source: palm/trunk/DOC/app/chapter_5.0.html @ 339

Last change on this file since 339 was 336, checked in by raasch, 15 years ago

several small bugfixes; some more dvrp changes

  • Property svn:keywords set to Id
File size: 32.7 KB
RevLine 
[5]1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
[40]2<html><head>
[336]3<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM chapter 5.0</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Siegfried Raasch"> <meta name="CREATED" content="20041103;12380720"> <meta name="CHANGED" content="20041123;15532356"> <meta name="KEYWORDS" content="parallel LES model"> <style>
[62]4<!--
5@page { size: 21cm 29.7cm }
6-->
7</style></head>
8<body style="direction: ltr;" lang="en-US"><h2 style="line-height: 100%;"><font size="4">5.0
9Installation of the
[5]10model</font></h2>
[41]11<font color="#000000">This chapter
[62]12describes the installation of PALM on a Linux workstation (local host)
13and a suitable remote computer, on which the
[40]14model runs are to be carried out. The local host is used to
[62]15start batch jobs with <b>mrun</b> and to analyze the
16results
17which are produced by the model on the remote host and send back to the
18local host. Alternatively, <span style="font-weight: bold;">mrun</span>
19can also be used to start PALM on the local host in interactive mode or
[290]20as a batch job (if a queueing system like NQS, PBS, or LoadLeveler is
21available).</font><p style="line-height: 100%;"></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Requirements</span></font></p><p style="line-height: 100%;"><font color="#000000">The
[62]22installation and operation of PALM requires at mimimum (on both, the
[290]23local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The Korn-shell (AT&amp;T ksh or public
24domain ksh) must be
[83]25available under<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">/bin/ksh</font><font color="#000000">.<span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-family: Courier New,Courier,monospace;"></span></font><font color="#000000"><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span></font></li><li><font color="#000000">The
[62]26NetCDF-library with version number not earlier than 3.6.0-p1 (for
27NetCDF, see under <a href="http://www.unidata.ucar.edu/software/netcdf/">www.unidata.ucar.edu</a>).</font></li><li><font color="#000000">A FORTRAN90/95 compiler.</font></li><li><font color="#000000">The Message Passing Interface (MPI), at
28least on the remote host, if the parallel version of PALM shall be used.</font></li><li><font color="#000000">On the local host, the revision control
29system <span style="font-weight: bold;">subversion</span>
30(see <a href="http://subversion.tigris.org/">subversion.tigris.org</a>).
31This is already included in many Linux distributions (e.g. SuSe). <span style="font-weight: bold;">subversion requires port 3690 to
32be open for tcp/udp.</span> <span style="font-weight: bold;">If
33there are firewall restrictions concerning this port, the PALM code
34cannot be accessed.</span> The
[40]35user needs a permit to access the PALM repository. For getting a permit
36please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>)
37and define a username under which you like to access the repository.
38You will then receive a password which allows the access under this
[62]39name.</font></li><li><font color="#000000">A
40job queueing system must be available on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle
41LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).</font></li><li><font color="#000000">ssh/scp-connections to and from the remote
42host must not be blocked by a firewall.<br></font></li></ol><font color="#000000"><span style="font-weight: bold;"></span></font><font color="#000000"> Currently, <span style="font-weight: bold;">mrun</span> is configured
[290]43to be used on a limited number of selected machines. These are SGI-ICE
44systems at computing center HLRN in Hannover (<span style="font-style: italic;">lcsgih</span>), Berlin (<span style="font-style: italic;">lcsgib</span>),
45IBM-Regatta system<span style="font-style: italic;"></span>
[62]46at Yonsei University, Seoul (<span style="font-style: italic;">ibms</span>),
47on NEC-SX6/8 systems at DKRZ, Hamburg (<span style="font-style: italic;">nech</span>) and RIAM,
[287]48Kyushu University, Fukuoka (<span style="font-style: italic;">necriam</span>),
49as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>), Tokyo
[290]50Institute of Technology (<span style="font-style: italic;">lctit</span>),
51and the Bergen Center for Computational Science (<span style="font-style: italic;">lcxt4</span>).
