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6  <title>PALM chapter 5.0</title>
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19<h2 style="line-height: 100%;"><font size="4">5.0 Installation of the
20model</font></h2>
21<p style="line-height: 100%;"><font color="#000000">This chapter
22describes the installation of PALM on the Linux workstation
23cluster of IMUK and a suitable remote computer (host), on which the
24model runs are actually carried out. The local cluster is used to
25start the batch job with <b>mrun</b> and to analyze the results
26produced by the model. In batch mode, runs can be carried on the
27IBM-Regatta
28system of the HLRN, on an IBM-Regatta at KISTI, Korea </font><font
29 color="#000000">(via a local
30DEC-Alpha-workstation at the Department of Atmospheric Sciences of the
31Yonsei University, Seoul)</font><font color="#000000">, and on an
32NEC-SX6 at DKRZ. The examples given in this chapter refer to an
33installation of PALM on the IMUK cluster, considering the IBM-Regatta
34system of
35the HLRN as the remote computer. </font>
36</p>
37<p style="line-height: 100%;">The installation process requires a valid
38account on the IMUK cluster and on the remote host as well. In the
39following the IMUK workstation is called the “local host”. <br>
40&nbsp; </p>
41<ul>
42  <p style="line-height: 100%;">All hosts (local as well as remote) are
43accessed via the secure shell (ssh). The user must establish
44passwordless login using the private/public-key mechanism (see e.g. the
45  <a href="http://www.hlrn.de/doc/ssh/index.html">HLRN documentation</a>).
46  <b>To ensure proper function of mrun, passwordless login must be
47established in both directions, from the local to the remote host as
48well as from the remote to the local host!</b> Test this by carrying
49out e.g. on the local host:</p>
50  <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
51ssh&nbsp; &lt;username on remote host&gt;@&lt;remote IP-address&gt;</span><br>
52  </p>
53  <p style="line-height: 100%;">and on the remote host:<br>
54  </p>
55  <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
56ssh&nbsp; &lt;username on local host&gt;@&lt;local IP-adddress&gt;</span><br>
57  </p>
58  <p style="line-height: 100%;">In both cases you should nnot be
59prompted for a password. <b>Before continuing the further installation
60process, this must be absolutely guaranteed!</b> This must also be
61guaranteed for <b>all</b> other remote hosts, on which PALM shall run.</p>
62</ul>
63<p style="line-height: 100%;">In the <b>first installation step</b> a
64set of directories must be created both on the local and on the
65remote host. These directories are: </p>
66<ul>
67  <pre style="line-height: 100%;"><font size="2">~/job_queue</font><br><font
68 size="2">~/palm</font><br><font size="2">~/palm/current_version</font><br><font
69 size="2">~/palm/current_version/SOURCE</font><br><font size="2">~/palm/current_version/JOBS</font></pre>
70</ul>
71<p style="line-height: 100%;">The names of these directories are
72freely selectable (except <tt><font size="2">~/job_queue</font></tt>),
73however new users should use them as suggested, since many
74examples in this documentation as well as all example files are
75assuming these settings. </p>
76<p style="line-height: 100%;"><font color="#000000">In the <b>second
77step</b> the PALM source code must be copied into directory </font><tt><font
78 size="2"><font color="#000000">~/palm/current_version/SOURCE</font></font></tt><font
79 color="#000000"> on the local host by carrying out the following
80commands: </font>
81</p>
82<ul>
83  <pre style="line-height: 100%;"><font color="#000000">cd ~/palm/current_version/SOURCE</font><br><font
84 color="#000000">ln -s /home/raasch/public_html/PALM_group/INSTALL/RCS .</font><br><font
85 color="#000000">cp RCS/*,v .</font><br><font color="#000000">co *,v</font><br><font
86 color="#000000">rm -rf *,v</font></pre>
87</ul>
88<p style="line-height: 100%;"><font color="#000000">Afterwards, the
89directory</font><font color="#000000"> </font><tt><font size="2"><font
90 color="#000000">~/palm/current_version/SOURCE</font></font></tt><font
91 color="#000000">
92should contain</font><font color="#000000"> all PALM routines as well
93as a file with the name </font><tt><font size="2"><font color="#000000">Makefile</font></font></tt><font
94 color="#000000">. </font><font color="#000000">All files are
95write-protected, the source code files end on “</font><tt><font
96 style="font-size: 11pt;" size="2"><font color="#000000">.f90</font></font></tt><font
97 color="#000000">”.
