source: palm/trunk/DOC/app/chapter_5.0.html @ 493

Last change on this file since 493 was 493, checked in by raasch, 14 years ago

Output in NetCDF4-format. New d3par-parameter netcdf_data_format.

(check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin)

Modules to be loaded for compilation (mbuild) or job execution (mrun)
can be given in the configuration file using variable modules. Example:

%modules ifort/11.0.069:netcdf lcsgih parallel

This method replaces the (undocumented) mpilib-variable.

WARNING: All fixed settings of modules in the scripts mbuild, mrun, and subjob
have been removed! Please set the modules variable appropriately in your
configuration file. (mbuild, mrun, subjob)


Parameters netcdf_64bit and netcdf_64bit_3d have been removed. Use
netcdf_data_format = 2 for choosing the classic 64bit-offset format (this is
the default). The offset-format can not be set independently for the
3d-output-data any more.

Parameters netcdf_format_mask, netcdf_format_mask_av, and variables
nc_format_mask, format_parallel_io removed. They are replaced by the new
parameter netcdf_data_format. (check_open, close_file,
data_output_mask, header, init_masks, modules, parin)


bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config

Bugfix: timeseries data have to be collected by PE0 (user_statistics)

  • Property svn:keywords set to Id
File size: 32.7 KB
1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
5<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>
7@page { size: 21cm 29.7cm }
9</style></head><body style="direction: ltr;" lang="en-US"><h2 style="line-height: 100%;"><font size="4">5.0
10Installation of the
12<font color="#000000">This chapter
13describes the installation of PALM on a Linux workstation (local host)
14and a suitable remote computer, on which the
15model runs are to be carried out. The local host is used to
16start batch jobs with <b>mrun</b> and to analyze the
18which are produced by the model on the remote host and send back to the
19local host. Alternatively, <span style="font-weight: bold;">mrun</span>
20can also be used to start PALM on the local host in interactive mode or
21as a batch job (if a queueing system like NQS, PBS, or LoadLeveler is
22available).</font><p style="line-height: 100%;"></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Requirements</span></font></p><p style="line-height: 100%;"><font color="#000000">The
23installation and operation of PALM requires at mimimum (on both, the
24local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The Korn-shell (AT&amp;T ksh or public
25domain ksh) must be
26available under<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">/bin/ksh</font><font color="#000000">.<span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-family: Courier New,Courier,monospace;"></span></font><font color="#000000"><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span></font></li><li><font color="#000000">The
27NetCDF-library with version number not earlier than 3.6.0-p1 (for
28NetCDF, see under <a href=""></a>).</font></li><li><font color="#000000">A FORTRAN90/95 compiler.</font></li><li><font color="#000000">The Message Passing Interface (MPI), at
29least on the remote host, if the parallel version of PALM shall be used.</font></li><li><font color="#000000">On the local host, the revision control
30system <span style="font-weight: bold;">subversion</span>
31(see <a href=""></a>).
32This is already included in many Linux distributions (e.g. SuSe). <span style="font-weight: bold;">subversion requires port 3690 to
33be open for tcp/udp.</span> <span style="font-weight: bold;">If
34there are firewall restrictions concerning this port, the PALM code
35cannot be accessed.</span> The
36user needs a permit to access the PALM repository. For getting a permit
37please contact the PALM group (<a href=""></a>)
38and define a username under which you like to access the repository.
39You will then receive a password which allows the access under this
40name.</font></li><li><font color="#000000">A
41job queueing system must be available on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle
42LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).</font></li><li><font color="#000000">ssh/scp-connections to and from the remote
43host must not be blocked by a firewall.<br></font></li></ol><font color="#000000"><span style="font-weight: bold;"></span></font><font color="#000000"> Currently, <span style="font-weight: bold;">mrun</span> is configured
44to be used on a limited number of selected machines. These are SGI-ICE
45systems at computing center HLRN in Hannover (<span style="font-style: italic;">lcsgih</span>), Berlin (<span style="font-style: italic;">lcsgib</span>),
46IBM-Regatta system<span style="font-style: italic;"></span>
47at Yonsei University, Seoul (<span style="font-style: italic;">ibms</span>),
48on NEC-SX6/8 systems at DKRZ, Hamburg (<span style="font-style: italic;">nech</span>) and RIAM,
49Kyushu University, Fukuoka (<span style="font-style: italic;">necriam</span>),
50as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>), Tokyo
51Institute of Technology (<span style="font-style: italic;">lctit</span>),
52and the Bergen Center for Computational Science (<span style="font-style: italic;">lcxt4</span>).
53The strings given in brackets are the systems names (host identifiers)
54under which <span style="font-weight: bold;">mrun</span>
55identifies the
56different hosts.<br><br>You can also use <span style="font-weight: bold;">mrun</span>/PALM on other
57Linux-Cluster, IBM-AIX, or NEC-SX machines. See <a href="#configuration_for_other_machines">below</a> on
58how to configure <span style="font-weight: bold;">mrun</span>
59for other machines. However, these configurations currently (version
603.2a) allow to run PALM in interactive mode only.<br><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span></font><p style="line-height: 100%;"><font color="#000000">The
61examples given in this chapter refer to an
62installation of PALM on an IMUK Linux workstation and the SGI-ICE
63system of
64the HLRN used as&nbsp;remote host. They are just called local and
65remote host from now on. </font></p><p style="line-height: 100%;">
66</p><p style="line-height: 100%;">The installation
67process requires a valid
68account on the local and on the remote host as well.<br>
69&nbsp; </p>
70<ul> All hosts (local as well as remote) are
71accessed via the secure shell (ssh). The user must establish
72passwordless login using the private/public-key mechanism (see e.g. the
73<a href="">HLRN
74documentation</a>). <b>To ensure proper function of mrun,
75passwordless login must be
76established in both directions, from the local to the remote host as
77well as from the remote to the local host!</b> Test this by
79out e.g. on the local host: <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
80</span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp;
81&lt;username on remote host&gt;@&lt;remote
82IP-address&gt;</span><br> </p> <p style="line-height: 100%;">and on the remote host:<br>
83</p> <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
84</span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp;
85&lt;username on local host&gt;@&lt;local IP-adddress&gt;</span><br>
86</p> In both cases you should&nbsp;not be
87prompted for a password. <b>Before continuing the further
89process, this must be absolutely guaranteed!</b> This must also
91guaranteed for <b>all</b> other remote hosts, on which
92PALM shall run.<br><br>Please
93note that on many remote hosts, passwordless login must also be
94established <b>within the remote host</b>, i.e. from the
95remote host to itself. Test this by executing on the remote host: <span style="font-family: Courier New,Courier,monospace;">ssh
96&lt;remote IP-address&gt;</span>. You should not be prompted
97for a password.<br><br></ul><p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package
98Installation</span></p><p style="line-height: 100%;">In
99the <b>first installation step</b> a
100set of directories must be created both on the local and on the
101remote host. These directories are:</p><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/job_queue<br></div><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm<br></div><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm/current_version<br></div><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS</span><br></div><p style="line-height: 100%;">The names of these directories
103freely selectable (except <big><tt><font size="2"><big>~/job_queue</big></font></tt></big>),
104however new users should use them as suggested, since many
105examples in this documentation as well as all example files are
106assuming these settings. The directory <big><span style="font-family: monospace;">~/palm/current_version</span></big>
107on the local host will be called the working directory from now on. </p>
108<p style="line-height: 100%;"><font color="#000000">In
109the <b>second
111a working copy of the recent version of the PALM software package,
112including the source code, scripts, documentation, etc.&nbsp; must
114copied to the working directory (</font><font color="#000000">local
115host!) by executing the following
116commands. Replace &lt;your username&gt; by the name that you
117chose to
118access the repository, and &lt;#&gt; by any of the available
120releases, e.g. "<span style="font-style: italic;">3.1c</span>"
121(new releases will be anounced by email to the PALM mailing list).</font></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">cd
122~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn
123checkout --username &lt;your username&gt;
124svn://;#&gt; trunk</span><br></div><p style="line-height: 100%;"><font color="#000000">You
125will then be prompted for your password. After finishing, the
126subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">should
127appear in your working directory. It contains a number of further
128subdirectories which contain e.g. the PALM source code (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SOURCE</font><font color="#000000">)
129and the scripts for running PALM (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SCRIPTS</font><font color="#000000">).</font></p><p style="line-height: 100%;">Alternatively,&nbsp;executing</p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username &lt;your username&gt; svn://;#&gt; abcde</pre><p style="line-height: 100%;">will place your working copy in a
130directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span>instead
131of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span>.
132But keep in mind that you will have to adjust several paths given
133below, if you do not use the default directory<span style="font-family: Courier New,Courier,monospace;"> trunk</span>.</p><p style="line-height: 100%;">Please never touch any file in
134your working copy of PALM, unless you&nbsp;know exactly what you
