source: palm/trunk/DOC/app/chapter_5.0.html @ 97

Last change on this file since 97 was 97, checked in by raasch, 14 years ago

New:
---
ocean version including prognostic equation for salinity and equation of state for seawater. Routine buoyancy can be used with both temperature and density.
+ inipar-parameters bc_sa_t, bottom_salinityflux, ocean, sa_surface, sa_vertical_gradient, sa_vertical_gradient_level, top_salinityflux

advec_s_bc, average_3d_data, boundary_conds, buoyancy, check_parameters, data_output_2d, data_output_3d, diffusion_e, flow_statistics, header, init_grid, init_3d_model, modules, netcdf, parin, production_e, prognostic_equations, read_var_list, sum_up_3d_data, swap_timelevel, time_integration, user_interface, write_var_list, write_3d_binary

New:
eqn_state_seawater, init_ocean

Changed:


inipar-parameter use_pt_reference renamed use_reference

hydro_press renamed hyp, routine calc_mean_pt_profile renamed calc_mean_profile

format adjustments for the ocean version (run_control)

advec_particles, buoyancy, calc_liquid_water_content, check_parameters, diffusion_e, diffusivities, header, init_cloud_physics, modules, production_e, prognostic_equations, run_control

Errors:


Bugfix: height above topography instead of height above level k=0 is used for calculating the mixing length (diffusion_e and diffusivities).

Bugfix: error in boundary condition for TKE removed (advec_s_bc)

