LSC Data Analysis Software Working Groups: Repositories

Repositories

Last Update: 04/26/08

Software required for LSC data analysis is distributed from the DASWG server packaged for a variety of operating systems
(links of the form '[ i386 ] [ x86_64 ]' contain useful Technical Information about each installed packages; if shown in red
'[ i386 ] [ x86_64 ]' they're 'testing' repositories):

Red Hat based OS's
Fedora instructions: Admin, User.
Centos instructions: Admin, User.
RedHat instructions: Admin, User. [no longer supported; instead, use sources from Fedora/CentOS]
Debian instructions: Admin,
Mac OS X instructions: User,

Available Packages

The following packages are available, and if YUM is used as package manager they can be downloaded as group "LSCSOFT":

Built by LIGO
FrameL (for data_frame manipulation: libframe, libframe-devel, libframe-util)
MetaIO (for LIGO_LW files metadata manipulation: libmetaio, libmetaio-devel, libmetaio-matlab, libmetaio-util)
User Environment Scripts (lscsoft-user-env)
LIGO Algorithm Library - LAL (lal, lal-devel)
LAL based Applications - LALAPPS (lalapps)
Grid LSC User Environment - GLUE (glue)
Framecpp (C++ interface to access frame structures: framecpp, framecpp-devel)
Data Monitoring Tool (DMT) Off_Line - DOL (dol)

The following non-LIGO (external & open access) software (gsl, fftw, python-numarray, python-matplotlib) must be installed in your machine in order to set up LSCSOFT. The other two (ROOT, SQLObject) are optional. All or some of them must be already included in the corresponding OS's Repositories as Extra packages, or you can also get them from the provided links below:

GNU Scientific Library (gsl, gsl-devel)
http://www.gnu.org/software/gsl/

Fast Fourier Transform ["Fastest Fourier Transform in the West" - FFTW3 (fftw, fftw-devel)]
http://www.fftw.org/

Python-Numarray: numerical tools for python (python-numarray)
http://dries.ulyssis.org/rpm/packages/python-numarray/info.html

Python-Matplotlib: plotting tools for python (python-matplotlib)
& its 2 dependencies: numpy, atlas
http://rpmfind.net/linux/RPM/AByName.html

ROOT (CERN Objet-Oriented general framework environment for data analysis: root)
http://root.cern.ch/

SQLObject (Python_based Object Relational Manager for object-interface to databases: sqlobject)
http://www.sqlobject.org/

Binary versions get installed in /opt/lscsoft and users (according the "user instructions") should source the appropriate shell script to set up their environment variables, i.e. /opt/lscsoft-user-env.(c)sh. If you are a developer and you need a development version (stored in the '[ URL ]' link) of one of these packages, the directory structure was chosen to allow ease of development and use.

If you want to contribute a package to the repository, you should contact Patrick Brady for an account. Testing and release procedures will be developed over time.

Fedora [ Base URL ]

The LSC Data Analysis Software stack is available for the following Fedora distributions

Fedora Core 3 [ URL ] [ i386 ] [ x86_64 ]
Fedora Core 4 [ URL ] [ i386 ] [ x86_64 ]
Fedora Core 7 [ URL ] [ i386 ] [ x86_64 ]
Fedora Core 8 [ URL ] [ i386 ] [ x86_64 ]
Fedora Core 9 [ URL ] [ i386 ] [ x86_64 ]

Administrator Instructions

Fedora ships with Yum, an update tool which allows you to automatically download and install RPM packages and resolve various dependencies. If you don't have Yum for some reason, you can download it from Duke University as tarball, src.rpm .

I- Installation
To use Yum to manage the LSC data analysis software stack, log in as root and create your repo-files:

su root

On FC3/FC4, create the file /etc/yum.repos.d/lscsoft.repo with the following contents:

[lscsoft]
name=LSC Data Analysis Software
baseurl=http://www.lsc-group.phys.uwm.edu/daswg/download/software/fedora/$releasever/$basearch
enabled=1
gpgcheck=0

For 32bit and 64bit enable Fedora Extras Repo file /etc/yum.repos.d/fedora-extras.repo, or create one with the following contents:
FC3

[extras]
name=Fedora Extras 3 - $basearch
baseurl=http://download.fedora.redhat.com/pub/fedora/linux/extras/3/$basearch/
enabled=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-fedora-extras
gpgcheck=1