52The strings given in brackets are the systems names (host identifiers)
53under which <span style="font-weight: bold;">mrun</span>
54identifies the
55different hosts.<br><br>You can also use <span style="font-weight: bold;">mrun</span>/PALM on other
56Linux-Cluster, IBM-AIX, or NEC-SX machines. See <a href="#configuration_for_other_machines">below</a> on
57how to configure <span style="font-weight: bold;">mrun</span>
58for other machines. However, these configurations currently (version
593.2a) allow to run PALM in interactive mode only.<br><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span></font><p style="line-height: 100%;"><font color="#000000">The
[62]60examples given in this chapter refer to an
[287]61installation of PALM on an IMUK Linux workstation and the SGI-ICE
[5]62system of
[62]63the HLRN used as&nbsp;remote host. They are just called local and
64remote host from now on. </font></p><p style="line-height: 100%;">
65</p><p style="line-height: 100%;">The installation
66process requires a valid
[40]67account on the local and on the remote host as well.<br>
[5]68&nbsp; </p>
[62]69<ul> All hosts (local as well as remote) are
[5]70accessed via the secure shell (ssh). The user must establish
71passwordless login using the private/public-key mechanism (see e.g. the
[290]72<a href="http://www2.hlrn.de/doc/ssh/index.html">HLRN
[62]73documentation</a>). <b>To ensure proper function of mrun,
74passwordless login must be
[5]75established in both directions, from the local to the remote host as
[62]76well as from the remote to the local host!</b> Test this by
77carrying
78out e.g. on the local host: <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
79</span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp;
80&lt;username on remote host&gt;@&lt;remote
81IP-address&gt;</span><br> </p> <p style="line-height: 100%;">and on the remote host:<br>
82</p> <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
83</span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp;
84&lt;username on local host&gt;@&lt;local IP-adddress&gt;</span><br>
85</p> In both cases you should&nbsp;not be
86prompted for a password. <b>Before continuing the further
87installation
88process, this must be absolutely guaranteed!</b> This must also
89be
90guaranteed for <b>all</b> other remote hosts, on which
[290]91PALM shall run.<br><br>Please
92note that on many remote hosts, passwordless login must also be
93established <b>within the remote host</b>, i.e. from the
94remote host to itself. Test this by executing on the remote host: <span style="font-family: Courier New,Courier,monospace;">ssh
95&lt;remote IP-address&gt;</span>. You should not be prompted
96for a password.<br><br></ul><p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package
[62]97Installation</span></p><p style="line-height: 100%;">In
98the <b>first installation step</b> a
[5]99set of directories must be created both on the local and on the
[62]100remote host. These directories are:</p><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/job_queue<br></div><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm<br></div><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm/current_version<br></div><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS</span><br></div><p style="line-height: 100%;">The names of these directories
101are
[290]102freely selectable (except <big><tt><font size="2"><big>~/job_queue</big></font></tt></big>),
[5]103however new users should use them as suggested, since many
104examples in this documentation as well as all example files are
[290]105assuming these settings. The directory <big><span style="font-family: monospace;">~/palm/current_version</span></big>
[62]106on the local host will be called the working directory from now on. </p>
107<p style="line-height: 100%;"><font color="#000000">In
108the <b>second
[40]109step</b>
110a working copy of the recent version of the PALM software package,
[62]111including the source code, scripts, documentation, etc.&nbsp; must
112be
[44]113copied to the working directory (</font><font color="#000000">local
114host!) by executing the following
[62]115commands. Replace &lt;your username&gt; by the name that you
116chose to
117access the repository, and &lt;#&gt; by any of the available
118PALM
119releases, e.g. "<span style="font-style: italic;">3.1c</span>"
120(new releases will be anounced by email to the PALM mailing list).</font></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">cd
121~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn
122checkout --username &lt;your username&gt;
123svn://130.75.105.45/palm/tags/release-&lt;#&gt; trunk</span><br></div><p style="line-height: 100%;"><font color="#000000">You
124will then be prompted for your password. After finishing, the
125subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">should
[40]126appear in your working directory. It contains a number of further
[62]127subdirectories which contain e.g. the PALM source code (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SOURCE</font><font color="#000000">)
128and the scripts for running PALM (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SCRIPTS</font><font color="#000000">).</font></p><p style="line-height: 100%;">Alternatively,&nbsp;executing</p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username &lt;your username&gt; svn://130.75.105.45/palm/tags/release-&lt;#&gt; abcde</pre><p style="line-height: 100%;">will place your working copy in a
129directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span>instead
130of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span>.
