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[62]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
[5]11model</font></h2>
[41]12<font color="#000000">This chapter
[62]13describes the installation of PALM on a Linux workstation (local host)
14and a suitable remote computer, on which the
[40]15model runs are to be carried out. The local host is used to
[62]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.</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 AT&amp;T Korn-shell (ksh) must be
24available 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">.
25Most of the current Linux distributions are using the public domain
26Korn-shell (pdksh). The PALM scripts <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span> do not work
27with the pdksh! Please replace it by the AT&amp;T ksh. If the
28AT&amp;T ksh path is different from<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">,
29please modify the first lines in <span style="font-weight: bold;">mrun</span>
30and <span style="font-weight: bold;">mbuild</span>,
31respectively.</font></li><li><font color="#000000">The
32NetCDF-library with version number not earlier than 3.6.0-p1 (for
33NetCDF, 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
34least 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
35system <span style="font-weight: bold;">subversion</span>
36(see <a href="http://subversion.tigris.org/">subversion.tigris.org</a>).
37This is already included in many Linux distributions (e.g. SuSe). <span style="font-weight: bold;">subversion requires port 3690 to
38be open for tcp/udp.</span> <span style="font-weight: bold;">If
39there are firewall restrictions concerning this port, the PALM code
40cannot be accessed.</span> The
[40]41user needs a permit to access the PALM repository. For getting a permit
42please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>)
43and define a username under which you like to access the repository.
44You will then receive a password which allows the access under this
[62]45name.</font></li><li><font color="#000000">A
46job queueing system must be available on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle
47LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).</font></li><li><font color="#000000">ssh/scp-connections to and from the remote
48host 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
49to be used on a limited number of selected machines. These are
50IBM-Regatta at computing center HLRN in Hannover (<span style="font-style: italic;">ibmh</span>), Berlin (<span style="font-style: italic;">ibmb</span>), at KISTI,
51Korea (<span style="font-style: italic;">ibms</span>),
52at Yonsei University, Seoul (<span style="font-style: italic;">ibms</span>),
53on NEC-SX6/8 systems at DKRZ, Hamburg (<span style="font-style: italic;">nech</span>) and RIAM,
54Kyushu University, Fukuoka (<span style="font-style: italic;">neck</span>),
55as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>) and Tokyo
56Institute of Technology (<span style="font-style: italic;">lctit</span>).
57The strings given in brackets are the systems names under which <span style="font-weight: bold;">mrun</span> indentifies the
58different hosts. mrun should also work on other systems, but this
59requires some modifications in the scripts <span style="font-weight: bold;">mrun</span>, <span style="font-weight: bold;">mbuild</span>, and <span style="font-weight: bold;">subjob</span>. Future PALM
60versions will allow to configure the scripts for different kinds of
61systems by just using a configuration file.</font><p style="line-height: 100%;"><font color="#000000">The
62examples given in this chapter refer to an
[40]63installation of PALM on an IMUK Linux workstation and the IBM-Regatta
[5]64system of
[62]65the HLRN used as&nbsp;remote host. They are just called local and
66remote host from now on. </font></p><p style="line-height: 100%;">
67</p><p style="line-height: 100%;">The installation
68process requires a valid
[40]69account on the local and on the remote host as well.<br>
[5]70&nbsp; </p>
[62]71<ul> All hosts (local as well as remote) are
[5]72accessed via the secure shell (ssh). The user must establish
73passwordless login using the private/public-key mechanism (see e.g. the
[62]74<a href="http://www.hlrn.de/doc/ssh/index.html">HLRN
75documentation</a>). <b>To ensure proper function of mrun,
76passwordless login must be
[5]77established in both directions, from the local to the remote host as
[62]78well as from the remote to the local host!</b> Test this by
79carrying
80out e.g. on the local host: <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
81</span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp;
82&lt;username on remote host&gt;@&lt;remote
83IP-address&gt;</span><br> </p> <p style="line-height: 100%;">and on the remote host:<br>
84</p> <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
85</span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp;
86&lt;username on local host&gt;@&lt;local IP-adddress&gt;</span><br>
87</p> In both cases you should&nbsp;not be
88prompted for a password. <b>Before continuing the further
89installation
90process, this must be absolutely guaranteed!</b> This must also
91be
92guaranteed for <b>all</b> other remote hosts, on which
93PALM shall run.
