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	<title>Ionut's WebSpace &#187; HPC</title>
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	<link>http://www.vioan.ro/wp</link>
	<description>Exploring Creativity Is My Passion</description>
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		<title>Supercomputers #9 and #24</title>
		<link>http://www.vioan.ro/wp/2010/11/14/supercomputers-9-and-24/</link>
		<comments>http://www.vioan.ro/wp/2010/11/14/supercomputers-9-and-24/#comments</comments>
		<pubDate>Sun, 14 Nov 2010 21:21:22 +0000</pubDate>
		<dc:creator>ionut</dc:creator>
				<category><![CDATA[HPC]]></category>
		<category><![CDATA[Linux]]></category>
		<category><![CDATA[SciComputing]]></category>
		<category><![CDATA[SciVis]]></category>
		<category><![CDATA[scientificcomputing]]></category>
		<category><![CDATA[supercomputers]]></category>

		<guid isPermaLink="false">http://www.vioan.ro/wp/?p=477</guid>
		<description><![CDATA[


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 [...]]]></description>
			<content:encoded><![CDATA[<p>TOP500 list of the world’s most powerful supercomputers is <a href="http://www.top500.org/list/2010/11/100">here</a>. In the first place is  <em>Tianhe</em> 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 (<a href="http://www.fz-juelich.de/jsc/jugene">Jugene</a>) and #24 (<a href="http://www.fz-juelich.de/jsc/juropa/">Juropa</a>). As you probably know, they are hosted by <a href="http://www.fz-juelich.de">Forschungszentrum Juelich</a>, Germany, where I am working.</p>
]]></content:encoded>
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		</item>
		<item>
		<title>My ZFS Home NAS/HTPC Box Build</title>
		<link>http://www.vioan.ro/wp/2010/01/19/my-zfs-home-nashtpc-box-build/</link>
		<comments>http://www.vioan.ro/wp/2010/01/19/my-zfs-home-nashtpc-box-build/#comments</comments>
		<pubDate>Tue, 19 Jan 2010 13:43:19 +0000</pubDate>
		<dc:creator>ionut</dc:creator>
				<category><![CDATA[*BSD]]></category>
		<category><![CDATA[Apple/OS X]]></category>
		<category><![CDATA[HPC]]></category>
		<category><![CDATA[Linux]]></category>
		<category><![CDATA[OpenSolaris]]></category>
		<category><![CDATA[HAS]]></category>
		<category><![CDATA[HTPC]]></category>
		<category><![CDATA[ZFS]]></category>

