Wednesday, March 31, 2010

Installing gcc4 on CentOS 4 from the command line

This is a very simple entry today. I wanted to install gcc 4.x on CentOS 4. But whenever you do a yum install gcc, it gets gcc 3.4.6. Of course, I try yum install gcc4 and was not able to get the package either. I manage to get it only when I
yum install gcc*

Encountering LimitRequestBody and memory_limit for Gallery

When you are uploading file, you may encounter this error:
"You may need to set LimitRequestBody 16777216 and memory_limit = 64M in /etc/php.ini and /etc/httpd/conf.d/php.conf on your Gallery server"

To solve the issue, change the /etc/php.ini file to
vim /etc/php.ini
upload_max_filesize = 128M 

Edit the following as well for /etc/httpd/conf.d/php.conf
vim /etc/httpd/conf.d/php.conf
<Files *.php> SetOutputFilter PHP SetInputFilter PHP LimitRequestBody 33554432 </Files>

Monday, March 29, 2010

Force Rebooting Remotely without corrupting the file system

Must thanks to Gavin W. Burris for his interesing blog Remotely Force a Reboot which hightlighted Magic SysRq as a cool tool to force a reboot remotely.

Step 1: To enable SysRq key
# echo 1 > /proc/sys/kernel/sysrq

Step 2: Power cycle the machine
echo b > /proc/sysrq-trigger

For more information, read Wikipedia Magic SysRq

Testing for Saturated Network for NFS

How do we test for saturated network for NFS. Is there a systematic way of doing it? You can read my Linux Cluster blog entry Testing for Saturated Network for NFS

Saturday, March 27, 2010

Multi-core Strategies: MPI and OpenMP

Multi-core Strategies: MPI and OpenMP is an interesting article on MPI and OpenMP from

Friday, March 26, 2010

LAMMPS Molecular Dynamics Simulator

LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

It is a very fast MD simulator which is comparable with other packages like Gromacs and Amber

Thursday, March 25, 2010

Finding information about a program or application

Using Command Line find
To find general information about a program or application, you can use file. For example, if you use
file /usr/bin/mplayer

You will get
/usr/bin/mplayer: ELF 32-bit LSB executable, 
Intel 80386, version 1 (SYSV), 
dynamically linked (uses shared libs), 
for GNU/Linux 2.6.18, stripped
This information tells us on the platform, whether dyanmics are used and for which kernel

Use the Command ldd
If you wish to retrieve all the dynamic linked libraries associated with the program vim, you can type
ldd /usr/bin/vim

You will get the libraries that vim requires => (0x006cf000) => /lib/ (0x00a61000) => /lib/ (0x06fdb000) => /lib/ (0x06a09000) => /usr/lib/ (0x00df8000) => /usr/lib/perl5/5.10.0/i386-linux-thread-multi/CORE/libperl

Tuesday, March 23, 2010

Encountering "This account is locked due too much wrong login attempts" from Gallery

If you are using Gallery,

"This account is locked due too much wrong login attempts. Wait for automatic unlock"

To remove the error, just remove the file "logins.dat" from the albums folder, all logged login attempts will deleted.

Monday, March 22, 2010

Using Torque to launch Interactive Session

Some simple uses of Torque commands

To launch an Interactive session asking for 4 nodes with 8 cores each
$ qsub -N demo -I -l nodes=4:ppn=8,walltime=01:00:00 scriptfile
  • -I:  Interactive Session
  • nodes: Server
  • ppn: Cores
To launch Interactive X11 Session
$ qsub -I -X -l nodes=4:ppn=8,walltime:01:00:00 scriptfile
If you are using windows as your client and you wish to display X11 on your windows, do look at
using Putty, X11 to forward X11

Wednesday, March 17, 2010

Global Data Center Authorithy - The Uptime Institute

The Uptime Institute is a thought leadership in term of Data Center Operation and for Data Centre Professional. A important site for Data Center Manager and Professional

Tuesday, March 16, 2010

Eject DVD-ROM using the command line

Sometimes, if you have a lot of computers in the Data Center and if you forgot or have not to label the server, one of the easiest method is firing the eject command from the command line
eject -v
eject -h (for help)

Monday, March 15, 2010

Using root account on Debian 5.x

I know this is really basic. Most of you can even type with your eyes close. But being a Redhat/Fedora enthusasist for seveal years, stepping into Debian take a bit of adjustment....One simple is how do I sudo a root especially since by default Debian disable the root account.

