45. Compiling gromacs with mpich2 ver 1.2 on debian testing

If you are using mpich2 1.2.1.1-5 -- read the ** comment. Otherwise don't worry.
** In my example I've used mpich2 ver 1.2.1.1-5 -- install mpich2 and libmpich2-dev version 1.2.1.1-5 according to http://verahill.blogspot.com/2012/01/debian-testing-64-wheezy-nwhchem.html -- do everything in between "Edit these two files.." and "exit" if you want the same system as I've used. **

Start here:
This is basically a condensed and annotated version of http://www.gromacs.org/Downloads/Installation_Instructions

Have a look at
http://www.gromacs.org/Downloads
to see what file to download

Also, you may want to do
sudo apt-get install build-essential gfortran fftw3

Next, use the console:

mkdir ~/tmp
cd ~/tmp

wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz

tar -xvf gromacs-4.5.5.tar.gz

aptitude search fftw
I have libfftw3-3 so I'll pull libfftw3-dev
sudo apt-get install libfftw3-dev

cd gromacs-4.5.5/

create buildconf.sh and put the following in it to build four different versions of gromacs L
(without mpi and single precision, with mpi and single precision (_mpi), without mpi and double precision (_dd), with mpi and double precision (_ddmpi)).
Change N in make -jN to equal the number of cores+1, in my case six cores => N=7, so -j7.
##########################
./configure --with-fft=fftw3
make -j7
sudo make install
 ./configure --with-fft=fftw3 --enable-mpi --program-suffix=_mpi 
make -j7 mdrun
sudo make install

make distclean

./configure --with-fft=fftw3 --disable-float --program-suffix=_dd
make -j7
sudo make install
 ./configure --with-fft=fftw3 --enable-mpi --disable-float --program-suffix=_ddmpi 
make -j7 mdrun
sudo make install

##########################

Then run

sh buildconf.sh

Next, in ~/.bashrc put

PATH=$PATH:/usr/local/gromacs/bin

or, to install for everyone, put the above line in /etc/profile (and then do source /etc/profile)

Then run
source ~/.bashrc

You can download a test set from http://www.gromacs.org/Downloads/Test-Set
Currently the newest one is ftp://ftp.gromacs.org/pub/tests/gmxtest-4.0.4.tgz

Or using git, if you have that installed:
git clone git://git.gromacs.org/regressiontests.git

44. Apt-cache server on LAN on debian

Apt-caching allows you to share updates between different computers and, what is more important, allows you to update a machine that is not directly connected to the internet, but which can access a computer which is.

I've added almost nothing new to this post: http://ubuntuforums.org/showthread.php?t=564301

Ergo, all glory to 'coolen'. My only contribution, and a very small one at that, is showing a solution for a system, with a switch rather than a router.

Anyway, here's my reproduction of the prescribed method. I've changed almost nothing. The main purposes for reproducing the approach here are 1) so that I can remember it myself and 2) so that other people get independent verification that the method does indeed work.

The server ip address in the example is set to 192.168.1.2.

On server:
sudo apt-get install apt-cacher-ng
sudo vim /etc/services (or sudo nano, gksu gedit etc.)

(I had a whole lot of stuff in my /etc/services)

Add
apt-cacher   3142/tcp    #apt-cacher-ng service
apt-cacher   3142/udp   #apt-cacher-ng service

'coolen' adds AUTOSTART=1 to /etc/default/apt-cacher-ng
As far as I understand that's not necessary.

sudo /etc/init.d/apt-cacher-ng start

Make sure that your firewall is not blocking connections to port 3142 (e.g. configure gufw).

