spack.md

# 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

```