131But keep in mind that you will have to adjust several paths given
132below, if you do not use the default directory<span style="font-family: Courier New,Courier,monospace;"> trunk</span>.</p><p style="line-height: 100%;">Please never touch any file in
133your working copy of PALM, unless you&nbsp;know exactly what you
134are doing.</p><p style="line-height: 100%; font-weight: bold;"><span style="font-weight: normal;">You can also get a copy of the
135most recent code by executing</span></p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username &lt;your username&gt; svn://130.75.105.45/palm/trunk trunk</pre>However,
136this version may contain bugs and new features may not be documented. <span style="font-weight: bold;">In future PALM releases,
137repository access to this most recent&nbsp;version will
138probably be restricted to the PALM developers.</span><p style="line-height: 100%;"></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Package
139Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To
[290]140use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable
141has to be extended and the
142environment variable<span style="font-family: Courier New,Courier,monospace;">
143PALM_BIN </span>has to be set (on local and remote host)
[62]144in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>,
145if<span style="font-family: Courier New,Courier,monospace;">
146ksh </span>is used):</font></p><p style="line-height: 100%; margin-left: 40px;"><font style="font-family: Courier New,Courier,monospace;" color="#000000">export
147PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH</font><font color="#000000"><br><span style="font-family: Courier New,Courier,monospace;">export
148PALM_BIN=</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">$HOME/palm/current_version/trunk/SCRIPTS</font></p><p style="line-height: 100%;"><font color="#000000">You
[83]149may have to login again in order to activate these settings.</font></p><font color="#000000">On the local and on the remote host, some
[290]150small helper/utility programs have to be installed, which
151are&nbsp;later used by <span style="font-weight: bold;">mrun</span>&nbsp;e.g.
152for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script
[62]153requires a configuration file<span style="font-family: Courier New,Courier,monospace;">
154.mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the
155following. A copy has to be put into the working directory under the
156name<span style="font-family: Courier New,Courier,monospace;">
157.mrun.config </span>by</font><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">cp
158trunk/SCRIPTS/.mrun.config.default .mrun.config</span></font></p><font color="#000000">Beside many other things, this file contains
159typical installation parameters
[40]160like compiler name, compiler options, etc.
[83]161for a set of different (remote) hosts. Please edit this file, uncomment
[62]162lines like</font><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username
163&nbsp;&lt;replace by your ... username&gt; &nbsp;
[83]164&lt;host identifier&gt;</div><p style="line-height: 100%;"><font color="#000000">by
[62]165removing the first hash (<span style="font-family: Courier New,Courier,monospace;">#</span>)
166character and replace the string "<span style="font-family: Courier New,Courier,monospace;">&lt;replace
167by ...&gt;</span>" by your username on the respective host
[290]168given in the <span style="font-family: Courier New,Courier,monospace;">&lt;host
169identifier&gt;</span>.
[62]170You only have to uncomment lines for those hosts on which you intend to
[336]171use PALM.</font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">Warning:
172When editing the configuration file, please NEVER use the TAB key.
173Otherwise, very confusing errors in mrun execution may occur.</span></font></p><p style="line-height: 100%;"><font color="#000000">Beside the default configuration file</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> .mrun.config.default</font><font color="#000000">, the directory<span style="font-family: Courier New,Courier,monospace;">
[290]174trunk/SCRIPTS </span>contains additional configuration files
175which are already adjusted for special hosts:<span style="font-family: Courier New,Courier,monospace;">
176.mrun.config.imuk </span>can be used at Hannover University,<span style="font-family: Courier New,Courier,monospace;">
177.mrun.config.riam </span>can
[287]178be used at the Research Institute of Applied Mechanics, Kyushu
179University. These files have to be edited in the same way as described
180above.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the
[290]181respective executables are generated by executing</font></p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild -u -h lcmuk<br>mbuild -u -h
182lcsgih</font></p><p style="line-height: 100%;"><font color="#000000">The
