Trainings 2019 - Admin HPC - module 1 - Software Installation

Sotwares installation

Description	Ways to install softwares under Linux (Centos7)
Related-course materials	HPC Administration Module1
Authors	Ndomassi TANDO (ndomassi.tando@ird.fr)
Creation Date	23/09/2019
Last Modified Date	23/09/2019

Summary

RPM packages
Installation from sources
Installation of a python package
Installation via Conda
Perl Modules installation
Essential system softwares
Links
License

RPM packages

Rpm are used for distribution such as Centos, Redhat or fedora.

You can install them with several commands:

$ rpm -ivh rpm_package.rpm

To use the command above, the dependencies of the package to install have to be installed first.

To avoid that and if you have of the rpms of the deendencies , just use:

$ yum install rpm_package.rpm

Installation from sources:

A lot of linux softwares have their sources available.

It allows to compile the software to match with the server architecture.

Usually, the sources are compressed into a tarball.

You first have to decompress the tarball with the command:

$ tar xvfz package.tar.gz

Into the source package, you should find a README.md or INSTALL.md file that explain to you how to install the software.

Use the following lines to compile the package:

$  cd package/
  $ ./configure --prefix=/PATH_WHERE_TO install it
 $ make                   # do the compilation
 $ make test             # check that the compilation is OK with a set of test files
 $  make install           # to install the binaries to  the precised path

Installation of a python package:

We can use the command :

$ pip install python_package

From source, after decompressing the tarball:

$ python setup.py install

If you work with several versions of python or a cluster, you should use a virtual environment to install your python package.

The virtual environnement encapsulates a python environment for each python packages avoiding interferences with the other:

Create a folder for your python package in /usr/local

$ mkdir /usr/local/python_package-version

Create the virtual environment:

$ virtualenv venv

Activate the virtual environment to install the python package:

$     source venv/bin/activate
    pip install package or python setup.py install

Deactivate the environment:

$ deactivate

Installation via Conda:

URL: https://conda.io/docs/

Conda quickly installs, runs and updates packages and their dependencies. Conda easily creates, saves, loads and switches between environments on your local computer. It was created for Python programs, but it can package and distribute software for any language.

Install conda running the installer:

$ bash Miniconda3-latest-Linux-x86_64.sh

Once conda installed, you can create a new environment and install a package with the command:

$ conda create -n software software

To activate a environment:

$ source activate myenv

To deactivate a environment:

$ source deactivate

Perl Modules installation:

Use the following commands:

$ perl –MCPAN –e shell  
                 > install <Module>[::<Submodule>]

or from the source:

$ perl Makefile.PL PREFIX= <INSTALL_PERL_PATH>
$ make
$ make test
$ make install

Essential system softwares:

Python:

Python is a programming language

URL : https://www.python.org/

Installation :

ncurses-devel sqlite-devel readline-devel tk-devel gdbm-devel db4-devel 
      libpcap-devel xz-devel
 $ wget  https://www.python.org/ftp/python/3.7.1/Python-3.7.1.tar.xz
 $ tar xf Python-3.7.1.tar.xz
 $ cd Python-3.7.1
 $ ./configure --prefix=/usr/local/python-3.7.1 --enable-shared LDFLAGS="-Wl,-rpath /usr/local/python-3.7.1/lib"
 $ make
 $ make altinstall

Add /usr/local/python-3.7.1 to the path :

$ echo  'export PATH=$PATH:/usr/local/python-3.7.1/bin' >>/etc/profile
$ echo  'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/python-3.7.1/lib' >>/etc/profile
$ echo  'export PYTHONPATH=/usr/local/python-3.7.1/bin' >>/etc/profile
$ source /etc/profile

Usage :

$ python3 + arguments

Perl:

Perl 5 is a highly capable, feature-rich programming language with over 30 years of development

URL : https://www.perl.org/about.html

Installation :