98The user should never modify these files without further knowledge of
99the PALM code. </font>
100</p>
101<p style="line-height: 100%;"><font color="#000000">To avoid the
102re-compilation of the complete source code for each model run, PALM
103willl be pre-compiled once on the remote host. Due to the use of
104FORTRAN modules in the source code, the subroutines must be compiled
105in a certain sequence. Therefore the so-called <i>make</i> mechanism
106is used (see the respective man-page of the Unix operating system),
107requiring the file </font><tt><font color="#000000">Makefile</font></tt><font
108 color="#000000">,
109in which the dependencies are described. The compiled sources (object
110files) are
111stored on the remote computer in the directory
112</font><tt><font color="#000000">~/palm/current_version/SOURCE/MAKE_DEPOSITORY</font></tt><font
113 color="#000000">.<br>
114&nbsp;<br>
115For pre-compilation the user has to</font> call <font color="#000000">the
116command <b>mbuild</b>, which requires some pre-settings. The path
117variable must be extended on <b>both</b> computers, so that the
118commands <b>mbuild</b> and <b>mrun</b> as well as further routines
119needed by <span style="font-weight: bold;">mrun</span> can be found.
120This is achieved on the local computer via:: </font>
121</p>
122<ul>
123  <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
124 color="#000000">PATH=$PATH:/home/raasch/pub,</font></pre>
125</ul>
126<p style="line-height: 100%;"><font color="#000000">and on the IBM
127Regatta
128system of the HLRN via</font></p>
129<ul>
130  <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
131 color="#000000">PATH=$PATH:/home/h/niksiraa/pub.</font></pre>
132</ul>
133<p style="line-height: 100%;"><font color="#000000">These path
134extensions must be automatically set in the profiles of the local and
135remote host (file "~/.myprofile" at IMUK, file "~/.profile" at HLRN)</font><font
136 color="#000000">.
137</font></p>
138<p style="line-height: 100%;"><font color="#000000">It is now assumed
139that the working directory is
140</font><tt><font color="#000000">~/palm/current_version/SOURCE</font></tt><font
141 color="#000000">
142on the local host. Compilation of the PALM code via <b>mbuild </b>needs
143a </font><a
144 href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/.mrun.config"><font
145 color="#000080">configuration
146file</font></a><font color="#000080">,</font><font color="#000000">
147which must be copied to the working directory under name
148</font><tt><font color="#000000">.mrun.config</font></tt><font
149 color="#000000">
150(please click on the link with &lt;SHIFT&gt; + left mouse button)</font><font
151 color="#000000">. This file contains typical installation parameters
152like compiler name, compiler options, etc.
153for a set of different remote hosts. This file is also needed later on
154for starting the model runs. </font>
155</p>
156<p style="line-height: 100%;"><font color="#000000">In the
157configuration file </font><tt><font color="#000000">.mrun.config</font></tt><font
158 color="#000000">
159the user name on the respective remote host must be entered. In lines
160like</font>
161</p>
162<ul>
163  <p style="line-height: 100%;"><tt><font color="#000000">%
164remote_username &lt;username&gt; &lt;remote-computer-shortcut&gt;</font></tt></p>
165</ul>
166the string "<span style="font-family: monospace;">&lt;username&gt;</span>"
167has to be replaced by the actual name of the user on the respective
168remote host (e.g. "nik....." on HLRN).<font color="#000000">
169</font>
170<p style="line-height: 100%;"><font color="#000000">After this, the
171pre-compilation for the IBM-Regatta of HLRN can be started by entering</font><font
172 color="#000000"> </font>
173</p>
174<ul>
175  <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
176 color="#000000">mbuild - h ibmh  .</font></pre>
177</ul>
178<p style="line-height: 100%;"><span style="font-family: monospace;">mbuild</span>
179will prompt some queries<font color="#000000">, which must all be
180answered "y" by the user. The compiling process </font><font
181 color="#000000">will take some time. </font><font color="#000000"><span
182 style="font-family: monospace;">mbuild</span></font><font
183 color="#000000"> transfers the 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>
188</p>
189<blockquote style="line-height: 100%;"><tt><font color="#000000">mbuild</font></tt></blockquote>
190<p style="line-height: 100%;"><font color="#000000">PALM will
191be (consecutively) pre-compiled for all remote hosts listed in
192the configuration file. </font>
193</p>
194<p style="line-height: 100%;"><font color="#000000">As a last step,
195after the compilation has been finished, the PALM installation has to
196be verified. For this
197purpose a simple test run is carried out. This once again requires the <b>mrun
198</b>configuration file (described in </font><a href="chapter_3.2.html"><font
199 color="#000080">chapter
2003.2</font></a><font color="#000000">), as well as the </font><a
201 href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d"><font
202 color="#000080">parameter
203file</font></a><font color="#000000"> (described in </font><a
204 href="chapter_4.4.html"><font color="#000080">chapter
2054.4</font></a>)<font color="#000000">. The parameter file must be&nbsp;
206copied to<br>
207</font></p>
208<p style="line-height: 100%;"><tt><font color="#000000">&nbsp;&nbsp;&nbsp;
209~/palm/current_version/JOBS/example/INPUT/example_p3d</font></tt><font
210 color="#000000">&nbsp;&nbsp; .
