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4	<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	</style></head><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
21	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
22	installation and operation of PALM requires at mimimum (on both, the
23	local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The Korn-shell (AT&T ksh or public
24	domain ksh) must be
25	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
26	NetCDF-library with version number not earlier than 3.6.0-p1 (for
27	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
28	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
29	system <span style="font-weight: bold;">subversion</span>
30	(see <a href="http://subversion.tigris.org/">subversion.tigris.org</a>).
31	This is already included in many Linux distributions (e.g. SuSe). <span style="font-weight: bold;">subversion requires port 3690 to
32	be open for tcp/udp.</span> <span style="font-weight: bold;">If
33	there are firewall restrictions concerning this port, the PALM code
34	cannot be accessed.</span> The
35	user needs a permit to access the PALM repository. For getting a permit
36	please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>)
37	and define a username under which you like to access the repository.
38	You will then receive a password which allows the access under this
39	name.</font></li><li><font color="#000000">A
40	job queueing system must be available on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle
41	LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).</font></li><li><font color="#000000">ssh/scp-connections to and from the remote
42	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
43	to be used on a limited number of selected machines. These are SGI-ICE
44	systems at computing center HLRN in Hannover (<span style="font-style: italic;">lcsgih</span>), Berlin (<span style="font-style: italic;">lcsgib</span>),
45	IBM-Regatta system<span style="font-style: italic;"></span>
46	at Yonsei University, Seoul (<span style="font-style: italic;">ibms</span>),
47	on NEC-SX6/8 systems at DKRZ, Hamburg (<span style="font-style: italic;">nech</span>) and RIAM,
48	Kyushu University, Fukuoka (<span style="font-style: italic;">necriam</span>),
49	as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>), Tokyo
50	Institute of Technology (<span style="font-style: italic;">lctit</span>),
51	and the Bergen Center for Computational Science (<span style="font-style: italic;">lcxt4</span>).
52	The strings given in brackets are the systems names (host identifiers)
53	under which <span style="font-weight: bold;">mrun</span>
54	identifies the
55	different hosts.<br><br>You can also use <span style="font-weight: bold;">mrun</span>/PALM on other
56	Linux-Cluster, IBM-AIX, or NEC-SX machines. See <a href="#configuration_for_other_machines">below</a> on
57	how to configure <span style="font-weight: bold;">mrun</span>
58	for other machines. However, these configurations currently (version
59	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
60	examples given in this chapter refer to an
61	installation of PALM on an IMUK Linux workstation and the SGI-ICE
62	system of
63	the HLRN used as remote host. They are just called local and
64	remote host from now on. </font></p><p style="line-height: 100%;">
65	</p><p style="line-height: 100%;">The installation
66	process requires a valid
67	account on the local and on the remote host as well.<br>
68	</p>
69	<ul> All hosts (local as well as remote) are
70	accessed via the secure shell (ssh). The user must establish
71	passwordless login using the private/public-key mechanism (see e.g. the
72	<a href="http://www2.hlrn.de/doc/ssh/index.html">HLRN
73	documentation</a>). <b>To ensure proper function of mrun,
74	passwordless login must be
75	established in both directions, from the local to the remote host as
76	well as from the remote to the local host!</b> Test this by
77	carrying
78	out e.g. on the local host: <p style="line-height: 100%;"><span style="font-family: monospace;">
79	</span><span style="font-family: Courier New,Courier,monospace;">ssh
80	<username on remote host>@<remote
81	IP-address></span><br> </p> <p style="line-height: 100%;">and on the remote host:<br>
82	</p> <p style="line-height: 100%;"><span style="font-family: monospace;">
83	</span><span style="font-family: Courier New,Courier,monospace;">ssh
84	<username on local host>@<local IP-adddress></span><br>
85	</p> In both cases you should not be
86	prompted for a password. <b>Before continuing the further
87	installation
88	process, this must be absolutely guaranteed!</b> This must also
89	be
90	guaranteed for <b>all</b> other remote hosts, on which
91	PALM shall run.<br><br>Please
92	note that on many remote hosts, passwordless login must also be
93	established <b>within the remote host</b>, i.e. from the
94	remote host to itself. Test this by executing on the remote host: <span style="font-family: Courier New,Courier,monospace;">ssh