$ wget  https://www.cpan.org/src/5.0/perl-5.28.1.tar.gz
$ tar xvfz perl-5.28.1.tar.gz
$ cd perl-5.28.1
$ ./configure -des -Dprefix=/usr/local/perl-5.28.1
$ make test
$ make install

Add /usr/local/perl-5.28.1 to the path :

$ echo  'export PATH=$PATH:/usr/local/perl-5.28.1/bin' >>/etc/profile
$ echo  'export PERL5LIB=$PERL5LIB:/usr/local/perl-5.28.1/lib/perl5' >>/etc/profile
$ source /etc/profile{

Usage :

$ perl + scripts

Perlbrew (optional):

perlbrew is an admin-free perl installation management tool.

It is a tool to manage multiple perl installations.

URL : https://perlbrew.pl/

Installation :

$ export PERLBREW_ROOT=/usr/local/perlbrew-0.84
      \wget -O - https://install.perlbrew.pl | bash

Add /usr/local/perl-5.28.1 to the path :

$ echo  'export PATH=$PATH:/usr/local/perlbrew-0.84' >>/etc/profile

   source /etc/profile

Usage :

# Initialize
           $ perlbrew init

         # See what is available
           $ perlbrew available

        #  Install some Perls
           $ perlbrew install 5.18.2
           $ perlbrew install perl-5.8.1
           $ perlbrew install perl-5.19.9

        # See what were installed
           $ perlbrew list

        # Swith to an installation and set it as default
           $ perlbrew switch perl-5.18.2

        # Temporarily use another version only in current shell.
           $ perlbrew use perl-5.8.1
           $ perl -v

        # Or turn it off completely. Useful when you messed up too deep.
        # Or want to go back to the system Perl.
           $ perlbrew off

        # Use 'switch' command to turn it back on.
           $ perlbrew switch perl-5.12.2

        # Exec something with all perlbrew-ed perls
           $ perlbrew exec -- perl -E 'say $]'

java:

Java is a programming language web oriented.

URL : https://www.java.com/fr/download/linux_manual.jsp

Installation :

Download the tarball form the interface (jre ou jdk)

$ cd /usr/java
$ tar zxvf jre-8u191-linux-x64.tar.gz

Add /usr/java/jre-8u191/ to the path :

$ echo  'export PATH=$PATH:/usr/java/jre-8u191/bin' >>/etc/profile
$ echo  'export PATH=$PATH:/usr/java/jre-8u191/lib' >>/etc/profile
$ source /etc/profile

Usage :

$ java -jar + file.jar

gcc:

The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, Go, and D, as well as libraries for these languages (libstdc++,...). GCC was originally written as the compiler for the GNU operating system.

URL : http://gcc.gnu.org/install/

Installation :

$ wget  ftp://ftp.lip6.fr/pub/gcc/releases/gcc-7.4.0/gcc-7.4.0.tar.gz
 $ tar zxvf gcc-7.4.0.tar.gz
 $ cd gcc-7.4.0
 $ mkdir build
 $ cd build
 $ ../configure --prefix=/usr/local/gcc-7.4.0
 $ make --disable-werror
 $ make install

Add /usr/local/gcc-7.4.0 to the path :

$ echo  'export PATH=$PATH/usr/local/gcc-7.4.0/bin' >>/etc/profile
$ echo  'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/gcc-7.4.0/lib' >>/etc/profile
$ source /etc/profile

Bioperl:

Installation

$ cpan
      cpan>d /bioperl/

Choose the most recent version:

cpan>install C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz

License

The resource material is licensed under the Creative Commons Attribution 4.0 International License (here).

Trainings 2019 – Admin HPC – module 1 – Software Installation

Sotwares installation

Summary

RPM packages

Installation from sources:

Installation of a python package:

Installation via Conda:

Perl Modules installation:

Essential system softwares:

Python:

Installation :

Usage :

Perl:

Installation :

Usage :

Perlbrew (optional):

Installation :

Usage :

java:

Installation :

Usage :

gcc:

Installation :

Bioperl:

Installation

Links

License

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