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1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
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>
5@page { size: 21cm 29.7cm }
8<body style="direction: ltr;" lang="en-US"><h2 style="line-height: 100%;"><font size="4">5.0
9Installation of the
11<font color="#000000">This chapter
12describes the installation of PALM on a Linux workstation (local host)
13and a suitable remote computer, on which the
14model runs are to be carried out. The local host is used to
15start batch jobs with <b>mrun</b> and to analyze the
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
20as a batch job (if a queueing system like NQS, PBS, or LoadLeveler is available).</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
21installation and operation of PALM requires at mimimum (on both, the
22local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The Korn-shell (AT&amp;T ksh or public domain ksh) must be
23available 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
24NetCDF-library with version number not earlier than 3.6.0-p1 (for
25NetCDF, see under <a href=""></a>).</font></li><li><font color="#000000">A FORTRAN90/95 compiler.</font></li><li><font color="#000000">The Message Passing Interface (MPI), at
26least 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
27system <span style="font-weight: bold;">subversion</span>
28(see <a href=""></a>).
29This is already included in many Linux distributions (e.g. SuSe). <span style="font-weight: bold;">subversion requires port 3690 to
30be open for tcp/udp.</span> <span style="font-weight: bold;">If
31there are firewall restrictions concerning this port, the PALM code
32cannot be accessed.</span> The
33user needs a permit to access the PALM repository. For getting a permit
34please contact the PALM group (<a href=""></a>)
35and define a username under which you like to access the repository.
36You will then receive a password which allows the access under this
37name.</font></li><li><font color="#000000">A
38job queueing system must be available on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle
39LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).</font></li><li><font color="#000000">ssh/scp-connections to and from the remote
40host 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
41to be used on a limited number of selected machines. These are SGI-ICE systems at computing center HLRN in Hannover (<span style="font-style: italic;">lcsgih</span>), Berlin (<span style="font-style: italic;">lcsgib</span>), IBM-Regatta system<span style="font-style: italic;"></span>
42at Yonsei University, Seoul (<span style="font-style: italic;">ibms</span>),
43on NEC-SX6/8 systems at DKRZ, Hamburg (<span style="font-style: italic;">nech</span>) and RIAM,
44Kyushu University, Fukuoka (<span style="font-style: italic;">necriam</span>),
45as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>), Tokyo
46Institute of Technology (<span style="font-style: italic;">lctit</span>), and the Bergen Center for Computational Science (<span style="font-style: italic;">lcxt4</span>).
47The strings given in brackets are the systems names (host identifiers) under which <span style="font-weight: bold;">mrun</span> identifies the
48different hosts.<br><br>You can also use <span style="font-weight: bold;">mrun</span>/PALM on other Linux-Cluster, IBM-AIX, or NEC-SX machines. See <a href="#configuration_for_other_machines">below</a> on how to configure <span style="font-weight: bold;">mrun</span> for other machines. However, these configurations currently (version 3.2a) 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
49examples given in this chapter refer to an
50installation of PALM on an IMUK Linux workstation and the SGI-ICE
51system of
52the HLRN used as&nbsp;remote host. They are just called local and
53remote host from now on. </font></p><p style="line-height: 100%;">
54</p><p style="line-height: 100%;">The installation
55process requires a valid
56account on the local and on the remote host as well.<br>
57&nbsp; </p>
58<ul> All hosts (local as well as remote) are
59accessed via the secure shell (ssh). The user must establish
60passwordless login using the private/public-key mechanism (see e.g. the
61<a href="">HLRN
62documentation</a>). <b>To ensure proper function of mrun,
63passwordless login must be
64established in both directions, from the local to the remote host as
65well as from the remote to the local host!</b> Test this by
67out e.g. on the local host: <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
68</span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp;
69&lt;username on remote host&gt;@&lt;remote
70IP-address&gt;</span><br> </p> <p style="line-height: 100%;">and on the remote host:<br>
71</p> <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
72</span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp;
73&lt;username on local host&gt;@&lt;local IP-adddress&gt;</span><br>
74</p> In both cases you should&nbsp;not be
75prompted for a password. <b>Before continuing the further
77process, this must be absolutely guaranteed!</b> This must also
79guaranteed for <b>all</b> other remote hosts, on which
80PALM shall run.