183second call also copies the PALM scripts (like <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span>) to the
184remote
[62]185host.</font></p><p style="line-height: 100%;"></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Pre-Compilation
186of PALM Code</span></font></p><font color="#000000">
187</font><br><font color="#000000">To avoid the
[5]188re-compilation of the complete source code for each model run, PALM
[62]189willl be pre-compiled once on the remote host by again using the script
190<span style="font-weight: bold;">mbuild</span>. Due
191to the use of
[5]192FORTRAN modules in the source code, the subroutines must be compiled
[62]193in a certain order. Therefore the so-called <i>make</i>
194mechanism
[5]195is used (see the respective man-page of the Unix operating system),
[62]196requiring a<span style="font-family: Courier New,Courier,monospace;">
197</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">Makefile</font><font color="#000000">,
198in which the dependencies are described. This file is found in
[290]199subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span></font><font color="#000000">, where
200also the PALM code is stored.</font><font color="#000000"> The compiled
[62]201sources (object
[5]202files) are
[40]203stored&nbsp;on the remote computer in the default directory
[41]204</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">~/palm/current_version/MAKE_DEPOSITORY</font>.<font color="#000000"><span style="font-weight: bold;"></span></font><p style="line-height: 100%;"><font color="#000000">The
[290]205pre-compilation for the remote host (here the SGI-ICE system of HLRN)
206is
[62]207done by</font><span style="font-family: monospace;"></span></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">mbuild
[287]208-h lcsgih &nbsp;</span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild
[62]209</span>will prompt some queries<font color="#000000">,
210which must all be
211answered "y" by the user. The compiling process </font><font color="#000000">will take some time.<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">mbuild</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"> </span>transfers
212the respective compiler calls to the remote
[5]213host where they are carried out interactively. You can follow the
214progress at the terminal window, where also error messages
215are displayed (hopefully not for this standard installation). By just
[41]216entering </font></p><p style="line-height: 100%;">
[62]217</p><blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote>
218<p style="line-height: 100%;"><font color="#000000">PALM
219will
[5]220be (consecutively) pre-compiled for all remote hosts listed in
[62]221the configuration file. If you want to compile for the local host only,
222please enter</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">mbuild
223-h lcmuk</span> </font>
224</p><p style="line-height: 100%;"></p><p style="line-height: 100%; font-weight: bold; text-decoration: underline;"><font color="#000000">Installation Verification</font></p><font color="#000000">As a last step,
[5]225after the compilation has been finished, the PALM installation has to
226be verified. For this
227purpose a simple test run is carried out. This once again requires the <b>mrun
[40]228</b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter
[62]2293.2</font></a><font color="#000000">), as well
[244]230as the </font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_cbl_p3d"><font color="#000080">parameter
[62]231file</font></a><font color="#000000">
[97]232(described in </font><a href="chapter_4.4.1.html"><font color="#000080">chapter
2334.4.1</font></a>)<font color="#000000">. The
[62]234parameter file must be
[40]235copied from the PALM working copy by<br>
[244]236</font><div style="margin-left: 40px;"><span style="font-family: monospace;"></span><font style="font-family: Courier New,Courier,monospace;" color="#000000">mkdir -p JOBS/example_cbl/INPUT<br>cp
237trunk/INSTALL/example_cbl_p3d&nbsp;JOBS/example_cbl/INPUT/example_cbl_p3d</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"></span></font></div>
[62]238<p style="line-height: 100%;"><font color="#000000">The
239test run can
[40]240now be started by executing the command </font>
[290]241</p><pre style="margin-left: 1cm; margin-right: 1cm; margin-bottom: 0.5cm; line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mrun -d example_cbl -h lcsgih -K parallel -X 8 -T 8 -t 500 -q testq -r &ldquo;d3# pr#&rdquo;</font></pre><font color="#000000">This specific run
[5]242will be carried out on 8 PEs and is allowed to use up to 500 seconds
[62]243CPU time. After pressing &lt;return&gt;, the most important
244settings of
[5]245the job are displayed at the terminal window
[62]246and the user is prompted for o.k. (&ldquo;</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">y</font><font color="#000000">&rdquo;).