95	<remote IP-address></span>. You should not be prompted
96	for a password.<br><br></ul><p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package
97	Installation</span></p><p style="line-height: 100%;">In
98	the <b>first installation step</b> a
99	set of directories must be created both on the local and on the
100	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
101	are
102	freely selectable (except <big><tt><font size="2"><big>~/job_queue</big></font></tt></big>),
103	however new users should use them as suggested, since many
104	examples in this documentation as well as all example files are
105	assuming these settings. The directory <big><span style="font-family: monospace;">~/palm/current_version</span></big>
106	on the local host will be called the working directory from now on. </p>
107	<p style="line-height: 100%;"><font color="#000000">In
108	the <b>second
109	step</b>
110	a working copy of the recent version of the PALM software package,
111	including the source code, scripts, documentation, etc.  must
112	be
113	copied to the working directory (</font><font color="#000000">local
114	host!) by executing the following
115	commands. Replace <your username> by the name that you
116	chose to
117	access the repository, and <#> by any of the available
118	PALM
119	releases, e.g. "<span style="font-style: italic;">3.1c</span>"
120	(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
121	~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn
122	checkout --username <your username>
123	svn://130.75.105.2/palm/tags/release-<#> trunk</span><br></div><p style="line-height: 100%;"><font color="#000000">You
124	will then be prompted for your password. After finishing, the
125	subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">should
126	appear in your working directory. It contains a number of further
127	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">)
128	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://130.75.105.2/palm/tags/release-<#> abcde</pre><p style="line-height: 100%;">will place your working copy in a
129	directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span>instead
130	of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span>.
131	But keep in mind that you will have to adjust several paths given
132	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
133	your working copy of PALM, unless you know exactly what you
134	are doing.</p><p style="line-height: 100%; font-weight: bold;"><span style="font-weight: normal;">You can also get a copy of the
135	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://130.75.105.2/palm/trunk trunk</pre>However,
136	this version may contain bugs and new features may not be documented. <span style="font-weight: bold;">In future PALM releases,
137	repository access to this most recent version will
138	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
139	Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To
140	use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable
141	has to be extended and the
142	environment variable<span style="font-family: Courier New,Courier,monospace;">
143	PALM_BIN </span>has to be set (on local and remote host)
144	in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>,
145	if<span style="font-family: Courier New,Courier,monospace;">
146	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
147	PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH</font><font color="#000000"><br><span style="font-family: Courier New,Courier,monospace;">export
148	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
149	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
150	small helper/utility programs have to be installed, which
151	are later used by <span style="font-weight: bold;">mrun</span> e.g.
152	for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script
153	requires a configuration file<span style="font-family: Courier New,Courier,monospace;">
154	.mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the
155	following. A copy has to be put into the working directory under the
156	name<span style="font-family: Courier New,Courier,monospace;">
157	.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
158	trunk/SCRIPTS/.mrun.config.default .mrun.config</span></font></p><font color="#000000">Beside many other things, this file contains
159	typical installation parameters
160	like compiler name, compiler options, etc.
161	for a set of different (remote) hosts. Please edit this file, uncomment
162	lines like</font><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username
163	<replace by your ... username>
164	<host identifier></div><p style="line-height: 100%;"><font color="#000000">by
165	removing the first hash (<span style="font-family: Courier New,Courier,monospace;">#</span>)
166	character and replace the string "<span style="font-family: Courier New,Courier,monospace;"><replace
167	by ...></span>" by your username on the respective host
168	given in the <span style="font-family: Courier New,Courier,monospace;"><host
169	identifier></span>.
