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Commit 70c1af8a authored by David Hrbáč's avatar David Hrbáč
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Merge branch 'new_modules' into 'master' 

New modules

See merge request !155
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6 merge requests!368Update prace.md to document the change from qprace to qprod as the default...,!367Update prace.md to document the change from qprace to qprod as the default...,!366Update prace.md to document the change from qprace to qprod as the default...,!323extended-acls-storage-section,!196Master,!155New modules
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# 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 is at [https://spack.io/](https://spack.io/)
Documentation is at [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 `~/Spack` folder. You can set the configuration by modifying ~/.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
Packages in Spack are written in pure Python, so you can do anything in Spack that you can do in Python. Python was chosen as the implementation language for two reasons. First, Python is becoming ubiquitous in the scientific software community. Second, it’s a modern language and has many powerful features to help make package writing easy.
### Search for Available Software
To install software with Spack, you need to know what software is available. Use 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 `spack graph` command to display dependency graph. 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 `spack install git` for default version or `spack install git@version` to chose the particular one.
```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 Rule
```console
$ spack edit git
```
!!! note
To change source link (ftp:// to http://) use `spack create URL -f` to regenerates 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
```
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mkdocs.yml
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......@@ -62,6 +62,7 @@ pages:
- Modules Matrix: modules-matrix.md
- Singularity Container: software/singularity.md
- EasyBuild: software/easybuild.md
- Spack: software/spack.md
- Salomon Software:
- Available Modules: modules-salomon.md
- Available Modules on UV: modules-salomon-uv.md
......
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