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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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8	<body style="direction: ltr;" lang="en-US"><h2 style="line-height: 100%;"><font size="4">5.0
9	Installation of the
10	model</font></h2>
11	<font color="#000000">This chapter
12	describes the installation of PALM on a Linux workstation (local host)
13	and a suitable remote computer, on which the
14	model runs are to be carried out. The local host is used to
15	start batch jobs with <b>mrun</b> and to analyze the
16	results
17	which are produced by the model on the remote host and send back to the
18	local host. Alternatively, <span style="font-weight: bold;">mrun</span>
19	can also be used to start PALM on the local host in interactive mode or
20	as 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
21	installation and operation of PALM requires at mimimum (on both, the
22	local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The Korn-shell (AT&T ksh or public domain ksh) must be
23	available 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
24	NetCDF-library with version number not earlier than 3.6.0-p1 (for
25	NetCDF, 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
26	least 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
27	system <span style="font-weight: bold;">subversion</span>
28	(see <a href="http://subversion.tigris.org/">subversion.tigris.org</a>).
29	This is already included in many Linux distributions (e.g. SuSe). <span style="font-weight: bold;">subversion requires port 3690 to
30	be open for tcp/udp.</span> <span style="font-weight: bold;">If
31	there are firewall restrictions concerning this port, the PALM code
32	cannot be accessed.</span> The
33	user needs a permit to access the PALM repository. For getting a permit
34	please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>)
35	and define a username under which you like to access the repository.
36	You will then receive a password which allows the access under this
37	name.</font></li><li><font color="#000000">A
38	job queueing system must be available on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle
39	LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).</font></li><li><font color="#000000">ssh/scp-connections to and from the remote
40	host 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
41	to be used on a limited number of selected machines. These are SGI-ICE systems at computing center HLRN in Hannover (<span style="font-style: italic;">lcsgih</span>), Berlin (<span style="font-style: italic;">lcsgib</span>), IBM-Regatta system<span style="font-style: italic;"></span>
42	at Yonsei University, Seoul (<span style="font-style: italic;">ibms</span>),
43	on NEC-SX6/8 systems at DKRZ, Hamburg (<span style="font-style: italic;">nech</span>) and RIAM,
44	Kyushu University, Fukuoka (<span style="font-style: italic;">necriam</span>),
45	as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>), Tokyo
46	Institute of Technology (<span style="font-style: italic;">lctit</span>), and the Bergen Center for Computational Science (<span style="font-style: italic;">lcxt4</span>).
47	The strings given in brackets are the systems names (host identifiers) under which <span style="font-weight: bold;">mrun</span> identifies the
48	different 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
49	examples given in this chapter refer to an
50	installation of PALM on an IMUK Linux workstation and the SGI-ICE
51	system of
52	the HLRN used as remote host. They are just called local and
53	remote host from now on. </font></p><p style="line-height: 100%;">
54	</p><p style="line-height: 100%;">The installation
55	process requires a valid
56	account on the local and on the remote host as well.<br>
57	</p>
58	<ul> All hosts (local as well as remote) are
59	accessed via the secure shell (ssh). The user must establish
60	passwordless login using the private/public-key mechanism (see e.g. the
61	<a href="http://www.hlrn.de/doc/ssh/index.html">HLRN
62	documentation</a>). <b>To ensure proper function of mrun,
63	passwordless login must be
64	established in both directions, from the local to the remote host as
65	well as from the remote to the local host!</b> Test this by
66	carrying
67	out e.g. on the local host: <p style="line-height: 100%;"><span style="font-family: monospace;">