170	You only have to uncomment lines for those hosts on which you intend to
171	use PALM.</font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">Warning:
172	When editing the configuration file, please NEVER use the TAB key.
173	Otherwise, very confusing errors in mrun execution may occur.</span></font></p><p style="line-height: 100%;"><font color="#000000">Beside the default configuration file</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> .mrun.config.default</font><font color="#000000">, the directory<span style="font-family: Courier New,Courier,monospace;">
174	trunk/SCRIPTS </span>contains additional configuration files
175	which are already adjusted for special hosts:<span style="font-family: Courier New,Courier,monospace;">
176	.mrun.config.imuk </span>can be used at Hannover University,<span style="font-family: Courier New,Courier,monospace;">
177	.mrun.config.riam </span>can
178	be used at the Research Institute of Applied Mechanics, Kyushu
179	University. These files have to be edited in the same way as described
180	above.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the
181	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
182	lcsgih</font></p><p style="line-height: 100%;"><font color="#000000">The
183	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
184	remote
185	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
186	of PALM Code</span></font></p><font color="#000000">
187	</font><br><font color="#000000">To avoid the
188	re-compilation of the complete source code for each model run, PALM
189	willl be pre-compiled once on the remote host by again using the script
190	<span style="font-weight: bold;">mbuild</span>. Due
191	to the use of
192	FORTRAN modules in the source code, the subroutines must be compiled
193	in a certain order. Therefore the so-called <i>make</i>
194	mechanism
195	is used (see the respective man-page of the Unix operating system),
196	requiring a<span style="font-family: Courier New,Courier,monospace;">
197	</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">Makefile</font><font color="#000000">,
198	in which the dependencies are described. This file is found in
199	subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span></font><font color="#000000">, where
200	also the PALM code is stored.</font><font color="#000000"> The compiled
201	sources (object
202	files) are
203	stored on the remote computer in the default directory
204	</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
205	pre-compilation for the remote host (here the SGI-ICE system of HLRN)
206	is
207	done by</font><span style="font-family: monospace;"></span></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">mbuild
208	-h lcsgih  </span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild
209	</span>will prompt some queries<font color="#000000">,
210	which must all be
211	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
212	the respective compiler calls to the remote
213	host where they are carried out interactively. You can follow the
214	progress at the terminal window, where also error messages
215	are displayed (hopefully not for this standard installation). By just
216	entering </font></p><p style="line-height: 100%;">
217	</p><blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote>
218	<p style="line-height: 100%;"><font color="#000000">PALM
219	will
220	be (consecutively) pre-compiled for all remote hosts listed in
221	the configuration file. If you want to compile for the local host only,
222	please enter</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">mbuild
223	-h lcmuk</span> </font>
224	</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,
225	after the compilation has been finished, the PALM installation has to
226	be verified. For this
227	purpose a simple test run is carried out. This once again requires the <b>mrun
228	</b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter
229	3.2</font></a><font color="#000000">), as well
230	as the </font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_cbl_p3d"><font color="#000080">parameter
231	file</font></a><font color="#000000">
232	(described in </font><a href="chapter_4.4.1.html"><font color="#000080">chapter
233	4.4.1</font></a>)<font color="#000000">. The
234	parameter file must be
235	copied from the PALM working copy by<br>
236	</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
237	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>
238	<p style="line-height: 100%;"><font color="#000000">The
239	test run can
240	now be started by executing the command </font>
241	</p><pre style="margin-left: 1cm; margin-right: 1cm; margin-bottom: 0.5cm; line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mrun -d example_cbl -h lcsgih -K parallel -X 8 -T 8 -t 500 -q testq -r d3# pr#</font></pre><font color="#000000">This specific run
242	will be carried out on 8 PEs and is allowed to use up to 500 seconds
243	CPU time. After pressing <return>, the most important
244	settings of
245	the job are displayed at the terminal window
246	and the user is prompted for o.k. (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">y</font><font color="#000000">).