247Next, a message of the queuing system like &ldquo;<i>Request</i>
248&hellip;
249<i>Submitted to queue&hellip; by&hellip;&rdquo; </i>should
250be displayed. Now the job is
251queued and either started immediately or at a later time, depending on
252the
[5]253current workload of the remote host. Provided that it is executed
254immediately and that all things work as designed, the job protocol of
[287]255this run will appear under the file name<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">~/job_queue/lcsgih_example</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"> </span>no
[62]256more than a few minutes later. The content of this
[41]257file should be carefully examined for any error messages.</font><p style="line-height: 100%;">
[62]258</p><p style="line-height: 100%;">Beside the job
259protocol and according to
[5]260the configuration file and arguments given for <b>mrun</b>
[62]261options<span style="font-family: Courier New,Courier,monospace;">
262-d </span>and<span style="font-family: Courier New,Courier,monospace;"> -r</span><tt>,</tt>further
263files should be found in
[5]264the
[244]265directories</p><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/MONITORING</div><p style="line-height: 100%;">and</p>
[5]266<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
[244]267</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/OUTPUT</span><span style="font-family: monospace;"></span><br>
[62]268</p><p style="line-height: 100%;">Please compare the
269contents of file</p>
[5]270<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
[287]271</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/MONITORING/lcsgih_example_rc</span><br>
[62]272</p><p style="line-height: 100%;">with those of the
273example result file which can be found under<span style="font-family: Courier New,Courier,monospace;">
[244]274trunk/INSTALL/example_cbl_rc</span>., e.g. by using the<span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;"> standard</span>
[62]275diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff
[287]276&nbsp;JOBS/example_cbl/MONITORING/lcsgih_example_cbl_rc
[244]277trunk/INSTALL/example_cbl_rc</p><p style="line-height: 100%;">where
[62]278it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;">
279~/palm/current_version</span>.</p><span style="font-weight: bold;">You should not find any
280difference between these two files</span>, except of the run date
281and time displayed at the top of the file header. <font color="#000000">If
[5]282the file contents are identical, the installation is successfully
[290]283completed.<br><br></font><p style="line-height: 100%;"></p><p style="line-height: 100%; font-weight: bold; text-decoration: underline;"><font color="#000000"><a name="configuration_for_other_machines"></a>Configuration
284for other machines</font></p><font color="#000000">Starting
[83]285from version 3.2a, beside the default hosts (HLRN, etc.), PALM can also
286be installed and run on other Linux-Cluster-, IBM-AIX, or
287NEC-SX-systems. To configure PALM for a non-default host only requires
[290]288to add some lines to the configuration file<span style="font-family: Courier New,Courier,monospace;">
289.mrun.config</span>.<br><br>First,
[83]290you have to define the host identifier (a string of arbitrary length)
[290]291under which your local host shall be identified by adding a line<br><br></font><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">%host_identifier
292&nbsp;&lt;hostname&gt; &nbsp;&lt;host
293identifier&gt;</span><br></div><br>to the
294configuration file (best to do this in the section where the other
295default host identifiers are defined). Here<span style="font-family: Courier New,Courier,monospace;">
296&lt;hostname&gt; </span>must be the name of your local
297host as provided by the unix-command "<span style="font-family: Courier New,Courier,monospace;">hostname</span>".
298The first characters of<span style="font-family: Courier New,Courier,monospace;">
299&lt;host identifier&gt; </span>have to be "<span style="font-family: Courier New,Courier,monospace;">lc</span>",
300if your system is (part of) a linux-cluster, "<span style="font-family: Courier New,Courier,monospace;">ibm</span>",
301or "<span style="font-family: Courier New,Courier,monospace;">nec</span>"
[83]302in case of an IBM-AIX- or NEC-SX-system, respectively. For example, if
[290]303you want to install on a linux-cluster, the line may read as<br><br><div style="margin-left: 40px;">%host_identifier &nbsp;foo
304&nbsp;lc_bar<br></div><br>In
[83]305the second step, you have to give all informations neccessary to
306compile and run PALM on your local host by adding an additional section
[290]307to the configuration file:<br><br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username&nbsp;&nbsp;
308&lt;1&gt;&nbsp; &nbsp; &nbsp; &lt;host
309identifier&gt; parallel<br>%tmp_user_catalog&nbsp;
310&lt;2&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host
311identifier&gt; parallel<br>%compiler_name&nbsp;&nbsp;&nbsp;&nbsp;
312&lt;3&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host
313identifier&gt; parallel<br>%compiler_name_ser
314&lt;4&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host
315identifier&gt; parallel<br>%cpp_options&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
316&lt;5&gt; &nbsp; &nbsp; &nbsp;&lt;host
317identifier&gt;&nbsp;parallel<br>%netcdf_inc&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
318&lt;6&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host
319identifier&gt; parallel<br>%netcdf_lib&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
320&lt;7&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host
321identifier&gt; parallel<br>%fopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
322&lt;8&gt; &nbsp;&nbsp;&nbsp; &nbsp;&lt;host
323identifier&gt; parallel<br>%lopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
324&nbsp;&lt;9&gt; &nbsp; &nbsp;
325&nbsp;&lt;host identifier&gt; parallel<br></div><br>The
[83]326section consists of four columns each separated by one or more blanks.
327The first column gives the name of the respective environment variable
[290]328used by <span style="font-weight: bold;">mrun</span>
329and <span style="font-weight: bold;">mbuild</span>,
[83]330while the second column defines its value. The third column has to be
331the host identifier as defined above, and the last column in each line
332must contain the string "<span style="font-family: Courier New,Courier,monospace;">parallel</span>".
