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3<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM
4chapter 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>
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9<body style="direction: ltr;" lang="en-US"><h2 style="line-height: 100%;"><font size="4">5.0
10Installation of the
11model</font></h2>
12<font color="#000000">This chapter
13describes the installation of PALM on a Linux workstation (local host)
14and a suitable remote computer, on which the
15model runs are to be carried out. The local host is used to
16start batch jobs with <b>mrun</b> and to analyze the
17results
18which are produced by the model on the remote host and send back to the
19local host. Alternatively, <span style="font-weight: bold;">mrun</span>
20can also be used to start PALM on the local host in interactive mode or
21as a batch job (if a queueing system like NQS, PBS, or LoadLeveler is
22available).</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
23installation and operation of PALM requires at mimimum (on both, the
24local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The Korn-shell (AT&amp;T ksh or public
25domain ksh) must be
26available 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
27NetCDF-library with version number not earlier than 3.6.0-p1 (for
28NetCDF, 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
29least 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
30system <span style="font-weight: bold;">subversion</span>
31(see <a href="http://subversion.tigris.org/">subversion.tigris.org</a>).
32This is already included in many Linux distributions (e.g. SuSe). <span style="font-weight: bold;">subversion requires port 3690 to
33be open for tcp/udp.</span> <span style="font-weight: bold;">If
34there are firewall restrictions concerning this port, the PALM code
35cannot be accessed.</span> The
36user needs a permit to access the PALM repository. For getting a permit
37please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>)
38and define a username under which you like to access the repository.
39You will then receive a password which allows the access under this
40name.</font></li><li><font color="#000000">A
41job queueing system must be available on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle
42LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).</font></li><li><font color="#000000">ssh/scp-connections to and from the remote
43host 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
44to be used on a limited number of selected machines. These are SGI-ICE
45systems at computing center HLRN in Hannover (<span style="font-style: italic;">lcsgih</span>), Berlin (<span style="font-style: italic;">lcsgib</span>),
46IBM-Regatta system<span style="font-style: italic;"></span>
47at Yonsei University, Seoul (<span style="font-style: italic;">ibms</span>),
48on NEC-SX6/8 systems at DKRZ, Hamburg (<span style="font-style: italic;">nech</span>) and RIAM,
49Kyushu University, Fukuoka (<span style="font-style: italic;">necriam</span>),
50as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>), Tokyo
51Institute of Technology (<span style="font-style: italic;">lctit</span>),
52and the Bergen Center for Computational Science (<span style="font-style: italic;">lcxt4</span>).
53The strings given in brackets are the systems names (host identifiers)
54under which <span style="font-weight: bold;">mrun</span>
55identifies the
56different hosts.<br><br>You can also use <span style="font-weight: bold;">mrun</span>/PALM on other
57Linux-Cluster, IBM-AIX, or NEC-SX machines. See <a href="#configuration_for_other_machines">below</a> on
58how to configure <span style="font-weight: bold;">mrun</span>
59for other machines. However, these configurations currently (version
603.2a) 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
61examples given in this chapter refer to an
62installation of PALM on an IMUK Linux workstation and the SGI-ICE
63system of
64the HLRN used as&nbsp;remote host. They are just called local and
65remote host from now on. </font></p><p style="line-height: 100%;">
66</p><p style="line-height: 100%;">The installation
67process requires a valid
68account on the local and on the remote host as well.<br>
69&nbsp; </p>
70<ul> All hosts (local as well as remote) are
71accessed via the secure shell (ssh). The user must establish
72passwordless login using the private/public-key mechanism (see e.g. the
73<a href="http://www2.hlrn.de/doc/ssh/index.html">HLRN
74documentation</a>). <b>To ensure proper function of mrun,
75passwordless login must be
76established in both directions, from the local to the remote host as
77well as from the remote to the local host!</b> Test this by
78carrying
79out e.g. on the local host: <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
80</span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp;
81&lt;username on remote host&gt;@&lt;remote
82IP-address&gt;</span><br> </p> <p style="line-height: 100%;">and on the remote host:<br>
83</p> <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
84</span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp;
