November 13, 2012 by kittycool

Compiling and Installing GAP System for Computational Discrete Algebra

GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory. GAP provides a programming language, a library of thousands of functions implementing algebraic algorithms written in the GAP language as well as large data libraries of algebraic The objects.

The information is taken from Compilation

Step 1: Download the GAP Software

Download the GAP Software at http://www.gap-system.org/Releases/index.html Current version at point of writing is 4.5.6

# tar -zxvf gap4r5p6_2012_11_04-18_46.tar.gz

# cd gap4r5p6

Step 2: Configure and Install (Default Installation)

#./configure

# make

Step 3: Optional Installation – GMP packages.
If you wish to use the GAP internal GMP Packges, then the version of GMP bundled with this GAP will be used. This is the default.

# ./configure --with-gmp=yes|no|system|"path"

Step 4: Optional Installation – Readline Editing for better command-line Editing.
If the argument you supply is yes, then GAP will look in standard locations for a Readline installed on your system. Or you can specify a path to a Readline installation.

# ./configure --with-readline=yes|no|"path"

For more information,
See INSTALL when you unpacked the GAP.

November 8, 2012 by kittycool

Installing and Configuring Environment Modules on CentOS 6

This tutorial is very similar to Installing and Configuring Environment Modules on CentOS 5 and the steps are very similar for CentOS 6 except that the tcl/tk 8.5.x used in CentOS repository does not have tclConfig.sh which is needed when you compile the Modules packages. I used 8.4.x which is similar to the version used in the CentOS 5 repository. You can use more more updated version of tcl

Step 1: Download the modules packages

Download the latest modules packages from Modules Sourceforge Project Site.

Step 2. Download the tcl/tk package from tcl/tk download site

# tar -zxvf tcl8.4.19-src.tar.gz

# cd tcl8.4.19/unix

Step 2a. Compile the tcl package

# ./configure --prefix=/usr/local/tcl --enable-threads

# make && make install

Step 2b. Compile the tk package

# tar -zxvf tk8.4.19-src.tar.gz

# cd tk8.4.19

# ./configure --prefix=/usr/local/tk --with-tcl=/usr/local/tcl/lib

# make && make install

Make sure you put the tcl library in the /etc/ld.so.conf.d

# vim /etc/ld.so.conf.d/tclx-x86_64.conf

/usr/local/tcl/lib
/usr/local/tk/lib

Do a ldconfig to update dynamic linker run-time bindings

# /sbin/ldconfig

Step 3: Unpacked, Configure and Install

# tar -zxvf modules-3.2.9c.tar.gz

Go to the Modules folder ($ModuleHome)

# cd modules-3.2.9

I wanted to keep all my individual modules files at /usr/local/Modules/contents. You can keep module files anywhere you wish to keep.

# ./configure --with-module-path=/usr/local/Modules/contents

Make and install the configuration

# make && make install

Step 4: Amend .modulefiles

Edit . modules to let Modules know where all the customized module files will be kept

# vim /usr/local/Modules/3.2.9/init/.modulespath

Comment out all the lines except the directory where all the customised modules files will be kept.

.....
.....
/usr/local/Modules/contents                             # General module files
.....
.....

Step 5: Update /etc/profile.d of the Servers

Copy the profile.modules from the $ModuleHome Directory

# cp /$ModuleHome/modules-3.2.9/etc/global/profile.modules /etc/profile.d/modules.sh

The content of modules.sh are as followed

#----------------------------------------------------------------------#
# system-wide profile.modules                                          #
# Initialize modules for all sh-derivative shells                      #
#----------------------------------------------------------------------#
trap "" 1 2 3

case "$0" in
-bash|bash|*/bash) . /usr/local/Modules/default/init/bash ;;
-ksh|ksh|*/ksh) . /usr/local/Modules/default/init/ksh ;;
-zsh|zsh|*/zsh) . /usr/local/Modules/default/init/zsh ;;
*) . /usr/local/Modules/default/init/sh ;; # sh and default for scripts
esac

trap 1 2 3

Create a softlink at /usr/local/Modules

# cd /usr/local/Modules
# ln -s 3.2.9 default

Sample Installation of an application using Modules (Intel Compilers)

Step 1: Create a Module File.

Place the Module File for Intel in /usr/local/Modules/contents

a. Create an Intel Folder inside /usr/local/Modules/contents

# mkdir /usr/local/Modules/contents/intel

b. Create a module file for the version of Intel (In my case, “12.0.2″). To save some time, you can copy a “sample” file and you can edit

# cp $ModuleHome/modules-3.2.9/modulefiles/modulefile /usr/local/Modules/contents/intel/12.0.2

# vim /usr/local/Modules/contents/intel/12.0.2

#%Module1.0
proc ModulesHelp { } {
global version prefix

puts stderr "\tIntel XE 12.0.2 (icc, icpc, ifort)"
}

module-whatis   "Intel XE 12.0.2 (icc, icpc, ifort)"

prepend-path    PATH            /opt/intel/composerxe/bin
prepend-path    LIBRARY_PATH    /opt/intel/composerxe/lib/intel64
prepend-path    LD_LIBRARY_PATH /opt/intel/composerxe/lib/intel64:/opt/intel/mkl/10.2.6.038/lib/em64t
prepend-path    MANPATH         /opt/intel/composerxe/man
prepend-path    MKL_HOME        /opt/intel/mkl/10.2.6.038

setenv CC       icc
setenv CXX      icpc
setenv FC       ifort
setenv F77      ifort
setenv F90      ifort

Step 2: Setting the Default versions of Intel.

If you have different version of software you wish to present to the users, do the following

# vim /usr/local/Modules/contents/intel/.version

#%Module1.0
set ModuleVersion "12.0.2"

More Information

Part 2 – Usage of Environment Modules on CentOS and in Cluster

November 6, 2012 by kittycool

Usage of Environment Modules on CentOS and in Cluster

This is the 2nd part of “Installing and Configuring Environment Modules on CentOS 5”

1. List the Modules on System

# module avail

--------------------------- /usr/local/Modules/contents ----------------------------
R/R-2.15.1            intel/12.0.2(default) matlab/R2011b

2. Load the Modules on System

# module load intel/12.0.2

Checking the version

# icc -v
Version 12.0.2

3. Unload the Modules on System

# module unload  intel/12.0.2

November 5, 2012 by kittycool

Installing and Configuring Environment Modules on CentOS 5

What is User Environment Modules?

Taken from Environment Modules Project

The Environment Modules package provides for the dynamic modification of a user’s environment via modulefiles.

Each modulefile contains the information needed to configure the shell for an application. Once the Modules package is initialized, the environment can be modified on a per-module basis using the module command which interprets modulefiles. Typically modulefiles instruct the module command to alter or set shell environment variables such as PATH, MANPATH, etc. modulefiles may be shared by many users on a system and users may have their own collection to supplement or replace the shared modulefiles.