333Otherwise, the respective line(s) will be interpreted as belonging to
334the setup for compiling and running a serial (non-parallel) version of
[290]335PALM.<br><br>All brackets have to be replaced by the
336appropriate settings for your local host:<br><ul><li><span style="font-family: Courier New,Courier,monospace;">&lt;1&gt;
337</span>is the username on your LOCAL host</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;2&gt;
338</span>is the temporary directory in which PALM runs will be
339carried out</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;3&gt;
340</span>is the compiler name which generates parallel code</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;4&gt;
341</span>is the compiler name for generating serial code</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;5&gt;
342</span>are
[83]343the preprocessor options to be invoked. In most of the cases, it will
344be neccessary to adjust the MPI data types to double precision by
[290]345giving <span style="font-family: Courier New,Courier,monospace;">-DMPI_REAL=MPI_DOUBLE_PRECISION
346-DMPI_2REAL=MPI_2DOUBLE_PRECISION</span>. To switch on the NetCDF
347support, you also have to give <span style="font-family: Courier New,Courier,monospace;">-D__netcdf</span>
348and <span style="font-family: Courier New,Courier,monospace;">-D__netcdf_64bit</span>
349(if you like to have 64bit NetCDF output).</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;6&gt;
350</span>is the compiler option for specifying the include path to
351search for the NetCDF module/include files</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;7&gt;
352</span>are the linker options to search for the NetCDF library</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;8&gt;
353</span>are the general compiler options to be used. You should
354allways switch on double precision (e.g. <span style="font-family: Courier New,Courier,monospace;">-r8</span>)
355and code optimization (e.g. <span style="font-family: Courier New,Courier,monospace;">-O2</span>).</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;9&gt;
356</span>are the linker options</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;host
357identifier&gt; </span>is the host identifier as defined
358before</li></ul><br>A typical example may be:<br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username&nbsp;&nbsp;
359raasch &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
360&nbsp; &nbsp; &nbsp; &nbsp;
361&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
362&nbsp; &nbsp;lc_bar parallel<br>%tmp_user_catalog&nbsp;
[83]363/tmp&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;lc_bar
364parallel<br>%compiler_name&nbsp;&nbsp;&nbsp;&nbsp;
365mpif90&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;lc_bar
366parallel<br>%compiler_name_ser
367ifort&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;lc_bar
368parallel<br>%cpp_options&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
369-DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__netcdf_64bit&nbsp;&nbsp;
370lc_bar parallel<br>%netcdf_inc&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
371-I:/usr/local/netcdf/include&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
372lc_bar parallel<br>%netcdf_lib&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
373-L/usr/local/netcdf/lib:-lnetcdf&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
374lc_bar parallel<br>%fopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
[290]375-axW:-cpp:-openmp:-r8:-nbs &nbsp; &nbsp; &nbsp;
376&nbsp;&nbsp;
[83]377&nbsp;&nbsp;&nbsp; lc_bar parallel<br>%lopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
378-axW:-cpp:-openmp:-r8:-nbs:-Vaxlib&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;lc_bar
[290]379parallel<br></div><br>Currently (version 3.2a),
380depending on the MPI
[83]381version which is running on your local host, the options for the
[290]382execution command (which may be <span style="font-family: Courier New,Courier,monospace;">mpirun</span>
383or <span style="font-family: Courier New,Courier,monospace;">mpiexec</span>)
[83]384may have to be adjusted manually in the mrun-script. A future version
385will allow to give the respective settings in the configuration file.
[62]386<p style="line-height: 100%;">If you have any problems
387with the PALM
[5]388installation, the members of the PALM working group are pleased to
389help you. &nbsp; </p>
[290]390<hr><p style="line-height: 100%;"><font color="#000080"><font color="#000080"><a href="chapter_4.6.html"><font color="#000080"><img src="left.gif" name="Grafik1" align="bottom" border="2" height="32" width="32"></font></a><a href="index.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="up" src="up.gif" name="Grafik2"></font></a><a href="chapter_5.1.html"><font color="#000080"><img src="right.gif" name="Grafik3" align="bottom" border="2" height="32" width="32"></font></a></font></font></p><p style="line-height: 100%;"><i>Last
391change:&nbsp;</i> $Id: chapter_5.0.html 287 2009-04-09
39208:59:36Z raasch $</p>
[40]393</body></html>
Note: See TracBrowser for help on using the repository browser.