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Last change on this file since 493 was 493, checked in by raasch, 15 years ago

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

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

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

%modules ifort/11.0.069:netcdf lcsgih parallel

This method replaces the (undocumented) mpilib-variable.

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

Changed:

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

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

Errors:

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

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

Property svn:keywords set to Id

File size: 32.7 KB

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5	<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM chapter 5.0</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Siegfried Raasch"> <meta name="CREATED" content="20041103;12380720"> <meta name="CHANGED" content="20041123;15532356"> <meta name="KEYWORDS" content="parallel LES model"> <style>
6	<!--
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9	</style></head><body style="direction: ltr;" lang="en-US"><h2 style="line-height: 100%;"><font size="4">5.0
10	Installation of the
11	model</font></h2>
12	<font color="#000000">This chapter
13	describes the installation of PALM on a Linux workstation (local host)
14	and a suitable remote computer, on which the
15	model runs are to be carried out. The local host is used to
16	start batch jobs with <b>mrun</b> and to analyze the
17	results
18	which are produced by the model on the remote host and send back to the
19	local host. Alternatively, <span style="font-weight: bold;">mrun</span>
20	can also be used to start PALM on the local host in interactive mode or
21	as a batch job (if a queueing system like NQS, PBS, or LoadLeveler is
22	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
23	installation and operation of PALM requires at mimimum (on both, the
24	local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The Korn-shell (AT&T ksh or public
25	domain ksh) must be
26	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
27	NetCDF-library with version number not earlier than 3.6.0-p1 (for
28	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
29	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
30	system <span style="font-weight: bold;">subversion</span>
31	(see <a href="http://subversion.tigris.org/">subversion.tigris.org</a>).
32	This is already included in many Linux distributions (e.g. SuSe). <span style="font-weight: bold;">subversion requires port 3690 to
33	be open for tcp/udp.</span> <span style="font-weight: bold;">If
34	there are firewall restrictions concerning this port, the PALM code
35	cannot be accessed.</span> The
36	user needs a permit to access the PALM repository. For getting a permit
37	please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>)
38	and define a username under which you like to access the repository.
39	You will then receive a password which allows the access under this
40	name.</font></li><li><font color="#000000">A
41	job queueing system must be available on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle
42	LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).</font></li><li><font color="#000000">ssh/scp-connections to and from the remote
43	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
44	to be used on a limited number of selected machines. These are SGI-ICE
45	systems at computing center HLRN in Hannover (<span style="font-style: italic;">lcsgih</span>), Berlin (<span style="font-style: italic;">lcsgib</span>),
46	IBM-Regatta system<span style="font-style: italic;"></span>
47	at Yonsei University, Seoul (<span style="font-style: italic;">ibms</span>),
48	on NEC-SX6/8 systems at DKRZ, Hamburg (<span style="font-style: italic;">nech</span>) and RIAM,
49	Kyushu University, Fukuoka (<span style="font-style: italic;">necriam</span>),
50	as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>), Tokyo
51	Institute of Technology (<span style="font-style: italic;">lctit</span>),
52	and the Bergen Center for Computational Science (<span style="font-style: italic;">lcxt4</span>).
53	The strings given in brackets are the systems names (host identifiers)
54	under which <span style="font-weight: bold;">mrun</span>
55	identifies the
56	different hosts.<br><br>You can also use <span style="font-weight: bold;">mrun</span>/PALM on other
57	Linux-Cluster, IBM-AIX, or NEC-SX machines. See <a href="#configuration_for_other_machines">below</a> on
58	how to configure <span style="font-weight: bold;">mrun</span>
59	for other machines. However, these configurations currently (version
60	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
61	examples given in this chapter refer to an
62	installation of PALM on an IMUK Linux workstation and the SGI-ICE
63	system of
64	the HLRN used as remote host. They are just called local and
65	remote host from now on. </font></p><p style="line-height: 100%;">
66	</p><p style="line-height: 100%;">The installation
67	process requires a valid
68	account on the local and on the remote host as well.<br>
69	</p>
70	<ul> All hosts (local as well as remote) are
71	accessed via the secure shell (ssh). The user must establish
72	passwordless login using the private/public-key mechanism (see e.g. the
73	<a href="http://www2.hlrn.de/doc/ssh/index.html">HLRN
74	documentation</a>). <b>To ensure proper function of mrun,
75	passwordless login must be
76	established in both directions, from the local to the remote host as