FC4

[extras]
name=Fedora Extras 4 - $basearch
baseurl=http://download.fedora.redhat.com/pub/fedora/linux/extras/4/$basearch/
mirrorlist=http://fedora.redhat.com/download/mirrors/fedora-extras-4
enabled=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-fedora-extras
gpgcheck=1

On 64 bit FC3/FC4 machines (only), you must add the following line to /etc/yum.conf because a 32bit version of gsl is released in the fedora base repository:

exclude=gsl.i386

Make sure fftw3 and fftw3-devel are removed from your system

yum remove fftw3 fftw3-devel
yum clean all

On FC7/FC8, create the file /etc/yum.repos.d/lscsoft.repo with the following contents:

[lscsoft]
name=LSC Data Analysis Software
baseurl=http://www.lsc-group.phys.uwm.edu/daswg/download/software/fedora/$releasever/$basearch
enabled=1
gpgcheck=0

As of Fedora 7 there is no Fedora Extras anymore, because it has merged with Fedora Core into the "Everything" package collection, so neither FC7 nor FC8 need to configure an extra repository. There are some bugs in the FC8 release concerning the updating and upgrading of packages that can be solved using the info at bugs.

However, there exist a very useful repository, the "Extra Packages for Enterprise Linux" (EPEL). This repository can provide packages such as fftw3, gsl, numpy, python-matplotlib, etc. To enable it, just intall it

rpm -Uvh http://download.fedora.redhat.com/pub/epel/5/i386/epel-release-5-2.noarch.rpm

Yum may ask you to import the EPEL GPG key. If not, import it via rpm

rpm --import /etc/pki/rpm-gpg/RPM-GPG-KEY-EPEL

If you've done that, install all of the released LSC Data Analysis Software by doing (as root):

yum groupinstall "LSCSOFT"

II- Updates

You can set Yum up to run a nightly update by doing

cd /etc/init.d/
/sbin/chkconfig --level 3 yum on
/sbin/chkconfig --level 5 yum on
/sbin/chkconfig --add yum
/sbin/service yum restart

Or you can manually update only the LSC Data Analysis Software by doing

yum groupupdate "LSCSOFT"

III- Optional

To enable LSCSoft Fedora Testing Repo, create the file /etc/yum.repos.d/lscsoft-testing.repo with the contents:

[lscsoft-testing]
name=LSC Data Analysis Software
baseurl=http://www.lsc-group.phys.uwm.edu/daswg/download/software/fedora/testing/$releasever/$basearch
enabled=1
gpgcheck=0

User Instructions

Users can set up their environments to use the software that has been installed by adding the following to their .profile if they use a bourne shell (e.g. bash):

if [ -f /opt/lscsoft/lscsoft-user-env.sh ] ; then
  . /opt/lscsoft/lscsoft-user-env.sh
fi

Users that use a C shell (e.g., tcsh), instead add these lines to your .login:

if ( -r /opt/lscsoft/lscsoft-user-env.csh ) then
	source /opt/lscsoft/lscsoft-user-env.csh
endif

On some LSC clusters, these setup scripts are sources at the system level. This is not yet uniform however.

You can selectively disable packages from /opt/lscsoft by creating various files in your home directory as follows, for example:

If ~/.noanything exists, then automatic setup of lscsoft is *disabled*
If ~/.nonothing exists, then automatic setup of lscsoft is *disabled*
If ~/.nolscsoft exists, then automatic setup of lscsoft is *disabled*
If ~/.nolscsoft-libmetaio exists, then /opt/lscsoft/libmetaio is *disabled*
If ~/.nolscsoft-libframe exists, then /opt/lscsoft/libframe is *disabled*
If ~/.nolscsoft-lal exists, then /opt/lscsoft/lal is *disabled*

... and so on. As more packages become available via the lscsoft yum repository, the user-env script will be updated to provide similar functionality

Centos [ Base URL ]

CentOS 5 [ URL ] [ i386 ] [ x86_64 ]

Administrator Instructions

Centos 5 ships with Yum, an update tool which allows you to automatically download and install RPM packages and resolve various dependencies. If you don't have Yum for some reason, you can download it from Duke University as tarball, src.rpm .

