From 0430934118227891e27e2096d4243a324d696f7e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= <lukas.krupcik@vsb.cz>
Date: Fri, 7 Jul 2017 13:25:32 +0200
Subject: [PATCH] add spack
---
docs.it4i/software/spack.md | 355 ++++++++++++++++++++++++++++++++++++
mkdocs.yml | 1 +
2 files changed, 356 insertions(+)
create mode 100644 docs.it4i/software/spack.md
diff --git a/docs.it4i/software/spack.md b/docs.it4i/software/spack.md
new file mode 100644
index 000000000..4ef2bb55a
--- /dev/null
+++ b/docs.it4i/software/spack.md
@@ -0,0 +1,355 @@
+# Spack
+
+Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine.
+
+Homepage: [https://spack.io/](https://spack.io/)
+Documentation: [https://spack.readthedocs.io/en/latest/](https://spack.readthedocs.io/en/latest/)
+
+## Spack On IT4Innovations Clusters
+
+```console
+
+~]$ ml av Spack
+
+---------------------- /apps/modules/devel ------------------------------
+ Spack/default
+
+```
+
+! note
+ Spack/default is rule for setting up local installation
+
+
+## First Usage Module Spack/default
+
+The Spack will be installed into your /home, create folder Spack for installing software and set the configuration into ~/.spack/configure.yml
+
+```console
+~]$ ml Spack
+== Settings for first use
+Couldn't import dot_parser, loading of dot files will not be possible.
+== temporary log file in case of crash /tmp/eb-wLh1RT/easybuild-54vEn3.log
+== processing EasyBuild easyconfig /apps/easybuild/easyconfigs-it4i/s/Spack/Spack-0.10.0.eb
+== building and installing Spack/0.10.0...
+== fetching files...
+== creating build dir, resetting environment...
+== unpacking...
+== patching...
+== preparing...
+== configuring...
+== building...
+== testing...
+== installing...
+== taking care of extensions...
+== postprocessing...
+== sanity checking...
+== cleaning up...
+== creating module...
+== permissions...
+== packaging...
+== COMPLETED: Installation ended successfully
+== Results of the build can be found in the log file(s) ~/.local/easybuild/software/Spack/0.10.0/easybuild/easybuild-Spack-0.10.0-20170707.122650.log
+== Build succeeded for 1 out of 1
+== Temporary log file(s) /tmp/eb-wLh1RT/easybuild-54vEn3.log* have been removed.
+== Temporary directory /tmp/eb-wLh1RT has been removed.
+== Create folder ~/Spack
+
+The following have been reloaded with a version change:
+ 1) Spack/default => Spack/0.10.0
+
+~]$ spack --version
+0.10.0
+```
+
+## Usage Module Spack/default
+
+```console
+~]$ ml Spack
+
+The following have been reloaded with a version change:
+ 1) Spack/default => Spack/0.10.0
+
+~]$ spack --version
+0.10.0
+```
+
+## Build Software Package
+
+### Search For Available Software
+
+To install software with Spack, you need to know what software is available. Using the `spack list` command.
+
+```console
+~]$ spack list
+==> 1114 packages.
+abinit font-bh-100dpi libffi npm py-ply r-maptools tetgen
+ack font-bh-75dpi libfontenc numdiff py-pmw r-markdown tethex
+activeharmony font-bh-lucidatypewriter-100dpi libfs nwchem py-prettytable r-mass texinfo
+adept-utils font-bh-lucidatypewriter-75dpi libgcrypt ocaml py-proj r-matrix texlive
+adios font-bh-ttf libgd oce py-prompt-toolkit r-matrixmodels the-platinum-searcher
+adol-c font-bh-type1 libgpg-error oclock py-protobuf r-memoise the-silver-searcher
+allinea-forge font-bitstream-100dpi libgtextutils octave py-psutil r-mgcv thrift
+allinea-reports font-bitstream-75dpi libhio octave-splines py-ptyprocess r-mime tinyxml
+ant font-bitstream-speedo libice octopus py-pudb r-minqa tinyxml2
+antlr font-bitstream-type1 libiconv ompss py-py r-multcomp tk
+ape font-cronyx-cyrillic libint ompt-openmp py-py2cairo r-munsell tmux
+apex font-cursor-misc libjpeg-turbo opari2 py-py2neo r-mvtnorm tmuxinator
+applewmproto font-daewoo-misc libjson-c openblas py-pychecker r-ncdf4 transset
+appres font-dec-misc liblbxutil opencoarrays py-pycodestyle r-networkd3 trapproto
+apr font-ibm-type1 libmesh opencv py-pycparser r-nlme tree
+...
