/usr/bin/ld cannot find -lf2c for CentOS 5

If you encounter this error "/usr/bin/ld: cannot find -lf2c", you are obviously missing f2c package. Do download the f2c-20031026-3.0.1.el5.x86_64.rpm package found at  f2c-20031026-3.0.1.el5.x86_64.rpm - CentOS 5 (RHEL 5) - ATrpms

# wget http://dl.atrpms.net/el5-x86_64/atrpms/stable/f2c-20031026-3.0.1.el5.x86_64.rpm
# rpm -Uvh f2c-20031026-3.0.1.el5.x86_64.rpm
# ldconfig

Free Full version of ILOG Optimization products via IBM's Academic Initiative Program

Since 15th February 2010, , IBM is offering no-charge full-version ILOG Optimization products via IBM's Academic Initiative Program. The ILOG Optimization provides registered members with renewable one-year access to IBM ILOG OPL-CPLEX, CPLEX, CP Optimizer and CP for both teaching and research use.

Registered members can access and obtain ILOG Optimization software at: https://www.ibm.com/developerworks/university/software/get_software.html, where they can search for ILOG Optimization or individual solvers

To run the software, members will also need to download a key from: https://www.ibm.com/developerworks/university/support/ilog.html, but are no longer required to install ILM. Note that as part of Academic Initiative, IBM also makes its professionally-developed training materials available for use in classrooms and labs at: https://www14.software.ibm.com/webapp/devtool/scholar/web/coursewarePickPage.do?source=ai-course-websphere.

For ILOG support, you can go to IBM Academic Initiative Support for more information

Installing Subversion on Fedora 11

I was installing Subversion on Fedora 11 using the "Subversion from CentOS" taken from CentOS Wiki and the instruction set work without a hitch. Just a few important commands to take note

Importing commands to take note:

1. Initial repository layout for MyTestProject
   # svn import /tmp/mytestproject to file://var/www/svn/repos/mytestproject -m
   
   
2. Checking Out
   $ svn co http://yoursvnserver/repos/mytestproject
   
   
3. Edit and Commit
   $ svn co http://yoursvnserver/repos/mytestproject
   $ svn commit -m "Added a line to testconf1.cfg."
   
   
4. Adding and Commit
   $ svn co http://yoursvnserver/repos/mytestproject
   $ svn add configurations/AnotherTestConf2.cfg
   $ svn commit -m "Added something else"
   
   
5. Deleting
   $ svn co http://yoursvnserver/repos/mytestproject
   $ svn delete configurations/AnotherTestConf2.cfg
   $ svn commit -m "Delete something"
   
   
6. Reverting to Previous Version
   $ svn log http://yoursvnserver/repos/mytestproject
   (You will see a complete list of revision numbers along with the comments)
   $ svn co -r (some number) http://yoursvnserver/repos/mytestproject
   
   
7. To add back files to the current repository
   $ svn copy http://yoursvnserver/repos/mytestproject/oldversionfile@NNN ./oldversionfile (where NNN is the revision number)
   

For more informatio

1. Version Control with Subversion (Free Online Documents and Ebook)
   

Compiling MPI BLACS on CentOS 5

An interesting article from Linux Cluster on Compiling MPI BLACS on CentOS 5. BLACS is compiled with OpenMPI 1.4.x with g77 and gfortran.

For more information see Compiling BLACS on CentOS 5

Compiling LAPACK on CentOS 5

Download the lapack latest stable version (lapack-3.3.0.tgz) from http://www.netlib.org/lapack/

# cd /root
# tar -xzvf lapack-3.3.0.tgz
# cd /root/lapack-3.3.0
# cp make.inc.example make.inc

Assuming Edit make.inc. Assuming the Compiling ATLAS on CentOS 5

#BLASLIB = ../../blas$(PLAT).a
BLASLIB = /usr/local/atlas/lib/libf77blas.a /usr/local/atlas/lib/libatlas.a

Compile lapack package

# make

Copy the libraries to

# mkdir /usr/local/lapack/lib
# cp /root/lapack-3.3.0/*.a /usr/local/lapack/lib
# cd /usr/local/lapack/lib/
# chmod 555 *.a

Other related Information

1. Compiling ATLAS on CentOS 5

Tex4ht for CentOS, Redhat and Fedora

TeX4ht is a highly configurable TeX-based authoring system dedicated mainly to produce hypertext.