68	</span><span style="font-family: Courier New,Courier,monospace;">ssh
69	<username on remote host>@<remote
70	IP-address></span><br> </p> <p style="line-height: 100%;">and on the remote host:<br>
71	</p> <p style="line-height: 100%;"><span style="font-family: monospace;">
72	</span><span style="font-family: Courier New,Courier,monospace;">ssh
73	<username on local host>@<local IP-adddress></span><br>
74	</p> In both cases you should not be
75	prompted for a password. <b>Before continuing the further
76	installation
77	process, this must be absolutely guaranteed!</b> This must also
78	be
79	guaranteed for <b>all</b> other remote hosts, on which
80	PALM shall run.
81	</ul><p style="line-height: 100%;"></p><p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package
82	Installation</span></p><p style="line-height: 100%;">In
83	the <b>first installation step</b> a
84	set of directories must be created both on the local and on the
85	remote 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
86	are
87	freely selectable (except <tt><font size="2">~/job_queue</font></tt>),
88	however new users should use them as suggested, since many
89	examples in this documentation as well as all example files are
90	assuming these settings. The directory <span style="font-family: monospace;">~/palm/current_version</span>
91	on the local host will be called the working directory from now on. </p>
92	<p style="line-height: 100%;"><font color="#000000">In
93	the <b>second
94	step</b>
95	a working copy of the recent version of the PALM software package,
96	including the source code, scripts, documentation, etc.  must
97	be
98	copied to the working directory (</font><font color="#000000">local
99	host!) by executing the following
100	commands. Replace <your username> by the name that you
101	chose to
102	access the repository, and <#> by any of the available
103	PALM
104	releases, e.g. "<span style="font-style: italic;">3.1c</span>"
105	(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
106	~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn
107	checkout --username <your username>
108	svn://130.75.105.45/palm/tags/release-<#> trunk</span><br></div><p style="line-height: 100%;"><font color="#000000">You
109	will then be prompted for your password. After finishing, the
110	subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">should
111	appear in your working directory. It contains a number of further
112	subdirectories which contain e.g. the PALM source code (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SOURCE</font><font color="#000000">)
113	and 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, executing</p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username <your username> svn://130.75.105.45/palm/tags/release-<#> abcde</pre><p style="line-height: 100%;">will place your working copy in a
114	directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span>instead
115	of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span>.
116	But keep in mind that you will have to adjust several paths given
117	below, 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
118	your working copy of PALM, unless you know exactly what you
119	are doing.</p><p style="line-height: 100%; font-weight: bold;"><span style="font-weight: normal;">You can also get a copy of the
120	most recent code by executing</span></p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username <your username> svn://130.75.105.45/palm/trunk trunk</pre>However,
121	this version may contain bugs and new features may not be documented. <span style="font-weight: bold;">In future PALM releases,
122	repository access to this most recent version will
123	probably 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
124	Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To
125	use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable has to be extended and the
126	environment variable<span style="font-family: Courier New,Courier,monospace;"> PALM_BIN </span>has to be set (on local and remote host)
127	in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>,
128	if<span style="font-family: Courier New,Courier,monospace;">
129	ksh </span>is used):</font></p><p style="line-height: 100%; margin-left: 40px;"><font style="font-family: Courier New,Courier,monospace;" color="#000000">export
130	PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH</font><font color="#000000"><br><span style="font-family: Courier New,Courier,monospace;">export
131	PALM_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
132	may have to login again in order to activate these settings.</font></p><font color="#000000">On the local and on the remote host, some
133	small helper/utility programs have to be installed, which are later used by <span style="font-weight: bold;">mrun</span> e.g. for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script
134	requires a configuration file<span style="font-family: Courier New,Courier,monospace;">
135	.mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the
136	following. A copy has to be put into the working directory under the
137	name<span style="font-family: Courier New,Courier,monospace;">
138	.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
139	trunk/SCRIPTS/.mrun.config.default .mrun.config</span></font></p><font color="#000000">Beside many other things, this file contains
140	typical installation parameters
141	like compiler name, compiler options, etc.
142	for a set of different (remote) hosts. Please edit this file, uncomment
143	lines like</font><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username
144	<replace by your ... username>
145	<host identifier></div><p style="line-height: 100%;"><font color="#000000">by
146	removing the first hash (<span style="font-family: Courier New,Courier,monospace;">#</span>)
147	character and replace the string "<span style="font-family: Courier New,Courier,monospace;"><replace
148	by ...></span>" by your username on the respective host
149	given in the <span style="font-family: Courier New,Courier,monospace;"><host identifier></span>.
