-block:: console - - $ spack versions zlib - ==> Safe versions (already checksummed): - 1.2.11 1.2.8 1.2.3 - ==> Remote versions (not yet checksummed): - 1.2.10 1.2.7 1.2.5.1 1.2.4.2 1.2.3.7 - ... - -The ``@`` sigil is used to specify versions, both of packages and of -compilers. - -.. code-block:: console - - $ spack install zlib@1.2.8 - ==> Installing zlib - ==> Searching for binary cache of zlib - ==> Finding buildcaches in /mirror/build_cache - ==> Installing zlib from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-zlib-1.2.8-bkyl5bhuep6fmhuxzkmhqy25qefjcvzc.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:18:30 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed zlib from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-bkyl5bhuep6fmhuxzkmhqy25qefjcvzc - - $ spack install zlib %gcc@4.7 - ==> Installing zlib - ==> Searching for binary cache of zlib - ==> Finding buildcaches in /mirror/build_cache - ==> Installing zlib from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-4.7/zlib-1.2.11/linux-ubuntu16.04-x86_64-gcc-4.7-zlib-1.2.11-bq2wtdxakpjytk2tjr7qu23i4py2fi2r.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 04:55:30 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed zlib from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-4.7/zlib-1.2.11-bq2wtdxakpjytk2tjr7qu23i4py2fi2r - -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 zlib @1.2.8 cppflags=-O3 - ==> Installing zlib - ==> Searching for binary cache of zlib - ==> Finding buildcaches in /mirror/build_cache - ==> Installing zlib from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:31:54 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed zlib from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu - -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-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - zlib@1.2.11 - - -- linux-ubuntu16.04-x86_64 / gcc@4.7 --------------------------- - zlib@1.2.11 - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - zlib@1.2.8 zlib@1.2.8 zlib@1.2.11 - - - $ spack find -lf - ==> 5 installed packages. - -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - 4pt75q7 zlib@1.2.11%clang - - - -- linux-ubuntu16.04-x86_64 / gcc@4.7 --------------------------- - bq2wtdx zlib@1.2.11%gcc - - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - bkyl5bh zlib@1.2.8%gcc - - 64mns5m zlib@1.2.8%gcc cppflags="-O3" - - 5nus6kn zlib@1.2.11%gcc - -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 tcl - ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - ==> Installing tcl - ==> Searching for binary cache of tcl - ==> Finding buildcaches in /mirror/build_cache - ==> Installing tcl from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-tcl-8.6.8-qhwyccywhx2i6s7ob2gvjrjtj3rnfuqt.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:07:15 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed tcl from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-qhwyccywhx2i6s7ob2gvjrjtj3rnfuqt - -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 tcl ^zlib @1.2.8 %clang - ==> Installing zlib - ==> Searching for binary cache of zlib - ==> Finding buildcaches in /mirror/build_cache - ==> Installing zlib from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.8/linux-ubuntu16.04-x86_64-clang-3.8.0-2ubuntu4-zlib-1.2.8-i426yu3o6lyau5fv5ljwsajfkqxj5rl5.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:09:01 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed zlib from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.8-i426yu3o6lyau5fv5ljwsajfkqxj5rl5 - ==> Installing tcl - ==> Searching for binary cache of tcl - ==> Installing tcl from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/tcl-8.6.8/linux-ubuntu16.04-x86_64-clang-3.8.0-2ubuntu4-tcl-8.6.8-6wc66etr7y6hgibp2derrdkf763exwvc.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:10:21 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed tcl from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/tcl-8.6.8-6wc66etr7y6hgibp2derrdkf763exwvc - -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 zlib (``cppflags="-O3"``) began with -``64mns5m``. 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 tcl ^/64mn - ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu - ==> Installing tcl - ==> Searching for binary cache of tcl - ==> Finding buildcaches in /mirror/build_cache - ==> Installing tcl from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-tcl-8.6.8-am4pbatrtga3etyusg2akmsvrswwxno2.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:11:53 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed tcl from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-am4pbatrtga3etyusg2akmsvrswwxno2 - -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-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - 6wc66et tcl@8.6.8%clang - i426yu3 ^zlib@1.2.8%clang - - i426yu3 zlib@1.2.8%clang - - 4pt75q7 zlib@1.2.11%clang - - - -- linux-ubuntu16.04-x86_64 / gcc@4.7 --------------------------- - bq2wtdx zlib@1.2.11%gcc - - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - am4pbat tcl@8.6.8%gcc - 64mns5m ^zlib@1.2.8%gcc cppflags="-O3" - - qhwyccy tcl@8.6.8%gcc - 5nus6kn ^zlib@1.2.11%gcc - - bkyl5bh zlib@1.2.8%gcc - - 64mns5m zlib@1.2.8%gcc cppflags="-O3" - - 5nus6kn zlib@1.2.11%gcc - - -Let's move on to slightly more complicated packages. ``HDF5`` is a -good 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 hdf5 - ==> Installing libsigsegv - ==> Searching for binary cache of libsigsegv - ==> Finding buildcaches in /mirror/build_cache - ==> Installing libsigsegv from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11/linux-ubuntu16.04-x86_64-gcc-5.4.0-libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:08:01 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed libsigsegv from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz - ==> Installing m4 - ==> Searching for binary cache