247	Next, a message of the queuing system like <i>Request</i>
248
249	<i>Submitted to queue by </i>should
250	be displayed. Now the job is
251	queued and either started immediately or at a later time, depending on
252	the
253	current workload of the remote host. Provided that it is executed
254	immediately and that all things work as designed, the job protocol of
255	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
256	more than a few minutes later. The content of this
257	file should be carefully examined for any error messages.</font><p style="line-height: 100%;">
258	</p><p style="line-height: 100%;">Beside the job
259	protocol and according to
260	the configuration file and arguments given for <b>mrun</b>
261	options<span style="font-family: Courier New,Courier,monospace;">
262	-d </span>and<span style="font-family: Courier New,Courier,monospace;"> -r</span><tt>,</tt>further
263	files should be found in
264	the
265	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>
266	<p style="line-height: 100%;"><span style="font-family: monospace;">
267	</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/OUTPUT</span><span style="font-family: monospace;"></span><br>
268	</p><p style="line-height: 100%;">Please compare the
269	contents of file</p>
270	<p style="line-height: 100%;"><span style="font-family: monospace;">
271	</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/MONITORING/lcsgih_example_rc</span><br>
272	</p><p style="line-height: 100%;">with those of the
273	example result file which can be found under<span style="font-family: Courier New,Courier,monospace;">
274	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>
275	diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff
276	JOBS/example_cbl/MONITORING/lcsgih_example_cbl_rc
277	trunk/INSTALL/example_cbl_rc</p><p style="line-height: 100%;">where
278	it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;">
279	~/palm/current_version</span>.</p><span style="font-weight: bold;">You should not find any
280	difference between these two files</span>, except of the run date
281	and time displayed at the top of the file header. <font color="#000000">If
282	the file contents are identical, the installation is successfully
283	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
284	for other machines</font></p><font color="#000000">Starting
285	from version 3.2a, beside the default hosts (HLRN, etc.), PALM can also
286	be installed and run on other Linux-Cluster-, IBM-AIX, or
287	NEC-SX-systems. To configure PALM for a non-default host only requires
288	to add some lines to the configuration file<span style="font-family: Courier New,Courier,monospace;">
289	.mrun.config</span>.<br><br>First,
290	you have to define the host identifier (a string of arbitrary length)
291	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
292	<hostname>  <host
293	identifier></span><br></div><br>to the
294	configuration file (best to do this in the section where the other
295	default host identifiers are defined). Here<span style="font-family: Courier New,Courier,monospace;">
296	<hostname> </span>must be the name of your local
297	host as provided by the unix-command "<span style="font-family: Courier New,Courier,monospace;">hostname</span>".
298	The first characters of<span style="font-family: Courier New,Courier,monospace;">
299	<host identifier> </span>have to be "<span style="font-family: Courier New,Courier,monospace;">lc</span>",
300	if your system is (part of) a linux-cluster, "<span style="font-family: Courier New,Courier,monospace;">ibm</span>",
301	or "<span style="font-family: Courier New,Courier,monospace;">nec</span>"
302	in case of an IBM-AIX- or NEC-SX-system, respectively. For example, if
303	you want to install on a linux-cluster, the line may read as<br><br><div style="margin-left: 40px;">%host_identifier  foo
304	lc_bar<br></div><br>In
305	the second step, you have to give all informations neccessary to
306	compile and run PALM on your local host by adding an additional section
307	to the configuration file:<br><br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username
308	<1>      <host
309	identifier> parallel<br>%tmp_user_catalog
310	<2>      <host
311	identifier> parallel<br>%compiler_name
312	<3>      <host
313	identifier> parallel<br>%compiler_name_ser
314	<4>      <host
315	identifier> parallel<br>%cpp_options
316	<5>      <host
317	identifier> parallel<br>%netcdf_inc
318	<6>      <host
319	identifier> parallel<br>%netcdf_lib
320	<7>      <host
321	identifier> parallel<br>%fopts
322	<8>      <host
323	identifier> parallel<br>%lopts
324	<9>
325	<host identifier> parallel<br></div><br>The
326	section consists of four columns each separated by one or more blanks.
327	The first column gives the name of the respective environment variable
328	used by <span style="font-weight: bold;">mrun</span>
329	and <span style="font-weight: bold;">mbuild</span>,
330	while the second column defines its value. The third column has to be
331	the host identifier as defined above, and the last column in each line
332	must contain the string "<span style="font-family: Courier New,Courier,monospace;">parallel</span>".
