Sunday, January 29, 2017

Parallel Debugging with a Serial Debugger

Parallel Debuggers are important tools when trying to eliminate bugs in parallel programs. Commercial parallel debuggers are expensive.
In this blog post I will show you a free and open source alternative which is good enough for education purposes and for small codes.
Suppose you want to debug the famous cpi.c code which computes an approximation to pi by a parallel numerical integration. This demo uses the free Data Display Debugger (ddd) which is based on gdb but has a nice GUI.

Step 1, compile:
mpicc -g -o cpi ./cpi.c

Step 2, run (without a debugger):
mpirun -np 2 ./cpi

Step 3, run with the free Data Display Debugger (ddd):
mpirun -np 2 ddd ./cpi

The last command will open two MPI processes (instances) of ddd each running cpi,
see screen capture:

Finally, I enclose here a short video which I hope is convincing:

hi-res version:

Happy (Free) MPI debugging!

Saturday, September 03, 2016

OpenFOAM in a container

OpenFOAM up and running in 5 minutes!

Get the instructions and the container from 

MYLAPTOP> ~/Downloads/startOpenFoam+

non-network local connections being added to access control list of_v1606_plus
bash-4.1$ echo 'now I am inside the container'

now I am inside the container

bash-4.1$ cd /home/telzur/OpenFOAM/telzur-v1606+/run/cavity/cavity

That's it!

Monday, December 28, 2015

Subversion installation problem in Linux Mint 17.3

sudo apt-get install subversion
[sudo] password for telzur:
Reading package lists... Done
Building dependency tree      
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 subversion : Depends: libsvn1 (= 1.8.8-1ubuntu3.2) but it is not going to be installed
              Depends: libapr1 (>= 1.4.8-2~) but it is not installable
              Depends: libaprutil1 (>= 1.2.7+dfsg) but it is not installable
E: Unable to correct problems, you have held broken packages.

Any ideas...?

Wednesday, April 09, 2014

Scientific Python versus Matlab: Geographical differences in interest

Scientific Python versus Matlab: Geographical differences in interest  according to Google trends.

Scientific Python:


Do you think what I think?

Saturday, September 07, 2013

Ubuntu / Mint software updates problems

If you get error messages of the following kind:

"E: Encountered a section with no Package: header...."

Do the following:

sudo rm /var/lib/apt/lists/* -vf
sudo apt-get update

It worked for me!

Saturday, July 06, 2013

Gnome3 packagekit problem

if you are in a situation where you want to install software using packagekit but nothing happens or you see a message that it is "waiting in queue" forever try the following which worked for me:

Open terminal as root and type:

pkcon refresh


this will let yum complete it's unfinished business and then packagekit will get back to life.

Good luck

Saturday, June 22, 2013

Supercomputing breakthroughs are correlated with the Sun activity

If you want to predict major breakthroughs in Supercomputing look at the sun.
It is well accepted by now that every 11 years there is a 3 orders of magnitude mile stone in supercomputers. However, about 11 years is also the cycle of the Sun activity when counting for example the number of sunspots.
Surprisingly enough whenever there is a deep in the sunspots count a major supercomputing milestone takes place.
The chart below says it all

The Wisdom behind Small Data Mining