source: palm/trunk/DOC/app/chapter_5.0.html @ 144

Last change on this file since 144 was 97, checked in by raasch, 17 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
RevLine 
[5]1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
[40]2<html><head>
[83]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>
[62]4<!--
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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
[5]10model</font></h2>
[41]11<font color="#000000">This chapter
[62]12describes the installation of PALM on a Linux workstation (local host)
13and a suitable remote computer, on which the
[40]14model runs are to be carried out. The local host is used to
[62]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
[83]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
[62]21installation and operation of PALM requires at mimimum (on both, the
[83]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
[62]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
[40]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
[62]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>).
[83]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
[62]51examples given in this chapter refer to an
[40]52installation of PALM on an IMUK Linux workstation and the IBM-Regatta
[5]53system of
[62]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
[40]58account on the local and on the remote host as well.<br>
[5]59&nbsp; </p>
[62]60<ul> All hosts (local as well as remote) are
[5]61accessed via the secure shell (ssh). The user must establish
62passwordless login using the private/public-key mechanism (see e.g. the
[62]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
[5]66established in both directions, from the local to the remote host as
[62]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
[5]86set of directories must be created both on the local and on the
[62]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
[5]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
[62]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
[40]96step</b>
97a working copy of the recent version of the PALM software package,
[62]98including the source code, scripts, documentation, etc.&nbsp; must
99be
[44]100copied to the working directory (</font><font color="#000000">local
101host!) by executing the following
[62]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
[40]113appear in your working directory. It contains a number of further
[62]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
[83]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)
[62]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
[83]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
[62]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
[40]143like compiler name, compiler options, etc.
[83]144for a set of different (remote) hosts. Please edit this file, uncomment
[62]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;
[83]147&lt;host identifier&gt;</div><p style="line-height: 100%;"><font color="#000000">by
[62]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
[83]151given in the <span style="font-family: Courier New,Courier,monospace;">&lt;host identifier&gt;</span>.
[62]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
[83]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
[62]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
[5]159re-compilation of the complete source code for each model run, PALM
[62]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
[5]163FORTRAN modules in the source code, the subroutines must be compiled
[62]164in a certain order. Therefore the so-called <i>make</i>
165mechanism
[5]166is used (see the respective man-page of the Unix operating system),
[62]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
[5]173files) are
[40]174stored&nbsp;on the remote computer in the default directory
[41]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
[62]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
[5]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
[41]186entering </font></p><p style="line-height: 100%;">
[62]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
[5]190be (consecutively) pre-compiled for all remote hosts listed in
[62]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,
[5]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
[40]198</b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter
[62]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">
[97]202(described in </font><a href="chapter_4.4.1.html"><font color="#000080">chapter
2034.4.1</font></a>)<font color="#000000">. The
[62]204parameter file must be
[40]205copied from the PALM working copy by<br>
[62]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
[40]210now be started by executing the command </font>
[62]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>
[41]212<font color="#000000">This specific run
[5]213will be carried out on 8 PEs and is allowed to use up to 500 seconds
[62]214CPU time. After pressing &lt;return&gt;, the most important
215settings of
[5]216the job are displayed at the terminal window
[62]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
[5]224current workload of the remote host. Provided that it is executed
225immediately and that all things work as designed, the job protocol of
[62]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
[41]228file should be carefully examined for any error messages.</font><p style="line-height: 100%;">
[62]229</p><p style="line-height: 100%;">Beside the job
230protocol and according to
[5]231the configuration file and arguments given for <b>mrun</b>
[62]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
[5]235the
[40]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>
[5]237<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
[40]238</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/OUTPUT</span><span style="font-family: monospace;"></span><br>
[62]239</p><p style="line-height: 100%;">Please compare the
240contents of file</p>
[5]241<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
[40]242</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/MONITORING/ibmh_example_rc</span><br>
[62]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
[5]253the file contents are identical, the installation is successfully
[83]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.
[62]303<p style="line-height: 100%;">If you have any problems
304with the PALM
[5]305installation, the members of the PALM working group are pleased to
306help you. &nbsp; </p>
[83]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>
[62]308<p style="line-height: 100%;"><i>Last
309change:&nbsp;</i> $Id: chapter_5.0.html 97 2007-06-21 08:23:15Z letzel $</p>
[40]310</body></html>
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