Rocks 5.4.2 – Ganglia’s gmond Python module for monitoring NVIDIA GPU

Disclaimer

The instructions/steps given below worked for me (and Michigan Technological University) running Rocks 5.4.2 (with CentOS 5.5) – as has been a common practice for several years now, a full version of Operating System was installed. These instructions may very well work for you (or your institution), on Rocks-like or other linux clusters. Please note that if you decide to use these instructions on your machine, you are doing so entirely at your very own discretion and that neither this site, sgowtham.com, nor its author (or Michigan Technological University) is responsible for any/all damage – intellectual and/or otherwise.

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CUDA/C – Hello, World!

Disclaimer

The instructions/steps/programs given below worked for me (and Michigan Technological University) running site licensed Red Hat Enterprise Linux 6.2, with NVIDIA CUDA SDK 4.1.28, NVIDIA GPU Driver v290.10 & two NVIDIA GeForce GTX 570 cards – as has been a common practice for several years now, a full version of Operating System was installed and all necessary patches/upgrades have been applied. These instructions may very well work for you (or your institution), on Red Hat-like or other linux distributions. Please note that if you decide to use these instructions on your machine, you are doing so entirely at your very own discretion and that neither this site, sgowtham.com, nor its author (or Michigan Technological University) is responsible for any/all damage – intellectual and/or otherwise.

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RHEL 6.2 – Ganglia’s gmond Python module for monitoring NVIDIA GPU

Disclaimer

The instructions/steps given below worked for me (and Michigan Technological University) running site licensed Red Hat Enterprise Linux 6.2 – as has been a common practice for several years now, a full version of Operating System was installed and all necessary patches/upgrades have been applied. These instructions may very well work for you (or your institution), on Red Hat-like or other linux distributions. Please note that if you decide to use these instructions on your machine, you are doing so entirely at your very own discretion and that neither this site, sgowtham.com, nor its author (or Michigan Technological University) is responsible for any/all damage – intellectual and/or otherwise.

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BASH – vasp2xyz, a script to extract coordinates from VASP

Users of VASP are often familiar with the struggles/hardships to easily visualize the coordinates from the output file OUTCAR. To that effect, I wrote the following script … with help at a crucial stage from Pat Krogel, Center for Experimental Computation at Michigan Technological University. It requires the OUTCAR and POSCAR files from a VASP simulation to be in the same folder and when successfully completed, it generates in OUTPUT_FILENAME.xyz – containing frame-by-frame XYZ coordinate information corresponding to each (optimization) step.

The script is part of a GitHub repository.

BASH – Wrappers For qstat In NPACI ROCKS 5.2.2

What is ROCKS?

Rocks Cluster Distribution (originally called NPACI Rocks) is a Linux distribution intended for high-performance computing clusters. It was started by NPACI and the SDSC in 2000, and was initially funded in part by an NSF grant (2000-2007) but is currently funded by the followup NSF grant. Rocks was initially based on the Red Hat Linux distribution, however modern versions of Rocks are now based on CentOS, with a modified Anaconda installer that simplifies mass installation onto many computers. Rocks includes many tools (such as MPI) which are not part of CentOS but are integral components that make a group of computers into a cluster. Installations can be customized with additional software packages at install-time by using special user-supplied CDs (called Roll CDs). The Rolls extend the system by integrating seamlessly and automatically into the management and packaging mechanisms used by base software, greatly simplifying installation and configuration of large numbers of computers. Over a dozen Rolls have been created, including the SGE roll, the Condor roll, the Lustre roll, the Java roll, and the ganglia roll.

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PHP – Computing Total Travel Distance From GPS Tracks

Amongst other things, I like to keep a detailed track of where I have been [especially during hiking in the woods, venturing into areas that I have never been before, etc.]. For this purpose, I have configured my Garmin GPSMap 60CSx to record location/date-time data every three seconds and a while ago, I described another API I wrote to store these track points in MySQL. Added advantage of this, as I have mentioned before in previous posts, is that it can be used for geotagging my photographs. For completeness sake, the MySQL table structure that holds track data is given below:

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PHP – Calculating Distance Between Two Locations Given Their GPS Coordinates

Amongst other things, I have the habit of geotagging my photographs and for this purpose, I use my Garmin GPSMap 60CSx, an API I wrote to store tracks in MySQL & Geonames data in a MySQL [please refer to this if you wish to do so as well]. For completeness sake, the MySQL table structure that holds Geonames data is given below:

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PERL – Retrieving Data From MySQL Databases In Different Servers

Fruit Basket Let us consider the following (hypothetical/real) case: we have a fruit basket with an assortment of fruits in it. Over a period of time, let us suppose we accumulate so much fruit [will they not stink? may be – but that’s a problem beyond the scope of PERL & MySQL] that one basket can no longer hold all the fruits. One possible [and meaningful] way to solve this problem is to introduce another basket and segregate fruits into either one of the two baskets. To make it bit more elegant, we should probably make sure that a given kind of fruit is stored in only one of the baskets. Then, when someone asks us for a fruit – say an Apple – we know which basket contains apples and we can readily pick them out; when someone else asks for an Orange, we can repeat the process; and so on.