of m4 - ==> Installing m4 from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18/linux-ubuntu16.04-x86_64-gcc-5.4.0-m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:24:11 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed m4 from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel - ==> Installing libtool - ==> Searching for binary cache of libtool - ==> Installing libtool from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6/linux-ubuntu16.04-x86_64-gcc-5.4.0-libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:12:47 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed libtool from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu - ==> Installing pkgconf - ==> Searching for binary cache of pkgconf - ==> Installing pkgconf from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:00:47 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed pkgconf from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v - ==> Installing util-macros - ==> Searching for binary cache of util-macros - ==> Installing util-macros from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/util-macros-1.19.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-util-macros-1.19.1-milz7fmttmptcic2qdk5cnel7ll5sybr.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:31:54 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed util-macros from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/util-macros-1.19.1-milz7fmttmptcic2qdk5cnel7ll5sybr - ==> Installing libpciaccess - ==> Searching for binary cache of libpciaccess - ==> Installing libpciaccess from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/libpciaccess-0.13.5/linux-ubuntu16.04-x86_64-gcc-5.4.0-libpciaccess-0.13.5-5urc6tcjae26fbbd2wyfohoszhgxtbmc.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:09:34 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed libpciaccess from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libpciaccess-0.13.5-5urc6tcjae26fbbd2wyfohoszhgxtbmc - ==> Installing xz - ==> Searching for binary cache of xz - ==> Installing xz from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/xz-5.2.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-xz-5.2.4-teneqii2xv5u6zl5r6qi3pwurc6pmypz.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:05:03 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed xz from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/xz-5.2.4-teneqii2xv5u6zl5r6qi3pwurc6pmypz - ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - ==> Installing libxml2 - ==> Searching for binary cache of libxml2 - ==> Installing libxml2 from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/libxml2-2.9.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-libxml2-2.9.8-wpexsphdmfayxqxd4up5vgwuqgu5woo7.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 04:56:04 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed libxml2 from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libxml2-2.9.8-wpexsphdmfayxqxd4up5vgwuqgu5woo7 - ==> Installing ncurses - ==> Searching for binary cache of ncurses - ==> Installing ncurses from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:04:49 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed ncurses from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh - ==> Installing readline - ==> Searching for binary cache of readline - ==> Installing readline from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:04:56 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed readline from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi - ==> Installing gdbm - ==> Searching for binary cache of gdbm - ==> Installing gdbm from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:18:34 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed gdbm from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes - ==> Installing perl - ==> Searching for binary cache of perl - ==> Installing perl from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:12:45 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed perl from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo - ==> Installing autoconf - ==> Searching for binary cache of autoconf - ==> Installing autoconf from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69/linux-ubuntu16.04-x86_64-gcc-5.4.0-autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:24:03 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed autoconf from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q - ==> Installing automake - ==> Searching for binary cache of automake - ==> Installing automake from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:12:03 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed automake from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy - ==> Installing numactl - ==> Searching for binary cache of numactl - ==> Installing numactl from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/numactl-2.0.11/linux-ubuntu16.04-x86_64-gcc-5.4.0-numactl-2.0.11-ft463odrombnxlc3qew4omckhlq7tqgc.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:30:34 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed numactl from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/numactl-2.0.11-ft463odrombnxlc3qew4omckhlq7tqgc - ==> Installing hwloc - ==> Searching for binary cache of hwloc - ==> Installing hwloc from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hwloc-1.11.9/linux-ubuntu16.04-x86_64-gcc-5.4.0-hwloc-1.11.9-43tkw5mt6huhv37vqnybqgxtkodbsava.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:08:00 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed hwloc from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hwloc-1.11.9-43tkw5mt6huhv37vqnybqgxtkodbsava - ==> Installing openmpi - ==> Searching for binary cache of openmpi - ==> Installing openmpi from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:01:54 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed openmpi from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx - ==> Installing hdf5 - ==> Searching for binary cache of hdf5 - ==> Installing hdf5 from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.4-ozyvmhzdew66byarohm4p36ep7wtcuiw.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:23:04 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed hdf5 from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-ozyvmhzdew66byarohm4p36ep7wtcuiw - -Spack packages can also have build options, called 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 hdf5~mpi - ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - ==> Installing hdf5 - ==> Searching for binary cache of hdf5 - ==> Finding buildcaches in /mirror/build_cache - ==> Installing hdf5 from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.4-5vcv5r67vpjzenq4apyebshclelnzuja.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:23:24 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed hdf5 from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-5vcv5r67vpjzenq4apyebshclelnzuja - -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 hdf5+hl+mpi ^mpich - ==> libsigsegv is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz - ==> m4 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel - ==> pkgconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v - ==> ncurses is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh - ==> readline is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi - ==> gdbm is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes - ==> perl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo - ==> autoconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q - ==> automake is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy - ==> libtool is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu - ==> Installing texinfo - ==> Searching for binary cache of texinfo - ==> Finding buildcaches in /mirror/build_cache - ==> Installing texinfo from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/texinfo-6.5/linux-ubuntu16.04-x86_64-gcc-5.4.0-texinfo-6.5-zs7a2pcwhq6ho2cj2x26uxfktwkpyucn.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:18:29 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed texinfo from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/texinfo-6.5-zs7a2pcwhq6ho2cj2x26uxfktwkpyucn - ==> Installing findutils - ==> Searching for binary cache of findutils - ==> Installing findutils from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/findutils-4.6.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-findutils-4.6.0-d4iajxsopzrlcjtasahxqeyjkjv5jx4v.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:07:17 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed findutils from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/findutils-4.6.0-d4iajxsopzrlcjtasahxqeyjkjv5jx4v - ==> Installing mpich - ==> Searching for binary cache of mpich - ==> Installing mpich from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpich-3.2.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-mpich-3.2.1-p3f7p2r5ntrynqibosglxvhwyztiwqs5.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:23:57 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed mpich from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpich-3.2.1-p3f7p2r5ntrynqibosglxvhwyztiwqs5 - ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - ==> Installing hdf5 - ==> Searching for binary cache of hdf5 - ==> Installing hdf5 from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.4-xxd7syhgej6onpyfyewxqcqe7ltkt7ob.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:07:32 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed hdf5 from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-xxd7syhgej6onpyfyewxqcqe7ltkt7ob - -We'll do a quick check in on what we have installed so far. - -.. code-block:: console - - $ spack find -ldf - ==> 32 installed packages - -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - 6wc66et tcl@8.6.8%clang - i426yu3 ^zlib@1.2.8%clang - - i426yu3 zlib@1.2.8%clang - - 4pt75q7 zlib@1.2.11%clang - - - -- linux-ubuntu16.04-x86_64 / gcc@4.7 --------------------------- - bq2wtdx zlib@1.2.11%gcc - - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - 3sx2gxe autoconf@2.69%gcc - suf5jtc ^m4@1.4.18%gcc - fypapcp ^libsigsegv@2.11%gcc - ic2kyoa ^perl@5.26.2%gcc - q4fpyuo ^gdbm@1.14.1%gcc - nxhwrg7 ^readline@7.0%gcc - 3o765ou ^ncurses@6.1%gcc - - rymw7im automake@1.16.1%gcc - ic2kyoa ^perl@5.26.2%gcc - q4fpyuo ^gdbm@1.14.1%gcc - nxhwrg7 ^readline@7.0%gcc - 3o765ou ^ncurses@6.1%gcc - - d4iajxs findutils@4.6.0%gcc - - q4fpyuo gdbm@1.14.1%gcc - nxhwrg7 ^readline@7.0%gcc - 3o765ou ^ncurses@6.1%gcc - - 5vcv5r6 hdf5@1.10.4%gcc - 5nus6kn ^zlib@1.2.11%gcc - - ozyvmhz hdf5@1.10.4%gcc - 3njc4q5 ^openmpi@3.1.3%gcc - 43tkw5m ^hwloc@1.11.9%gcc - 5urc6tc ^libpciaccess@0.13.5%gcc - wpexsph ^libxml2@2.9.8%gcc - teneqii ^xz@5.2.4%gcc - 5nus6kn ^zlib@1.2.11%gcc - ft463od ^numactl@2.0.11%gcc - - xxd7syh hdf5@1.10.4%gcc - p3f7p2r ^mpich@3.2.1%gcc - 5nus6kn ^zlib@1.2.11%gcc - - 43tkw5m hwloc@1.11.9%gcc - 5urc6tc ^libpciaccess@0.13.5%gcc - wpexsph ^libxml2@2.9.8%gcc - teneqii ^xz@5.2.4%gcc - 5nus6kn ^zlib@1.2.11%gcc - ft463od ^numactl@2.0.11%gcc - - 5urc6tc libpciaccess@0.13.5%gcc - - fypapcp libsigsegv@2.11%gcc - - o2pfwjf libtool@2.4.6%gcc - - wpexsph libxml2@2.9.8%gcc - teneqii ^xz@5.2.4%gcc - 5nus6kn ^zlib@1.2.11%gcc - - suf5jtc m4@1.4.18%gcc - fypapcp ^libsigsegv@2.11%gcc - - p3f7p2r mpich@3.2.1%gcc - - 3o765ou ncurses@6.1%gcc - - ft463od numactl@2.0.11%gcc - - 3njc4q5 openmpi@3.1.3%gcc - 43tkw5m ^hwloc@1.11.9%gcc - 5urc6tc ^libpciaccess@0.13.5%gcc - wpexsph ^libxml2@2.9.8%gcc - teneqii ^xz@5.2.4%gcc - 5nus6kn ^zlib@1.2.11%gcc - ft463od ^numactl@2.0.11%gcc - - ic2kyoa perl@5.26.2%gcc - q4fpyuo ^gdbm@1.14.1%gcc - nxhwrg7 ^readline@7.0%gcc - 3o765ou ^ncurses@6.1%gcc - - fovrh7a pkgconf@1.4.2%gcc - - nxhwrg7 readline@7.0%gcc - 3o765ou ^ncurses@6.1%gcc - - am4pbat tcl@8.6.8%gcc - 64mns5m ^zlib@1.2.8%gcc cppflags="-O3" - - qhwyccy tcl@8.6.8%gcc - 5nus6kn ^zlib@1.2.11%gcc - - zs7a2pc texinfo@6.5%gcc - ic2kyoa ^perl@5.26.2%gcc - q4fpyuo ^gdbm@1.14.1%gcc - nxhwrg7 ^readline@7.0%gcc - 3o765ou ^ncurses@6.1%gcc - - milz7fm util-macros@1.19.1%gcc - - teneqii xz@5.2.4%gcc - - bkyl5bh zlib@1.2.8%gcc - - 64mns5m zlib@1.2.8%gcc cppflags="-O3" - - 5nus6kn zlib@1.2.11%gcc - - -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+hl+mpi ^mpich - o hdf5 - |\ - o | zlib - / - o mpich - o findutils - |\ - | |\ - | | |\ - | | | |\ - o | | | | texinfo - | | | o | automake - | |_|/| | - |/| | | | - | | | |/ - | | | o autoconf - | |_|/| - |/| |/ - | |/| - o | | perl - o | | gdbm - o | | readline - o | | ncurses - o | | pkgconf - / / - | o libtool - |/ - o m4 - o libsigsegv - -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 zlib and -openssl, 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 an even more complicated package. - -.. code-block:: console - - $ spack install trilinos - ==> Installing diffutils - ==> Searching for binary cache of diffutils - ==> Finding buildcaches in /mirror/build_cache - ==> Installing diffutils from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/diffutils-3.6/linux-ubuntu16.04-x86_64-gcc-5.4.0-diffutils-3.6-2rhuivgjrna2nrxhntyde6md2khcvs34.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:30:17 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed diffutils from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/diffutils-3.6-2rhuivgjrna2nrxhntyde6md2khcvs34 - ==> Installing bzip2 - ==> Searching for binary cache of bzip2 - ==> Installing bzip2 from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/bzip2-1.0.6/linux-ubuntu16.04-x86_64-gcc-5.4.0-bzip2-1.0.6-ufczdvsqt6edesm36xiucyry7myhj7e7.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:34:37 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed bzip2 from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/bzip2-1.0.6-ufczdvsqt6edesm36xiucyry7myhj7e7 - ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - ==> Installing boost - ==> Searching for binary cache of boost - ==> Installing boost from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/boost-1.68.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-boost-1.68.0-zbgfxapchxa4awxdwpleubfuznblxzvt.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 04:58:55 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed boost from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/boost-1.68.0-zbgfxapchxa4awxdwpleubfuznblxzvt - ==> pkgconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v - ==> ncurses is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh - ==> readline is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi - ==> gdbm is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes - ==> perl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo - ==> Installing openssl - ==> Searching for binary cache of openssl - ==> Installing openssl from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/openssl-1.0.2o/linux-ubuntu16.04-x86_64-gcc-5.4.0-openssl-1.0.2o-b4y3w3bsyvjla6eesv4vt6aplpfrpsha.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:24:10 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed openssl from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openssl-1.0.2o-b4y3w3bsyvjla6eesv4vt6aplpfrpsha - ==> Installing cmake - ==> Searching for binary cache of cmake - ==> Installing cmake from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/cmake-3.12.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-cmake-3.12.3-otafqzhh4xnlq2mpakch7dr3tjfsrjnx.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:33:15 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed cmake from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/cmake-3.12.3-otafqzhh4xnlq2mpakch7dr3tjfsrjnx - ==> Installing glm - ==> Searching for binary cache of glm - ==> Installing glm from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/glm-0.9.7.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-glm-0.9.7.1-jnw622jwcbsymzj2fsx22omjl7tmvaws.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:30:33 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed glm from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/glm-0.9.7.1-jnw622jwcbsymzj2fsx22omjl7tmvaws - ==> libsigsegv is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz - ==> m4 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel - ==> libtool is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu - ==> util-macros is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/util-macros-1.19.1-milz7fmttmptcic2qdk5cnel7ll5sybr - ==> libpciaccess is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libpciaccess-0.13.5-5urc6tcjae26fbbd2wyfohoszhgxtbmc - ==> xz is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/xz-5.2.4-teneqii2xv5u6zl5r6qi3pwurc6pmypz - ==> libxml2 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libxml2-2.9.8-wpexsphdmfayxqxd4up5vgwuqgu5woo7 - ==> autoconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q - ==> automake is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy - ==> numactl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/numactl-2.0.11-ft463odrombnxlc3qew4omckhlq7tqgc - ==> hwloc is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hwloc-1.11.9-43tkw5mt6huhv37vqnybqgxtkodbsava - ==> openmpi is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx - ==> Installing hdf5 - ==> Searching for binary cache of hdf5 - ==> Installing hdf5 from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.4-oqwnui7wtovuf2id4vjwcxfmxlzjus6y.