31. Update flash -- chrome on debian wheezy/testing 64 bit

You may have had problems playing flash videos recently and have been presented with a message saying that your player is out of date, and that you can either play (just this time) or upgrade. Clicking on upgrade takes you to the adobe website -- downloading the file is easy enough, but then what?

Well, here's how to upgrade.
Download the file install_flash_player_11_linux.x86_64.tar.gz
extract the libflashplayer.so file from the root of the compressed file

Figure out what files to replace:

locate libflashplayer.so
yields
/usr/lib/chromium-browser/plugins/libflashplayer.so
/usr/lib/flashplugin-nonfree/libflashplayer.so

So, in the directory where you put your new libflashplayer.so
sudo cp libflashplayer.so usr/lib/chromium-browser/plugins/libflashplayer.so
and
sudo cp libflashplayer.so /usr/lib/flashplugin-nonfree/libflashplayer.so


Restart your browser, and you should be good to go.

30. "Bench-marking" nwchem with mpich2 on debian wheezy

For various reasons my beowulf has been dismantled and in boxes for most of the year, with only the six-core node seeing use a normal work computer.

Anyhow, here's a very unscientific test of the performance of my six-core (phenom II, 2.8 GHz, 8Gb RAM) running the nwchem code compiled in the previous post.

The speed-tests were performed by starting up mpd
mpd --ncpus=6&
and then executing with
time mpdrun -n x ./nwchem input.nw
where x is an integer signifying the number of cores

The nwchem.nw files I used was

nwchem.nw
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

Here are the results:

(x is number of cores; times in seconds)
x   Run 1   Run 2    Run 3   Run 4   Run 5
1* 40.8     37.9     40.7     40.3      39.9
1   22.2     40.7      40.6    44.8      38.2
2   22.8     22.4     16.3     23.5       21.5
3   14.1     12.3     15.7     15.5       15.1
4   14.5     11.5     12.0     14.9       14.7
5   11.4     11.5     8.9       11.9       12.5
6   16.0     12.2     13.4     9.9        9.6

* No mpd running; executed using time nwchem nwchem.nw



So here's the unscientific part -- the computer is running a full desktop environment with evolution, chrome etc open in the background so that each run sees a slightly different system. I've tried to vary the order in which the runs were made though.

 A guess would be that a longer run would yield more reproducible results. As it is now, the length of the runs vary significantly. The only lesson that can be obtained is that it doesn't help much throwing more cores at a problem as the optimisation times only drop off slowly past a certain point.

Edit: I've run the same file using an almost identical set-up on two more boxes
Don't compare the benchmarks when running at maximum numbers of cpu, since this will be heavily affected by other processes.

Optiplex 990 (Intel i5 2400, 4 cores @ 3.1 GHz, 8 Gb RAM)

x   Run 1   Run 2    Run 3   Run 4   Run 5
1   45.80   46.97  46.56   46.95   39.01
2   22.77  25.81   26.93  26.61   25.81
3   17.18  16.48   18.89  19.26  19.18
4   11.62  16.62   15.82  15.86   16.03

Homebuilt (3 core AMD Athlon 2 X3 @ 3.1 GHz, 4 Gb RAM)

x   Run 1   Run 2    Run 3   Run 4   Run 5   Run 6   Run 7
1   43.74   57.02   40.22   47.89   53.87
2   31.41   22.31   25.83   32.31   33.00
3   36.19   31.01   43.55   24.75   37.82   33.95   27.06

29. Compiling/Building nwchem with mpich on debian testing 64 bit (Wheezy -- 15/12/2011)

So, as seen in the previous post, mpich2 ver 1.4 and nwchem 6.0 don't play nicely together.

Continuing with the virtual machine in the previous post, I added a line referencing the stable version to /etc/apt/sources.list:
deb ftp://ftp.au.debian.org/debian/ stable main contrib non-free

Important: I ADDED that line -- all lines referencing the testing version (or wheezy) are left untouched.
Do
sudo apt-get update
Since the versions in stable are older adding that line won't affect your system.

Now,
apt-cache showpkg mpich2

Under provides it should say:
1.4.1-1+b1
1.2.1.1-5

Now,
sudo apt-get install mpich2=1.2.1.1-5

You'll get a warning that you're about to downgrade, which is what we're trying to do.

sudo apt-get autoremove (will downgrade dependent packages. Just go with it)
aptitude search mpich2
check what's installed and what version
aptitude show libmpich2-dev
If it's 1.4.1 or not installed, make sure to set it to 1.2.1.1-5 just like for mpich2

Run sh myconfig.sh (see here for the script). Seems to build ok. All the mpd tools are where they should be.
NOTE: according to this post mpd isn't needed in newer (>=1.3) versions.

In summary, this seems to be the way to build nwchem on wheezy -- by downgrading the mpich2 and mpich2-dev packages. Since downgrading those packages may affect other packages as well, it may cause problems, but so far so good.

Testing the built binary:
mpd --ncpus=4 &
mptrace -l
mpdrun -n 4 ./nwchem ../../examples/dirdyvtst/h3/h3tr1.nw

All is good

EDIT (16/12/2011):
So, you've installed an older version of a package. apt-get will want to upgrade it, so you should put the packages on 'hold'. Every time you upgrade your system apt-get will warn you that there are packages on hold, so don't worry about forgetting about it

sudo su
echo "mpich2 hold"|dpkg --set-selections
echo "libmpich2-dev hold"|dpkg --set-selections

(taken from http://forums.debian.net/viewtopic.php?f=20&t=71448&start=15)

As an aside, you may want to downgrade gromacs-mpich to use mpich2-1.2 as well:
sudo apt-get install gromacs-mpich=4.0.7-3