I - Installation
To use Yum to manage the LSC data analysis software stack, log in as root

su root

Create the file /etc/yum.repos.d/lscsoft.repo with the following contents:

[lscsoft]
name=LSC Data Analysis Software
baseurl=http://www.lsc-group.phys.uwm.edu/daswg/download/software/centos/5/$basearch
enabled=1
gpgcheck=0

If you want access to the testing repo, create the file /etc/yum.repos.d/lscsoft-testing.repo with the following contents:

[lscsoft-testing]
name=LSC Data Analysis Software
baseurl=http://www.lsc-group.phys.uwm.edu/daswg/download/software/centos/testing/5/$basearch
enabled=1
gpgcheck=0

You will also need to enable "Extra Packages for Enterprise Linux" (EPEL). This repository will provide packages such as fftw3, gsl, numpy, python-matplotlib, etc.

rpm -Uvh http://download.fedora.redhat.com/pub/epel/5/i386/epel-release-5-2.noarch.rpm

Yum may ask you to import the EPEL GPG key. If not, import it via rpm

rpm --import /etc/pki/rpm-gpg/RPM-GPG-KEY-EPEL

If you've done that, install all of the released LSC Data Analysis Software by doing (as root):

yum groupinstall "LSCSOFT"

II - Updates
You can set Yum up to run a nightly update by doing

cd /etc/init.d/
/sbin/chkconfig --level 3 yum on
/sbin/chkconfig --level 5 yum on
/sbin/chkconfig --add yum
/sbin/service yum restart

Or you can manually update only the LSC Data Analysis Software by doing

yum groupupdate "LSCSOFT"

User Instructions

Users can set up their environments to use the software that has been installed by adding the following to their .profile if they use a bourne shell (e.g. bash):

if [ -f /opt/lscsoft/lscsoft-user-env.sh ] ; then
  . /opt/lscsoft/lscsoft-user-env.sh
fi

Users that use a C shell (e.g., tcsh), instead add these lines to your .login:

if ( -r /opt/lscsoft/lscsoft-user-env.csh ) then
        source /opt/lscsoft/lscsoft-user-env.csh
endif

On some LSC clusters, these setup scripts are sources at the system level. This is not yet uniform however.

You can selectively disable packages from /opt/lscsoft by creating various files in your home directory as follows:

If ~/.noanything exists, then automatic setup of lscsoft is *disabled*
If ~/.nonothing exists, then automatic setup of lscsoft is *disabled*
If ~/.nolscsoft exists, then automatic setup of lscsoft is *disabled*
If ~/.nolscsoft-libmetaio exists, then /opt/lscsoft/libmetaio is *disabled*
If ~/.nolscsoft-libframe exists, then /opt/lscsoft/libframe is *disabled*
If ~/.nolscsoft-lal exists, then /opt/lscsoft/lal is *disabled*

As more packages become available via the lscsoft yum repository, the user-env script will be updated to provide similar functionality

RedHat [ Base URL ]

Redhat 9.0 [ URL ] [ i386 ] [ x86_64 ] (no longer supported)
Redhat Enterprise WS3 [ URL ] [ i386 ] [ x86_64 ] (no longer supported; packages from Fedora/CentOS must run well in RedHat-based boxes)

Administrator Instructions

Redhat 9.0 ships with Yum, an update tool which allows you to automatically download and install RPM packages and resolve various dependencies. If you don't have Yum for some reason, you can download it from Duke University as tarball, src.rpm .

I - Install
To use Yum to manage the LSC data analysis software stack, log in as root

su root

Then add the following section to /etc/yum.conf:

[lscsoft]
name=LSC Data Analysis Software
baseurl=http://www.lsc-group.phys.uwm.edu/daswg/download/software/redhat/$releasever/

If you've done that, install all of the released LSC Data Analysis Software by doing (as root):

yum groupinstall "LSCSOFT"

II - Updates
You can set Yum up to run a nightly update by doing

cd /etc/init.d/
/sbin/chkconfig --level 3 yum on
/sbin/chkconfig --level 5 yum on
/sbin/chkconfig --add yum
/sbin/service yum restart

Or you can manually update only the LSC Data Analysis Software by doing

yum groupupdate "LSCSOFT"

User Instructions

Users can set up their environments to use the software that has been installed by adding the following to your .profile if they use a bourne shell (e.g. bash):

if [ -f /opt/lscsoft/lscsoft-user-env.sh ] ; then
  . /opt/lscsoft/lscsoft-user-env.sh
fi

Users that use a C shell (e.g., tcsh), instead add these lines to your .login:

if ( -r /opt/lscsoft/lscsoft-user-env.csh ) then
	source /opt/lscsoft/lscsoft-user-env.csh
endif

On some LSC clusters, these setup scripts are sources at the system level. This is not yet uniform however.