To install text4ht, make sure you install the repository from http://centos.karan.org/

#yum install tex4ht (That's it)

Installing lammps using Intel Compilers, OpenMPI and FFTW

This is a entry on how I install LAMMPS using Intel, OpenMPI and FFTW

1. If you are eligible for the Intel Compiler Free Download. Download the Free Non-Commercial Intel Compiler Download
2. Build OpenMPI with Intel Compiler
3. Install FFTW. Remember to install FFTW-2.1.x and not FFTW-3.x or you will face an issue fft3d.h(164): catastrophic error: could not open source file "fftw.h" . Read the LAMMPS "Getting Started" Section for more information
4. When you are ready and about to compile, there are several "Make" selection found at "$SOURCE/lammps-30Mar10/src/MAKE". I chose the makefile.openmpi. Be default you do not need to edit the Makefile.openmpi. But if you are a guru and want to edit the file, feel free to
5. Finally go to the preceding directory by typing
   

   cd .. (ie $SOURCE/lammps-30Mar10/src)
   make openmpi -j (-j for parallel compilation)

6. At the end of the compilation, you should see a lmp_openmpi binary at the src directory. You are almost done
7. Check that the executable are properly linked by doing a
   

   # ldd lmp_openmpi

8. Remember to include /usr/local/lib in the LD_LIBRARY_PATH if libmpi_cxx.so.0 is located at /usr/local/lib

Compiling ATLAS on CentOS 5

This tutorial is to help you compile ATLAS (Automatically Tuned Linear Algebra Software) with gFortran. For those who are using Intel Compiler, you have the reliable Intel MKL (Math Kernel Library)

First thing first, some comparison between ATLAS and MKL.

ATLAS

ATLAS The Automatically Tuned Linear Algebra Software (ATLAS) provides a complete implementation of the BLAS API 3 and a subset of LAPACK 3. A big number of instructions-set specific optimizations are used throughout the library to achieve peak-performance on a wide variety of HW-platforms.

ATLAS provides both C and Fortran interfaces.

ATLAS is available for all HW-platforms capable of running UNIX or UNIX-like operating systems as well as Windows (tm).

MKL

Intel's Math Kernel Library (MKL) implements a set of linear algebra, fast Fourier transforms and vector math functions. It includes LAPACK 3, BLAS 3 and extended BLAS and provides both C and Fortran interfaces.

MKL is available for Windows (tm) and Linux (x86/i686 and above) only.

Download the latest stable package from ATLAS (http://sourceforge.net/projects/math-atlas/files/Stable/). The current stable version is atlas3.8.0.tar.gz. Do note that ATLAS don't like configuration on its original location, hence the need to create ATLAS_BUILD directory.

# cd /root
# tar -xzvf atlas3.8.3.tar.gz
# mkdir /root/ATLAS_BUILD
# cd /root/ATLAS_BUILD
# /root/ATLAS/configure

You will need to turn off CPU Throttling. For CentOS and Fedora, you will use

# /usr/bin/cpufreq-selector -g performance

For more information, you can see my blog entry Switching off CPU Throttling on CentOS or Fedora

Compile ATLAS

make
make check
make ptcheck
make time
make install

By default, ATLAS installed to /usr/local/atlas

Finally remember to add /usr/local/atlas/lib to your LD_LIBRARY_PATH

fft3d.h(164): catastrophic error: could not open source file "fftw.h"

I was compiling LAMMPS Molecular Dynamics Simulator.

1. Using $SOURCE/lammps-30Mar10/src
2. I compiled using make.linux. Quite soon, I encounter the following error fft3d.h(164): catastrophic error: could not open source file "fftw.h"
3. I have compiled my fftw3 and my Intel Math Kernel library properly and was able to locate the header in my Intel Math Kernel Library. I've correctly "source" the path at LD_LIBRARY_PATH and /etc/ld.so.conf.d. But the LAMMPS is still not able to locate the library.
4. I realise the cruz of the problem was that LAMPS requires FFTW-2.1.x. configuring and compiling fftw-2.x, the problem went away

Problem eliminated. My compilation is not done yet. But this fftw initial problem is settle for now :)

Scalpel - Recover lost file

Scalpel is a fast file carver that reads a database of header and footerdefinitions and extracts matching files from a set of image files or rawdevice files. Scalpel is filesystem-independent and will carve files fromFATx, NTFS, ext2/3, or raw partitions. It is useful for both digitalforensics investigation and file recovery

Step 1: Install scalpel
# yum install scalpel

Step 2: Define the file type you wish to recover by uncommenting it.
# vim /etc/scalpel.conf

Step 3: Recover the file
# scalpel /dev/mapper/VolGroup00-LogVol00 -o output

Note:

1. Make sure you do not have a directory output or scalpel will not work.
2. Scalpel search by partition and not directory. So don't specify directory. It simply cannot work
3. to know which partition yo have, type # mount

Article: For more information, see Recover Deleted Files With Scalpel by HowToForge

CPMD consortium

The CPMD code is a parallelized plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.

Compiling Grace: checking for a Motif >= 1002 compatible API... no

When you are compiling source package from Grace, you may encounter error during compiling on CentOS 5.x "checking for a Motif >= 1002 compatible API... no"

To resolve the issues, you will need to install the

# yum install openmotif openmotif-devel

Grace plotting tool for X Window System

Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif. Grace runs on practically any version of Unix-like OS. As well, it has been successfully ported to VMS, OS/2, and Win9*/NT/2000/XP (some minor functionality may be missing, though).

Grace is a descendant of ACE/gr, also known as Xmgr.

