Ionut's WebSpace » SciVis

Avogadro: Segmentation fault – solved

ionut — Wed, 20 May 2009 21:17:36 +0000

That’s my first post to the great Planet, so “Hello PlanetSuse!!!”. If you are curios and you would like to know more about me, check my website and you will find many interesting things, my work, my research and so on.

I was running Avogadro on my openSUSE 11.1 box, but I have got a “segmentation fault”. If you have the same problem, in order to solve the issue just update your python-numpy package. That’s all.

If you don’t know what Avogadro is:

“Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.”

and three nice pictures:

Installing Intel Compiler Suite on OpenSUSE 11.1

ionut — Fri, 27 Mar 2009 11:47:15 +0000

Here are the basic steps to install Intel C/C++ and Fortran Compilers on OpenSUSE 11.1:

1. download Intel C/C++ and Fortran Compilers from their website. They are free for non-commercial use
2. unpack and start the installer
3. at some point I received:

Step no: 4 of 7 | Installation configuration - Missing Critical Pre-requisite
--------------------------------------------------------------------------------
The following required for installation commands are missing:
libstdc++.so.5 (library)
--------------------------------------------------------------------------------
1. Finish with prerequisites and back to Critical Pre-requisites dialog
[default]
2. Back to Pre-requisite summary dialog
 
h. Help
b. Back to the previous menu
q. Quit
--------------------------------------------------------------------------------
Please type a selection or press "Enter" to accept default choice [1]:

4. let’s stop the installer and install the necessary packages

vaio:/home/ionut # zypper install libstdc++33
 
vaio:/home/ionut # whereis libstdc++.so.5
libstdc++.so: /usr/lib/libstdc++.so.6 /usr/lib64/libstdc++.so.5 /usr/lib64/libstdc++.so.6
 
vaio:/home/ionut # zypper install libstdc++33-32bit
 
vaio:/home/ionut # zypper install binutils-32bit binutils-devel

5. let’s run again the installer, now we have all packages installed

[...skip...]
Step no: 4 of 7 | Installation configuration - Missing Optional Pre-requisite
--------------------------------------------------------------------------------
There is one or more optional unresolved issues. It is highly recommended to fix
it all before you continue the installation. You can fix it without exiting from
the installation and re-check. Or you can quit from the installation, fix it and
run the installation again.
--------------------------------------------------------------------------------
Missing optional pre-requisite
-- cannot determine operating system type
-- system glibc or kernel version not supported or not detectable
-- binutils version not supported or not detectable
------------------------------------------------------------
1. Skip missing optional pre-requisites [default]
2. Show the detailed info about issue(s)
3. Re-check the pre-requisites
 
h. Help
b. Back to the previous menu
q. Quit
--------------------------------------------------------------------------------
Please type a selection or press "Enter" to accept default choice [1]:

5. accept default choice and press Enter
6. Intel compiler is installed, do the same for the other compiler
7. enjoy

Parallel Programming with MPI in Bristol

ionut — Thu, 26 Mar 2009 21:00:35 +0000

I spent the last 4 days in Bristol to attend to “Parallel Programming with MPI” course, provided by HECToR which is the UK’s high-end computing resource, funded by the Research Councils and available for researchers at UK universities, and by NAG – The Numerical Algorithms Group specialized in the provision of software for the solution of mathematical, statistical and data mining problems.

The course covered the Introduction to MPI and Advanced MPI. MPI (Message Passing Interface) is the de facto standard for parallel programming. I have also some experience with PVM (Parallel Virtual Machine) my Master Thesis was based on that, and I learnt a lot about OpenMP, so I wanted to extend my knowledge for Parallel Programming with MPI.

The course introduced the concepts and terminology of High Performance Computing (HPC). After an detailed look at point-to-point and collective communication, we learnt some more advanced topics: Cartesian topologies, MPI derived data types, user-defined binary operators, groups and communicators. We also had a lot of practical exercises to solve. It was a great course.

High End Computing and Scientific Visualization at NASA

ionut — Mon, 24 Nov 2008 19:47:15 +0000

I found an interesting video. If you have about a hour to spend and if you work in scientific computing, maybe these talks would be useful for you: