Bug in Gaussian 09 revision A.02

There is a bug in Gaussian09 revision A.02, which makes the single electron integral very slow, sometimes even fail. Our scientist has verified this. To solve this issue, Upgrade to Gaussian 09 to B.01.

Encountering State Initializing after installing Voltaire Drivers

First thing first,

For more information on downloading the appropriate Voltaire Drivers, see blog entry Download Voltaire OFED Drivers for CentOS. After you have downloaded the appropriate and install Voltaire Drivers, you may encounter something like:

CA 'mlx4_0'
        CA type: MT26428
        Number of ports: 1
        Firmware version: 2.6.0
        Hardware version: a0
        Node GUID: 0x0008f1476328oaf0
        System image GUID: 0x0008fd6478a5af3
        Port 1:
                State: Initializing
                Physical state: LinkUp
                Rate: 40
                Base lid: 2
                LMC: 0
                SM lid: 14
                Capability mask: 0x0251086a
                Port GUID: 0x0008f103467a5af1

It is due to the Subnet Manager (opensm) not being installed. Voltaire OFED Installation package installed only the OpenIB Packages. Even if you have install the opensm before installing the Voltaire OFED Package, the Voltaire OFED Package will uninstall the existing opensm packages to ensure openib packages are fully compatible.

To install the Opensm packages nicely, do read on the blog entry Installing Voltaire QDR Infiniband Drivers for CentOS 5.4

Other good reasing materials:

1. RHEL and Infiniband - basic diagnostics

Installing Voltaire QDR Infiniband Drivers for CentOS 5.4

This blog writeup Installing Voltaire QDR Infiniband Drivers for CentOS 5.4 (linuxcluster.wordpress.com) is on how you can

1. Download the drivers from the Voltaire Website
2. Install the Infiniband Drivers
3. Install the Subnet Manager - opensmd
4. Test the State is "Active"
5. Connectivity Test between Server and Client

For more information, on Voltaire Infiniband installation, do read on

1. Voltaire OFED 1.5 User Manual
2. Infiniband HOWTO by Guy Coates

Download Voltaire OFED Drivers for CentOS

Here is the FTP site for downloading Voltaire OFED Drivers Listing. The latest drivers for CentOS is for CentOS 5.4
http://www.voltaire.com/ftp/versions/current/Software/Server_Products/VoltaireOFED-Linux/1.5/

BashGuide Wiki

BashGuide Wiki by Greg is an excellent material for beginner. According to the wiki which is still work-in-progress

This guide aims to become a starting point for people interested in learning to work with BASH. It aspires to teach its readers good practice techniques for developing scripts for the BASH interpreter, and to educate them about the internal operation of BASH......

To read it.

Making Disc Images using mkisofs

I've got this tip from Linux Format Edition 137. Very useful indeed.

mkisofs is a wonderful utility to generate ISO images. To generate a compatible ISO images on a disc which are readable everywhere, consider the following commands

$ mkisofs -rdlJ -o disc_directory_image.iso directory/

1. -r : "Rock Ridge" format is enabled to allow long filenames on UNIX systems
2. -J : allow long filenames on Windows Systems
3. -l : Allow full 31-character filenames.
4. -d : Do not append a period to files that do not have one which violate ISO9660

Using Yum Provides

This is a continuation of Using Yum effectively (Part 1) and Using Yum effectively (Part 2)

I have learned a cool command line "yum provides". "yum provides" help you search for the packages that will install either a file or directory. For example

# yum provides bash

bash-3.2-24.el5.x86_64 : The GNU Bourne Again shell (bash) version 3.2
Repo : base
Matched from:

bash-3.2-24.el5.x86_64 : The GNU Bourne Again shell (bash) version 3.1.
Repo : installed
Matched from:
Other : Provides-match: bash

Linux Advice Site

Unix and Linux is a collaboratively edited question and answer site for people who love Unix and Linux. No registration is required. Quite an interesting site especially when the site stack have 95% of questions answered

CPLEX Installation with Python on CentOS

Following up on this blog entry Free Full version of ILOG Optimization products via IBM's Academic Initiative Program

1. After getting the necessary software and license from IBM Academic Initiative, you should install the CPLEX binary

# ./cplex_studio122.acad.linux-x86.bin

2. For the license file, make use your license file name is "access.ilm" (without the quotation)

3. Create a folder to house the license. CPLEX needs this folder to be present

# mkdir -p /usr/ilog/ilm
# mv access.ilm /usr/ilog/ilm

4. You should be able to run your CPLEX now. To verify, go to the CPLEX binary folder and run it. In my case

# /usr/local/cplex_studio_122/cplex/bin/x86-64_sles10.4.1/cplex

5. To install the Python API of CPLEX, do read up on IBM iLOG Optimization Studio Documentation

# cd /usr/local/cplex_studio_122/cplex/python/x86-64_sles10_4.1/
# python setup.py install --home ./cplex/

You will need to add the path to your PYTHONPATH by running

export PYTHONPATH=$PYTHONPATH:/usr/local/cplex_studio_v12/cplex/python/x86-64_sles10_4.1

ChameleonOS Alpha Changeable Skins for Linux

ChameleonOS is a light-weight linux operating system with changeable skins that mimics other Operating Systems including MS and Mac-OS X. ChameleonOS is based on Unity Linux RC2.

Quite neat.

Changing a Partition Label on Linux

If you need to re-label a partition, you can use the command e2label

Firstly to display the label of a partition

# e2label /dev/sda1

To change the label of a partition

# e2label /dev/sda1 data

Remember to update the partition label at /etc/fstab file

Loading Mod_Python on Apache 2.x on CentOS 4.x and CentOS 5.x

Loading Python on Apache is easy. The material is taken from Mod Python ArchLinux Wiki

Configure Apache

# vim /etc/httpd/conf/httpd.conf

LoadModule python_module modules/mod_python.so

Restart Apache

# service restart httpd

Test Mod_Python
1. Add this block to /etc/httpd/conf/httpd.conf

<Directory /home/www/html> 
   AddHandler mod_python .py
   PythonHandler mod_python.publisher 
   PythonDebug On 
</Directory>

2. Create a file in /home/www/html/ called mptest.py and add this as contents

from mod_python import apache
def handler(req):
req.content_type = 'text/plain'
req.send_http_header()
req.write("Hello World!")
return apache.OK

Restart Apache again

# service restart httpd

Navigate to http://www.yoursite.com/mphandler.py/handler and you should see a site that says
Hello World!

Unzipping file with bz2 extension

If you encounter files that is compressed with bz2 only, use the following commands

$ bunzip2 file.bz2

If however, you encounter files that is compressed with .tar.bz2, use the following commands

$ tar -xvjpf file.bz2

Installing HandBrake on Fedora 13

Handbrake is an open-source, GPL-licensed, multiplatform, multithreaded video transcoder, available for MacOS X, Linux and Windows.

Installation is straight-forward and much of this material is taken from Compiling HandBrake on Linux

Install the following packages

# yum groupinstall "Development Tools" "Development Libraries" \
"X Software Development" "GNOME Software Development"

# yum install yasm zlib-devel bzip2-devel \
dbus-glib-devel libgudev1-devel webkitgtk-devel libnotify-devel \
gstreamer-devel gstreamer-plugins-base-devel

More Information

1. HandBrake Wiki
2. HandBrake Wiki FAQs
3. HandBrake Site

Another Useful DVD-Backup or DVD-ripping tool is Thoggen. For more information, see Installing Thoggen on Fedora 11