The instruction set to install the source can be found in the User Guide

Gnome evine - Document Viewer

Evine is a simple document viewer that support a number of format such as PDF, Postscript, DjVu, DVI, tiff. he goal of evince is to replace the multiple document viewers that exist on the GNOME Desktop with a single simple application.

Evine comes by default when you install GNOME for most Linux Distribution. If evine is not installed by default, just do a
# apt-get install evine (for debian variants) OR
# yum install evine (RH variants)

Amaha Linux Home Server

Amaha Linux Home Server is not a Linux Distro but a collection of software packed as presented with a web-managed console. It sits on top of the version of Fedora 12.

The Amahi Linux Home Server core purpose makes your home networking simple. According to the Project website, it has a number of features that

1. Audio Streaming with the Amahi Tunes, a customised Firefly Media Server.
2. VPN using preconfigured OpenVPN
3. Networking including DNS, Web Servers and NAS Server
4. File Sharing
5. Hardware monitoring
6. Amaha Private Wiki
7. Backup to a network share
8. Vista Calendar Integration 
9. Outlook Integration
10. ICal Integration
11. For more information, do look at Amahi Feature Gallery

Before you install Amahi Linux Home Server, you have to install Fedora 12 and add the Amahi repository in. Use the web-based console to configure the services you need.

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

Sage - an Open Source Mathematics Software System

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.

Additional Documentation:

1. Sage Tutorial
2. Sage Installation Guide
3. Sage FAQ
4. Download for Linux

UNIX Binary Gaussian 09 Revision A.02 Installation instructions

Taken and modified from the README.BIN for my environment. This deserve hightlight for adminstrators to setup it quickly.

1. Check that you have the correct versions of the OS, and libraries for your machine, as listed in the website G09 platform list
2. Select or create a group (e.g. g09) which will own the Gaussian files inside the /etc/group. Users who will run Gaussian should either already be in this group, or should have this added to their list of groups.
3. Create a Directory to place g09 and gv (For example gaussian). You can do it by using a command
   

   mkdir gaussian

4. Mount the Gaussian CD  using commands like this one
   

   mount /mnt/cdrom 

5. Within the CD, you can copy the gaussian binary contents (E64_930N.TGZ) out into your newly created gaussian directory.
6. Untar it by using the command
   

   tar -zxvf E64_930N.TGZ

7. Change ownership for the newly created g09 directory from step 6.
   

   chgrp -Rv g09 g09

8. Install
   

   cd g09
   ./bsd/install

9. Set the environment for users login
   

   touch .login

   Place the below contents into the .login
   

   g09root=/usr/local/gaussian/ 
   GAUSS_SCRDIR=/scratch/$USER
   export g09root GAUSS_SCRDIR
   . $g09root/g09/bsd/g09.profile

10. Put it in your .bash_profile
    

    source .login

Manual setup of TCP LINDA for Gaussian
To configure for TCP Linda for Gaussian to run Parallel on Nodes, all you need is to tweak the ntsnet and LindaLauncher file found at g09 directory. For TCP Linda to work in Gaussian, just make sure the LINDA_PATH is correct.

1. ntsnet is found $g09root/ntsnet (where $g09root = /usr/local/gaussian/g09 in my installation)
2. LindaLauncher is found in $g09root/linda8.2/opteron-linux/bin/LindaLauncher (where $g09root = /usr/local/gaussian/g09 in my installation)
3. flc is found at $g09root/opteron-linux/bin/flc
4. pmbuild is found at $g09root/opteron-linux/bin/pmbuild
5. vntsnet is found at $g09root/opteron-linux/bin/vntsnet

LINDA_PATH=/usr/local/gaussian/g09/linda8.2/opteron-linux/

Auto-Install for Gaussian. This can also be found at Gaussian Installation Notes

# cd /usr/local/gaussian/g09
# ./bsd/install

Put the .tsnet.config in your home directory.

# touch .tsnet.config

Tsnet.Appl.nodelist: n01 n02
Tsnet.Appl.verbose: True
Tsnet.Appl.veryverbose: True
Tsnet.Node.lindarsharg: ssh
Tsnet.Appl.useglobalconfig: True

Smokescreen - Flash.... without plugin

What on earth is Smokescreen?
Smokescreen is a new open-source project aimed at converting Flash to JavaScript/HTML5 to run on devices that does not support adobe flash....

Smokescreen will soon be released for free under an open source license. So look out for more information.
Yes, do look at the Smokescreen Demo

Scientific Software for Python - Numpy, scipy, pyMPI

NumPy is the fundamental package needed for scientific computing with Python. It contains among other things:

SciPy  is open-source software for mathematics, science, and engineering. It is also the name of a very popular conference on scientific programming with Python. The SciPy library depends on NumPy, which provides convenient and fast N-dimensional array manipulation. The SciPy library is built to work with NumPy arrays, and provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization.

pyMPI is a project integrating the Message Passing Interface (MPI) into the Python interpreter.