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1<?xml version='1.0' encoding="UTF-8"?> 1<?xml version='1.0' encoding="UTF-8"?>
2<!-- $Header: /var/cvsroot/gentoo/xml/htdocs/doc/en/hpc-howto.xml,v 1.14 2008/05/19 20:56:20 swift Exp $ --> 2<!-- $Header: /var/cvsroot/gentoo/xml/htdocs/doc/en/hpc-howto.xml,v 1.15 2010/06/07 09:08:37 nightmorph Exp $ -->
3<!DOCTYPE guide SYSTEM "/dtd/guide.dtd"> 3<!DOCTYPE guide SYSTEM "/dtd/guide.dtd">
4 4
5<guide link="/doc/en/hpc-howto.xml"> 5<guide>
6<title>High Performance Computing on Gentoo Linux</title> 6<title>High Performance Computing on Gentoo Linux</title>
7 7
8<author title="Author"> 8<author title="Author">
9 <mail link="marc@adelielinux.com">Marc St-Pierre</mail> 9 <mail link="marc@adelielinux.com">Marc St-Pierre</mail>
10</author> 10</author>
18 <mail link="olivier@adelielinux.com">Olivier Crete</mail> 18 <mail link="olivier@adelielinux.com">Olivier Crete</mail>
19</author> 19</author>
20<author title="Reviewer"> 20<author title="Reviewer">
21 <mail link="dberkholz@gentoo.org">Donnie Berkholz</mail> 21 <mail link="dberkholz@gentoo.org">Donnie Berkholz</mail>
22</author> 22</author>
23<author title="Editor">
24 <mail link="nightmorph"/>
25</author>
23 26
24<!-- No licensing information; this document has been written by a third-party 27<!-- No licensing information; this document has been written by a third-party
25 organisation without additional licensing information. 28 organisation without additional licensing information.
26 29
27 In other words, this is copyright adelielinux R&D; Gentoo only has 30 In other words, this is copyright adelielinux R&D; Gentoo only has
33This document was written by people at the Adelie Linux R&amp;D Center 36This document was written by people at the Adelie Linux R&amp;D Center
34&lt;http://www.adelielinux.com&gt; as a step-by-step guide to turn a Gentoo 37&lt;http://www.adelielinux.com&gt; as a step-by-step guide to turn a Gentoo
35System into a High Performance Computing (HPC) system. 38System into a High Performance Computing (HPC) system.
36</abstract> 39</abstract>
37 40
38<version>1.6</version> 41<version>1.7</version>
39<date>2006-12-18</date> 42<date>2010-06-07</date>
40 43
41<chapter> 44<chapter>
42<title>Introduction</title> 45<title>Introduction</title>
43<section> 46<section>
44<body> 47<body>
86 89
87<p> 90<p>
88During the installation process, you will have to set your USE variables in 91During the installation process, you will have to set your USE variables in
89<path>/etc/make.conf</path>. We recommended that you deactivate all the 92<path>/etc/make.conf</path>. We recommended that you deactivate all the
90defaults (see <path>/etc/make.profile/make.defaults</path>) by negating them in 93defaults (see <path>/etc/make.profile/make.defaults</path>) by negating them in
91make.conf. However, you may want to keep such use variables as x86, 3dnow, gpm, 94make.conf. However, you may want to keep such use variables as 3dnow, gpm,
92mmx, nptl, nptlonly, sse, ncurses, pam and tcpd. Refer to the USE documentation 95mmx, nptl, nptlonly, sse, ncurses, pam and tcpd. Refer to the USE documentation
93for more information. 96for more information.
94</p> 97</p>
95 98
96<pre caption="USE Flags"> 99<pre caption="USE Flags">
97USE="-oss 3dnow -apm -arts -avi -berkdb -crypt -cups -encode -gdbm -gif gpm -gtk 100USE="-oss 3dnow -apm -avi -berkdb -crypt -cups -encode -gdbm -gif gpm -gtk
98-imlib -java -jpeg -kde -gnome -libg++ -libwww -mikmod mmx -motif -mpeg ncurses 101-imlib -java -jpeg -kde -gnome -libg++ -libwww -mikmod mmx -motif -mpeg ncurses
99-nls nptl nptlonly -oggvorbis -opengl pam -pdflib -png -python -qt3 -qt4 -qtmt 102-nls nptl nptlonly -ogg -opengl pam -pdflib -png -python -qt4 -qtmt
100-quicktime -readline -sdl -slang -spell -ssl -svga tcpd -truetype -X -xml2 -xv 103-quicktime -readline -sdl -slang -spell -ssl -svga tcpd -truetype -vorbis -X
101-zlib" 104-xml2 -xv -zlib"
102</pre> 105</pre>
103 106
104<p> 107<p>
105Or simply: 108Or simply:
106</p> 109</p>
119released on <uri>http://www.kernel.org/</uri>, unless you require special 122released on <uri>http://www.kernel.org/</uri>, unless you require special
120support such as xfs. 123support such as xfs.