+```
+
+#### Specify Software Version (for package)
+
+To see more available versions of a package, run `spack versions`.
+
+```console
+~]$ spack versions git
+==> Safe versions (already checksummed):
+ 2.11.0 2.9.3 2.9.2 2.9.1 2.9.0 2.8.4 2.8.3 2.8.2 2.8.1 2.8.0 2.7.3 2.7.1
+==> Remote versions (not yet checksummed):
+ Found no versions for git
+```
+
+## Graph For Software Package
+
+Spack provides the `spack graph` command for graphing dependencies. The command by default generates an ASCII rendering of a spec’s dependency graph.
+
+```console
+~]$ spack graph git
+o git
+|\
+| |\
+| | |\
+| | | |\
+| | | | |\
+| | | | | |\
+| | | | | | |\
+| | | | | | | |\
+| | | | | | | o | curl
+| |_|_|_|_|_|/| |
+|/| | | |_|_|/ /
+| | | |/| | | |
+| | | o | | | | openssl
+| |_|/ / / / /
+|/| | | | | |
+| | | | o | | gettext
+| | | | |\ \ \
+| | | | | |\ \ \
+| | | | | | |\ \ \
+| | | | | | | |\ \ \
+| | | | | | | o | | | libxml2
+| |_|_|_|_|_|/| | | |
+|/| | | | |_|/| | | |
+| | | | |/| | | | | |
+o | | | | | | | | | | zlib
+ / / / / / / / / / /
+| | | o | | | | | | xz
+| | | / / / / / /
+| | | o | | | | | tar
+| | | / / / / /
+| | | | o | | | pkg-config
+| | | | / / /
+o | | | | | | perl
+ / / / / / /
+o | | | | | pcre
+ / / / / /
+| o | | | ncurses
+| / / /
+| | | o autoconf
+| | | o m4
+| | | o libsigsegv
+| | |
+o | | libiconv
+ / /
+| o expat
+|
+o bzip2
+```
+
+### Information For Software Package
+
+To get more information on a particular package from `spack list`, use `spack info`.
+
+```console
+~]$ spack info git
+Package: git
+Homepage: http://git-scm.com
+
+Safe versions:
+ 2.11.0 https://github.com/git/git/tarball/v2.11.0
+ 2.9.3 https://github.com/git/git/tarball/v2.9.3
+ 2.9.2 https://github.com/git/git/tarball/v2.9.2
+ 2.9.1 https://github.com/git/git/tarball/v2.9.1
+ 2.9.0 https://github.com/git/git/tarball/v2.9.0
+ 2.8.4 https://github.com/git/git/tarball/v2.8.4
+ 2.8.3 https://github.com/git/git/tarball/v2.8.3
+ 2.8.2 https://github.com/git/git/tarball/v2.8.2
+ 2.8.1 https://github.com/git/git/tarball/v2.8.1
+ 2.8.0 https://github.com/git/git/tarball/v2.8.0
+ 2.7.3 https://github.com/git/git/tarball/v2.7.3
+ 2.7.1 https://github.com/git/git/tarball/v2.7.1
+
+Variants:
+ None
+
+Installation Phases:
+ install
+
+Build Dependencies:
+ autoconf curl expat gettext libiconv openssl pcre perl zlib
+
+Link Dependencies:
+ curl expat gettext libiconv openssl pcre perl zlib
+
+Run Dependencies:
+ None
+
+Virtual Packages:
+ None
+
+Description:
+ Git is a free and open source distributed version control system
+ designed to handle everything from small to very large projects with
+ speed and efficiency.
+```
+
+### Install Software Package
+
+`spack install` will install any package shown by `spack list`. For example, To install the latest version of the `git` package, you might type this.
+
+Use `spack install git` for default version or `spack install git@version`.
+
+```console
+~]$ spack install git@2.11.0
+==> Installing git
+==> Installing pcre
+==> Fetching http://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.39.tar.bz2
+...
+```
+
+! warning
+ `ftp` on cluster is not allowed, you must edit source link (edit)[#Edit Rule]
+
+### Edit Rule
+
+```console
+~]$ spack edit git
+```
+
+! note
+ For change source link (ftp:// to http://) use `spack create URL -f`. Automatically generates rules.