333	Otherwise, the respective line(s) will be interpreted as belonging to
334	the setup for compiling and running a serial (non-parallel) version of
335	PALM.<br><br>All brackets have to be replaced by the
336	appropriate settings for your local host:<br><ul><li><span style="font-family: Courier New,Courier,monospace;"><1>
337	</span>is the username on your LOCAL host</li><li><span style="font-family: Courier New,Courier,monospace;"><2>
338	</span>is the temporary directory in which PALM runs will be
339	carried out</li><li><span style="font-family: Courier New,Courier,monospace;"><3>
340	</span>is the compiler name which generates parallel code</li><li><span style="font-family: Courier New,Courier,monospace;"><4>
341	</span>is the compiler name for generating serial code</li><li><span style="font-family: Courier New,Courier,monospace;"><5>
342	</span>are
343	the preprocessor options to be invoked. In most of the cases, it will
344	be neccessary to adjust the MPI data types to double precision by
345	giving <span style="font-family: Courier New,Courier,monospace;">-DMPI_REAL=MPI_DOUBLE_PRECISION
346	-DMPI_2REAL=MPI_2DOUBLE_PRECISION</span>. To switch on the NetCDF
347	support, you also have to give <span style="font-family: Courier New,Courier,monospace;">-D__netcdf</span>
348	and <span style="font-family: Courier New,Courier,monospace;">-D__netcdf_64bit</span>
349	(if you like to have 64bit NetCDF output).</li><li><span style="font-family: Courier New,Courier,monospace;"><6>
350	</span>is the compiler option for specifying the include path to
351	search for the NetCDF module/include files</li><li><span style="font-family: Courier New,Courier,monospace;"><7>
352	</span>are the linker options to search for the NetCDF library</li><li><span style="font-family: Courier New,Courier,monospace;"><8>
353	</span>are the general compiler options to be used. You should
354	allways switch on double precision (e.g. <span style="font-family: Courier New,Courier,monospace;">-r8</span>)
355	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>
356	</span>are the linker options</li><li><span style="font-family: Courier New,Courier,monospace;"><host
357	identifier> </span>is the host identifier as defined
358	before</li></ul><br>A typical example may be:<br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username
359	raasch
360
361
362	lc_bar parallel<br>%tmp_user_catalog
363	/tmp                                    lc_bar
364	parallel<br>%compiler_name
365	mpif90                                  lc_bar
366	parallel<br>%compiler_name_ser
367	ifort                                   lc_bar
368	parallel<br>%cpp_options
369	-DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__netcdf_64bit
370	lc_bar parallel<br>%netcdf_inc
371	-I:/usr/local/netcdf/include
372	lc_bar parallel<br>%netcdf_lib
373	-L/usr/local/netcdf/lib:-lnetcdf
374	lc_bar parallel<br>%fopts
375	-axW:-cpp:-openmp:-r8:-nbs
376
377	lc_bar parallel<br>%lopts
378	-axW:-cpp:-openmp:-r8:-nbs:-Vaxlib      lc_bar
379	parallel<br></div><br>Currently (version 3.2a),
380	depending on the MPI
381	version which is running on your local host, the options for the
382	execution command (which may be <span style="font-family: Courier New,Courier,monospace;">mpirun</span>
383	or <span style="font-family: Courier New,Courier,monospace;">mpiexec</span>)
384	may have to be adjusted manually in the mrun-script. A future version
385	will allow to give the respective settings in the configuration file.
386	<p style="line-height: 100%;">If you have any problems
387	with the PALM
388	installation, the members of the PALM working group are pleased to
389	help you.   </p>
390	<hr><p style="line-height: 100%;"><font color="#000080"><font color="#000080"><a href="chapter_4.6.html"><font color="#000080"><img src="left.gif" name="Grafik1" align="bottom" border="2" height="32" width="32"></font></a><a href="index.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="up" src="up.gif" name="Grafik2"></font></a><a href="chapter_5.1.html"><font color="#000080"><img src="right.gif" name="Grafik3" align="bottom" border="2" height="32" width="32"></font></a></font></font></p><p style="line-height: 100%;"><i>Last
391	change: </i> $Id: chapter_5.0.html 287 2009-04-09
392	08:59:36Z raasch $</p>
393	</body></html>

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