121</p> 124</p>
122 125
123<pre caption="Installing vanilla-sources"> 126<pre caption="Installing vanilla-sources">
124# <i>emerge -p syslog-ng vanilla-sources</i> 127# <i>emerge -a syslog-ng vanilla-sources</i>
125</pre> 128</pre>
126 129
127<p> 130<p>
128When you install miscellaneous packages, we recommend installing the 131When you install miscellaneous packages, we recommend installing the
129following: 132following:
130</p> 133</p>
131 134
132<pre caption="Installing necessary packages"> 135<pre caption="Installing necessary packages">
133# <i>emerge -p nfs-utils portmap tcpdump ssmtp iptables xinetd</i> 136# <i>emerge -a nfs-utils portmap tcpdump ssmtp iptables xinetd</i>
134</pre> 137</pre>
135 138
136</body> 139</body>
137</section> 140</section>
138<section> 141<section>
257The advantage of NFS today is that it is mature, standard, well understood, 260The advantage of NFS today is that it is mature, standard, well understood,
258and supported robustly across a variety of platforms. 261and supported robustly across a variety of platforms.
259</p> 262</p>
260 263
261<pre caption="Ebuilds for NFS-support"> 264<pre caption="Ebuilds for NFS-support">
262# <i>emerge -p nfs-utils portmap</i> 265# <i>emerge -a nfs-utils portmap</i>
263# <i>emerge nfs-utils portmap</i>
264</pre> 266</pre>
265 267
266<p> 268<p>
267Configure and install a kernel to support NFS v3 on all nodes: 269Configure and install a kernel to support NFS v3 on all nodes:
268</p> 270</p>
404HostKey /etc/ssh/ssh_host_rsa_key 406HostKey /etc/ssh/ssh_host_rsa_key
405</pre> 407</pre>
406 408
407<p> 409<p>
408If your application require RSH communications, you will need to emerge 410If your application require RSH communications, you will need to emerge
409net-misc/netkit-rsh and sys-apps/xinetd. 411<c>net-misc/netkit-rsh</c> and <c>sys-apps/xinetd</c>.
410</p> 412</p>
411 413
412<pre caption="Installing necessary applicaitons"> 414<pre caption="Installing necessary applicaitons">
413# <i>emerge -p xinetd</i> 415# <i>emerge -a xinetd</i>
414# <i>emerge xinetd</i>
415# <i>emerge -p netkit-rsh</i> 416# <i>emerge -a netkit-rsh</i>
416# <i>emerge netkit-rsh</i>
417</pre> 417</pre>
418 418
419<p> 419<p>
420Then configure the rsh deamon. Edit your <path>/etc/xinet.d/rsh</path> file. 420Then configure the rsh deamon. Edit your <path>/etc/xinet.d/rsh</path> file.
421</p> 421</p>
621<p> 621<p>
622To setup a firewall on your cluster, you will need iptables. 622To setup a firewall on your cluster, you will need iptables.
623</p> 623</p>
624 624
625<pre caption="Installing iptables"> 625<pre caption="Installing iptables">
626# <i>emerge -p iptables</i> 626# <i>emerge -a iptables</i>
627# <i>emerge iptables</i>
628</pre> 627</pre>
629 628
630<p> 629<p>
631Required kernel configuration: 630Required kernel configuration:
632</p> 631</p>
697workstations, supercomputers, and massively parallel systems. Development of 696workstations, supercomputers, and massively parallel systems. Development of
698PBS is provided by Altair Grid Technologies. 697PBS is provided by Altair Grid Technologies.
699</p> 698</p>
700 699
701<pre caption="Installing openpbs"> 700<pre caption="Installing openpbs">
702# <i>emerge -p openpbs</i> 701# <i>emerge -a openpbs</i>
703</pre> 702</pre>
704 703
705<note> 704<note>
706OpenPBS ebuild does not currently set proper permissions on var-directories 705OpenPBS ebuild does not currently set proper permissions on var-directories
707used by OpenPBS. 706used by OpenPBS.
814installed, while <e>crypt</e> will configure MPICH to use <c>ssh</c> instead 813installed, while <e>crypt</e> will configure MPICH to use <c>ssh</c> instead
815of <c>rsh</c>. 814of <c>rsh</c>.
816</p> 815</p>
817 816
818<pre caption="Installing the mpich application"> 817<pre caption="Installing the mpich application">
819# <i>emerge -p mpich</i> 818# <i>emerge -a mpich</i>
820# <i>emerge mpich</i>
821</pre> 819</pre>
822 820
823<p> 821<p>
824You may need to export a mpich work directory to all your slave nodes in 822You may need to export a mpich work directory to all your slave nodes in
825<path>/etc/exports</path>: 823<path>/etc/exports</path>:

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