Thursday, September 30, 2010

Configuring SSH to use Protocol 2 or SSHv2 in CentOS

To disable SSHv1 or SSH Protocol 1, do the following:

Check for Protocol configuration
# cat /etc/ssh/sshd_config |grep Protocol

Ensure that you should get only Protocol 2
Protocol 2

If not, Edit the /etc/ssh/sshd_config to reflect only Protocol 2
# vim /etc/ssh/sshd_config
Search for the word Protocol and make the necessary changes.

Restart OpeenSSH Server
# service sshd restart

Tuesday, September 28, 2010

Unable to clear the offline mode for Compute node using pbsnodes command

If you try to make a node online after you deliberately off-line the node perhaps for some repair work and unable to online again. Instead on your Torque Server,  you see errors such as these

PBS_Server: LOG_ERROR::is_request, bad attempt to connect from (address not trusted - check entry in server_priv/nodes

As the log says, there is some issue in the server_priv configuration. If all your nodes are working well except that, you should take a look at the client settings. Maybe your server_priv has the wrong configration.

Once you have cleared the error, just fire off the command
# pbsnodes -c node_name

Monday, September 27, 2010

Donate unused Computer Cycles to World Community Grid

You can join the World Community Grid (WCG) and donate your unused computer cycles and support innovative humanitarian research being conducted all over the world. WCG is a community of over 600,000 people and 1.4 million machines and is the world's largest, free, volunteer super-computer dedicated solely to addressing global medical and scientific issues.

Free Technical Resources at IBM Student Portal

No-charge technical resources are available for students at IBM Student Portal. You can access software downloads and eBooks to learn about leading technologies.

Sunday, September 26, 2010

Installing lapack, blas and atlas on CentOS 5

Installing lapack, blas and atlas on CentOS 5.4 is very simple.Firstly you must enable the follow repositories:

  1. atlas package - EPEL (For more information on how to download EPEL, see Red Hat Enterprise Linux / CentOS Linux Enable EPEL Repository
  2. blas and lapack packages - RPMForge (For more information on how to download RPMForge, See Install RPMForge
Installing atlas, blas and lapack x86_64 packages
# yum install atlas.x86_64 blas.x86_64 lapack.x86_64

Saturday, September 25, 2010

Installing GNU Compilers for CentOS 4.x

If you are installing GNU compilers from yum for CentOS 4.x, here is the yum command to achieve it

GNU Compilers for 3.x (C, C++, Fortran 77, Java)
# yum install gcc, gcc-c++, gcc-g77, gcc-java

GNU Compilers for 4.x (C, C++, Fortran 77, Java)
# yum install gcc4, gcc4-c++, gcc4-gfortran, gcc4-java
#yum install gcc4*

Thursday, September 23, 2010

Resolving Warning Remote Identification has changed!

If you encounter the following error, this can be easily resolve....


Someone could be eavesdropping on you right now (man-in-the-middle attack)!
It is also possible that the RSA host key has just been changed.
The fingerprint for the RSA key sent by the remote host is
Please contact your system administrator.
Add correct host key in /root/.ssh/known_hosts to get rid of this message.
Offending key in /root/.ssh/known_hosts:6
Password authentication is disabled to avoid man-in-the-middle attacks.
Keyboard-interactive authentication is disabled to avoid man-in-the-middle attacks.
Permission denied (publickey,gssapi-with-mic,password).

You can do a quick fix. In my case, I just simply edit the known_hosts file
# vim /root/.ssh/known_hosts
Search for the remote host that is having the issue. In this case (
Delete the "offending" line
Save the file known_hosts


Managing F5 LTM TCP Profile Idle Timeout Settings

For those running Remote Desktop Protocol and facing idle timeout problems, may want to take a look at the Article "Investigating the LTM TCP Profile: Max Syn Retransmissions & Idle Timeout". The default 300 seconds is good enough for most application, but for applications with long-lived connections like remote desktop protocol, the settings should be tweaked to a larger figures or configure to "indefinite"

Wednesday, September 22, 2010

Unable to update glibc for CentOS 4.x

I was trying to update glibc package on my old CentOS 4.x Server, but I seem to encounter errors such as these and unable to

Error: Unable to satisfy dependencies
Error: Package glibc-devel needs glibc = 2.3.4-2.43.el4_8.2, this is not available.
Error: Package glibc-devel needs glibc-headers = 2.3.4-2.43.el4_8.2, this is not available.

To allow the smooth update of glibc package first,
# yum remove glibc-devel glibc-headers glibc-kernheaders

Then finally update the glibc packages
# yum install glibc*

I've got the materials for this blog entry from Bug 6018 - Missing dependency in glibc packages yum not updating

Tuesday, September 21, 2010

Hangs at "UEFI platform initialization" for IBM BladeCenter HS22

Taken from IBM  at "UEFI platform initialization" after backflash - IBM BladeCenter HS22"

After a series of reset and reboot, one of my HS22 suffered a hang at UEFI platform initialization and cannot boot into the OS. Looked around for solution.

After flashing blade Unified Extensible Firmware Interface (UEFI) from version 1.07 (build 46A) to any earlier version, the blade hangs in Power On Self Test (POST) during the next reboot. The following message is displayed at the top of the screen "UEFI Platform Initialization"

Immediate Workaround:
If the blade is in the hung condition, then it can be recovered by removing the system board battery to reset the blade settings to default.

Complete the following steps:
  1. Remove the blade from the chassis.
  2. Remove the system board battery.
  3. Wait 30 seconds and reinstall the battery.
  4. Reinstall the blade and power on.
  5. Last but not least, please take a good look at the BIOS and reconfigure your BIOS serttings if necessary.

Download the fixes patches from IBM Fix Central Site

Have tried it work...

Monday, September 20, 2010

Mount an ISO File in Linux

You do not need to burn an ISO file into a CD before you can use it for its intended purposes. A simple command like this can allow you to see and execute the content in the ISO file

$ mount -o loop -t iso9660 myISO.iso /mnt/mount/point

Sunday, September 19, 2010

Uninstalling Nouveau driver and Installing NVIDIA Drivers on Fedora 13

I was trying to install the proprietary NVIDIA Driver for my workstation with Fedora 13, but was unable to install due to the presence of Nouveau Driver which Fedora installed by default and this installation by Fedora caused a conflict with the intended installation of NVIDIA Driver

Source for this information is derived from a Forum

Step 1: Blacklist Nouveau Driver
# vim /etc/modprobe.d/blacklist.conf
Add the below line to the end of /etc/modprobe.d/blacklist.conf
blacklist nouveau

Step 2: Edit /boot/grub/grub.conf and add the following to the end of the kernel line
rdblacklist=nouveau vga=31B
Replace 31B with the desired mode:
1600x1200 - 346
1280x1024 - 31B
1400x1050 - 348
1024x768 - 318
800x600 - 315

For example:
kernel /vmlinuz- ro 
root=/dev/mapper/vg_kittycool-lv_root rd_LVM_LV=vg_kittycool/lv_root rd_LVM_LV=vg_kittycool/lv_swap 
rd_NO_LUKS rd_NO_MD rd_NO_DM 
LANG=en_US.UTF-8 SYSFONT=latarcyrheb-sun16 
KEYBOARDTYPE=pc KEYTABLE=us rhgb quiet rdblacklist=nouveau vga=31B

Step 3: Download and Install NVIDIA Drivers
# chmod 755

# ./

# reboot

Monday, September 13, 2010

Chelsio iWARP Installation and Setup Guide for CentOS 5.4

Most of this material for this blog entry is taken the documentation Guide named Chelsio iWARP installation and setup guide (pdf) . The Blog Entry ”Chelsio iWARP Installation and Setup Guide for CentOS 5.4” (Linux Cluster) is an modification from a user’s perspective of the original document from Chelsio.

Sunday, September 12, 2010

Chelsio iWARP Drivers compatibility with Chelsio Linux drivers

The documentation is extracted from Chelsio iWARP Installation and Setup Guide and is formatted on my blog  Chelsio iWARP Drivers compatibility with Chelsio Linux drivers (Linux Cluster)

Here is a listing for the latest OFED to the latest Chelsio Drivers and Firmware

OFED Package Cxgb3toe-W.X.YY.ZZZ driver Firmware Supported/Not Supported/Not Tested
OFED-1.5.1 Cxgb3toe- 7.10.0 Not Supported
OFED-1.5.1 Cxgb3toe- 7.8.0 Supported
OFED-1.5.1 Cxgb3toe- 7.4.0 Not Supported

Wednesday, September 8, 2010

Installing Chelsio T3 10GE Driver on CentOS 5.4

Here the documentation on installing Chelsio Chelsio T3 10GE Driver on CentOS 5.4 (x86-64). For more information, see Installing Chelsio 10GE Driver on CentOS 5.4