135are doing.</p><p style="line-height: 100%; font-weight: bold;"><span style="font-weight: normal;">You can also get a copy of the
136most recent code by executing</span></p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username &lt;your username&gt; svn:// trunk</pre>However,
137this version may contain bugs and new features may not be documented. <span style="font-weight: bold;">In future PALM releases,
138repository access to this most recent&nbsp;version will
139probably be restricted to the PALM developers.</span><p style="line-height: 100%;"></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Package
140Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To
141use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable
142has to be extended and the
143environment variable<span style="font-family: Courier New,Courier,monospace;">
144PALM_BIN </span>has to be set (on local and remote host)
145in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>,
146if<span style="font-family: Courier New,Courier,monospace;">
147ksh </span>is used):</font></p><p style="line-height: 100%; margin-left: 40px;"><font style="font-family: Courier New,Courier,monospace;" color="#000000">export
148PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH</font><font color="#000000"><br><span style="font-family: Courier New,Courier,monospace;">export
149PALM_BIN=</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">$HOME/palm/current_version/trunk/SCRIPTS</font></p><p style="line-height: 100%;"><font color="#000000">You
150may have to login again in order to activate these settings.</font></p><font color="#000000">On the local and on the remote host, some
151small helper/utility programs have to be installed, which
152are&nbsp;later used by <span style="font-weight: bold;">mrun</span>&nbsp;e.g.
153for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script
154requires a configuration file<span style="font-family: Courier New,Courier,monospace;">
155.mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the
156following. A copy has to be put into the working directory under the
157name<span style="font-family: Courier New,Courier,monospace;">
158.mrun.config </span>by</font><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">cp
159trunk/SCRIPTS/.mrun.config.default .mrun.config</span></font></p><font color="#000000">Beside many other things, this file contains
160typical installation parameters
161like compiler name, compiler options, etc.
162for a set of different (remote) hosts. Please edit this file, uncomment
163lines like</font><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username
164&nbsp;&lt;replace by your ... username&gt; &nbsp;
165&lt;host identifier&gt;</div><p style="line-height: 100%;"><font color="#000000">by
166removing the first hash (<span style="font-family: Courier New,Courier,monospace;">#</span>)
167character and replace the string "<span style="font-family: Courier New,Courier,monospace;">&lt;replace
168by ...&gt;</span>" by your username on the respective host
169given in the <span style="font-family: Courier New,Courier,monospace;">&lt;host
171You only have to uncomment lines for those hosts on which you intend to
172use PALM.</font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">Warning:
173When editing the configuration file, please NEVER use the TAB key.
174Otherwise, 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;">
175trunk/SCRIPTS </span>contains additional configuration files
176which are already adjusted for special hosts:<span style="font-family: Courier New,Courier,monospace;">
177.mrun.config.imuk </span>can be used at Hannover University,<span style="font-family: Courier New,Courier,monospace;">
178.mrun.config.riam </span>can
179be used at the Research Institute of Applied Mechanics, Kyushu
180University. These files have to be edited in the same way as described
181above.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the
182respective 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
183lcsgih</font></p><p style="line-height: 100%;"><font color="#000000">The
184second call also copies the PALM scripts (like <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span>) to the
186host.</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
187of PALM Code</span></font></p><font color="#000000">
188</font><br><font color="#000000">To avoid the
189re-compilation of the complete source code for each model run, PALM
190willl be pre-compiled once on the remote host by again using the script
191<span style="font-weight: bold;">mbuild</span>. Due
192to the use of
193FORTRAN modules in the source code, the subroutines must be compiled
194in a certain order. Therefore the so-called <i>make</i>
196is used (see the respective man-page of the Unix operating system),
197requiring a<span style="font-family: Courier New,Courier,monospace;">
198</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">Makefile</font><font color="#000000">,
199in which the dependencies are described. This file is found in
200subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span></font><font color="#000000">, where
201also the PALM code is stored.</font><font color="#000000"> The compiled
202sources (object
203files) are
204stored&nbsp;on the remote computer in the default directory
205</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
206pre-compilation for the remote host (here the SGI-ICE system of HLRN)