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:09:10 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed hdf5 from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-oqwnui7wtovuf2id4vjwcxfmxlzjus6y - ==> Installing openblas - ==> Searching for binary cache of openblas - ==> Installing openblas from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/openblas-0.3.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-openblas-0.3.3-cyeg2yiitpuqglhvbox5gtbgsim2v5vn.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:32:04 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed openblas from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openblas-0.3.3-cyeg2yiitpuqglhvbox5gtbgsim2v5vn - ==> Installing hypre - ==> Searching for binary cache of hypre - ==> Installing hypre from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hypre-2.15.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-hypre-2.15.1-fshksdpecwiq7r6vawfswpboedhbisju.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:07:34 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed hypre from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hypre-2.15.1-fshksdpecwiq7r6vawfswpboedhbisju - ==> Installing matio - ==> Searching for binary cache of matio - ==> Installing matio from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/matio-1.5.9/linux-ubuntu16.04-x86_64-gcc-5.4.0-matio-1.5.9-lmzdgssvobdljw52mtahelu2ju7osh6h.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:05:13 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed matio from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/matio-1.5.9-lmzdgssvobdljw52mtahelu2ju7osh6h - ==> Installing metis - ==> Searching for binary cache of metis - ==> Installing metis from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/metis-5.1.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-metis-5.1.0-3wnvp4ji3wwu4v4vymszrhx6naehs6jc.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:31:42 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed metis from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/metis-5.1.0-3wnvp4ji3wwu4v4vymszrhx6naehs6jc - ==> Installing netlib-scalapack - ==> Searching for binary cache of netlib-scalapack - ==> Installing netlib-scalapack from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-netlib-scalapack-2.0.2-wotpfwfctgfkzzn2uescucxvvbg3tm6b.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:07:22 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed netlib-scalapack from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2-wotpfwfctgfkzzn2uescucxvvbg3tm6b - ==> Installing mumps - ==> Searching for binary cache of mumps - ==> Installing mumps from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mumps-5.1.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-mumps-5.1.1-acsg2dzroox2swssgc5cwgkvdy6jcm5q.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:18:32 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed mumps from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mumps-5.1.1-acsg2dzroox2swssgc5cwgkvdy6jcm5q - ==> Installing netcdf - ==> Searching for binary cache of netcdf - ==> Installing netcdf from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.6.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-netcdf-4.6.1-mhm4izpogf4mrjidyskb6ewtzxdi7t6g.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:11:57 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed netcdf from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.6.1-mhm4izpogf4mrjidyskb6ewtzxdi7t6g - ==> Installing parmetis - ==> Searching for binary cache of parmetis - ==> Installing parmetis from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/parmetis-4.0.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-parmetis-4.0.3-uv6h3sqx6quqg22hxesi2mw2un3kw6b7.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:12:04 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed parmetis from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/parmetis-4.0.3-uv6h3sqx6quqg22hxesi2mw2un3kw6b7 - ==> Installing suite-sparse - ==> Searching for binary cache of suite-sparse - ==> Installing suite-sparse from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/suite-sparse-5.3.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-suite-sparse-5.3.0-zaau4kifha2enpdcn3mjlrqym7hm7yon.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:22:54 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed suite-sparse from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/suite-sparse-5.3.0-zaau4kifha2enpdcn3mjlrqym7hm7yon - ==> Installing trilinos - ==> Searching for binary cache of trilinos - ==> Installing trilinos from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-trilinos-12.12.1-rlsruavxqvwk2tgxzxboclbo6ykjf54r.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:18:10 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed trilinos from binary cache - -Now we're starting to see the power of Spack. Trilinos in its default -configuration has 23 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 -binary installation for the tutorial, a source 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 trilinos +hdf5 ^hdf5+hl+mpi ^mpich - ==> diffutils is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/diffutils-3.6-2rhuivgjrna2nrxhntyde6md2khcvs34 - ==> bzip2 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/bzip2-1.0.6-ufczdvsqt6edesm36xiucyry7myhj7e7 - ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - ==> boost is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/boost-1.68.0-zbgfxapchxa4awxdwpleubfuznblxzvt - ==> pkgconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v - ==> ncurses is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh - ==> readline is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi - ==> gdbm is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes - ==> perl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo - ==> openssl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openssl-1.0.2o-b4y3w3bsyvjla6eesv4vt6aplpfrpsha - ==> cmake