81</ul><p style="line-height: 100%;"></p><p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package
82Installation</span></p><p style="line-height: 100%;">In
83the <b>first installation step</b> a
84set of directories must be created both on the local and on the
85remote 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
87freely selectable (except <tt><font size="2">~/job_queue</font></tt>),
88however new users should use them as suggested, since many
89examples in this documentation as well as all example files are
90assuming these settings. The directory <span style="font-family: monospace;">~/palm/current_version</span>
91on the local host will be called the working directory from now on. </p>
92<p style="line-height: 100%;"><font color="#000000">In
93the <b>second
95a working copy of the recent version of the PALM software package,
96including the source code, scripts, documentation, etc.&nbsp; must
98copied to the working directory (</font><font color="#000000">local
99host!) by executing the following
100commands. Replace &lt;your username&gt; by the name that you
101chose to
102access the repository, and &lt;#&gt; by any of the available
104releases, e.g. "<span style="font-style: italic;">3.1c</span>"
105(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
106~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn
107checkout --username &lt;your username&gt;
108svn://;#&gt; trunk</span><br></div><p style="line-height: 100%;"><font color="#000000">You
109will then be prompted for your password. After finishing, the
110subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">should
111appear in your working directory. It contains a number of further
112subdirectories which contain e.g. the PALM source code (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SOURCE</font><font color="#000000">)
113and 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://;#&gt; abcde</pre><p style="line-height: 100%;">will place your working copy in a
114directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span>instead
115of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span>.
116But keep in mind that you will have to adjust several paths given
117below, 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
118your working copy of PALM, unless you&nbsp;know exactly what you
119are doing.</p><p style="line-height: 100%; font-weight: bold;"><span style="font-weight: normal;">You can also get a copy of the
120most 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:// trunk</pre>However,
121this version may contain bugs and new features may not be documented. <span style="font-weight: bold;">In future PALM releases,
122repository access to this most recent&nbsp;version will
123probably 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
124Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To
125use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable has to be extended and the
126environment variable<span style="font-family: Courier New,Courier,monospace;"> PALM_BIN </span>has to be set (on local and remote host)
127in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>,
128if<span style="font-family: Courier New,Courier,monospace;">
129ksh </span>is used):</font></p><p style="line-height: 100%; margin-left: 40px;"><font style="font-family: Courier New,Courier,monospace;" color="#000000">export
130PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH</font><font color="#000000"><br><span style="font-family: Courier New,Courier,monospace;">export
131PALM_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
132may have to login again in order to activate these settings.</font></p><font color="#000000">On the local and on the remote host, some
133small helper/utility programs have to be installed, which are&nbsp;later used by <span style="font-weight: bold;">mrun</span>&nbsp;e.g. for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script
134requires a configuration file<span style="font-family: Courier New,Courier,monospace;">
135.mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the
136following. A copy has to be put into the working directory under the
137name<span style="font-family: Courier New,Courier,monospace;">
138.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
139trunk/SCRIPTS/.mrun.config.default .mrun.config</span></font></p><font color="#000000">Beside many other things, this file contains
140typical installation parameters
141like compiler name, compiler options, etc.
142for a set of different (remote) hosts. Please edit this file, uncomment
143lines like</font><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username
144&nbsp;&lt;replace by your ... username&gt; &nbsp;
145&lt;host identifier&gt;</div><p style="line-height: 100%;"><font color="#000000">by
146removing the first hash (<span style="font-family: Courier New,Courier,monospace;">#</span>)
147character and replace the string "<span style="font-family: Courier New,Courier,monospace;">&lt;replace
148by ...&gt;</span>" by your username on the respective host
149given in the <span style="font-family: Courier New,Courier,monospace;">&lt;host identifier&gt;</span>.