208done by</font><span style="font-family: monospace;"></span></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">mbuild
209-h lcsgih &nbsp;</span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild
210</span>will prompt some queries<font color="#000000">,
211which must all be
212answered "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
213the respective compiler calls to the remote
214host where they are carried out interactively. You can follow the
215progress at the terminal window, where also error messages
216are displayed (hopefully not for this standard installation). By just
217entering </font></p><p style="line-height: 100%;">
218</p><blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote>
219<p style="line-height: 100%;"><font color="#000000">PALM
221be (consecutively) pre-compiled for all remote hosts listed in
222the configuration file. If you want to compile for the local host only,
223please enter</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">mbuild
224-h lcmuk</span> </font>
225</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,
226after the compilation has been finished, the PALM installation has to
227be verified. For this
228purpose a simple test run is carried out. This once again requires the <b>mrun
229</b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter
2303.2</font></a><font color="#000000">), as well
231as the </font><a href=""><font color="#000080">parameter
232file</font></a><font color="#000000">
233(described in </font><a href="chapter_4.4.1.html"><font color="#000080">chapter
2344.4.1</font></a>)<font color="#000000">. The
235parameter file must be
236copied from the PALM working copy by<br>
237</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
238trunk/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>
239<p style="line-height: 100%;"><font color="#000000">The
240test run can
241now be started by executing the command </font>
242</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 “d3# pr#”</font></pre><font color="#000000">This specific run
243will be carried out on 8 PEs and is allowed to use up to 500 seconds
244CPU time. After pressing &lt;return&gt;, the most important
245settings of
246the job are displayed at the terminal window
247and the user is prompted for o.k. (“</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">y</font><font color="#000000">”).
248Next, a message of the queuing system like “<i>Request</i>
250<i>Submitted to queue… by…” </i>should
251be displayed. Now the job is
252queued and either started immediately or at a later time, depending on
254current workload of the remote host. Provided that it is executed
255immediately and that all things work as designed, the job protocol of
256this 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
257more than a few minutes later. The content of this
258file should be carefully examined for any error messages.</font><p style="line-height: 100%;">
259</p><p style="line-height: 100%;">Beside the job
260protocol and according to
261the configuration file and arguments given for <b>mrun</b>
262options<span style="font-family: Courier New,Courier,monospace;">
263-d </span>and<span style="font-family: Courier New,Courier,monospace;"> -r</span><tt>,</tt>further
264files should be found in
266directories</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>
267<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
268</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/OUTPUT</span><span style="font-family: monospace;"></span><br>
269</p><p style="line-height: 100%;">Please compare the
270contents of file</p>
271<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
272</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/MONITORING/lcsgih_example_rc</span><br>
273</p><p style="line-height: 100%;">with those of the
274example result file which can be found under<span style="font-family: Courier New,Courier,monospace;">
275trunk/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>
276diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff
278trunk/INSTALL/example_cbl_rc</p><p style="line-height: 100%;">where
279it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;">
280~/palm/current_version</span>.</p><span style="font-weight: bold;">You should not find any
281difference between these two files</span>, except of the run date
282and time displayed at the top of the file header. <font color="#000000">If
283the file contents are identical, the installation is successfully
284completed.<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
285for other machines</font></p><font color="#000000">Starting
286from version 3.2a, beside the default hosts (HLRN, etc.), PALM can also
287be installed and run on other Linux-Cluster-, IBM-AIX, or
288NEC-SX-systems. To configure PALM for a non-default host only requires
289to add some lines to the configuration file<span style="font-family: Courier New,Courier,monospace;">
291you have to define the host identifier (a string of arbitrary length)
292under 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
293&nbsp;&lt;hostname&gt; &nbsp;&lt;host
294identifier&gt;</span><br></div><br>to the
295configuration file (best to do this in the section where the other
296default host identifiers are defined). Here<span style="font-family: Courier New,Courier,monospace;">
297&lt;hostname&gt; </span>must be the name of your local
298host as provided by the unix-command "<span style="font-family: Courier New,Courier,monospace;">hostname</span>".