85&lt;username on local host&gt;@&lt;local IP-adddress&gt;</span><br>
86</p> In both cases you should&nbsp;not be
87prompted for a password. <b>Before continuing the further
88installation
89process, this must be absolutely guaranteed!</b> This must also
90be
91guaranteed for <b>all</b> other remote hosts, on which
92PALM shall run.<br><br>Please
93note that on many remote hosts, passwordless login must also be
94established <b>within the remote host</b>, i.e. from the
95remote host to itself. Test this by executing on the remote host: <span style="font-family: Courier New,Courier,monospace;">ssh
96&lt;remote IP-address&gt;</span>. You should not be prompted
97for a password.<br><br></ul><p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package
98Installation</span></p><p style="line-height: 100%;">In
99the <b>first installation step</b> a
100set of directories must be created both on the local and on the
101remote 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
102are
103freely selectable (except <big><tt><font size="2"><big>~/job_queue</big></font></tt></big>),
104however new users should use them as suggested, since many
105examples in this documentation as well as all example files are
106assuming these settings. The directory <big><span style="font-family: monospace;">~/palm/current_version</span></big>
107on the local host will be called the working directory from now on. </p>
108<p style="line-height: 100%;"><font color="#000000">In
109the <b>second
110step</b>
111a working copy of the recent version of the PALM software package,
112including the source code, scripts, documentation, etc.&nbsp; must
113be
114copied to the working directory (</font><font color="#000000">local
115host!) by executing the following
116commands. Replace &lt;your username&gt; by the name that you
117chose to
118access the repository, and &lt;#&gt; by any of the available
119PALM
120releases, e.g. "<span style="font-style: italic;">3.1c</span>"
121(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
122~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn
123checkout --username &lt;your username&gt;
124svn://130.75.105.45/palm/tags/release-&lt;#&gt; trunk</span><br></div><p style="line-height: 100%;"><font color="#000000">You
125will then be prompted for your password. After finishing, the
126subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">should
127appear in your working directory. It contains a number of further
128subdirectories which contain e.g. the PALM source code (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SOURCE</font><font color="#000000">)
129and 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
130directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span>instead
131of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span>.
132But keep in mind that you will have to adjust several paths given
133below, 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
134your working copy of PALM, unless you&nbsp;know exactly what you
135are doing.</p><p style="line-height: 100%; font-weight: bold;"><span style="font-weight: normal;">You can also get a copy of the
136most 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,
137this version may contain bugs and new features may not be documented. <span style="font-weight: bold;">In future PALM releases,
138repository access to this most recent&nbsp;version will
139probably 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
140Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To
141use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable
142has to be extended and the
143environment variable<span style="font-family: Courier New,Courier,monospace;">
144PALM_BIN </span>has to be set (on local and remote host)
145in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>,
146if<span style="font-family: Courier New,Courier,monospace;">
147ksh </span>is used):</font></p><p style="line-height: 100%; margin-left: 40px;"><font style="font-family: Courier New,Courier,monospace;" color="#000000">export
148PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH</font><font color="#000000"><br><span style="font-family: Courier New,Courier,monospace;">export
149PALM_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
150may have to login again in order to activate these settings.</font></p><font color="#000000">On the local and on the remote host, some
151small helper/utility programs have to be installed, which
152are&nbsp;later used by <span style="font-weight: bold;">mrun</span>&nbsp;e.g.
153for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script
154requires a configuration file<span style="font-family: Courier New,Courier,monospace;">
155.mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the
156following. A copy has to be put into the working directory under the
157name<span style="font-family: Courier New,Courier,monospace;">
158.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
159trunk/SCRIPTS/.mrun.config.default .mrun.config</span></font></p><font color="#000000">Beside many other things, this file contains
160typical installation parameters
161like compiler name, compiler options, etc.
