Rocks 6.1 – IPoIB

Disclaimer

The instructions/steps given below worked for me (and Michigan Technological University) running Rocks 6.1 (with Service Pack 1, CentOS 6.3 and GE 2011.11p1) – as has been a common practice for several years now, a full version of Operating System was installed. The HPC cluster (wigner) used to prepare this documentation has Mellanox 56 Gb/s FDR InfiniBand switches and ports. Further, it is assumed the eth0 interface is used for private ethernet network and ib0 is the InfiniBand interface. 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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Rocks 5.4.2 – Scheduling GPU jobs via SGE

Disclaimer

The instructions/steps given below worked for me (and Michigan Technological University) running Rocks 5.4.2 (with CentOS 5.5 and SGE 6.2u5) – 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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SC12 in Salt Lake City

The description of the conference didn’t change – SC12 is still The International Conference for High Performance Computing, Networking, Storage and Analysis, but the location did: Salt Lake City in Utah, known to the historically inclined as the crossroads of the west. I had never been to SLC ever before but the last time I was in Utah was August of 2005 – a momentary step in and out of state border as part of Glenn Canyon Dam tour which, in itself, was part of a 3 day trip to the Grand Canyon.

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Rocks 5.4.2 – HPCC 1.4.1 benchmark with GCC 4.1.2

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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Rocks 5.4.2 – HPL 2.0 benchmark with GCC 4.1.2

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.

Continue reading … “Rocks 5.4.2 – HPL 2.0 benchmark with GCC 4.1.2”

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.

Continue reading … “Rocks 5.4.2 – Ganglia’s gmond Python module for monitoring NVIDIA GPU”

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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SC11, fond memories from a fantastic nerd fest

Apart from what I could infer from the title, SC11, The International Conference for High Performance Computing, Networking, Storage and Analysis, that it was being held in a city that I had already been to once before (and had gained some familiarity, with at least parts of it) as part of The Great American Road Trip with dear friend Nils Stenvig (@UPBeaches), that the city had more than its fair share of friendly & familiar faces and that the event would offer the first of opportunities to put a face to many a names that I had known & interacted with for many years, I knew little about SC11 and of what I wanted from it.

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Subversion – Changing Repository Location

Subversion Subversion (SVN) is a version control system initiated in 2000 by CollabNet Inc. It is used to maintain current and historical versions of files such as source code, web pages, and documentation. Its goal is to be a mostly-compatible successor to the widely used Concurrent Versions System (CVS). Subversion is well-known in the open source community and is used on many open source projects.

Subversion was started in 2000 as an effort to write a free version control system which operated much like CVS but with fixed bugs and misfeatures in CVS. By 2001, Subversion was sufficiently developed to be capable of hosting its own source code. More information, including this above paragraph, is here.

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BASH – Extracting Subversion Log

Subversion

Subversion Subversion (SVN) is a version control system initiated in 2000 by CollabNet Inc. It is used to maintain current and historical versions of files such as source code, web pages, and documentation. Its goal is to be a mostly-compatible successor to the widely used Concurrent Versions System (CVS). Subversion is well-known in the open source community and is used on many open source projects.

Subversion was started in 2000 as an effort to write a free version control system which operated much like CVS but with fixed bugs and misfeatures in CVS. By 2001, Subversion was sufficiently developed to be capable of hosting its own source code. More information, including this above paragraphs, is here.

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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, CEC @ MTU]. It expects OUTCAR & POSCAR from a calculation to be in the same folder and when successfully completed, it results in OUTPUT_FILENAME.xyz – containing frame-by-frame [corresponding to each (optimization) step] XYZ co-ordinates of the system.

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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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CSS – Floating Next/Previous Links On Images

Why is this necessary, you ask? Ever since I first used PixelPost and deliciously delicious theme, I had been wanting to do something similar for my own photo gallery. Since PixelPost [nor any other photoblog software] ever came close to satisfying my needs, I ended up writing [still a work in progress to some extent] one on my own and the desire to have a jazzy Next and Previous links floating on images. Not reading through the CSS and trying to understand how exactly it was to be accomplished, I was under the [wrong] assumption that knowledge of Javascript was necessary/mandatory.

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MAC – Upgrading MacPorts

Wondering why is this necessary? Citing MacPorts,

An installation of MacPorts and the ports installed by it are only designed to work on a single OS release and a single CPU architecture. If you upgrade to a new OS version (e.g. from Tiger to Leopard) or migrate to a new machine with a different type of CPU (e.g. PowerPC to Intel), you may get lucky and have your ports keep working, but in general, things will break.

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