It is that simple.
# sudo -s

Saturday, March 13, 2010

Friday, March 12, 2010

Installing Gallery 1.5 on CentOS 5 and Apache

Gallery is a open source web based photo album organizer. Gallery gives you an intuitive way to blend photo management seamlessly into your own website whether you're running a small personal site or a large community site.

There are coexistence for 2 version of Gallery. Gallery 1.x and Gallery 2.x One question you may ask is why 2 versions. For more information on the 2 version comparison, do take a look G1-G2 Comparison from Gallery
This blog entry will focus on the Gallery 1.5 which uses File Metadata Storage. This documentation is a modification of the original documentation Gallery1:Installation on a Unix/Linux Server with Shell Access
Step 1: Change your current working directory to the directory where you want to install Gallery, and download the Gallery tarball

cd /var/html/www 

Step 2: Change to your fresh gallery directory
cd gallery 

Step 3: Create two blank files, .htaccess and config.php, and chmod them 0666
touch .htaccess
touch config.php
chmod 0666 .htaccess config.php 

Step 4: Assuming you are saving the album in the home directory of user named "photo" /home/photo
cd /home/photo/public_html 
mkdir albums
chmod 0777 albums
cd /home
chmod 711 /home/photo

Create a softlink from /var/www/html/albums to /home/photo/public_html/albums
cd /var/www/html/
ln -s /home/photo/public_html/albums albums

Step 5: Configure Apache
vim /etc/httpd/conf/httpd.conf
Type the following in httpd.conf
Restart Apache
Service httpd restart

Step 6: Install the latest version of jhead
You have to enable your EPEL repository to get the latest jhead 2.87
yum install jhead

Step 7: Launch the Gallery web-based configuration......
http://yourwebsite/gallery/setup and follow through...

Your Gallery should be up and running in no-time

Encountering Yum error in CentOS 5.x - Traceback (most recent call last) : File "/usr/bin/yum", line 28, in ?

After I have installed CentOS 5.4, and do a yum update, I encountered an error
Traceback (most recent call last) :
     File "/usr/bin/yum", line 28, in ?
     import yummain
ImportError: No module named yummain

I tried doing yum clean all, but the error came up even for this command. To solve the issue, I've used rpm and re-install yum-3.2.22-20.el5.centos.noarch.rpm from the CentOS 5.4 DVD again and the problem ceased.
rpm -Uvh yum-3.2.22-20.el5.centos.noarch.rpm

On another note, there were some solution on Google suggesting to install yum-complete-transaction. Now that was quite painful. I did a yum install yum-complete-transaction. But it actually  meant a

yum install yum-utils

Thursday, March 11, 2010

Installing Linux Mint 8 Universal Edition on HP 2133

Installing Linux Mint 8 was a breeze on HP 2133 (WXGA). According to Linux blogs, HP 2133 has propriety Via Chrome 9 graphic controller which causes a lot of issues of getting the graphics to display properly for earlier version of Ubuntu or Linux Mint.

But with Linux Mint 8, the installation was very smooth. The only minor issue was that the Broadcom Wifi has to be installed via the "Hardware Drivers" found in the control panel.  Choose the "Broadcom STA wireless driver" and your HP 2133 will be up with no time.

Linux Mint 8 works flawlessly with mobile broadband such as the Huawei E220.

My favorite desktop OS with my favourite netbook.....

Tuesday, March 9, 2010

Compiling other compilers with OpenMPI

To compile Intel Compiler with OpenMPI, see blog entry Building OpenMPI with Intel Compiler (Ver 2)

For more information on compiling with other compilers: see FAQ No 65 "Open MPI seems to default to building with the GNU compiler set. Can I use other compilers?"

In summary, the 4 switches on the configure command line are used to specify the compiler suite:

•CC: Specifies the C compiler
•CXX: Specifies the C++ compiler
•F77: Specifies the Fortran 77 compiler
•FC: Specifies the Fortran 90 compiler

For Portland Group Compiler,
# Portland compilers 
# ./configure CC=pgcc CXX=pgCC F77=pgf77 FC=pgf90

For Pathscale Compilers
# Pathscale compilers
# ./configure CC=pathcc CXX=pathCC F77=pathf90 FC=pathf90

For Sun Compilers
# Sun compilers
# ./configure CC=cc CXX=CC F77=f77 FC=f90

Note: The Open MPI team recommends using a single compiler suite whenever possible. Unexpeced or undefined behavior can occur when you mix compiler suites in unsupported ways (e.g., mixing Fortran 77 and Fortran 90 compilers between different compiler suites is almost guaranteed not to work).