94</ul><p style="line-height: 100%;"></p><p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package
95Installation</span></p><p style="line-height: 100%;">In
96the <b>first installation step</b> a
[5]97set of directories must be created both on the local and on the
[62]98remote 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
99are
[5]100freely selectable (except <tt><font size="2">~/job_queue</font></tt>),
101however new users should use them as suggested, since many
102examples in this documentation as well as all example files are
[62]103assuming these settings. The directory <span style="font-family: monospace;">~/palm/current_version</span>
104on the local host will be called the working directory from now on. </p>
105<p style="line-height: 100%;"><font color="#000000">In
106the <b>second
[40]107step</b>
108a working copy of the recent version of the PALM software package,
[62]109including the source code, scripts, documentation, etc.&nbsp; must
110be
[44]111copied to the working directory (</font><font color="#000000">local
112host!) by executing the following
[62]113commands. Replace &lt;your username&gt; by the name that you
114chose to
115access the repository, and &lt;#&gt; by any of the available
116PALM
117releases, e.g. "<span style="font-style: italic;">3.1c</span>"
118(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
119~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn
120checkout --username &lt;your username&gt;
121svn://130.75.105.45/palm/tags/release-&lt;#&gt; trunk</span><br></div><p style="line-height: 100%;"><font color="#000000">You
122will then be prompted for your password. After finishing, the
123subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">should
[40]124appear in your working directory. It contains a number of further
[62]125subdirectories which contain e.g. the PALM source code (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SOURCE</font><font color="#000000">)
126and 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
127directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span>instead
128of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span>.
129But keep in mind that you will have to adjust several paths given
130below, 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
131your working copy of PALM, unless you&nbsp;know exactly what you
132are doing.</p><p style="line-height: 100%; font-weight: bold;"><span style="font-weight: normal;">You can also get a copy of the
133most 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,
134this version may contain bugs and new features may not be documented. <span style="font-weight: bold;">In future PALM releases,
135repository access to this most recent&nbsp;version will
136probably 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
137Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To
[40]138use the PALM scripts, the PATH variable has to be extended and the
139environment variable PALM_BIN has to be set (on local and remote host)
[62]140in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>,
141if<span style="font-family: Courier New,Courier,monospace;">
142ksh </span>is used):</font></p><p style="line-height: 100%; margin-left: 40px;"><font style="font-family: Courier New,Courier,monospace;" color="#000000">export
143PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH</font><font color="#000000"><br><span style="font-family: Courier New,Courier,monospace;">export
144PALM_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
145may habe to login again in order to activate these settings.</font></p><font color="#000000">On the local and on the remote host, some
146small helper/utility programs have to be installed, which are e.g.
147later used by <span style="font-weight: bold;">mrun</span>
148or for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script
149requires a configuration file<span style="font-family: Courier New,Courier,monospace;">
150.mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the
151following. A copy has to be put into the working directory under the
152name<span style="font-family: Courier New,Courier,monospace;">
153.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
154trunk/SCRIPTS/.mrun.config.default .mrun.config</span></font></p><font color="#000000">Beside many other things, this file contains
155typical installation parameters
[40]156like compiler name, compiler options, etc.
[62]157for a set of different remote hosts. Please edit this file, uncomment
158lines like</font><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username
159&nbsp;&lt;replace by your ... username&gt; &nbsp;
160&lt;remote-computer-shortcut&gt;</div><p style="line-height: 100%;"><font color="#000000">by
161removing the first hash (<span style="font-family: Courier New,Courier,monospace;">#</span>)
162character and replace the string "<span style="font-family: Courier New,Courier,monospace;">&lt;replace
163by ...&gt;</span>" by your username on the respective host
164given in the <span style="font-family: Courier New,Courier,monospace;">&lt;remote-computer-shortcut&gt;</span>.