advec_s_bc, diffusion_e, prognostic_equations

  • Property svn:keywords set to Id
File size: 31.2 KB
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1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
2<html><head>
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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7</style></head>
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 available).</font><p style="line-height: 100%;"></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Requirements</span></font></p><p style="line-height: 100%;"><font color="#000000">The
21installation and operation of PALM requires at mimimum (on both, the
22local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The Korn-shell (AT&amp;T ksh or public domain ksh) must be
23available under<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">/bin/ksh</font><font color="#000000">.<span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-family: Courier New,Courier,monospace;"></span></font><font color="#000000"><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span></font></li><li><font color="#000000">The
24NetCDF-library with version number not earlier than 3.6.0-p1 (for
25NetCDF, see under <a href="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
26least on the remote host, if the parallel version of PALM shall be used.</font></li><li><font color="#000000">On the local host, the revision control
27system <span style="font-weight: bold;">subversion</span>
28(see <a href="http://subversion.tigris.org/">subversion.tigris.org</a>).
29This is already included in many Linux distributions (e.g. SuSe). <span style="font-weight: bold;">subversion requires port 3690 to
30be open for tcp/udp.</span> <span style="font-weight: bold;">If
31there are firewall restrictions concerning this port, the PALM code
32cannot be accessed.</span> The
33user needs a permit to access the PALM repository. For getting a permit
34please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>)
35and define a username under which you like to access the repository.
36You will then receive a password which allows the access under this
37name.</font></li><li><font color="#000000">A
38job queueing system must be available on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle
39LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).</font></li><li><font color="#000000">ssh/scp-connections to and from the remote
40host must not be blocked by a firewall.<br></font></li></ol><font color="#000000"><span style="font-weight: bold;"></span></font><font color="#000000"> Currently, <span style="font-weight: bold;">mrun</span> is configured
41to be used on a limited number of selected machines. These are
42IBM-Regatta at computing center HLRN in Hannover (<span style="font-style: italic;">ibmh</span>), Berlin (<span style="font-style: italic;">ibmb</span>), at KISTI,
43Korea (<span style="font-style: italic;">ibms</span>),
44at Yonsei University, Seoul (<span style="font-style: italic;">ibms</span>),
45on NEC-SX6/8 systems at DKRZ, Hamburg (<span style="font-style: italic;">nech</span>) and RIAM,
46Kyushu University, Fukuoka (<span style="font-style: italic;">neck</span>),
47as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>) and Tokyo
48Institute of Technology (<span style="font-style: italic;">lctit</span>).
49The strings given in brackets are the systems names (host identifiers) under which <span style="font-weight: bold;">mrun</span> identifies the
50different hosts.<br><br>You can also use <span style="font-weight: bold;">mrun</span>/PALM on other Linux-Cluster, IBM-AIX, or NEC-SX machines. See <a href="#configuration_for_other_machines">below</a> on how to configure <span style="font-weight: bold;">mrun</span> for other machines. However, these configurations currently (version 3.2a) allow to run PALM in interactive mode only.<br><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span></font><p style="line-height: 100%;"><font color="#000000">The
51examples given in this chapter refer to an
52installation of PALM on an IMUK Linux workstation and the IBM-Regatta
53system of
54the HLRN used as&nbsp;remote host. They are just called local and
55remote host from now on. </font></p><p style="line-height: 100%;">
56</p><p style="line-height: 100%;">The installation
57process requires a valid
58account on the local and on the remote host as well.<br>
59&nbsp; </p>
60<ul> All hosts (local as well as remote) are
61accessed via the secure shell (ssh). The user must establish
62passwordless login using the private/public-key mechanism (see e.g. the
63<a href="http://www.hlrn.de/doc/ssh/index.html">HLRN
64documentation</a>). <b>To ensure proper function of mrun,
65passwordless login must be
66established in both directions, from the local to the remote host as
67well as from the remote to the local host!</b> Test this by
68carrying
69out e.g. on the local host: <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
70</span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp;
71&lt;username on remote host&gt;@&lt;remote
72IP-address&gt;</span><br> </p> <p style="line-height: 100%;">and on the remote host:<br>
73</p> <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
74</span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp;
75&lt;username on local host&gt;@&lt;local IP-adddress&gt;</span><br>
76</p> In both cases you should&nbsp;not be
77prompted for a password. <b>Before continuing the further
78installation
79process, this must be absolutely guaranteed!</b> This must also
80be
81guaranteed for <b>all</b> other remote hosts, on which
82PALM shall run.
83</ul><p style="line-height: 100%;"></p><p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package
84Installation</span></p><p style="line-height: 100%;">In
85the <b>first installation step</b> a
86set of directories must be created both on the local and on the
87remote 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
88are
89freely selectable (except <tt><font size="2">~/job_queue</font></tt>),
90however new users should use them as suggested, since many
91examples in this documentation as well as all example files are
92assuming these settings. The directory <span style="font-family: monospace;">~/palm/current_version</span>