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PHP – Storing GPS Track Points In MySQL

Garmin GPSMap 60CSxThough the term waypoint has come into fairly common use in recent times, the concept has existed for as long as we have been navigating. Waypoints have traditionally been associated with distinctive features of the physical world – such as mountains, rock formations, lakes, buildings, and so on. With the advancement of technology and times, waypoints have become increasingly abstract, often having no obvious relationship to any distinctive feature of the physical world. Such waypoints are used to define invisible routing paths for navigation. And for the sake of this discussion/article, we will stick to the following definition of a waypoint: a set of co-ordinates – latitude & longitude, and sometimes altitude – to uniquely identify a point in our physical universe.

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PHP – Storing GPS Waypoints In MySQL

Garmin GPSMap 60CSxThough the term waypoint has come into fairly common use in recent times, the concept has existed for as long as we have been navigating. Waypoints have traditionally been associated with distinctive features of the physical world – such as mountains, rock formations, lakes, buildings, and so on. With the advancement of technology and times, waypoints have become increasingly abstract, often having no obvious relationship to any distinctive feature of the physical world. Such waypoints are used to define invisible routing paths for navigation. And for the sake of this discussion/article, we will stick to the following definition of a waypoint: a set of co-ordinates – latitude & longitude, and sometimes altitude – to uniquely identify a point in our physical universe.

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String2Image – A Web Utility To Convert Strings Into Graphics

Why Strings As Graphics, you ask? There are a myriad of reasons and/or applications where strings need to converted to graphics and one such, probably most commonly seen, application is to put our email address on the web. We want it there but we don’t want anyone (the bots) stealing it. If nothing else, this web based utility should help us a bit in that regard.

As I have done previously for other utilities – LaTeX2Graphics and KannadaLaTeX2Graphics – I have used Andreas Reigber‘s simple yet elegant (command line) utility called TeX2Im. Using this web-based utility is pretty simple. Just type-in (or paste) the string in the form and copy/save the graphic to your computer.

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WordPress – Plugin To Keep Track Of Visitors

I understand there are very many plugins available for WordPress that help keep track of a variety of stats. This one, wp-visitors, is simple and light-weight. Myself and couple friends (Adam & Karen and Tim Obermann) have been using it without any trouble – in some form or the other – for over a year now. I am sure this plugin will see further updates – a few bells and whistles (geographical resolution of IP address), etc. As with all WordPress hosted plugins, this too is released under GPL. So, if you like it and like to make it better, please be my guest 🙂

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WordPress – Legacy of comments.php For 2.7 And Beyond

During the State Of The Word address in not-so-recently held WordCamp New York, Matt Mullenweg gave a sneak preview of a plethora of new (and cool) features being included into the next WordPress release (2.7). I had since then been toying around with the almost ? version (of nightly builds) for a while and now that it is in ? stage, I believe I can discuss one of the really cool features and some code-change required to make some pre-2.7 themes incorporate it.

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PHP – Displaying Gravatars In A Non-WordPress Application

Citing their website, an Automattic.com joint:,

A gravatar, or globally recognized avatar, is quite simply an avatar image that follows you from weblog to weblog appearing beside your name when you comment on gravatar enabled sites. Avatars help identify your posts on web forums, so why not on weblogs?

It’s free and with one account, one can register and assign multiple email address the same (or different) avatar(s).

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BASH – GZIP or BZIP2?

BASH is a free software Unix shell written for the GNU Project. Its name is an acronym which stands for Bourne-again shell. The name is a pun on the name of the Bourne shell (sh), an early and important UNIX shell written by Stephen Bourne and distributed with Version 7 Unix circa 1978, and the concept of being born again. BASH was created in 1987 by Brian Fox. In 1990 Chet Ramey became the primary maintainer. BASH is the default shell on most GNU/Linux systems as well as on Mac OS X and it can be run on most UNIX-like operating systems. It has also been ported to Microsoft Windows using the POSIX emulation provided by Cygwin, to MS-DOS by the DJGPP project and to Novell NetWare.

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BASH – Wrappers For qstat In NPACI ROCKS

BASH is a free software UNIX shell written for the GNU Project. Its name is an acronym which stands for Bourne-again shell. The name is a pun on the name of the Bourne shell (sh), an early and important UNIX shell written by Stephen Bourne and distributed with Version 7 UNIX circa 1978, and the concept of being born again. BASH was created in 1987 by Brian Fox. In 1990 Chet Ramey became the primary maintainer. BASH is the default shell on most GNU/Linux systems as well as on Mac OS X and it can be run on most UNIX-like operating systems. It has also been ported to Microsoft Windows using the POSIX emulation provided by Cygwin, to MS-DOS by the DJGPP project and to Novell NetWare.

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