GROMACS with Intel compilers

Thanks to craigb I managed to compile GROMACS 4.0 using intel compilers.

In a simple test run GROMACS with intel compilers was atleast 33% faster than GNU compilers. IT CAN SAVE YOU 1/3rd OF YOUR TIME!!


Download and install intel compilers and math kernel libraries from Intel.
Note down your version numbers and change it where ever necessary.

Download gromacs and unzip/untar it.

Here is the step-by-step procedure I followed for installation:

1) Make changes at two place in the "configure" file

Alter
LIBS="-lmkl $LIBS"
to
LIBS="-lmkl_intel -lmkl_sequential -lmkl_core $LIBS"


2) Add the following to the ~/.bashrc file

export LD_LIBRARY_PATH="/opt/intel/mkl/10.0.4.023/lib/32"



3) To install GROMACS: (install dir is /usr/local/gromacs)

./configure CC="icc" CPPFLAGS="-I/opt/intel/mkl/10.0.4.023/include" LDFLAGS="-L/opt/intel/mkl/10.0.4.023/lib/32" --with-fft=mkl

make

make install


4) To enable mpi with mdrun: ("mdrun_mpi" will be installed)

make clean

./configure CC="icc" CPPFLAGS="-I/opt/intel/mkl/10.0.4.023/include" LDFLAGS="-L/opt/intel/mkl/10.0.4.023/lib/32" --with-fft=mkl --enable-mpi --program-suffix="_mpi"

make mdrun

make install-mdrun


5) To install GROMACS with double-precession and enable mpi: (install dir is /usr/local/gromacs_d)

make clean

./configure CC="icc" CPPFLAGS="-I/opt/intel/mkl/10.0.4.023/include" LDFLAGS="-L/opt/intel/mkl/10.0.4.023/lib/32" --with-fft=mkl --enable-mpi --program-suffix="_d" --prefix=/usr/local/gromacs_d

make

make install

Gnome-do: For keyboard lovers

Gnome-do is a fantastic software which will be equally appreciated by command line-ers and GUI users. It can be addictive and will make life so much easier with a variety of plug-ins. With a simple and elegant look it can search a file from any corner in your drive or play your favorite music in matter of seconds at a few keyboard strokes (not at the click of you mouse - which will be slower!!!)

Try it Today!

Linux Mint: A beautiful distro

Linux Mint is a spin-off of Debian linux and is probably the best distro for a linux newbie. It has all the features of Ubuntu and more. As I read somewhere Linux Mint is 97% Ubuntu, but that 3% extra makes it better. It comes with a very elegant Gnome theme compared to the dull brownish Ubuntu theme.

Notably it comes with "giver", which is a great way to share files and folders within a network (specially between room-mates!) without using a memory stick. If you haven't tried "giver", I highly recommend it (even for fedora and debian users)

If you are trying to convince anyone to use linux instead of Windows or Mac, Linux Mint is your answer...It will make the transition much easier than you might expect.

Configuring Tamu VPN in Linux

First step is to install vpnc.

Install “vpnc” through apt (ubuntu, debian) or yum (fedora, redhat) or manually.

example: yum install vpnc (fedora)

apt-get install vpnc (ubuntu, debian)

1) Command line option:

To run TAMU vpn through command line is very very simple. Just run vpnc:

$ vpnc

This will prompt you a series of questions:

Enter IPSec gateway address: vpn-master.tamu.edu

Enter IPSec ID for vpn-master.tamu.edu: tamu

Enter IPSec secret for tamu@vpn-master.tamu.edu : tamuvpn

Enter username for vpn-master.tamu.edu: (your neo-id)

Enter password for @vpn-master.tamu.edu: (your neo-password)

Thats it! You are done...

You can store this as a configuration file and load it as: $ vpnc tamu.conf

example configuration file tamu.conf:

IPSec gateway vpn-master.tamu.edu
IPSec ID tamu
IPSec secret tamuvpn
Xauth username
Xauth password

To disconnect vpn type command: vpnc-disconnect

2) GUI Option:

Requirement: You need NetworkManager running in your system.

STEPS:

Open your network configuration and choose VPN menu:

Click on Add menu and create new VPN connection:

Add the required details as shown in the figure and create the new VPN setting:

Fill in your neo ID and password at the required places. And click OK.

Now a new VPN connection should appear on your NetworkManager icon in your desktop

when you left-click on the icon. Click on it and enjoy TAMU-VPN.