You can selectively disable packages from /opt/lscsoft by creating various files in your home directory as follows:

If ~/.noanything exists, then automatic setup of lscsoft is *disabled*
If ~/.nonothing exists, then automatic setup of lscsoft is *disabled*
If ~/.nolscsoft exists, then automatic setup of lscsoft is *disabled*
If ~/.nolscsoft-libmetaio exists, then /opt/lscsoft/libmetaio is *disabled*
If ~/.nolscsoft-libframe exists, then /opt/lscsoft/libframe is *disabled*
If ~/.nolscsoft-lal exists, then /opt/lscsoft/lal is *disabled*

As more packages become available via the lscsoft yum repository, the user-env script will be updated to provide similar functionality

Debian [ Base URL ]

The LSC data analysis software stack is available for the following Debian distributions

Sarge [ URL ] [ i386 ] [ x86_64 ] still testing...

Administrator Instructions

I - Installation
By default, Debian ships with Apt or Aptitude, instead of Yum (although this can be also installed), so this instructions will use this tool. You must be root to perform this installation (type su and enter the root password). It is recommended that you add the LSCSoft Debian repository to your /etc/apt/sources.list file by adding the following lines:

deb     http://www.lsc-group.phys.uwm.edu/daswg/download/software/debian/dist/sarge/ main contrib non-free
deb-src http://www.lsc-group.phys.uwm.edu/daswg/download/software/debian/dist/sarge/ main contrib non-free

This will give you automated access to the LSCSoft Debian repository.

First install GSL and FFTW3. These software packages are provided by Debian and so are almost certainly available from one of the repositories listed in your /etc/apt/sources.list.

If these packages are already installed on your system, these instructions will upgrade you to the latest versions. You can use either apt-get or aptitude to get the packages, and we'll use the former (as reference) to fetch and install the software:

apt-get update
apt-get install fftw3 fftw3-dev
apt-get install libgsl0 libgsl-dev

Now install the LSC software. If you have added the LSCSoft Debian repository to your /etc/apt/sources.list file, then you can retrieve and install the packges with apt-get:

apt-get install libframe0 libframe-dev libframe-utils
apt-get install libmetaio0 libmetaio-dev

Your installation is now complete. (X)

Other
Some other Debian repositories that LSC users might be interested in adding to their sources.list file are

- ROOT
- Cernlib (source packages are also available) CERNLIB is already available on your local Debian mirror. To download and install the packages, run apt-get install cernlib as root For more info link to Debian_CERNLib

Mac OS X [ Base URL ]

The LSC data analysis software stack has been tested on the following Mac OS X versions

10.4.x (Tiger)

This OS X distribution does not currently include LAL, LALApps, Numarray or Matplotlib.

User Instructions

Download LSC Software Suite The LSCsoft repostiory for Mac OS X is provided as a disk image [Version 1.3 (lscsoft-1.3.dmg) contains Universal Binaries and so it willwork on PowerPC or Intel Macs]. Click on the icon to the left to download the disk image.

Once the image has downloaded, double-click to mount the disk image.

A volume called "LSC Software Suite" should appear on your desktop. Double click to open it.

You should see the following packages contained in the disk image. The package called LSC Software Suite.mpkg is the master package for the lscsoft repository. Double click the LSC Software Suite.mpkg to run the OS X installer.

The first screen of the installer wizard (shown below) contains instruction on how to set up your environment. Copy and paste the relevant lines to either you .profile (for bash users) or your .login (for C shell users).

Click continue and chose select a destination volume to install the software. This should be your startup volume (i.e. the volume that contains your System Folder)

Click install (or upgrade, if you have previously installed the software) to begin the installation process. Type your password when prompted. Once the install is finished, click Close. You do not need to re-boot, but you will need to close and re-open any terminals to get your new enviornment variables.

When you are finished, drag the LSC Software Suite volume to the Trash to unmount it.

$Id: repositories.html,v 1.104 2008/04/28 17:07:08 xavier Exp $

LSC Data Analysis Software Working Groups

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Fedora [ Base URL ]

Centos [ Base URL ]

RedHat [ Base URL ]

Debian [ Base URL ]

Mac OS X [ Base URL ]