93on the local host will be called the working directory from now on. </p>
94<p style="line-height: 100%;"><font color="#000000">In
95the <b>second
96step</b>
97a working copy of the recent version of the PALM software package,
98including the source code, scripts, documentation, etc.&nbsp; must
99be
100copied to the working directory (</font><font color="#000000">local
101host!) by executing the following
102commands. Replace &lt;your username&gt; by the name that you
103chose to
104access the repository, and &lt;#&gt; by any of the available
105PALM
106releases, e.g. "<span style="font-style: italic;">3.1c</span>"
107(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
108~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn
109checkout --username &lt;your username&gt;
110svn://130.75.105.45/palm/tags/release-&lt;#&gt; trunk</span><br></div><p style="line-height: 100%;"><font color="#000000">You
111will then be prompted for your password. After finishing, the
112subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">should
113appear in your working directory. It contains a number of further
114subdirectories which contain e.g. the PALM source code (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SOURCE</font><font color="#000000">)
115and 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
116directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span>instead
117of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span>.
118But keep in mind that you will have to adjust several paths given
119below, 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
120your working copy of PALM, unless you&nbsp;know exactly what you
121are doing.</p><p style="line-height: 100%; font-weight: bold;"><span style="font-weight: normal;">You can also get a copy of the
122most 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,
123this version may contain bugs and new features may not be documented. <span style="font-weight: bold;">In future PALM releases,
124repository access to this most recent&nbsp;version will
125probably 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
126Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To
127use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable has to be extended and the
128environment variable<span style="font-family: Courier New,Courier,monospace;"> PALM_BIN </span>has to be set (on local and remote host)
129in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>,
130if<span style="font-family: Courier New,Courier,monospace;">
131ksh </span>is used):</font></p><p style="line-height: 100%; margin-left: 40px;"><font style="font-family: Courier New,Courier,monospace;" color="#000000">export
132PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH</font><font color="#000000"><br><span style="font-family: Courier New,Courier,monospace;">export
133PALM_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
134may have to login again in order to activate these settings.</font></p><font color="#000000">On the local and on the remote host, some
135small helper/utility programs have to be installed, which are&nbsp;later used by <span style="font-weight: bold;">mrun</span>&nbsp;e.g. for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script
136requires a configuration file<span style="font-family: Courier New,Courier,monospace;">
137.mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the
138following. A copy has to be put into the working directory under the
139name<span style="font-family: Courier New,Courier,monospace;">
140.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
141trunk/SCRIPTS/.mrun.config.default .mrun.config</span></font></p><font color="#000000">Beside many other things, this file contains
142typical installation parameters
143like compiler name, compiler options, etc.
144for a set of different (remote) hosts. Please edit this file, uncomment
145lines like</font><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username
146&nbsp;&lt;replace by your ... username&gt; &nbsp;
147&lt;host identifier&gt;</div><p style="line-height: 100%;"><font color="#000000">by
148removing the first hash (<span style="font-family: Courier New,Courier,monospace;">#</span>)
149character and replace the string "<span style="font-family: Courier New,Courier,monospace;">&lt;replace
150by ...&gt;</span>" by your username on the respective host
151given in the <span style="font-family: Courier New,Courier,monospace;">&lt;host identifier&gt;</span>.
152You only have to uncomment lines for those hosts on which you intend to
153use PALM.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the
154respective 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
155second 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
156host.</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
157of PALM Code</span></font></p><font color="#000000">
158</font><br><font color="#000000">To avoid the
159re-compilation of the complete source code for each model run, PALM
160willl be pre-compiled once on the remote host by again using the script
161<span style="font-weight: bold;">mbuild</span>. Due
162to the use of
163FORTRAN modules in the source code, the subroutines must be compiled
164in a certain order. Therefore the so-called <i>make</i>
165mechanism
166is used (see the respective man-page of the Unix operating system),
167requiring a<span style="font-family: Courier New,Courier,monospace;">
168</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">Makefile</font><font color="#000000">,
169in which the dependencies are described. This file is found in
170subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE<span style="font-family: Times New Roman,Times,serif;">, where
171also the PALM code is stored</span></span>. The compiled
172sources (object
173files) are
174stored&nbsp;on the remote computer in the default directory
175</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
176pre-compilation for the remote host (here the IBM-Regatta of HLRN) is
177done by</font><span style="font-family: monospace;"></span></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">mbuild
178-h ibmh&nbsp;&nbsp;</span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild
179</span>will prompt some queries<font color="#000000">,
180which must all be
181answered "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
182the respective compiler calls to the remote
183host where they are carried out interactively. You can follow the
184progress at the terminal window, where also error messages
185are displayed (hopefully not for this standard installation). By just
186entering </font></p><p style="line-height: 100%;">
187</p><blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote>
188<p style="line-height: 100%;"><font color="#000000">PALM
189will
190be (consecutively) pre-compiled for all remote hosts listed in
191the configuration file. If you want to compile for the local host only,
192please enter</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">mbuild
193-h lcmuk</span> </font>
194</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,
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 color="#000080">chapter
1993.2</font></a><font color="#000000">), as well
200as the </font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d"><font color="#000080">parameter
201file</font></a><font color="#000000">
202(described in </font><a href="chapter_4.4.1.html"><font color="#000080">chapter
2034.4.1</font></a>)<font color="#000000">. The
204parameter file must be
205copied from the PALM working copy by<br>
206</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
207trunk/INSTALL/example_p3d&nbsp;JOBS/example/INPUT/example_p3d</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"></span></font></div>
208<p style="line-height: 100%;"><font color="#000000">The
209test run can
210now be started by executing the command </font>
211</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>
212<font color="#000000">This specific run
213will be carried out on 8 PEs and is allowed to use up to 500 seconds
214CPU time. After pressing &lt;return&gt;, the most important
215settings of
216the job are displayed at the terminal window
217and 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;).
218Next, a message of the queuing system like &ldquo;<i>Request</i>
219&hellip;
220<i>Submitted to queue&hellip; by&hellip;&rdquo; </i>should
221be displayed. Now the job is
222queued and either started immediately or at a later time, depending on
223the
224current workload of the remote host. Provided that it is executed
225immediately and that all things work as designed, the job protocol of
226this 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
227more than a few minutes later. The content of this
228file should be carefully examined for any error messages.</font><p style="line-height: 100%;">
229</p><p style="line-height: 100%;">Beside the job
230protocol and according to
231the configuration file and arguments given for <b>mrun</b>
232options<span style="font-family: Courier New,Courier,monospace;">
233-d </span>and<span style="font-family: Courier New,Courier,monospace;"> -r</span><tt>,</tt>further
234files should be found in
235the
236directories</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>
237<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
238</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/OUTPUT</span><span style="font-family: monospace;"></span><br>
239</p><p style="line-height: 100%;">Please compare the
240contents of file</p>
241<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
242</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/MONITORING/ibmh_example_rc</span><br>
243</p><p style="line-height: 100%;">with those of the
244example result file which can be found under<span style="font-family: Courier New,Courier,monospace;">
245trunk/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>
246diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff
247&nbsp;JOBS/example/MONITORING/ibmh_example_rc
248trunk/INSTALL/example_rc</p><p style="line-height: 100%;">where
249it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;">
250~/palm/current_version</span>.</p><span style="font-weight: bold;">You should not find any
251difference between these two files</span>, except of the run date
252and time displayed at the top of the file header. <font color="#000000">If
253the file contents are identical, the installation is successfully
254completed.<br><br></font><p style="line-height: 100%;"></p><p style="line-height: 100%; font-weight: bold; text-decoration: underline;"><font color="#000000"><a name="configuration_for_other_machines"></a>Configuration for other machines</font></p><font color="#000000">Starting
255from version 3.2a, beside the default hosts (HLRN, etc.), PALM can also
256be installed and run on other Linux-Cluster-, IBM-AIX, or
257NEC-SX-systems. To configure PALM for a non-default host only requires
258to add some lines to the configuration file<span style="font-family: Courier New,Courier,monospace;"> .mrun.config</span>.<br><br>First,
259you have to define the host identifier (a string of arbitrary length)
260under which your local host shall be identified by adding a line<br><br></font><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">%host_identifier &nbsp;&lt;hostname&gt; &nbsp;&lt;host identifier&gt;</span><br></div><br>to the configuration file (best to do this in the section where the other default host identifiers are defined). Here<span style="font-family: Courier New,Courier,monospace;"> &lt;hostname&gt; </span>must be the name of your local host as provided by the unix-command "<span style="font-family: Courier New,Courier,monospace;">hostname</span>". The first characters of<span style="font-family: Courier New,Courier,monospace;"> &lt;host identifier&gt; </span>have to be "<span style="font-family: Courier New,Courier,monospace;">lc</span>", if your system is (part of) a linux-cluster, "<span style="font-family: Courier New,Courier,monospace;">ibm</span>", or "<span style="font-family: Courier New,Courier,monospace;">nec</span>"
261in case of an IBM-AIX- or NEC-SX-system, respectively. For example, if
262you want to install on a linux-cluster, the line may read as<br><br><div style="margin-left: 40px;">%host_identifier &nbsp;foo &nbsp;lc_bar<br></div><br>In
263the second step, you have to give all informations neccessary to
264compile and run PALM on your local host by adding an additional section