150	You only have to uncomment lines for those hosts on which you intend to
151	use PALM.</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;"> trunk/SCRIPTS </span>contains additional configuration files which are already adjusted for special hosts:<span style="font-family: Courier New,Courier,monospace;"> .mrun.config.imuk </span>can be used at Hannover University,<span style="font-family: Courier New,Courier,monospace;"> .mrun.config.riam </span>can
152	be used at the Research Institute of Applied Mechanics, Kyushu
153	University. These files have to be edited in the same way as described
154	above.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the
155	respective 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 lcsgih</font></p><p style="line-height: 100%;"><font color="#000000">The
156	second 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
157	host.</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
158	of PALM Code</span></font></p><font color="#000000">
159	</font><br><font color="#000000">To avoid the
160	re-compilation of the complete source code for each model run, PALM
161	willl be pre-compiled once on the remote host by again using the script
162	<span style="font-weight: bold;">mbuild</span>. Due
163	to the use of
164	FORTRAN modules in the source code, the subroutines must be compiled
165	in a certain order. Therefore the so-called <i>make</i>
166	mechanism
167	is used (see the respective man-page of the Unix operating system),
168	requiring a<span style="font-family: Courier New,Courier,monospace;">
169	</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">Makefile</font><font color="#000000">,
170	in which the dependencies are described. This file is found in
171	subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE<span style="font-family: Times New Roman,Times,serif;">, where
172	also the PALM code is stored</span></span>. The compiled
173	sources (object
174	files) are
175	stored on the remote computer in the default directory
176	</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
177	pre-compilation for the remote host (here the SGI-ICE system of HLRN) is
178	done by</font><span style="font-family: monospace;"></span></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">mbuild
179	-h lcsgih  </span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild
180	</span>will prompt some queries<font color="#000000">,
181	which must all be
182	answered "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
183	the respective compiler calls to the remote
184	host where they are carried out interactively. You can follow the
185	progress at the terminal window, where also error messages
186	are displayed (hopefully not for this standard installation). By just
187	entering </font></p><p style="line-height: 100%;">
188	</p><blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote>
189	<p style="line-height: 100%;"><font color="#000000">PALM
190	will
191	be (consecutively) pre-compiled for all remote hosts listed in
192	the configuration file. If you want to compile for the local host only,
193	please enter</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">mbuild
194	-h lcmuk</span> </font>
195	</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,
196	after the compilation has been finished, the PALM installation has to
197	be verified. For this
198	purpose a simple test run is carried out. This once again requires the <b>mrun
199	</b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter
200	3.2</font></a><font color="#000000">), as well
201	as the </font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_cbl_p3d"><font color="#000080">parameter
202	file</font></a><font color="#000000">
203	(described in </font><a href="chapter_4.4.1.html"><font color="#000080">chapter
204	4.4.1</font></a>)<font color="#000000">. The
205	parameter file must be
206	copied from the PALM working copy by<br>
207	</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
208	trunk/INSTALL/example_cbl_p3d JOBS/example_cbl/INPUT/example_cbl_p3d</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"></span></font></div>
209	<p style="line-height: 100%;"><font color="#000000">The
210	test run can
211	now be started by executing the command </font>
212	</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>
213	<font color="#000000">This specific run
214	will be carried out on 8 PEs and is allowed to use up to 500 seconds
215	CPU time. After pressing <return>, the most important
216	settings of
217	the job are displayed at the terminal window
218	and the user is prompted for o.k. (“</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">y</font><font color="#000000">”).
219	Next, a message of the queuing system like “<i>Request</i>
220	…
221	<i>Submitted to queue… by…” </i>should
222	be displayed. Now the job is
223	queued and either started immediately or at a later time, depending on
224	the
225	current workload of the remote host. Provided that it is executed
226	immediately and that all things work as designed, the job protocol of
227	this 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
228	more than a few minutes later. The content of this
229	file should be carefully examined for any error messages.</font><p style="line-height: 100%;">
230	</p><p style="line-height: 100%;">Beside the job
231	protocol and according to
232	the configuration file and arguments given for <b>mrun</b>
233	options<span style="font-family: Courier New,Courier,monospace;">
234	-d </span>and<span style="font-family: Courier New,Courier,monospace;"> -r</span><tt>,</tt>further
235	files should be found in
236	the
237	directories</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>
238	<p style="line-height: 100%;"><span style="font-family: monospace;">
239	</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/OUTPUT</span><span style="font-family: monospace;"></span><br>
240	</p><p style="line-height: 100%;">Please compare the
241	contents of file</p>