		<guid isPermaLink="false">http://www.vioan.ro/wp/?p=408</guid>
		<description><![CDATA[I was looking to build a NAS (Network Attached Storage) to store all my music, photos, files, e-books and important work related files. I also wanted to have a central place for my backups and to be used sometimes as HTPC. So, a &#8220;two in one&#8221; solution (NAS and HTPC).
Even if there are many ready-to-go [...]]]></description>
			<content:encoded><![CDATA[<p>I was looking to build a NAS (Network Attached Storage) to store all my music, photos, files, e-books and important work related files. I also wanted to have a central place for my backups and to be used sometimes as HTPC. So, a &#8220;two in one&#8221; solution (NAS and HTPC).</p>
<p>Even if there are many ready-to-go NAS solutions I decided to build myself one and having the HTPC on the same machine. Here is mainly what I wanted:</p>
<ul>
<li>low powered system (64-bit microprocessor)</li>
<li>used as a media server (stream movies/music)</li>
<li>to be used sometimes as a HTPC, so I wanted HDMI (for HD video)</li>
<li>ZFS file system with all its goodies</li>
<li>gigabit ethernet interface to take advantage of the network bandwidth</li>
<li>nice chassis with four hot-swappable 3.5&#8243; SATA HDD (I am using just two HDD right now because the motherboard has only 3 SATA)</li>
</ul>
<p>My NAS/HTPC specs are here:</p>
<ul>
<li> <a href="http://www.chenbro.com/corporatesite/products_detail.php?sku=79">Chenbro ES34069 chassis</a></li>
<li><a href="http://www.zotacusa.com/zotac-ionitx-a-u-atom-n330-1-6ghz-dual-core-mini-itx-intel-motherboard.html">Zotac ION-ITX-A Wi-Fi Dual Core 1.6GHz</a> motherboard</li>
<li>2 GB Kingston DDR2 800MHz RAM</li>
<li>2 x Western Digital Caviar Green 1.0 TB</li>
<li>1x Toshiba 2.5&#8243; HDD 100 GB (for OS)</li>
</ul>
<p><img class="aligncenter size-medium wp-image-410" title="home_server1" src="http://www.vioan.ro/wp/wp-content/uploads/2010/01/home_server1-300x225.jpg" alt="home_server1" width="300" height="225" /><img class="aligncenter size-medium wp-image-411" title="es34069" src="http://www.vioan.ro/wp/wp-content/uploads/2010/01/es34069-214x300.jpg" alt="es34069" width="214" height="300" /></p>
<p>I choosed <a href="http://www.freebsd.org"><strong>FreeBSD</strong></a> as operating system, because I am more familiar with it than with Solaris. I recompiled <strong>mplayer</strong> with <strong>vdpau</strong> support (for HD video).</p>
<p>Here are the steps:</p>
<ul>
<li>download the latest mplayer snapshot from their website</li>
<li>download these two files (<a href="ftp://download.nvidia.com/XFree86/vdpau/include/vdpau/">ftp://download.nvidia.com/XFree86/vdpau/include/vdpau/</a>) and put them in <em>/usr/include/vdpau</em> (create that directory)</li>
<li>./configure &#8211;disable-x264-lavc &#8211;disable-x264 -–enable-vdpau</li>
<li>gmake</li>
<li>gmake install</li>
<li>check to see if you have vdpau support with: &#8220;<em>mplayer -vo help</em>&#8220;. If you see something like: &#8220;<em>vdpau VDPAU with X11</em>&#8221; then everything is ok.</li>
</ul>
<p>Some additional steps/configs:</p>
<ul>
<li>add zfs_enable=&#8221;YES&#8221; in /etc/rc.conf</li>
<li>add  the following in /boot/loader.conf:</li>
</ul>
<p>vm.kmem_size_max=&#8221;1024M&#8221;</p>
<p>vm.kmem_size=&#8221;1024M&#8221;</p>
<p>vfs.zfs.arc_max=&#8221;100M&#8221;</p>
<ul>
<li>zpool create storage mirror ad4 ad10</li>
<li>zfs create storage/archives</li>
<li>zfs create storage/backups</li>
<li>install samba, duplicity, rsnapshots, rsync, unison, ushare, &#8230;</li>
</ul>
<p>Right now, everything is working very well, I am very happy with the setup, but I still didn&#8217;t manage to have sound over HDMI, so, a temporary solution will be to connect an additional speaker system to it.</p>
<p>I don&#8217;t need any fancy remote control, I have a logitech wifi keyboard/mouse, because I like to be able to read the news in the morning (during cofee time) using google reader</p>
<p>The total power consumption is about 35W idle / 45W load which is pretty good, I think.</p>
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		</item>
		<item>
		<title>Installing Intel Compiler Suite on OpenSUSE 11.1</title>
		<link>http://www.vioan.ro/wp/2009/03/27/installing-intel-compiler-suite-on-opensuse-111/</link>
		<comments>http://www.vioan.ro/wp/2009/03/27/installing-intel-compiler-suite-on-opensuse-111/#comments</comments>
		<pubDate>Fri, 27 Mar 2009 11:47:15 +0000</pubDate>
		<dc:creator>ionut</dc:creator>
				<category><![CDATA[HPC]]></category>
		<category><![CDATA[Linux]]></category>
		<category><![CDATA[SciComputing]]></category>
		<category><![CDATA[SciVis]]></category>
		<category><![CDATA[C]]></category>
		<category><![CDATA[compilers]]></category>
		<category><![CDATA[fortran]]></category>
		<category><![CDATA[intel]]></category>

		<guid isPermaLink="false">http://www.vioan.ro/wp/?p=355</guid>
		<description><![CDATA[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:

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Step no: 4 of 7 &#124; Installation configuration - Missing Critical Pre-requisite
--------------------------------------------------------------------------------
The following required for installation [...]]]></description>
			<content:encoded><![CDATA[<p>Here are the basic steps to install Intel C/C++ and Fortran Compilers on OpenSUSE 11.1:</p>
<p>1. download Intel C/C++ and Fortran Compilers from their website. They are free for non-commercial use<br />
2. unpack and start the installer<br />
3. at some point I received:</p>