162for a set of different (remote) hosts. Please edit this file, uncomment
163lines like</font><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username
164&nbsp;&lt;replace by your ... username&gt; &nbsp;
165&lt;host identifier&gt;</div><p style="line-height: 100%;"><font color="#000000">by
166removing the first hash (<span style="font-family: Courier New,Courier,monospace;">#</span>)
167character and replace the string "<span style="font-family: Courier New,Courier,monospace;">&lt;replace
168by ...&gt;</span>" by your username on the respective host
169given in the <span style="font-family: Courier New,Courier,monospace;">&lt;host
170identifier&gt;</span>.
171You only have to uncomment lines for those hosts on which you intend to
172use PALM.</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;">
173trunk/SCRIPTS </span>contains additional configuration files
174which are already adjusted for special hosts:<span style="font-family: Courier New,Courier,monospace;">
175.mrun.config.imuk </span>can be used at Hannover University,<span style="font-family: Courier New,Courier,monospace;">
176.mrun.config.riam </span>can
177be used at the Research Institute of Applied Mechanics, Kyushu
178University. These files have to be edited in the same way as described
179above.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the
180respective 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
181lcsgih</font></p><p style="line-height: 100%;"><font color="#000000">The
182second call also copies the PALM scripts (like <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span>) to the
183remote
184host.</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
185of PALM Code</span></font></p><font color="#000000">
186</font><br><font color="#000000">To avoid the
187re-compilation of the complete source code for each model run, PALM
188willl be pre-compiled once on the remote host by again using the script
189<span style="font-weight: bold;">mbuild</span>. Due
190to the use of
191FORTRAN modules in the source code, the subroutines must be compiled
192in a certain order. Therefore the so-called <i>make</i>
193mechanism
194is used (see the respective man-page of the Unix operating system),
195requiring a<span style="font-family: Courier New,Courier,monospace;">
196</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">Makefile</font><font color="#000000">,
197in which the dependencies are described. This file is found in
198subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span></font><font color="#000000">, where
199also the PALM code is stored.</font><font color="#000000"> The compiled
200sources (object
201files) are
202stored&nbsp;on the remote computer in the default directory
203</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
204pre-compilation for the remote host (here the SGI-ICE system of HLRN)
205is
206done by</font><span style="font-family: monospace;"></span></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">mbuild
207-h lcsgih &nbsp;</span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild
208</span>will prompt some queries<font color="#000000">,
209which must all be
210answered "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
211the respective compiler calls to the remote
212host where they are carried out interactively. You can follow the
213progress at the terminal window, where also error messages
214are displayed (hopefully not for this standard installation). By just
215entering </font></p><p style="line-height: 100%;">
216</p><blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote>
217<p style="line-height: 100%;"><font color="#000000">PALM
218will
219be (consecutively) pre-compiled for all remote hosts listed in
220the configuration file. If you want to compile for the local host only,
221please enter</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">mbuild
222-h lcmuk</span> </font>
223</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,
224after the compilation has been finished, the PALM installation has to
225be verified. For this
226purpose a simple test run is carried out. This once again requires the <b>mrun
227</b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter
2283.2</font></a><font color="#000000">), as well
229as the </font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_cbl_p3d"><font color="#000080">parameter
230file</font></a><font color="#000000">
231(described in </font><a href="chapter_4.4.1.html"><font color="#000080">chapter
2324.4.1</font></a>)<font color="#000000">. The
233parameter file must be
234copied from the PALM working copy by<br>
235</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
236trunk/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>
237<p style="line-height: 100%;"><font color="#000000">The
238test run can
239now be started by executing the command </font>
240</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
241will be carried out on 8 PEs and is allowed to use up to 500 seconds
242CPU time. After pressing &lt;return&gt;, the most important
243settings of
244the job are displayed at the terminal window
245and 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;).
246Next, a message of the queuing system like &ldquo;<i>Request</i>
247&hellip;
248<i>Submitted to queue&hellip; by&hellip;&rdquo; </i>should
249be displayed. Now the job is
250queued and either started immediately or at a later time, depending on
251the
252current workload of the remote host. Provided that it is executed
253immediately and that all things work as designed, the job protocol of
254this 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
255more than a few minutes later. The content of this
256file should be carefully examined for any error messages.</font><p style="line-height: 100%;">
257</p><p style="line-height: 100%;">Beside the job
258protocol and according to
259the configuration file and arguments given for <b>mrun</b>
260options<span style="font-family: Courier New,Courier,monospace;">
261-d </span>and<span style="font-family: Courier New,Courier,monospace;"> -r</span><tt>,</tt>further
262files should be found in
263the
264directories</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>
265<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
266</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/OUTPUT</span><span style="font-family: monospace;"></span><br>
267</p><p style="line-height: 100%;">Please compare the
268contents of file</p>
269<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
270</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/MONITORING/lcsgih_example_rc</span><br>
271</p><p style="line-height: 100%;">with those of the
272example result file which can be found under<span style="font-family: Courier New,Courier,monospace;">
273trunk/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>
274diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff
275&nbsp;JOBS/example_cbl/MONITORING/lcsgih_example_cbl_rc
276trunk/INSTALL/example_cbl_rc</p><p style="line-height: 100%;">where
277it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;">
278~/palm/current_version</span>.</p><span style="font-weight: bold;">You should not find any
279difference between these two files</span>, except of the run date
280and time displayed at the top of the file header. <font color="#000000">If
281the file contents are identical, the installation is successfully
282completed.<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
283for other machines</font></p><font color="#000000">Starting
284from version 3.2a, beside the default hosts (HLRN, etc.), PALM can also
285be installed and run on other Linux-Cluster-, IBM-AIX, or
286NEC-SX-systems. To configure PALM for a non-default host only requires
287to add some lines to the configuration file<span style="font-family: Courier New,Courier,monospace;">
288.mrun.config</span>.<br><br>First,
289you have to define the host identifier (a string of arbitrary length)
290under 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
291&nbsp;&lt;hostname&gt; &nbsp;&lt;host
292identifier&gt;</span><br></div><br>to the
293configuration file (best to do this in the section where the other
294default host identifiers are defined). Here<span style="font-family: Courier New,Courier,monospace;">
295&lt;hostname&gt; </span>must be the name of your local
296host as provided by the unix-command "<span style="font-family: Courier New,Courier,monospace;">hostname</span>".
297The first characters of<span style="font-family: Courier New,Courier,monospace;">
298&lt;host identifier&gt; </span>have to be "<span style="font-family: Courier New,Courier,monospace;">lc</span>",
299if your system is (part of) a linux-cluster, "<span style="font-family: Courier New,Courier,monospace;">ibm</span>",
300or "<span style="font-family: Courier New,Courier,monospace;">nec</span>"
301in case of an IBM-AIX- or NEC-SX-system, respectively. For example, if
302you want to install on a linux-cluster, the line may read as<br><br><div style="margin-left: 40px;">%host_identifier &nbsp;foo
303&nbsp;lc_bar<br></div><br>In
304the second step, you have to give all informations neccessary to
305compile and run PALM on your local host by adding an additional section
306to the configuration file:<br><br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username&nbsp;&nbsp;
307&lt;1&gt;&nbsp; &nbsp; &nbsp; &lt;host
308identifier&gt; parallel<br>%tmp_user_catalog&nbsp;
309&lt;2&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host
310identifier&gt; parallel<br>%compiler_name&nbsp;&nbsp;&nbsp;&nbsp;
311&lt;3&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host
312identifier&gt; parallel<br>%compiler_name_ser
313&lt;4&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host
314identifier&gt; parallel<br>%cpp_options&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
315&lt;5&gt; &nbsp; &nbsp; &nbsp;&lt;host
316identifier&gt;&nbsp;parallel<br>%netcdf_inc&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
317&lt;6&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host
318identifier&gt; parallel<br>%netcdf_lib&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
319&lt;7&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host
320identifier&gt; parallel<br>%fopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
321&lt;8&gt; &nbsp;&nbsp;&nbsp; &nbsp;&lt;host
322identifier&gt; parallel<br>%lopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
323&nbsp;&lt;9&gt; &nbsp; &nbsp;
324&nbsp;&lt;host identifier&gt; parallel<br></div><br>The
325section consists of four columns each separated by one or more blanks.