299The first characters of<span style="font-family: Courier New,Courier,monospace;">
300&lt;host identifier&gt; </span>have to be "<span style="font-family: Courier New,Courier,monospace;">lc</span>",
301if your system is (part of) a linux-cluster, "<span style="font-family: Courier New,Courier,monospace;">ibm</span>",
302or "<span style="font-family: Courier New,Courier,monospace;">nec</span>"
303in case of an IBM-AIX- or NEC-SX-system, respectively. For example, if
304you want to install on a linux-cluster, the line may read as<br><br><div style="margin-left: 40px;">%host_identifier &nbsp;foo
306the second step, you have to give all informations neccessary to
307compile and run PALM on your local host by adding an additional section
308to the configuration file:<br><br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username&nbsp;&nbsp;
309&lt;1&gt;&nbsp; &nbsp; &nbsp; &lt;host
310identifier&gt; parallel<br>%tmp_user_catalog&nbsp;
311&lt;2&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host
312identifier&gt; parallel<br>%compiler_name&nbsp;&nbsp;&nbsp;&nbsp;
313&lt;3&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host
314identifier&gt; parallel<br>%compiler_name_ser
315&lt;4&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host
316identifier&gt; parallel<br>%cpp_options&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
317&lt;5&gt; &nbsp; &nbsp; &nbsp;&lt;host
319&lt;6&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host
320identifier&gt; parallel<br>%netcdf_lib&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
321&lt;7&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host
322identifier&gt; parallel<br>%fopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
323&lt;8&gt; &nbsp;&nbsp;&nbsp; &nbsp;&lt;host
324identifier&gt; parallel<br>%lopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
325&nbsp;&lt;9&gt; &nbsp; &nbsp;
326&nbsp;&lt;host identifier&gt; parallel<br></div><br>The
327section consists of four columns each separated by one or more blanks.
328The first column gives the name of the respective environment variable
329used by <span style="font-weight: bold;">mrun</span>
330and <span style="font-weight: bold;">mbuild</span>,
331while the second column defines its value. The third column has to be
332the host identifier as defined above, and the last column in each line
333must contain the string "<span style="font-family: Courier New,Courier,monospace;">parallel</span>".
334Otherwise, the respective line(s) will be interpreted as belonging to
335the setup for compiling and running a serial (non-parallel) version of
336PALM.<br><br>All brackets have to be replaced by the
337appropriate settings for your local host:<br><ul><li><span style="font-family: Courier New,Courier,monospace;">&lt;1&gt;
338</span>is the username on your LOCAL host</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;2&gt;
339</span>is the temporary directory in which PALM runs will be
340carried out</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;3&gt;
341</span>is the compiler name which generates parallel code</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;4&gt;
342</span>is the compiler name for generating serial code</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;5&gt;
344the preprocessor options to be invoked. In most of the cases, it will
345be neccessary to adjust the MPI data types to double precision by
346giving <span style="font-family: Courier New,Courier,monospace;">-DMPI_REAL=MPI_DOUBLE_PRECISION
347-DMPI_2REAL=MPI_2DOUBLE_PRECISION</span>. To switch on the NetCDF
348support, you also have to give <span style="font-family: Courier New,Courier,monospace;">-D__netcdf</span>
349and <span style="font-family: Courier New,Courier,monospace;">-D__netcdf4</span>
350(if you like to have NetCDF4/HDF5 data format; this requires a NetCDF4 library!).</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;6&gt;
351</span>is the compiler option for specifying the include path to
352search for the NetCDF module/include files</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;7&gt;
353</span>are the linker options to search for the NetCDF library</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;8&gt;
354</span>are the general compiler options to be used. You should
355allways switch on double precision (e.g. <span style="font-family: Courier New,Courier,monospace;">-r8</span>)
356and 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;
357</span>are the linker options</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;host
358identifier&gt; </span>is the host identifier as defined
359before</li></ul><br>A typical example may be:<br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username&nbsp;&nbsp;
360raasch &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
361&nbsp; &nbsp; &nbsp; &nbsp;
362&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
363&nbsp; &nbsp;lc_bar parallel<br>%tmp_user_catalog&nbsp;
370-DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf&nbsp; lc_bar parallel<br>%netcdf_inc&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
372lc_bar parallel<br>%netcdf_lib&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;
377&nbsp;&nbsp;&nbsp; lc_bar parallel<br>%lopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
379parallel<br></div><br>Currently (version 3.7a),
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>
Note: See TracBrowser for help on using the repository browser.