<div class="wp_syntax"><table><tr><td class="line_numbers"><pre>1
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</pre></td><td class="code"><pre class="bash" style="font-family:monospace;">Step no: <span style="color: #000000;">4</span> of <span style="color: #000000;">7</span> <span style="color: #000000; font-weight: bold;">|</span> Installation configuration - Missing Critical Pre-requisite
<span style="color: #660033;">--------------------------------------------------------------------------------</span>
The following required <span style="color: #000000; font-weight: bold;">for</span> installation commands are missing:
libstdc++.so.5 <span style="color: #7a0874; font-weight: bold;">&#40;</span>library<span style="color: #7a0874; font-weight: bold;">&#41;</span>
<span style="color: #660033;">--------------------------------------------------------------------------------</span>
1. Finish with prerequisites and back to Critical Pre-requisites <span style="color: #c20cb9; font-weight: bold;">dialog</span>
<span style="color: #7a0874; font-weight: bold;">&#91;</span>default<span style="color: #7a0874; font-weight: bold;">&#93;</span>
2. Back to Pre-requisite summary <span style="color: #c20cb9; font-weight: bold;">dialog</span>
&nbsp;
h. Help
b. Back to the previous menu
q. Quit
<span style="color: #660033;">--------------------------------------------------------------------------------</span>
Please <span style="color: #7a0874; font-weight: bold;">type</span> a selection or press <span style="color: #ff0000;">&quot;Enter&quot;</span> to accept default choice <span style="color: #7a0874; font-weight: bold;">&#91;</span><span style="color: #000000;">1</span><span style="color: #7a0874; font-weight: bold;">&#93;</span>:</pre></td></tr></table></div>

<p>4. let&#8217;s stop the installer and install the necessary packages</p>

<div class="wp_syntax"><table><tr><td class="line_numbers"><pre>1
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</pre></td><td class="code"><pre class="bash" style="font-family:monospace;">vaio:<span style="color: #000000; font-weight: bold;">/</span>home<span style="color: #000000; font-weight: bold;">/</span>ionut <span style="color: #666666; font-style: italic;"># zypper install libstdc++33</span>
&nbsp;
vaio:<span style="color: #000000; font-weight: bold;">/</span>home<span style="color: #000000; font-weight: bold;">/</span>ionut <span style="color: #666666; font-style: italic;"># whereis libstdc++.so.5</span>
libstdc++.so: <span style="color: #000000; font-weight: bold;">/</span>usr<span style="color: #000000; font-weight: bold;">/</span>lib<span style="color: #000000; font-weight: bold;">/</span>libstdc++.so.6 <span style="color: #000000; font-weight: bold;">/</span>usr<span style="color: #000000; font-weight: bold;">/</span>lib64<span style="color: #000000; font-weight: bold;">/</span>libstdc++.so.5 <span style="color: #000000; font-weight: bold;">/</span>usr<span style="color: #000000; font-weight: bold;">/</span>lib64<span style="color: #000000; font-weight: bold;">/</span>libstdc++.so.6
&nbsp;
vaio:<span style="color: #000000; font-weight: bold;">/</span>home<span style="color: #000000; font-weight: bold;">/</span>ionut <span style="color: #666666; font-style: italic;"># zypper install libstdc++33-32bit</span>
&nbsp;
vaio:<span style="color: #000000; font-weight: bold;">/</span>home<span style="color: #000000; font-weight: bold;">/</span>ionut <span style="color: #666666; font-style: italic;"># zypper install binutils-32bit binutils-devel</span></pre></td></tr></table></div>

<p>5. let&#8217;s run again the installer, now we have all packages installed</p>