is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/cmake-3.12.3-otafqzhh4xnlq2mpakch7dr3tjfsrjnx - ==> glm is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/glm-0.9.7.1-jnw622jwcbsymzj2fsx22omjl7tmvaws - ==> libsigsegv is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz - ==> m4 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel - ==> autoconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q - ==> automake is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy - ==> libtool is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu - ==> texinfo is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/texinfo-6.5-zs7a2pcwhq6ho2cj2x26uxfktwkpyucn - ==> findutils is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/findutils-4.6.0-d4iajxsopzrlcjtasahxqeyjkjv5jx4v - ==> mpich is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpich-3.2.1-p3f7p2r5ntrynqibosglxvhwyztiwqs5 - ==> hdf5 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-xxd7syhgej6onpyfyewxqcqe7ltkt7ob - ==> openblas is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openblas-0.3.3-cyeg2yiitpuqglhvbox5gtbgsim2v5vn - ==> Installing hypre - ==> Searching for binary cache of hypre - ==> Finding buildcaches in /mirror/build_cache - ==> Installing hypre from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hypre-2.15.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-hypre-2.15.1-obewuozolon7tkdg4cfxc6ae2tzkronb.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:34:36 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed hypre from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hypre-2.15.1-obewuozolon7tkdg4cfxc6ae2tzkronb - ==> Installing matio - ==> Searching for binary cache of matio - ==> Installing matio from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/matio-1.5.9/linux-ubuntu16.04-x86_64-gcc-5.4.0-matio-1.5.9-gvyqldhifflmvcrtui3b6s64jcczsxxh.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:25:11 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed matio from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/matio-1.5.9-gvyqldhifflmvcrtui3b6s64jcczsxxh - ==> metis is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/metis-5.1.0-3wnvp4ji3wwu4v4vymszrhx6naehs6jc - ==> Installing netlib-scalapack - ==> Searching for binary cache of netlib-scalapack - ==> Installing netlib-scalapack from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-netlib-scalapack-2.0.2-p7iln2pcosw2ipyqoyr7ie6lpva2oj7r.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:32:20 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed netlib-scalapack from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2-p7iln2pcosw2ipyqoyr7ie6lpva2oj7r - ==> Installing mumps - ==> Searching for binary cache of mumps - ==> Installing mumps from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mumps-5.1.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-mumps-5.1.1-cumcj5a75cagsznpjrgretxdg6okxaur.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:33:18 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed mumps from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mumps-5.1.1-cumcj5a75cagsznpjrgretxdg6okxaur - ==> Installing netcdf - ==> Searching for binary cache of netcdf - ==> Installing netcdf from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.6.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-netcdf-4.6.1-wmmx5sgwfds34v7bkkhiduar5yecrnnd.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:24:01 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed netcdf from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.6.1-wmmx5sgwfds34v7bkkhiduar5yecrnnd - ==> Installing parmetis - ==> Searching for binary cache of parmetis - ==> Installing parmetis from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/parmetis-4.0.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-parmetis-4.0.3-jehtatan4y2lcobj6waoqv66jj4libtz.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:07:41 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed parmetis from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/parmetis-4.0.3-jehtatan4y2lcobj6waoqv66jj4libtz - ==> suite-sparse is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/suite-sparse-5.3.0-zaau4kifha2enpdcn3mjlrqym7hm7yon - ==> Installing trilinos - ==> Searching for binary cache of trilinos - ==> Installing trilinos from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-trilinos-12.12.1-kqc52moweigxqxzwzfqajc6ocxwdwn4w.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:30:15 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed trilinos from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-kqc52moweigxqxzwzfqajc6ocxwdwn4w - - -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-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - trilinos@12.12.1 - ^boost@1.68.0 - ^bzip2@1.0.6 - ^zlib@1.2.11 - ^glm@0.9.7.1 - ^hdf5@1.10.4 - ^openmpi@3.1.3 - ^hwloc@1.11.9 - ^libpciaccess@0.13.5 - ^libxml2@2.9.8 - ^xz@5.2.4 - ^numactl@2.0.11 - ^hypre@2.15.1 - ^openblas@0.3.3 - ^matio@1.5.9 - ^metis@5.1.0 - ^mumps@5.1.1 - ^netlib-scalapack@2.0.2 - ^netcdf@4.6.1 - ^parmetis@4.0.3 - ^suite-sparse@5.3.0 - - trilinos@12.12.1 - ^boost@1.68.0 - ^bzip2@1.0.6 - ^zlib@1.2.11 - ^glm@0.9.7.1 - ^hdf5@1.10.4 - ^mpich@3.2.1 - ^hypre@2.15.1 - ^openblas@0.3.3 - ^matio@1.5.9 - ^metis@5.1.0 - ^mumps@5.1.1 - ^netlib-scalapack@2.0.2 - ^netcdf@4.6.1 - ^parmetis@4.0.3 - ^suite-sparse@5.3.0 - - -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 | | | | | | | | | | | | | suite-sparse - |\ \ \ \ \ \ \ \ \ \ \ \ \ \ - | |_|_|/ / / / / / / / / / / - |/| | | | | | | | | | | | | - | |\ \ \ \ \ \ \ \ \ \ \ \ \ - | | |_|_|_|_|_|/ / / / / / / - | |/| | | | | | | | | | | | - | | | |_|_|_|_|_|_|_|/ / / - | | |/| | | | | | | | | | - | | | o | | | | | | | | | parmetis - | | |/| | | | | | | | | | - | |/|/| | | | | | | | | | - | | | |/ / / / / / / / / - | | | | | | o | | | | | mumps - | |_|_|_|_|/| | | | | | - |/| | | |_|/| | | | | | - | | | |/| |/ / / / / / - | | | | |/| | | | | | - | | | | o | | | | | | netlib-scalapack - | |_|_|/| | | | | | | - |/| | |/| | | | | | | - | | |/|/ / / / / / / - | o | | | | | | | | metis - | |/ / / / / / / / - | | | | | | | o | glm - | | |_|_|_|_|/ / - | |/| | | | | | - | o | | | | | | cmake - | |\ \ \ \ \ \ \ - | o | | | | | | | openssl - | |\ \ \ \ \ \ \ \ - | | | | | o | | | | netcdf - | | |_|_|/| | | | | - | |/| | |/| | | | | - | | | | | |\ \ \ \ \ - | | | | | | | |_|/ / - | | | | | | |/| | | - | | | | | | | o | | matio - | | |_|_|_|_|/| | | - | |/| | | | |/ / / - | | | | | | | o | hypre - | |_|_|_|_|_|/| | - |/| | | | |_|/ / - | | | | |/| | | - | | | | | | o | hdf5 - | | |_|_|_|/| | - | |/| | | |/ / - | | | | |/| | - | | | | o | | openmpi - | | |_|/| | | - | |/| | | | | - | | | | |\ \ \ - | | | | | o | | hwloc - | | | | |/| | | - | | | | | |\ \ \ - | | | | | | |\ \ \ - | | | | | | o | | | libxml2 - | | |_|_|_|/| | | | - | |/| | | |/| | | | - | | | | | | | | | o boost - | | |_|_|_|_|_|_|/| - | |/| | | | | | | | - | o | | | | | | | | zlib - | / / / / / / / / - | | | | | o | | | xz - | | | | | / / / - | | | | | o | | libpciaccess - | | | | |/| | | - | | | | | |\ \ \ - | | | | | o | | | util-macros - | | | | | / / / - | | | o | | | | numactl - | | | |\ \ \ \ \ - | | | | |_|_|/ / - | | | |/| | | | - | | | | |\ \ \ \ - | | | | | |_|/ / - | | | | |/| | | - | | | | | |\ \ \ - | | | | | o | | | automake - | | |_|_|/| | | | - | |/| | | | | | | - | | | | | |/ / / - | | | | | o | | autoconf - | | |_|_|/| | | - | |/| | |/ / / - | | | |/| | | - | o | | | | | perl - | o | | | | | gdbm - | o | | | | | readline - | |/ / / / / - | o | | | | ncurses - | | |_|/ / - | |/| | | - | o | | | pkgconf - | / / / - o | | | openblas - / / / - | o | libtool - |/ / - o | m4 - o | libsigsegv - / - o bzip2 - o diffutils - -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 zlib and tcl. Now we -will go through and uninstall some of those packages that we didn't -really need. - -.. code-block:: console - - $ spack find -d tcl - ==> 3 installed packages - -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - tcl@8.6.8 - ^zlib@1.2.8 - - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - tcl@8.6.8 - ^zlib@1.2.8 - - tcl@8.6.8 - ^zlib@1.2.11 - - - $ spack find zlib - ==> 6 installed packages. - -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - zlib@1.2.8 zlib@1.2.11 - - -- linux-ubuntu16.04-x86_64 / gcc@4.7 --------------------------- - zlib@1.2.11 - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - zlib@1.2.8 zlib@1.2.8 zlib@1.2.11 - -We can uninstall packages by spec using the same syntax as install. - -.. code-block:: console - - $ spack uninstall zlib %gcc@4.7 - ==> The following packages will be uninstalled: - - -- linux-ubuntu16.04-x86_64 / gcc@4.7 --------------------------- - bq2wtdx zlib@1.2.11%gcc+optimize+pic+shared - - ==> Do you want to proceed? [y/N] y - ==> Successfully uninstalled zlib@1.2.11%gcc@4.7+optimize+pic+shared arch=linux-ubuntu16.04-x86_64 /bq2wtdx - - $ spack find -lf zlib - ==> 5 installed packages. - -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - i426yu3 zlib@1.2.8%clang - 4pt75q7 zlib@1.2.11%clang - - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - bkyl5bh zlib@1.2.8%gcc - 64mns5m zlib@1.2.8%gcc cppflags="-O3" - 5nus6kn zlib@1.2.11%gcc - -We can also uninstall packages by referring only to their hash. - -We can use either ``-f`` (force) or ``-R`` (remove dependents as well) to -remove packages that are required by another installed package. - -.. code-block:: console - - $ spack uninstall zlib/i426 - ==> Error: Will not uninstall zlib@1.2.8%clang@3.8.0-2ubuntu4/i426yu3 - - The following packages depend on it: - -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - 6wc66et tcl@8.6.8%clang - - ==> Error: Use \`spack uninstall --dependents\` to uninstall these dependencies as well. - - $ spack uninstall -R zlib/i426 - ==> The following packages will be uninstalled: - - -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - 6wc66et tcl@8.6.8%clang - i426yu3 zlib@1.2.8%clang+optimize+pic+shared - ==> Do you want to proceed? [y/N] y - ==> Successfully uninstalled tcl@8.6.8%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 /6wc66et - ==> Successfully uninstalled zlib@1.2.8%clang@3.8.0-2ubuntu4+optimize+pic+shared arch=linux-ubuntu16.04-x86_64 /i426yu3 - -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-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - rlsruav trilinos@12.12.1%gcc~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2 - kqc52mo trilinos@12.12.1%gcc~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2 - - ==> Error: You can either: - a) use a more specific spec, or - b) use `spack uninstall --all` to uninstall ALL matching specs. - - - $ spack uninstall /rlsr - ==> The following packages will be uninstalled: - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - rlsruav trilinos@12.12.1%gcc~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2 - ==> Do you want to proceed? [y/N] y - ==> Successfully uninstalled trilinos@12.12.1%gcc@5.4.0~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2 arch=linux-ubuntu16.04-x86_64 /rlsruav - ------------------------------ -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 ^mpich`` will return every installed -package that depends on mpich, and ``spack find cppflags="-O3"`` will -return every package which was built with ``cppflags="-O3"``. - -.. code-block:: console - - $ spack find ^mpich - ==> 8 installed packages - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - hdf5@1.10.4 matio@1.5.9 netcdf@4.6.1 parmetis@4.0.3 - hypre@2.15.1 mumps@5.1.1 netlib-scalapack@2.0.2 trilinos@12.12.1 - - $ spack find cppflags=-O3 - ==> 1 installed packages. - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - zlib@1.2.8 - -The ``find`` command can also show which packages were installed -explicitly (rather than pulled in as a dependency) using the ``-x`` -flag. The ``-X`` 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 -px - ==> 10 installed packages - -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 -------------- - zlib@1.2.11 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.11-4pt75q7qq6lygf3hgnona4lyc2uwedul - - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - hdf5@1.10.4 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-5vcv5r67vpjzenq4apyebshclelnzuja - hdf5@1.10.4 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-ozyvmhzdew66byarohm4p36ep7wtcuiw - hdf5@1.10.4 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-xxd7syhgej6onpyfyewxqcqe7ltkt7ob - tcl@8.6.8 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-am4pbatrtga3etyusg2akmsvrswwxno2 - tcl@8.6.8 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-qhwyccywhx2i6s7ob2gvjrjtj3rnfuqt - trilinos@12.12.1 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-kqc52moweigxqxzwzfqajc6ocxwdwn4w - zlib@1.2.8 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-bkyl5bhuep6fmhuxzkmhqy25qefjcvzc - zlib@1.2.8 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu - zlib@1.2.11 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - ---------------------- -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 - -- clang ubuntu16.04-x86_64 ------------------------------------- - clang@3.8.0-2ubuntu4 clang@3.7.1-2ubuntu2 - - -- gcc ubuntu16.04-x86_64 --------------------------------------- - gcc@5.4.0 gcc@4.7 - -The compilers are maintained in a YAML file. Later in the tutorial you -will learn how to configure compilers by hand 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 gcc @7.2.0 - ==> libsigsegv is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz - ==> m4 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel - ==> pkgconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v - ==> ncurses is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh - ==> readline is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi - ==> gdbm is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes - ==> perl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo - ==> autoconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q - ==> automake is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy - ==> libtool is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu - ==> Installing gmp - ==> Searching for binary cache of gmp - ==> Finding buildcaches in /mirror/build_cache - ==> Installing gmp from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/gmp-6.1.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-gmp-6.1.2-qc4qcfz4monpllc3nqupdo7vwinf73sw.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:18:16 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed gmp from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gmp-6.1.2-qc4qcfz4monpllc3nqupdo7vwinf73sw - ==> Installing isl - ==> Searching for binary cache of isl - ==> Installing isl from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/isl-0.18/linux-ubuntu16.04-x86_64-gcc-5.4.0-isl-0.18-vttqoutnsmjpm3ogb52rninksc7hq5ax.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:05:19 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed isl from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/isl-0.18-vttqoutnsmjpm3ogb52rninksc7hq5ax - ==> Installing mpfr - ==> Searching for binary cache of mpfr - ==> Installing mpfr from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpfr-3.1.6/linux-ubuntu16.04-x86_64-gcc-5.4.0-mpfr-3.1.6-jnt2nnp5pmvikbw7opueajlbwbhmjxyv.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:32:07 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed mpfr from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpfr-3.1.6-jnt2nnp5pmvikbw7opueajlbwbhmjxyv - ==> Installing mpc - ==> Searching for binary cache of mpc - ==> Installing mpc from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpc-1.1.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-mpc-1.1.0-iuf3gc3zpgr4n4mditnxhff6x3joxi27.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:30:35 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed mpc from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpc-1.1.0-iuf3gc3zpgr4n4mditnxhff6x3joxi27 - ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb - Installing gcc - ==> Searching for binary cache of gcc - ==> Finding buildcaches in /mirror/build_cache - ==> Installing gcc from binary cache - ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs.spack - ######################################################################## 100.0% - gpg: Signature made Sat Nov 10 05:22:47 2018 UTC using RSA key ID 3B7C69B2 - gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown] - gpg: WARNING: This key is not certified with a trusted signature! - gpg: There is no indication that the signature belongs to the owner. - Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2 - ==> Successfully installed gcc from binary cache - [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs - - $ spack find -p gcc - spack find -p gcc - ==> 1 installed package - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - gcc@7.2.0 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs - -We can add gcc to Spack as an available compiler using the ``spack -compiler add`` command. This will allow future packages to build with -gcc@7.2.0. - -.. code-block:: console - - $ spack compiler add `spack location -i gcc@7.2.0` - ==> Added 1 new compiler to /home/ubuntu/.spack/linux/compilers.yaml - gcc@7.2.0 - ==> Compilers are defined in the following files: - /home/ubuntu/.spack/linux/compilers.yaml - -We can also remove compilers from our configuration using ``spack compiler remove <compiler_spec>`` - -.. code-block:: console - - $ spack compiler remove gcc@7.2.0 - ==> Removed compiler gcc@7.2.0 |