165You only have to uncomment lines for those hosts on which you intend to
166use PALM.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the
167respective 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 ibmh</font></p><p style="line-height: 100%;"><font color="#000000">The
168second 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
169host.</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
170of PALM Code</span></font></p><font color="#000000">
171</font><br><font color="#000000">To avoid the
[5]172re-compilation of the complete source code for each model run, PALM
[62]173willl be pre-compiled once on the remote host by again using the script
174<span style="font-weight: bold;">mbuild</span>. Due
175to the use of
[5]176FORTRAN modules in the source code, the subroutines must be compiled
[62]177in a certain order. Therefore the so-called <i>make</i>
178mechanism
[5]179is used (see the respective man-page of the Unix operating system),
[62]180requiring a<span style="font-family: Courier New,Courier,monospace;">
181</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">Makefile</font><font color="#000000">,
182in which the dependencies are described. This file is found in
183subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE<span style="font-family: Times New Roman,Times,serif;">, where
184also the PALM code is stored</span></span>. The compiled
185sources (object
[5]186files) are
[40]187stored&nbsp;on the remote computer in the default directory
[41]188</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
[62]189pre-compilation for the remote host (here the IBM-Regatta of HLRN) is
190done by</font><span style="font-family: monospace;"></span></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">mbuild
191-h ibmh&nbsp;&nbsp;</span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild
192</span>will prompt some queries<font color="#000000">,
193which must all be
194answered "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
195the respective compiler calls to the remote
[5]196host where they are carried out interactively. You can follow the
197progress at the terminal window, where also error messages
198are displayed (hopefully not for this standard installation). By just
[41]199entering </font></p><p style="line-height: 100%;">
[62]200</p><blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote>
201<p style="line-height: 100%;"><font color="#000000">PALM
202will
[5]203be (consecutively) pre-compiled for all remote hosts listed in
[62]204the configuration file. If you want to compile for the local host only,
205please enter</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">mbuild
206-h lcmuk</span> </font>
207</p><p style="line-height: 100%;"></p><p style="line-height: 100%; font-weight: bold; text-decoration: underline;"><font color="#000000">Installation Verification</font></p><font color="#000000">As a last step,
[5]208after the compilation has been finished, the PALM installation has to
209be verified. For this
210purpose a simple test run is carried out. This once again requires the <b>mrun
[40]211</b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter
[62]2123.2</font></a><font color="#000000">), as well
213as the </font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d"><font color="#000080">parameter
214file</font></a><font color="#000000">
215(described in </font><a href="chapter_4.4.html"><font color="#000080">chapter
2164.4</font></a>)<font color="#000000">. The
217parameter file must be
[40]218copied from the PALM working copy by<br>
[62]219</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/INPUT<br>cp
220trunk/INSTALL/example_p3d&nbsp;JOBS/example/INPUT/example_p3d</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"></span></font></div>
221<p style="line-height: 100%;"><font color="#000000">The
222test run can
[40]223now be started by executing the command </font>
[62]224</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 -h ibmh -K parallel -X 8 -T 8 -t 500 -q cdev -r &ldquo;d3# pr#&rdquo;</font></pre>
[41]225<font color="#000000">This specific run
[5]226will be carried out on 8 PEs and is allowed to use up to 500 seconds
[62]227CPU time. After pressing &lt;return&gt;, the most important
228settings of
[5]229the job are displayed at the terminal window
[62]230and 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;).
231Next, a message of the queuing system like &ldquo;<i>Request</i>
232&hellip;
233<i>Submitted to queue&hellip; by&hellip;&rdquo; </i>should
234be displayed. Now the job is
235queued and either started immediately or at a later time, depending on
236the
[5]237current workload of the remote host. Provided that it is executed
238immediately and that all things work as designed, the job protocol of
[62]239this 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/ibmh_example</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"> </span>no
240more than a few minutes later. The content of this
[41]241file should be carefully examined for any error messages.</font><p style="line-height: 100%;">
[62]242</p><p style="line-height: 100%;">Beside the job
243protocol and according to
[5]244the configuration file and arguments given for <b>mrun</b>
[62]245options<span style="font-family: Courier New,Courier,monospace;">
246-d </span>and<span style="font-family: Courier New,Courier,monospace;"> -r</span><tt>,</tt>further
247files should be found in
[5]248the
[40]249directories</p><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/MONITORING</div><p style="line-height: 100%;">and</p>
[5]250<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
[40]251</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/OUTPUT</span><span style="font-family: monospace;"></span><br>
[62]252</p><p style="line-height: 100%;">Please compare the
253contents of file</p>
[5]254<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
[40]255</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/MONITORING/ibmh_example_rc</span><br>
[62]256</p><p style="line-height: 100%;">with those of the
257example result file which can be found under<span style="font-family: Courier New,Courier,monospace;">
258trunk/INSTALL/example_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>
259diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff
260&nbsp;JOBS/example/MONITORING/ibmh_example_rc
261trunk/INSTALL/example_rc</p><p style="line-height: 100%;">where
262it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;">
263~/palm/current_version</span>.</p><span style="font-weight: bold;">You should not find any
264difference between these two files</span>, except of the run date
265and time displayed at the top of the file header. <font color="#000000">If
[5]266the file contents are identical, the installation is successfully
[41]267completed.</font>
[62]268<p style="line-height: 100%;">If you have any problems
269with the PALM
[5]270installation, the members of the PALM working group are pleased to
271help you. &nbsp; </p>
[62]272<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="Inhaltsverzeichnis.html"><font color="#000080"><img src="up.gif" name="Grafik2" align="bottom" border="2" height="32" width="32"></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>
273<p style="line-height: 100%;"><i>Last
274change:&nbsp;</i> $Id: chapter_5.0.html 62 2007-03-13 02:52:40Z raasch $</p>
[40]275</body></html>
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