Ionut's WebSpace » SciComputing

Supercomputers #9 and #24

ionut — Sun, 14 Nov 2010 21:21:22 +0000

TOP500 list of the world’s most powerful supercomputers is here. In the first place is Tianhe hosted by National Supercomputing Center in Tianjin, China. I am glad to see that the supercomputers which I use every day for my simulations are #9 (Jugene) and #24 (Juropa). As you probably know, they are hosted by Forschungszentrum Juelich, Germany, where I am working.

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

My USB Memory Stick Companion

ionut — Thu, 26 Mar 2009 21:53:06 +0000

I have a Kingston Data Traveler 4 GB USB Drive, and a few days ago I decided to use it also as a rescue boot device (to be bootable in order to recover data when needed), as storage device (to move around some files, used on windows, mac, linux, freebsd), to have on it some personal files which I would like to be encrypted (for example: my ssh private keys, my bookmarks, my passwords, …), but also to have with me some applications which I use day by day (firefox, thunderbird, keypass, …).

So here is what I did:

As filesystem I used Fat32. I installed System RescueCD so I have a bootable linux distro with a lot of useful utilities like Partimage, GNU Parted, TestDisk, kernel for i386 and also for x86-64, … The instructions to install it on fat32 filesystem are here: Installation On USB Memory Stick, I used “Instalation from Windows” part.

Next step was to install Truecrypt for windows in portable mode, a step by step guide how to do it, is available here, to be able to open my encrypted volume.

Now I can create an encrypted volume, using truecrypt, where we store all my personal files, let’s say 2 giga.

In that encrypted volume I also installed PortableApps Suite and beeing a LaTeX user I also included USBTeX.

Ok, now I still have space to store some useful small iso images, like Clonezilla, Hiren Boot CD, Acronis True Image BootCD.

That’s my setup for USB Memory Stick, I have it with me all the time, I can use it on any system, mac, windows, linux, I have a bootable linux disto on it, and also my personal files encrypted with some useful software. Maybe I should mention that Portable Apps Suite works well also with wine on linux.

I did a dd copy of my complete usb stick configuration/setup, immediately after I finished to install everything I needed, because if I will lose it, then to be able to recover everything quickly.

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.

Eclipse Updates/Plugins on OpenSUSE 11.1

ionut — Wed, 18 Mar 2009 10:17:09 +0000

I have just installed Eclipse on OpenSUSE 11.1 from repository, but after that I could not install any plugins, the message has been:

Some people suggest that you have to remove the installed version from repo and download the latest version from eclipse website. I didn’t want to do that, so, If you have the same problem then try the following:

Go to Windows->Preferences, click the arrow by General and select Capabilities. Check the box labeled Classic Update. That should solve the problem and now you can add your preferred plugins.

That’s all!

Using LaTeX in Scribus for posters

ionut — Wed, 03 Dec 2008 20:13:16 +0000

I am using LaTeX and beamer class to make presentations and posters. A short introduction to start with latex is available. Sometimes I am using LaTeX just to produce eps/pdf text boxes and after that Scribus for poster layout. In the last development version of Scribus, which is 1.3.5svn, there is possible to use latex source/expressions directly in document, so is not necessary anymore the aditional step to create eps/pdf text boxes.

For OpenSUSE there is the last version here:
http://software.opensuse.org/ymp/home:mrdocs/openSUSE_11.0/scribus.ymp

but I don’t want to replace 1.3.3.12 stable version, so I will install the latest development version in my home directory

Warning: The documents saved in 1.3.5 will not be back compatible with the other versions, more here: http://scribus.info/svn/Scribus/trunk/Scribus/README

Let’s install the last development of Scribus (it is very stable for what I need, I didn’t have any problems with it):

$ mkdir ~/aplic/scribus_135
$ mkdir ~/tempsrc
$ cd ~/tempsrc
$ svn co svn://scribus.info/Scribus/trunk/Scribus
$ cd Scribus
$ cmake -DCMAKE_INSTALL_PREFIX:PATH=~/aplic/scribus_135

I obtained an error during the compilation because I didn’t have “libqt4-devel” so:

1	$ zypper install libqt4-devel

1
2
3

$ make
$ make install
$ ~/aplic/scribus_135/bin/scribus

Here are two screenshots, the main window and scribus latex editor:

That’s all.

References:

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:

Software I am using …

ionut — Fri, 14 Nov 2008 23:57:30 +0000

If you would like to see what software I am using on my desktop, laptop, workstation (Windows, Linux, Unix) in order to get my research/scientific work done, or if you want to know what software I am installing on my servers for customers, check this section of my website.

Scientific Software

ionut — Fri, 14 Nov 2008 15:41:13 +0000

If you are working in Scientific Computing, like me, then the next links are for you: