Installing Devede on Fedora 11

DeVeDe is a program to create video DVDs and CDs (VCD, sVCD or CVD), suitables for home players, from any number of video files, in any of the formats supported by Mplayer. The big advantage over other utilites is that it only needs Mplayer, Mencoder, DVDAuthor, VCDImager and MKisofs (well, and Python, PyGTK and PyGlade), so its dependencies are really small.

To install devede on Fedora 11, first you have to install RPM Fusion. For more information on RPM Fusion installation, see Blog Entry RPM Fusion Repository. Remember to do a "yum check-update" after you have install the repository

Step 1: Install devede

# yum install devede

Step 2: Launch devede

$ devede

Step 2: Explore the options. Some of the key features are

• Selection of Video output format (PAL, NTSC)
• Customised Menu Title Background, Music, Font
• Video Output size in relations to Video Medium
• Can burn to ISO or MPEG
• etc

SSH Error : Permission denied (publickey, gssapi-with-mic,password)

One of our Linux accounts was having this issue with SSH

"Permission denied (publickey,gssapi-with-mic,password)"

One obvious symptoms of this problem is that it was possible to SSH in from external machine, but was unable SSH out of the problematic machine

To resolve this issue, you have to go to

$ cd /home/youruserid/.ssh/
$ vim config

Change the configuration to

BatchMode no

The option BatchMode specifies whether a username and password querying on connect will be disabled. This option is useful when you create scripts and dont want to supply the password. e.g. Scripts that use the scp command to make backups over the network.

For more information on SSH configuration, see

• 15.3. Configure the /etc/ssh/ssh_config file

See also

1. Unspecified GSS failure from SSH causes slow login 
2. Resolving Slow SSH Login

libimf.so: warning: warning: feupdateenv is not implemented and will always fail

After you have compiled OpenMPI with the Intel Compilers, as
and when execuing mpirun on your program, you enconter "libimf.so: warning: warning: feupdateenv is not implemented and will always fail"

$ mpicc hello.c -o hello
libimf.so: warning: warning: feupdateenv is not implemented and will always fail

This resolution to the issue can be found at OpenMPI FAQ to resolve this issue, you have to include the

$ mpicc hello.c -o hello -shared-intel

The default behavior of Open MPI's wrapper compilers can be changed to automatically include this -shared-intel flag so that it is unnecessary to specify it on the command line when linking MPI applications.

RCSB Protein Database Bank

RCSB Protein Database Bank is a Resource for Studying Biological Macromolecules. The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies.

The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.

Pupil - Program for User Package Interface and Linking

PUPIL,Program for User Package Interface and Linking, is a software environment,- the program,- to allow developers to quickly and efficiently link together multiple pieces of software,- the user packages,- that have been and are actively being developed by researchers.

With its current 1.3 version, it is able to

• Graphic User Interface to build the main simulation input file.
• Simulation Manager to lead the multi-scale simulation between different Calculation Units.
• Interface with Amber v10
• Interface with DLPOLY v2.18
• Interface with Gaussian03
• Interface with deMon2k
• Interface with NWChem
• Interface with Siesta v2.0 (Start/Stop and CycleQM behaviors)
• Interface with mndo97 (Start/Stop QM role behaviors)
• stubMD. Stub program for interface sample and testing playing a Molecular Dynamics Calculation Unit role.
• stubQM. Stub program for interface sample and testing, playing a Cycle Quantum Mechanics Calculation Unit role.
• stubDI. Stub program for interface sample and testing, playing an external Domain Identifier Calculation Unit role.