150You only have to uncomment lines for those hosts on which you intend to
151use 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;"> trunk/SCRIPTS </span>contains additional configuration files which are already adjusted for special hosts:<span style="font-family: Courier New,Courier,monospace;"> .mrun.config.imuk </span>can be used at Hannover University,<span style="font-family: Courier New,Courier,monospace;"> .mrun.config.riam </span>can
152be used at the Research Institute of Applied Mechanics, Kyushu
153University. These files have to be edited in the same way as described
154above.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the
155respective 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 lcsgih</font></p><p style="line-height: 100%;"><font color="#000000">The
156second call also copies the PALM scripts (like <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span>) to the remote
157host.</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
158of PALM Code</span></font></p><font color="#000000">
159</font><br><font color="#000000">To avoid the
160re-compilation of the complete source code for each model run, PALM
161willl be pre-compiled once on the remote host by again using the script
162<span style="font-weight: bold;">mbuild</span>. Due
163to the use of
164FORTRAN modules in the source code, the subroutines must be compiled
165in a certain order. Therefore the so-called <i>make</i>
167is used (see the respective man-page of the Unix operating system),
168requiring a<span style="font-family: Courier New,Courier,monospace;">
169</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">Makefile</font><font color="#000000">,
170in which the dependencies are described. This file is found in
171subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE<span style="font-family: Times New Roman,Times,serif;">, where
172also the PALM code is stored</span></span>. The compiled
173sources (object
174files) are
175stored&nbsp;on the remote computer in the default directory
176</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
177pre-compilation for the remote host (here the SGI-ICE system of HLRN) is
178done by</font><span style="font-family: monospace;"></span></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">mbuild
179-h lcsgih &nbsp;</span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild
180</span>will prompt some queries<font color="#000000">,
181which must all be
182answered "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
183the respective compiler calls to the remote
184host where they are carried out interactively. You can follow the
185progress at the terminal window, where also error messages
186are displayed (hopefully not for this standard installation). By just
187entering </font></p><p style="line-height: 100%;">
188</p><blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote>
189<p style="line-height: 100%;"><font color="#000000">PALM
191be (consecutively) pre-compiled for all remote hosts listed in
192the configuration file. If you want to compile for the local host only,
193please enter</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">mbuild
194-h lcmuk</span> </font>
195</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,
196after the compilation has been finished, the PALM installation has to
197be verified. For this
198purpose a simple test run is carried out. This once again requires the <b>mrun
199</b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter
2003.2</font></a><font color="#000000">), as well
201as the </font><a href=""><font color="#000080">parameter
202file</font></a><font color="#000000">
203(described in </font><a href="chapter_4.4.1.html"><font color="#000080">chapter
2044.4.1</font></a>)<font color="#000000">. The
205parameter file must be
206copied from the PALM working copy by<br>
207</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
208trunk/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>
209<p style="line-height: 100%;"><font color="#000000">The
210test run can
211now be started by executing the command </font>
212</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>
213<font color="#000000">This specific run
214will be carried out on 8 PEs and is allowed to use up to 500 seconds
215CPU time. After pressing &lt;return&gt;, the most important
216settings of
217the job are displayed at the terminal window
218and 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;).
219Next, a message of the queuing system like &ldquo;<i>Request</i>
221<i>Submitted to queue&hellip; by&hellip;&rdquo; </i>should
222be displayed. Now the job is
223queued and either started immediately or at a later time, depending on
225current workload of the remote host. Provided that it is executed
226immediately and that all things work as designed, the job protocol of
227this 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
228more than a few minutes later. The content of this
229file should be carefully examined for any error messages.</font><p style="line-height: 100%;">
230</p><p style="line-height: 100%;">Beside the job
231protocol and according to
232the configuration file and arguments given for <b>mrun</b>
233options<span style="font-family: Courier New,Courier,monospace;">
234-d </span>and<span style="font-family: Courier New,Courier,monospace;"> -r</span><tt>,</tt>further
235files should be found in
237directories</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>
238<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
239</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/OUTPUT</span><span style="font-family: monospace;"></span><br>
240</p><p style="line-height: 100%;">Please compare the
241contents of file</p>
242<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
243</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/MONITORING/lcsgih_example_rc</span><br>
244</p><p style="line-height: 100%;">with those of the
245example result file which can be found under<span style="font-family: Courier New,Courier,monospace;">
246trunk/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>
247diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff
249trunk/INSTALL/example_cbl_rc</p><p style="line-height: 100%;">where
250it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;">
251~/palm/current_version</span>.</p><span style="font-weight: bold;">You should not find any
252difference between these two files</span>, except of the run date
253and time displayed at the top of the file header. <font color="#000000">If
254the file contents are identical, the installation is successfully
255completed.<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 for other machines</font></p><font color="#000000">Starting
256from version 3.2a, beside the default hosts (HLRN, etc.), PALM can also
257be installed and run on other Linux-Cluster-, IBM-AIX, or