77	well as from the remote to the local host!</b> Test this by
78	carrying
79	out e.g. on the local host: <p style="line-height: 100%;"><span style="font-family: monospace;">
80	</span><span style="font-family: Courier New,Courier,monospace;">ssh
81	<username on remote host>@<remote
82	IP-address></span><br> </p> <p style="line-height: 100%;">and on the remote host:<br>
83	</p> <p style="line-height: 100%;"><span style="font-family: monospace;">
84	</span><span style="font-family: Courier New,Courier,monospace;">ssh
85	<username on local host>@<local IP-adddress></span><br>
86	</p> In both cases you should not be
87	prompted for a password. <b>Before continuing the further
88	installation
89	process, this must be absolutely guaranteed!</b> This must also
90	be
91	guaranteed for <b>all</b> other remote hosts, on which
92	PALM shall run.<br><br>Please
93	note that on many remote hosts, passwordless login must also be
94	established <b>within the remote host</b>, i.e. from the
95	remote host to itself. Test this by executing on the remote host: <span style="font-family: Courier New,Courier,monospace;">ssh
96	<remote IP-address></span>. You should not be prompted
97	for a password.<br><br></ul><p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package
98	Installation</span></p><p style="line-height: 100%;">In
99	the <b>first installation step</b> a
100	set of directories must be created both on the local and on the
101	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
102	are
103	freely selectable (except <big><tt><font size="2"><big>~/job_queue</big></font></tt></big>),
104	however new users should use them as suggested, since many
105	examples in this documentation as well as all example files are
106	assuming these settings. The directory <big><span style="font-family: monospace;">~/palm/current_version</span></big>
107	on the local host will be called the working directory from now on. </p>
108	<p style="line-height: 100%;"><font color="#000000">In
109	the <b>second
110	step</b>
111	a working copy of the recent version of the PALM software package,
112	including the source code, scripts, documentation, etc.  must
113	be
114	copied to the working directory (</font><font color="#000000">local
115	host!) by executing the following
116	commands. Replace <your username> by the name that you
117	chose to
118	access the repository, and <#> by any of the available
119	PALM
120	releases, e.g. "<span style="font-style: italic;">3.1c</span>"
121	(new releases will be anounced by email to the PALM mailing list).</font></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">cd
122	~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn
123	checkout --username <your username>
124	svn://130.75.105.2/palm/tags/release-<#> trunk</span><br></div><p style="line-height: 100%;"><font color="#000000">You
125	will then be prompted for your password. After finishing, the
126	subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">should
127	appear in your working directory. It contains a number of further
128	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">)
129	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
130	directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span>instead
131	of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span>.
132	But keep in mind that you will have to adjust several paths given
133	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
134	your working copy of PALM, unless you know exactly what you
135	are doing.</p><p style="line-height: 100%; font-weight: bold;"><span style="font-weight: normal;">You can also get a copy of the
136	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,
137	this version may contain bugs and new features may not be documented. <span style="font-weight: bold;">In future PALM releases,
138	repository access to this most recent version will
139	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
140	Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To
141	use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable
142	has to be extended and the
143	environment variable<span style="font-family: Courier New,Courier,monospace;">
144	PALM_BIN </span>has to be set (on local and remote host)
145	in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>,
146	if<span style="font-family: Courier New,Courier,monospace;">
147	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
148	PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH</font><font color="#000000"><br><span style="font-family: Courier New,Courier,monospace;">export
149	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
150	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
151	small helper/utility programs have to be installed, which
152	are later used by <span style="font-weight: bold;">mrun</span> e.g.
153	for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script
154	requires a configuration file<span style="font-family: Courier New,Courier,monospace;">
155	.mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the
156	following. A copy has to be put into the working directory under the
157	name<span style="font-family: Courier New,Courier,monospace;">
158	.mrun.config </span>by</font><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">cp
159	trunk/SCRIPTS/.mrun.config.default .mrun.config</span></font></p><font color="#000000">Beside many other things, this file contains
160	typical installation parameters
161	like compiler name, compiler options, etc.
162	for a set of different (remote) hosts. Please edit this file, uncomment
163	lines like</font><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username
164	<replace by your ... username>