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</pre></td><td class="code"><pre class="bash" style="font-family:monospace;"><span style="color: #7a0874; font-weight: bold;">&#91;</span>...skip...<span style="color: #7a0874; font-weight: bold;">&#93;</span>
Step no: <span style="color: #000000;">4</span> of <span style="color: #000000;">7</span> <span style="color: #000000; font-weight: bold;">|</span> Installation configuration - Missing Optional Pre-requisite
<span style="color: #660033;">--------------------------------------------------------------------------------</span>
There is one or <span style="color: #c20cb9; font-weight: bold;">more</span> optional unresolved issues. It is highly recommended to fix
it all before you <span style="color: #7a0874; font-weight: bold;">continue</span> 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.
<span style="color: #660033;">--------------------------------------------------------------------------------</span>
Missing optional pre-requisite
<span style="color: #660033;">--</span> cannot determine operating system <span style="color: #7a0874; font-weight: bold;">type</span>
<span style="color: #660033;">--</span> system glibc or kernel version not supported or not detectable
<span style="color: #660033;">--</span> binutils version not supported or not detectable
<span style="color: #660033;">------------------------------------------------------------</span>
1. Skip missing optional pre-requisites <span style="color: #7a0874; font-weight: bold;">&#91;</span>default<span style="color: #7a0874; font-weight: bold;">&#93;</span>
2. Show the detailed info about issue<span style="color: #7a0874; font-weight: bold;">&#40;</span>s<span style="color: #7a0874; font-weight: bold;">&#41;</span>
3. Re-check the pre-requisites
&nbsp;
h. Help
b. Back to the previous menu
q. Quit
<span style="color: #660033;">--------------------------------------------------------------------------------</span>
Please <span style="color: #7a0874; font-weight: bold;">type</span> a selection or press <span style="color: #ff0000;">&quot;Enter&quot;</span> to accept default choice <span style="color: #7a0874; font-weight: bold;">&#91;</span><span style="color: #000000;">1</span><span style="color: #7a0874; font-weight: bold;">&#93;</span>:</pre></td></tr></table></div>

<p>5. accept default choice and press Enter<br />
6. Intel compiler is installed, do the same for the other compiler<br />
7. enjoy <img src='http://www.vioan.ro/wp/wp-includes/images/smilies/icon_smile.gif' alt=':)' class='wp-smiley' /> </p>
]]></content:encoded>
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		</item>
		<item>
		<title>Parallel Programming with MPI in Bristol</title>
		<link>http://www.vioan.ro/wp/2009/03/26/parallel-programming-with-mpi-in-bristol/</link>
		<comments>http://www.vioan.ro/wp/2009/03/26/parallel-programming-with-mpi-in-bristol/#comments</comments>
		<pubDate>Thu, 26 Mar 2009 21:00:35 +0000</pubDate>
		<dc:creator>ionut</dc:creator>
				<category><![CDATA[HPC]]></category>
		<category><![CDATA[Linux]]></category>
		<category><![CDATA[MacOS]]></category>
		<category><![CDATA[SciComputing]]></category>
		<category><![CDATA[SciVis]]></category>
		<category><![CDATA[mpi]]></category>
		<category><![CDATA[openmp]]></category>
		<category><![CDATA[pvm]]></category>
		<category><![CDATA[scientific computing]]></category>

		<guid isPermaLink="false">http://www.vioan.ro/wp/?p=339</guid>
		<description><![CDATA[I spent the last 4 days in Bristol to attend to &#8220;Parallel Programming with MPI&#8221; course, provided by HECToR which is the UK&#8217;s high-end computing resource, funded by the Research Councils and available for researchers at UK universities, and by NAG &#8211; The Numerical Algorithms Group specialized in the provision of software for the solution [...]]]></description>
			<content:encoded><![CDATA[<p>I spent the last 4 days in Bristol to attend to &#8220;Parallel Programming with <a href="http://en.wikipedia.org/wiki/Message_Passing_Interface">MPI</a>&#8221; course, provided by <a href="http://www.hector.ac.uk/about-us/"><abbr>HECToR</abbr></a> which is the UK&#8217;s high-end computing resource, funded by the Research Councils and available for researchers at UK universities, and by <a href="http://www.nag.co.uk">NAG &#8211; The Numerical Algorithms Group</a> specialized in the provision of software for the solution of mathematical, statistical and data mining problems.</p>
<p>The course covered the <strong>Introduction to MPI</strong> and <strong>Advanced MPI</strong>.  <a href="http://www.mcs.anl.gov/research/projects/mpi/">MPI (Message Passing Interface)</a> is the <em><em>de facto</em></em> standard for parallel programming. I have also some experience with <a href="http://www.csm.ornl.gov/pvm/">PVM (Parallel Virtual Machine)</a> my Master Thesis was based on that, and I learnt a lot about <a href="http://openmp.org/wp/">OpenMP</a>, so I wanted to extend my knowledge for Parallel Programming with MPI.</p>
<p>The course introduced the concepts and terminology of <a href="http://en.wikipedia.org/wiki/High-performance_computing">High Performance Computing (HPC)</a>.  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.</p>
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