+
+**Example**
+
+```console
+~]$ spack install git
+==> Installing git
+==> Installing pcre
+==> Fetching ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.39.tar.bz2
+curl: (7) couldn't connect to host
+==> Fetching from ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.39.tar.bz2 failed.
+==> Error: FetchError: All fetchers failed for pcre-8.39-bm3lumpbghly2l7bkjsi4n2l3jyam6ax
+...
+
+~]$ spack create http://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.39.tar.bz2 -f
+==> This looks like a URL for pcre
+==> Found 2 versions of pcre:
+
+ 8.41 http://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.41.tar.bz2
+ 8.40 http://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.40.tar.bz2
+
+How many would you like to checksum? (default is 1, q to abort) 1
+==> Downloading...
+==> Fetching http://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.41.tar.bz2
+######################################################################## 100,0%
+==> Checksummed 1 version of pcre
+==> This package looks like it uses the cmake build system
+==> Created template for pcre package
+==> Created package file: ~/.local/easybuild/software/Spack/0.10.0/var/spack/repos/builtin/packages/pcre/package.py
+~]$
+~]$ spack install git
+==> Installing git
+==> Installing pcre
+==> Installing cmake
+==> Installing ncurses
+==> Fetching http://ftp.gnu.org/pub/gnu/ncurses/ncurses-6.0.tar.gz
+######################################################################## 100,0%
+...
+```
+
+## Available Spack Module
+
+We know that `spack list` shows you the names of available packages, but how do you figure out which are already installed?
+
+```console
+==> 19 installed packages.
+-- linux-centos6-x86_64 / gcc@4.4.7 -----------------------------
+autoconf@2.69 cmake@3.7.1 expat@2.2.0 git@2.11.0 libsigsegv@2.10 m4@1.4.17 openssl@1.0.2j perl@5.24.0 tar@1.29 zlib@1.2.10
+bzip2@1.0.6 curl@7.50.3 gettext@0.19.8.1 libiconv@1.14 libxml2@2.9.4 ncurses@6.0 pcre@8.41 pkg-config@0.29.1 xz@5.2.2
+```
+
+**Spack colorizes output**
+
+```console
+~]$ spack find | less -R
+```
+
+`spack find` shows the specs of installed packages. A spec is like a name, but it has a version, compiler, architecture, and build options associated with it. In spack, you can have many installations of the same package with different specs.
+
+## Load And Unload Module
+
+Neither of these is particularly pretty, easy to remember, or easy to type. Luckily, Spack has its own interface for using modules and dotkits.
+
+```console
+~]$ spack load git
+==> This command requires spack's shell integration.
+
+ To initialize spack's shell commands, you must run one of
+ the commands below. Choose the right command for your shell.
+
+ For bash and zsh:
+ . ~/.local/easybuild/software/Spack/0.10.0/share/spack/setup-env.sh
+
+ For csh and tcsh:
+ setenv SPACK_ROOT ~/.local/easybuild/software/Spack/0.10.0
+ source ~/.local/easybuild/software/Spack/0.10.0/share/spack/setup-env.csh
+```
+
+**First usage**
+
+```console
+~]$ . ~/.local/easybuild/software/Spack/0.10.0/share/spack/setup-env.sh
+```
+
+```console
+~]$ git version 1.7.1
+~]$ spack load git
+~]$ git --version
+git version 2.11.0
+~]$ spack unload git
+~]$ git --version
+git version 1.7.1
+```
+
+## Uninstall Software Package
+
+Spack will ask you either to provide a version number to remove the ambiguity or use the `--all` option to uninstall all of the matching packages.
+
+You may force uninstall a package with the `--force` option
+
+``console
+~]$ spack uninstall git
+==> The following packages will be uninstalled :
+
+-- linux-centos6-x86_64 / gcc@4.4.7 -----------------------------
+xmh3hmb git@2.11.0%gcc
+
+
+==> Do you want to proceed ? [y/n]
+y
+==> Successfully uninstalled git@2.11.0%gcc@4.4.7 arch=linux-centos6-x86_64 -xmh3hmb
+
+```
+
diff --git a/mkdocs.yml b/mkdocs.yml
index 4b8091537..a670e39c7 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -62,6 +62,7 @@ pages:
- Modules Matrix: modules-matrix.md
- Singularity Container: software/singularity.md
- EasyBuild: software/easybuild.md
+ - EasyBuild: software/spack.md
- Salomon Software:
- Available Modules: modules-salomon.md
- Available Modules on UV: modules-salomon-uv.md
--
GitLab