258NEC-SX-systems. To configure PALM for a non-default host only requires
259to add some lines to the configuration file<span style="font-family: Courier New,Courier,monospace;"> .mrun.config</span>.<br><br>First,
260you have to define the host identifier (a string of arbitrary length)
261under 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 &nbsp;&lt;hostname&gt; &nbsp;&lt;host identifier&gt;</span><br></div><br>to the configuration file (best to do this in the section where the other default host identifiers are defined). Here<span style="font-family: Courier New,Courier,monospace;"> &lt;hostname&gt; </span>must be the name of your local host as provided by the unix-command "<span style="font-family: Courier New,Courier,monospace;">hostname</span>". The first characters of<span style="font-family: Courier New,Courier,monospace;"> &lt;host identifier&gt; </span>have to be "<span style="font-family: Courier New,Courier,monospace;">lc</span>", if your system is (part of) a linux-cluster, "<span style="font-family: Courier New,Courier,monospace;">ibm</span>", or "<span style="font-family: Courier New,Courier,monospace;">nec</span>"
262in case of an IBM-AIX- or NEC-SX-system, respectively. For example, if
263you want to install on a linux-cluster, the line may read as<br><br><div style="margin-left: 40px;">%host_identifier &nbsp;foo &nbsp;lc_bar<br></div><br>In
264the second step, you have to give all informations neccessary to
265compile and run PALM on your local host by adding an additional section
266to the configuration file:<br><br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username&nbsp;&nbsp; &lt;1&gt;&nbsp; &nbsp; &nbsp; &lt;host identifier&gt; parallel<br>%tmp_user_catalog&nbsp; &lt;2&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host identifier&gt; parallel<br>%compiler_name&nbsp;&nbsp;&nbsp;&nbsp; &lt;3&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host identifier&gt; parallel<br>%compiler_name_ser &lt;4&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host identifier&gt; parallel<br>%cpp_options&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
267&lt;5&gt; &nbsp; &nbsp; &nbsp;&lt;host identifier&gt;&nbsp;parallel<br>%netcdf_inc&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;6&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host identifier&gt; parallel<br>%netcdf_lib&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;7&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host identifier&gt; parallel<br>%fopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
268&lt;8&gt; &nbsp;&nbsp;&nbsp; &nbsp;&lt;host identifier&gt; parallel<br>%lopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
269&nbsp;&lt;9&gt; &nbsp; &nbsp; &nbsp;&lt;host identifier&gt; parallel<br></div><br>The
270section consists of four columns each separated by one or more blanks.
271The first column gives the name of the respective environment variable
272used by <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span>,
273while the second column defines its value. The third column has to be
274the host identifier as defined above, and the last column in each line
275must contain the string "<span style="font-family: Courier New,Courier,monospace;">parallel</span>".
276Otherwise, the respective line(s) will be interpreted as belonging to
277the setup for compiling and running a serial (non-parallel) version of
278PALM.<br><br>All brackets have to be replaced by the appropriate settings for your local host:<br><ul><li><span style="font-family: Courier New,Courier,monospace;">&lt;1&gt; </span>is the username on your LOCAL host</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;2&gt; </span>is the temporary directory in which PALM runs will be carried out</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;3&gt; </span>is the compiler name which generates parallel code</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;4&gt; </span>is the compiler name for generating serial code</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;5&gt; </span>are
279the preprocessor options to be invoked. In most of the cases, it will
280be neccessary to adjust the MPI data types to double precision by
281giving <span style="font-family: Courier New,Courier,monospace;">-DMPI_REAL=MPI_DOUBLE_PRECISION -DMPI_2REAL=MPI_2DOUBLE_PRECISION</span>. To switch on the NetCDF support, you also have to give <span style="font-family: Courier New,Courier,monospace;">-D__netcdf</span> and <span style="font-family: Courier New,Courier,monospace;">-D__netcdf_64bit</span> (if you like to have 64bit NetCDF output).</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;6&gt; </span>is the compiler option for specifying the include path to search for the NetCDF module/include files</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;7&gt; </span>are the linker options to search for the NetCDF library</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;8&gt; </span>are the general compiler options to be used. You should allways switch on double precision (e.g. <span style="font-family: Courier New,Courier,monospace;">-r8</span>) and 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; </span>are the linker options</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;host identifier&gt; </span>is the host identifier as defined before</li></ul><br>A typical example may be:<br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username&nbsp;&nbsp;
282raasch &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
283&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;lc_bar parallel<br>%tmp_user_catalog&nbsp;
291lc_bar parallel<br>%netcdf_inc&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
293lc_bar parallel<br>%netcdf_lib&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
295lc_bar parallel<br>%fopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
296-axW:-cpp:-openmp:-r8:-nbs &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;
297&nbsp;&nbsp;&nbsp; lc_bar parallel<br>%lopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
299parallel<br></div><br>Currently (version 3.2a), depending on the MPI
300version which is running on your local host, the options for the
301execution command (which may be <span style="font-family: Courier New,Courier,monospace;">mpirun</span> or <span style="font-family: Courier New,Courier,monospace;">mpiexec</span>)
302may have to be adjusted manually in the mrun-script. A future version
303will allow to give the respective settings in the configuration file.
304<p style="line-height: 100%;">If you have any problems
305with the PALM
306installation, the members of the PALM working group are pleased to
307help you. &nbsp; </p>
308<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>
309<p style="line-height: 100%;"><i>Last
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