242	<p style="line-height: 100%;"><span style="font-family: monospace;">
243	</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/MONITORING/lcsgih_example_rc</span><br>
244	</p><p style="line-height: 100%;">with those of the
245	example result file which can be found under<span style="font-family: Courier New,Courier,monospace;">
246	trunk/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>
247	diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff
248	JOBS/example_cbl/MONITORING/lcsgih_example_cbl_rc
249	trunk/INSTALL/example_cbl_rc</p><p style="line-height: 100%;">where
250	it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;">
251	~/palm/current_version</span>.</p><span style="font-weight: bold;">You should not find any
252	difference between these two files</span>, except of the run date
253	and time displayed at the top of the file header. <font color="#000000">If
254	the file contents are identical, the installation is successfully
255	completed.<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
256	from version 3.2a, beside the default hosts (HLRN, etc.), PALM can also
257	be installed and run on other Linux-Cluster-, IBM-AIX, or
258	NEC-SX-systems. To configure PALM for a non-default host only requires
259	to add some lines to the configuration file<span style="font-family: Courier New,Courier,monospace;"> .mrun.config</span>.<br><br>First,
260	you have to define the host identifier (a string of arbitrary length)
261	under 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  <hostname>  <host identifier></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;"> <hostname> </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;"> <host identifier> </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>"
262	in case of an IBM-AIX- or NEC-SX-system, respectively. For example, if
263	you want to install on a linux-cluster, the line may read as<br><br><div style="margin-left: 40px;">%host_identifier  foo  lc_bar<br></div><br>In
264	the second step, you have to give all informations neccessary to
265	compile and run PALM on your local host by adding an additional section
266	to the configuration file:<br><br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username   <1>      <host identifier> parallel<br>%tmp_user_catalog  <2>      <host identifier> parallel<br>%compiler_name     <3>      <host identifier> parallel<br>%compiler_name_ser <4>      <host identifier> parallel<br>%cpp_options
267	<5>      <host identifier> parallel<br>%netcdf_inc        <6>      <host identifier> parallel<br>%netcdf_lib        <7>      <host identifier> parallel<br>%fopts
268	<8>      <host identifier> parallel<br>%lopts
269	<9>      <host identifier> parallel<br></div><br>The
270	section consists of four columns each separated by one or more blanks.
271	The first column gives the name of the respective environment variable
272	used by <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span>,
273	while the second column defines its value. The third column has to be
274	the host identifier as defined above, and the last column in each line
275	must contain the string "<span style="font-family: Courier New,Courier,monospace;">parallel</span>".
276	Otherwise, the respective line(s) will be interpreted as belonging to
277	the setup for compiling and running a serial (non-parallel) version of
278	PALM.<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;"><1> </span>is the username on your LOCAL host</li><li><span style="font-family: Courier New,Courier,monospace;"><2> </span>is the temporary directory in which PALM runs will be carried out</li><li><span style="font-family: Courier New,Courier,monospace;"><3> </span>is the compiler name which generates parallel code</li><li><span style="font-family: Courier New,Courier,monospace;"><4> </span>is the compiler name for generating serial code</li><li><span style="font-family: Courier New,Courier,monospace;"><5> </span>are
279	the preprocessor options to be invoked. In most of the cases, it will
280	be neccessary to adjust the MPI data types to double precision by
281	giving <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;"><6> </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;"><7> </span>are the linker options to search for the NetCDF library</li><li><span style="font-family: Courier New,Courier,monospace;"><8> </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;"><9> </span>are the linker options</li><li><span style="font-family: Courier New,Courier,monospace;"><host identifier> </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
282	raasch
283	lc_bar parallel<br>%tmp_user_catalog
284	/tmp                                    lc_bar
285	parallel<br>%compiler_name
286	mpif90                                  lc_bar
287	parallel<br>%compiler_name_ser
288	ifort                                   lc_bar
289	parallel<br>%cpp_options
290	-DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__netcdf_64bit
291	lc_bar parallel<br>%netcdf_inc
292	-I:/usr/local/netcdf/include
293	lc_bar parallel<br>%netcdf_lib
294	-L/usr/local/netcdf/lib:-lnetcdf
295	lc_bar parallel<br>%fopts
296	-axW:-cpp:-openmp:-r8:-nbs
297	lc_bar parallel<br>%lopts
298	-axW:-cpp:-openmp:-r8:-nbs:-Vaxlib      lc_bar
299	parallel<br></div><br>Currently (version 3.2a), depending on the MPI
300	version which is running on your local host, the options for the
301	execution 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>)
302	may have to be adjusted manually in the mrun-script. A future version
303	will allow to give the respective settings in the configuration file.
304	<p style="line-height: 100%;">If you have any problems
305	with the PALM
306	installation, the members of the PALM working group are pleased to
307	help you.   </p>
308	<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>
309	<p style="line-height: 100%;"><i>Last
310	change: </i> $Id: chapter_5.0.html 287 2009-04-09 08:59:36Z raasch $</p>
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