Monday, March 8, 2010

MAUI: Cannot send request to server ...... (server may not be running)

ERROR: cannot send request to server ................42559 (server may not be running)
ERROR: cannot request service (status)

A few assumptions for this blog entry. You are using Torque and MAUI only for the resource manager and scheduler respectively.

Several things to check.
  1. Make sure your /etc/hostname reflect the correct entries for all the head and compute nodes
  2. For the Torque configuration, do follow the configuration seen in the blog entry Setting up Torque Server on xCAT 2.x. Pay particular attendtion to Step 2 and 3
  3. For the MAUI configuration, do follow the configuration seen in the blog entry MAUI Installation in xCAT 2.x
  4. Check the logs for MAUI at /usr/local/maui/log
After following Pointer 1-4, you are still unable to solve, you can get some hints if you can go to
# cd /opt/maui/sbin/
and type
In my particular situation, I encounter server must be started on host '' (currently on 'xxx') which is my short-name. I resolve it quickly by going to /usr/local/maui/maui.cfg and edit the

Sunday, March 7, 2010

Directory index forbidden by Options directive error for when displaying nagios

When you are unable to display the Nagios web after installation but encounter "Directory index forbidden by Options directive: .........." error. You need to set Apache to serve the file when the directory is requested.

To resolve the problem above. Go to
# vim /etc/httpd/conf/httpd.conf

Type the following into http.conf and restart apache and nagios

# service htpd restart
# service nagios restart

Friday, March 5, 2010

forrtl: severe (24): end-of-file during read & forrtl

forrtl: severe (24): end-of-file during read & forrtl: severe (67): input statement requires too much data....Read this forum entry for more information.

Solving error while loading shared libraries:

If you encontered this error "error while loading shared libraries: cannot open shared object file: No such file or directory".

This is due to missing /usr/local/lib files which are not accessible by the compute nodes. After you have made the libraries available, you may have to add /usr/local/lib to your LD_LIBRARY_PATH environment

You should be able to eliminate the error.

Thursday, March 4, 2010

Green Data Center and Structural Cabling by IBM

YouTube Training from IBM done at Ngee Ann Polytechnic
  1. Green Data Centre Overview
  2. Green Data Centre Containment Design Structural Cabling
  3. IBM Scalable Modular Data Center (SMDC)

Using Yum to install Nagios 3 for CentOS 5.4

I was trying to install Nagios 3.x for CentOS 5.4 but only nagios 2.x is surface. You must make sure you install the right repositories for CentOS to get nagios 3.x. To install Nagios 3.x, you will need to install RPMForge first. If you install EPEL only, you might only get nagios 2.x

Tuesday, March 2, 2010

Force fsck on the next reboot

fsck is used for checking and repairing Linux file system. To force a fsck after a reboot, do the following
# shutdown -rF now
(where F - Force fsck on reboot)

Monday, March 1, 2010

ClearOS - A Linux Server alterntive for Small and Medium Size Enterprise

ClearOS from Cloud Foundation is a powerful network and gateway server designed for small organizations and distributed environments.It is based on CentOS Linux

It has a wide arrays of applications that really helps the Small and Medium Enterprises. Some of the features taken from the ClearOS are listed here.

1. Directory Features
  • Integrated LDAP for User and Group Management
  • User Security Certificate Manager

2. Network Features
  • Multi-WAN
  • VPN - PPTP, IPsec, OpenVPN
  • DMZ and 1-to-1 NAT
  • Stateful Firewall
  • Local DHCP and DNS Servers
3. Gateway Features
  • Antimalware - Antivirus, Antiphishing, Antispyware
  • Antispam
  • Bandwidth Management
  • Intrusion Protection, Intrusion Prevention, Intrusion Detection
  • Protocol Filtering including Peer-to-Peer Detection
  • Content Filter
  • Web Proxy
  • Access Control
4. Server Features
  • Windows Networking with PDC Support
  • File and Print Services
  • Flexshares
  • Groupware with Outlook Connector
  • Mail Server - POP, IMAP, SMTP, Webmail, Retrieval
  • Mail Filtering - Antispam, Antimalware, Greylisting, Quarantine
  • Mail Archiving
  • Database with MySQL
  • Web Server with PHP Support