265to the configuration file:<br><br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username&nbsp;&nbsp; &lt;1&gt;&nbsp; &nbsp; &nbsp; &lt;host identifier&gt; parallel<br>%tmp_user_catalog&nbsp; &lt;2&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host identifier&gt; parallel<br>%compiler_name&nbsp;&nbsp;&nbsp;&nbsp; &lt;3&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host identifier&gt; parallel<br>%compiler_name_ser &lt;4&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host identifier&gt; parallel<br>%cpp_options&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
266&lt;5&gt; &nbsp; &nbsp; &nbsp;&lt;host identifier&gt;&nbsp;parallel<br>%netcdf_inc&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;6&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host identifier&gt; parallel<br>%netcdf_lib&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;7&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host identifier&gt; parallel<br>%fopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
267&lt;8&gt; &nbsp;&nbsp;&nbsp; &nbsp;&lt;host identifier&gt; parallel<br>%lopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
268&nbsp;&lt;9&gt; &nbsp; &nbsp; &nbsp;&lt;host identifier&gt; parallel<br></div><br>The
269section consists of four columns each separated by one or more blanks.
270The first column gives the name of the respective environment variable
271used by <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span>,
272while the second column defines its value. The third column has to be
273the host identifier as defined above, and the last column in each line
274must contain the string "<span style="font-family: Courier New,Courier,monospace;">parallel</span>".
275Otherwise, the respective line(s) will be interpreted as belonging to
276the setup for compiling and running a serial (non-parallel) version of
277PALM.<br><br>All brackets have to be replaced by the appropriate settings for your local host:<br><ul><li><span style="font-family: Courier New,Courier,monospace;">&lt;1&gt; </span>is the username on your LOCAL host</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;2&gt; </span>is the temporary directory in which PALM runs will be carried out</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;3&gt; </span>is the compiler name which generates parallel code</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;4&gt; </span>is the compiler name for generating serial code</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;5&gt; </span>are
278the preprocessor options to be invoked. In most of the cases, it will
279be neccessary to adjust the MPI data types to double precision by
280giving <span style="font-family: Courier New,Courier,monospace;">-DMPI_REAL=MPI_DOUBLE_PRECISION -DMPI_2REAL=MPI_2DOUBLE_PRECISION</span>. To switch on the NetCDF support, you also have to give <span style="font-family: Courier New,Courier,monospace;">-D__netcdf</span> and <span style="font-family: Courier New,Courier,monospace;">-D__netcdf_64bit</span> (if you like to have 64bit NetCDF output).</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;6&gt; </span>is the compiler option for specifying the include path to search for the NetCDF module/include files</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;7&gt; </span>are the linker options to search for the NetCDF library</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;8&gt; </span>are the general compiler options to be used. You should allways switch on double precision (e.g. <span style="font-family: Courier New,Courier,monospace;">-r8</span>) and code optimization (e.g. <span style="font-family: Courier New,Courier,monospace;">-O2</span>).</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;9&gt; </span>are the linker options</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;host identifier&gt; </span>is the host identifier as defined before</li></ul><br>A typical example may be:<br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username&nbsp;&nbsp;
281raasch &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
282&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;lc_bar parallel<br>%tmp_user_catalog&nbsp;
283/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
284parallel<br>%compiler_name&nbsp;&nbsp;&nbsp;&nbsp;
285mpif90&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
286parallel<br>%compiler_name_ser
287ifort&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
288parallel<br>%cpp_options&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
289-DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__netcdf_64bit&nbsp;&nbsp;
290lc_bar parallel<br>%netcdf_inc&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
291-I:/usr/local/netcdf/include&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
292lc_bar parallel<br>%netcdf_lib&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
293-L/usr/local/netcdf/lib:-lnetcdf&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
294lc_bar parallel<br>%fopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
295-axW:-cpp:-openmp:-r8:-nbs &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;
296&nbsp;&nbsp;&nbsp; lc_bar parallel<br>%lopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
297-axW:-cpp:-openmp:-r8:-nbs:-Vaxlib&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;lc_bar
298parallel<br></div><br>Currently (version 3.2a), depending on the MPI
299version which is running on your local host, the options for the
300execution command (which may be <span style="font-family: Courier New,Courier,monospace;">mpirun</span> or <span style="font-family: Courier New,Courier,monospace;">mpiexec</span>)
301may have to be adjusted manually in the mrun-script. A future version
302will allow to give the respective settings in the configuration file.
303<p style="line-height: 100%;">If you have any problems
304with the PALM
305installation, the members of the PALM working group are pleased to
306help you. &nbsp; </p>
307<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>
308<p style="line-height: 100%;"><i>Last
309change:&nbsp;</i> $Id: chapter_5.0.html 97 2007-06-21 08:23:15Z raasch $</p>
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