326The first column gives the name of the respective environment variable
327used by <span style="font-weight: bold;">mrun</span>
328and <span style="font-weight: bold;">mbuild</span>,
329while the second column defines its value. The third column has to be
330the host identifier as defined above, and the last column in each line
331must contain the string "<span style="font-family: Courier New,Courier,monospace;">parallel</span>".
332Otherwise, the respective line(s) will be interpreted as belonging to
333the setup for compiling and running a serial (non-parallel) version of
334PALM.<br><br>All brackets have to be replaced by the
335appropriate settings for your local host:<br><ul><li><span style="font-family: Courier New,Courier,monospace;">&lt;1&gt;
336</span>is the username on your LOCAL host</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;2&gt;
337</span>is the temporary directory in which PALM runs will be
338carried out</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;3&gt;
339</span>is the compiler name which generates parallel code</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;4&gt;
340</span>is the compiler name for generating serial code</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;5&gt;
341</span>are
342the preprocessor options to be invoked. In most of the cases, it will
343be neccessary to adjust the MPI data types to double precision by
344giving <span style="font-family: Courier New,Courier,monospace;">-DMPI_REAL=MPI_DOUBLE_PRECISION
345-DMPI_2REAL=MPI_2DOUBLE_PRECISION</span>. To switch on the NetCDF
346support, you also have to give <span style="font-family: Courier New,Courier,monospace;">-D__netcdf</span>
347and <span style="font-family: Courier New,Courier,monospace;">-D__netcdf_64bit</span>
348(if you like to have 64bit NetCDF output).</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;6&gt;
349</span>is the compiler option for specifying the include path to
350search for the NetCDF module/include files</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;7&gt;
351</span>are the linker options to search for the NetCDF library</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;8&gt;
352</span>are the general compiler options to be used. You should
353allways switch on double precision (e.g. <span style="font-family: Courier New,Courier,monospace;">-r8</span>)
354and 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;
355</span>are the linker options</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;host
356identifier&gt; </span>is the host identifier as defined
357before</li></ul><br>A typical example may be:<br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username&nbsp;&nbsp;
358raasch &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
359&nbsp; &nbsp; &nbsp; &nbsp;
360&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
361&nbsp; &nbsp;lc_bar parallel<br>%tmp_user_catalog&nbsp;
362/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
363parallel<br>%compiler_name&nbsp;&nbsp;&nbsp;&nbsp;
364mpif90&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
365parallel<br>%compiler_name_ser
366ifort&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
367parallel<br>%cpp_options&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
368-DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__netcdf_64bit&nbsp;&nbsp;
369lc_bar parallel<br>%netcdf_inc&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
370-I:/usr/local/netcdf/include&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
371lc_bar parallel<br>%netcdf_lib&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
372-L/usr/local/netcdf/lib:-lnetcdf&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
373lc_bar parallel<br>%fopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
374-axW:-cpp:-openmp:-r8:-nbs &nbsp; &nbsp; &nbsp;
375&nbsp;&nbsp;
376&nbsp;&nbsp;&nbsp; lc_bar parallel<br>%lopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
377-axW:-cpp:-openmp:-r8:-nbs:-Vaxlib&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;lc_bar
378parallel<br></div><br>Currently (version 3.2a),
379depending on the MPI
380version which is running on your local host, the options for the
381execution command (which may be <span style="font-family: Courier New,Courier,monospace;">mpirun</span>
382or <span style="font-family: Courier New,Courier,monospace;">mpiexec</span>)
383may have to be adjusted manually in the mrun-script. A future version
384will allow to give the respective settings in the configuration file.
385<p style="line-height: 100%;">If you have any problems
386with the PALM
387installation, the members of the PALM working group are pleased to
388help you. &nbsp; </p>
389<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
390change:&nbsp;</i> $Id: chapter_5.0.html 287 2009-04-09
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