Tuesday, September 7, 2010

Chelsio OEM-IBM Download

If you are using Chelsio OEM Driver for IBM Blade, X and P series, do go to  Chelsio OEM-IBM Download

The download page has some interesting articles
  1. Chelsio Cards & Cables Compatibility:-CX4 Adapters  
  2. IBM Redbooks
    Chelsio 10GbE Adapters for IBM System Cluster 1350 and IBM iDataPlex
    Chelsio 10 GbE Adapters for IBM Power Systems
  3. Chelsio Adapters driver Download, Installation, Configuration, troubleshooting, support  
  4. IBM iDataplex and Cluster 1350 - Drivers, Firmware and Software (Red Hat 5.3   
  5. IBM Announcement Letter
  6. IBM system Cluster 1350 Information Center

Monday, September 6, 2010

Weka - Data Mining Software in Java

What is Weka?
Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization.
To download and install Weka, see Download and installing Weka

Saturday, September 4, 2010

Installing Sage From Source

Sage is a free open-source mathematics software system licensed under the GPL. It combines the power of many existing open-source packages into a common Python-based interface.
Software Prerequisites:
  1. gcc 4.x and above
  2. g++
  3. gfortran
  4. make
  5. m4
  6. perl
  7. ranlib
  8. tar
  9. readline and its development headers
  10. ssh-keygen -- needed to run the notebook in secure mode.
  11. latex -- highly recommended, though not strictly required

OS and hardware Prerequisites:
  1. 2 GB of free disk space 
  2. Linux (32 bits or 64-bits or IA64 or 32-bit PPC or MAC OS X) 

Steps to install Sage:
# tar xvf sage-x.y.z.tar
# cd sage-x.y.z
# make
# ./sage

Finally add the directory of SAGE to your Path Directory
export PATH=$PATH:/usr/local/sage-x.y.z/

For more detailed information on installation of SAGE, do look at the Steps to Install from Source

Thursday, September 2, 2010

Multi Configuration Time Dependent Hartree (MCTDH)

Multi Configuration Time Dependent Hartree (MCTDH). MCTDH is a general algorithm to solve the time-dependent Schrödinger equation for multidimensional dynamical systems consisting of distinguishable particles. MCTDH can thus determine the quantal motion of the nuclei of a molecular system evolving on one or several coupled electronic potential energy surfaces. MCTDH by its very nature is an approximate method. However, it can be made as accurate as any competing method, but its numerical efficiency deteriorates with growing accuracy.
Do note that for interested researchers, the MCTDH package is distributed on request to interested researchers. If you want to work with MCTDH, please send an e-mail to Hans-Dieter.Meyer at

The User and Developer Manuals are comprehensive. In particular, the Installation and Compilation straightforward with steps to guide you along....

Wednesday, September 1, 2010

Deploying the MIT Photonic-Bands (MPB) package

The MIT Photonic-Bands (MPB) package is a free program for computing the band structures (dispersion relations) and electromagnetic modes of periodic dielectric structures, on both serial and parallel computers.

MPB Information:
  1. MPB Download Page
  2. MPB Installation Guide

Software Requisites:
  1. Basic linear Algebra Subroutines (BLAS). For more information on BLAS installation, see the Section on BLAS
  2. Linear Algebra PACKage (LAPACK). For more information see the Section on LAPACK
  3. FFTW For more information see my Blog Entry Installing FFTW
  4. HDF (Hierarchical Data Format)
  5. GNU Guile. Guile is a library designed to help programmers create flexible applications. Using Guile in an application allows programmers to write plug-ins, or modules
  6. libctl is a free Guile-based library implementing flexible control files for scientific simulations. 
Sample Installation of prerequisites using F77 - GNU Fortran:
# f77=gfortran CFLAGS="-I/usr/local/fftw-mpi-2.1.5/gnu/include -I/usr/local/hdf5-1.8.5/gnu/include" 
CPPFLAGS="-I/usr/local/fftw-mpi-2.1.5/gnu/include -I/usr/local/hdf5-1.8.5/gnu/include -DH5_USE_16_API=1" 
LDFLAGS="-L/usr/local/fftw-mpi-2.1.5/gnu/lib -L/usr/local/hdf5-1.8.5/gnu/lib"

Finally the Installtion of MIT PB, for our installation, we use some of the settings
# ./configure --prefix=/usr/local/mpb-1.4.2 --with-mpi