211</font></p>
212<p style="line-height: 100%;"><font color="#000000">The test run can
213now be started by entering the command: </font>
214</p>
215<pre
216 style="margin-left: 1cm; margin-right: 1cm; margin-bottom: 0.5cm; line-height: 100%;"><font
217 color="#000000">mrun -d example -h ibmh -K parallel -X 8 -T 8 -t 500 -q cdev -r “d3# pr#”</font></pre>
218<p style="line-height: 100%;"><font color="#000000">This specific run
219will be carried out on 8 PEs and is allowed to use up to 500 seconds
220CPU time. After pressing &lt;return&gt;, the most important settings of
221the job are displayed at the terminal window
222and the user is prompted for o.k. (“</font><tt><font color="#000000">y</font></tt><font
223 color="#000000">”).
224Afterwards a message of the queuing system like “<i>Request</i> …
225<i>Submitted to queue… by…” </i>should be displayed. Now the job is
226queued either started immediately or at a later time, depending on the
227current workload of the remote host. Provided that it is executed
228immediately and that all things work as designed, the job protocol of
229this run will appear under the file name </font><tt><font
230 color="#000000">~/job_queue/ibmh_example</font></tt><font
231 color="#000000"> no more than 3 minutes later. The content of this
232file should be carefully examined for any error messages.</font>
233</p>
234<p style="line-height: 100%;">Beside the job protocol and according to
235the configuration file and arguments given for <b>mrun</b>
236options <tt>-d</tt> and <tt>-r,</tt>further files should be found in
237the
238directories<br>
239</p>
240<p style="line-height: 100%; font-family: monospace;">&nbsp;&nbsp;&nbsp;
241~/palm/current_version/JOBS/example/MONITORING
242<br>
243</p>
244<p style="line-height: 100%;">and</p>
245<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
246~/palm/current_version/JOBS/example/OUTPUT&nbsp; .
247</span><br>
248</p>
249<p style="line-height: 100%;">Please compare the contents of file</p>
250<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
251~/palm/current_version/JOBS/example/MONITORING/ibmh_example_rc</span><br>
252</p>
253<p style="line-height: 100%;">with those of the <a
254 href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_rc">result
255example file</a> (e.g. with the help of the UNIX-command <span
256 style="font-family: monospace;">diff</span>). There should be not a
257single difference between these two files. <font color="#000000">If
258the file contents are identical, the installation is successfully
259completed.</font> </p>
260<p style="line-height: 100%;">If you have any problems with the PALM
261installation, the members of the PALM working group are pleased to
262help you. &nbsp; </p>
263<hr>
264<p style="line-height: 100%;"><font color="#000080"><font
265 color="#000080"><a href="chapter_4.6.html"><font color="#000080"><img
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270 color="#000080"><img src="right.gif" name="Grafik3" align="bottom"
271 border="2" height="32" width="32"></font></a></font></font></p>
272<p style="line-height: 100%;"><i>Last change:&nbsp;</i> 20/04/05 (SR) </p>
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