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

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 :)

CPMD consortium

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

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

Advancing the Power of Visualization.

This is an interview by HPwire with Steve Briggs, HPCD’s SVA product marketing manager on Visualisation from HP point of view. Interesting information

Advancing the Power of Visualization –Coming Soon to Linux Clusters: 100 Million Pixels and More