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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>
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8<body style="direction: ltr;" lang="en-US"><h2 style="line-height: 100%;"><font size="4">5.0
9Installation of the
10model</font></h2>
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
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
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
22installation and operation of PALM requires at mimimum (on both, the
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
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
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
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
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
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>
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,
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
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
60examples given in this chapter refer to an
61installation of PALM on an IMUK Linux workstation and the SGI-ICE
62system of
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
67account on the local and on the remote host as well.<br>
68&nbsp; </p>
69<ul> All hosts (local as well as remote) are
70accessed via the secure shell (ssh). The user must establish
71passwordless login using the private/public-key mechanism (see e.g. the
72<a href="http://www2.hlrn.de/doc/ssh/index.html">HLRN
73documentation</a>). <b>To ensure proper function of mrun,
74passwordless login must be
75established in both directions, from the local to the remote host as
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
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
97Installation</span></p><p style="line-height: 100%;">In
98the <b>first installation step</b> a
99set of directories must be created both on the local and on the
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
102freely selectable (except <big><tt><font size="2"><big>~/job_queue</big></font></tt></big>),
103however new users should use them as suggested, since many
104examples in this documentation as well as all example files are
105assuming these settings. The directory <big><span style="font-family: monospace;">~/palm/current_version</span></big>
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
109step</b>
110a working copy of the recent version of the PALM software package,
111including the source code, scripts, documentation, etc.&nbsp; must
112be
113copied to the working directory (</font><font color="#000000">local
114host!) by executing the following
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
126appear in your working directory. It contains a number of further
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
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)
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
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
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
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
160like compiler name, compiler options, etc.
161for a set of different (remote) hosts. Please edit this file, uncomment
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;
164&lt;host identifier&gt;</div><p style="line-height: 100%;"><font color="#000000">by
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
168given in the <span style="font-family: Courier New,Courier,monospace;">&lt;host
169identifier&gt;</span>.
170You only have to uncomment lines for those hosts on which you intend to
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;">
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
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
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
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
188re-compilation of the complete source code for each model run, PALM
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
192FORTRAN modules in the source code, the subroutines must be compiled
193in a certain order. Therefore the so-called <i>make</i>
194mechanism
195is used (see the respective man-page of the Unix operating system),
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
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
201sources (object
202files) are
203stored&nbsp;on the remote computer in the default directory
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
205pre-compilation for the remote host (here the SGI-ICE system of HLRN)
206is
207done by</font><span style="font-family: monospace;"></span></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">mbuild
208-h lcsgih &nbsp;</span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild
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
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
216entering </font></p><p style="line-height: 100%;">
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
220be (consecutively) pre-compiled for all remote hosts listed in
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,
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
228</b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter
2293.2</font></a><font color="#000000">), as well
230as the </font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_cbl_p3d"><font color="#000080">parameter
231file</font></a><font color="#000000">
232(described in </font><a href="chapter_4.4.1.html"><font color="#000080">chapter
2334.4.1</font></a>)<font color="#000000">. The
234parameter file must be
235copied from the PALM working copy by<br>
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>
238<p style="line-height: 100%;"><font color="#000000">The
239test run can
240now be started by executing the command </font>
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
242will be carried out on 8 PEs and is allowed to use up to 500 seconds
243CPU time. After pressing &lt;return&gt;, the most important
244settings of
245the job are displayed at the terminal window
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
253current workload of the remote host. Provided that it is executed
254immediately and that all things work as designed, the job protocol of
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
256more than a few minutes later. The content of this
257file should be carefully examined for any error messages.</font><p style="line-height: 100%;">
258</p><p style="line-height: 100%;">Beside the job
259protocol and according to
260the configuration file and arguments given for <b>mrun</b>
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
264the
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>
266<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
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>
268</p><p style="line-height: 100%;">Please compare the
269contents of file</p>
270<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
271</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/MONITORING/lcsgih_example_rc</span><br>
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;">
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>
275diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff
276&nbsp;JOBS/example_cbl/MONITORING/lcsgih_example_cbl_rc
277trunk/INSTALL/example_cbl_rc</p><p style="line-height: 100%;">where
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
282the file contents are identical, the installation is successfully
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
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
288to add some lines to the configuration file<span style="font-family: Courier New,Courier,monospace;">
289.mrun.config</span>.<br><br>First,
290you have to define the host identifier (a string of arbitrary length)
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>"
302in case of an IBM-AIX- or NEC-SX-system, respectively. For example, if
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
305the second step, you have to give all informations neccessary to
306compile and run PALM on your local host by adding an additional section
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
326section consists of four columns each separated by one or more blanks.
327The first column gives the name of the respective environment variable
328used by <span style="font-weight: bold;">mrun</span>
329and <span style="font-weight: bold;">mbuild</span>,
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
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
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
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;
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;
375-axW:-cpp:-openmp:-r8:-nbs &nbsp; &nbsp; &nbsp;
376&nbsp;&nbsp;
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
379parallel<br></div><br>Currently (version 3.2a),
380depending on the MPI
381version which is running on your local host, the options for the
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>)
384may have to be adjusted manually in the mrun-script. A future version
385will allow to give the respective settings in the configuration file.
386<p style="line-height: 100%;">If you have any problems
387with the PALM
388installation, the members of the PALM working group are pleased to
389help you. &nbsp; </p>
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>
393</body></html>
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