On client:

With ROUTER
To turn on:
sudo vim /etc/apt/apt.conf.d/01proxy
Acquire::http::Proxy "http://192.168.1.2:3142";

Do sudo apt-get update and you're done


(If you want to go back to the default repos, turn off  by changing to
Aquire::http::Proxy "http://";)


With SWITCH
(I basically looked at https://help.ubuntu.com/community/Apt-Cacher-Server)

sudo vim /etc/apt/sources.list

If your sources.list file currently looks like this:
deb ftp://ftp.au.debian.org/debian/ testing main contrib non-free
deb ftp://ftp.au.debian.org/debian/ stable main contrib non-free
deb ftp://ftp.au.debian.org/debian/ unstable main contrib non-free

change it so that it looks like this:

deb http://192.168.1.2:3142/ftp.au.debian.org/debian/ testing main contrib non-free
deb http://192.168.1.2:3142/ftp.au.debian.org/debian/ stable main contrib non-free
deb http://192.168.1.2:3142/ftp.au.debian.org/debian/ unstable main contrib non-free

Do sudo apt-get update and you're done.

43. nwchem revisited. Install on new debian machine

Here's a streamlined version of compiling and setting up nwchem with mpich2 support on a virgin debian testing (wheezy) 64 bit computer. I'm working on a build guide for nwchem 6.1 -- currently it builds fine but all jobs end with a Segmentation Violation error and exits with status 11.

Start by running
sudo apt-get install build-essential  gfortran
Edit these two files (the preferences one will most likely not exist)
/etc/apt/sources.list

deb ftp://ftp.au.debian.org/debian/ testing main contrib non-free
deb ftp://ftp.au.debian.org/debian/ stable main contrib non-free
deb ftp://ftp.au.debian.org/debian/ unstable main contrib non-free

/etc/apt/preferences

 Package: *
Pin: release a=testing
Pin-Priority: 990

Package: *
Pin: release a=unstable
Pin-Priority: -10

Package: *
Pin: release a=stable
Pin-Priority: 10

IMPORTANT: the pin-priority for stable must be positive (here +10), or it won't work.

Run
sudo apt-get install mpich2=1.2.1.1-5 libmpich2-dev=1.2.1.1-5

Set the Pin-priority to -10 for stable again.

sudo su
echo "mpich2 hold"|dpkg --set-selections
echo "libmpich2-dev hold"|dpkg --set-selections
mkdir ~/nwchem
cd ~/nwchem
touch buildconf.sh
chmod +x buildconf.sh

(EDIT 21/02/2012: I accidentally put a bad csh-formatted buildconf.sh file at the beginning. Then I put an incomplete bash version. It should work now.)

In buildconf.sh put
export LARGE_FILES=TRUE
export TCGRSH=/usr/local/bin/ssh
export NWCHEM_TOP=/home/myhome/nwchem/nwchem-6.0
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES=all
export USE_MPI=y
export USE_MPIF=y
export MPI_LOC=/usr
export MPI_INCLUDE=$MPI_LOC/include/mpich2

cd $NWCHEM_TOP/src
make clean
make nwchem_config
make FC=gfortran

Then download the source code for nwchem

wget http://www.nwchem-sw.org/images/Nwchem-6.0.tar.gz
tar -xvf Nwchem-6.0.tar.gz

To start building:
./buildconf.sh

Once it's built:
echo "PATH=$PATH:/home/myname/nwchem/nwchem-6.0/bin/LINUX64" >> ~/.bashrc
source ~/.bashrc

Prepare mpd
echo "MPD_SECRETWORD=jibberjabber" >> ~/.mpd.conf
chmod 600 ~/.mpd.conf
mpd --ncpus=3 &

Prepare for a test-run
touch nwchem.nw
Put the following in the nwchem.nw file:

start benzene 

geometry units angstroms
C  0.100  1.396  0.000
C  1.209  0.698  0.000
C  1.209 -0.698  0.000
C  0.000 -1.396  0.000
C -1.209 -0.698  0.000
C -1.209  0.698  0.000
H  0.000  2.479  0.000
H  2.147  1.240  0.000
H  2.147 -1.240  0.000
H  0.000 -2.479  0.000
H -2.147 -1.240  0.000
H -2.147  1.240  0.000
end
basis
 H library sto-3g
 c library sto-3g
end
dft
    xc b3lyp
end
task dft optimize

Launch the job:
mpdrun -n 2 nwchem nwchem.nw

And you should be ready to go

Edit: 12/02/2012 It looks like version of nwchem currently in SID is built with mpi support: http://packages.debian.org/sid/nwchem . I haven't checked it out.