165	<host identifier></div><p style="line-height: 100%;"><font color="#000000">by
166	removing the first hash (<span style="font-family: Courier New,Courier,monospace;">#</span>)
167	character and replace the string "<span style="font-family: Courier New,Courier,monospace;"><replace
168	by ...></span>" by your username on the respective host
169	given in the <span style="font-family: Courier New,Courier,monospace;"><host
170	identifier></span>.
171	You only have to uncomment lines for those hosts on which you intend to
172	use PALM.</font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">Warning:
173	When editing the configuration file, please NEVER use the TAB key.
174	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;">
175	trunk/SCRIPTS </span>contains additional configuration files
176	which are already adjusted for special hosts:<span style="font-family: Courier New,Courier,monospace;">
177	.mrun.config.imuk </span>can be used at Hannover University,<span style="font-family: Courier New,Courier,monospace;">
178	.mrun.config.riam </span>can
179	be used at the Research Institute of Applied Mechanics, Kyushu
180	University. These files have to be edited in the same way as described
181	above.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the
182	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
183	lcsgih</font></p><p style="line-height: 100%;"><font color="#000000">The
184	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
185	remote
186	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
187	of PALM Code</span></font></p><font color="#000000">
188	</font><br><font color="#000000">To avoid the
189	re-compilation of the complete source code for each model run, PALM
190	willl be pre-compiled once on the remote host by again using the script
191	<span style="font-weight: bold;">mbuild</span>. Due
192	to the use of
193	FORTRAN modules in the source code, the subroutines must be compiled
194	in a certain order. Therefore the so-called <i>make</i>
195	mechanism
196	is used (see the respective man-page of the Unix operating system),
197	requiring a<span style="font-family: Courier New,Courier,monospace;">
198	</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">Makefile</font><font color="#000000">,
199	in which the dependencies are described. This file is found in
200	subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span></font><font color="#000000">, where
201	also the PALM code is stored.</font><font color="#000000"> The compiled
202	sources (object
203	files) are
204	stored on the remote computer in the default directory
205	</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">~/palm/current_version/MAKE_DEPOSITORY</font>.<font color="#000000"><span style="font-weight: bold;"></span></font><p style="line-height: 100%;"><font color="#000000">The
206	pre-compilation for the remote host (here the SGI-ICE system of HLRN)
207	is
208	done by</font><span style="font-family: monospace;"></span></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">mbuild
209	-h lcsgih  </span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild
210	</span>will prompt some queries<font color="#000000">,
211	which must all be
212	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
213	the respective compiler calls to the remote
214	host where they are carried out interactively. You can follow the
215	progress at the terminal window, where also error messages
216	are displayed (hopefully not for this standard installation). By just
217	entering </font></p><p style="line-height: 100%;">
218	</p><blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote>
219	<p style="line-height: 100%;"><font color="#000000">PALM
220	will
221	be (consecutively) pre-compiled for all remote hosts listed in
222	the configuration file. If you want to compile for the local host only,
223	please enter</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">mbuild
224	-h lcmuk</span> </font>
225	</p><p style="line-height: 100%;"></p><p style="line-height: 100%; font-weight: bold; text-decoration: underline;"><font color="#000000">Installation Verification</font></p><font color="#000000">As a last step,
226	after the compilation has been finished, the PALM installation has to
227	be verified. For this
228	purpose a simple test run is carried out. This once again requires the <b>mrun
229	</b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter
230	3.2</font></a><font color="#000000">), as well
231	as the </font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_cbl_p3d"><font color="#000080">parameter
232	file</font></a><font color="#000000">
233	(described in </font><a href="chapter_4.4.1.html"><font color="#000080">chapter
234	4.4.1</font></a>)<font color="#000000">. The
235	parameter file must be
236	copied from the PALM working copy by<br>
237	</font><div style="margin-left: 40px;"><span style="font-family: monospace;"></span><font style="font-family: Courier New,Courier,monospace;" color="#000000">mkdir -p JOBS/example_cbl/INPUT<br>cp
238	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>
239	<p style="line-height: 100%;"><font color="#000000">The
240	test run can
241	now be started by executing the command </font>
242	</p><pre style="margin-left: 1cm; margin-right: 1cm; margin-bottom: 0.5cm; line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mrun -d example_cbl -h lcsgih -K parallel -X 8 -T 8 -t 500 -q testq -r d3# pr#</font></pre><font color="#000000">This specific run
243	will be carried out on 8 PEs and is allowed to use up to 500 seconds
244	CPU time. After pressing <return>, the most important
245	settings of
246	the job are displayed at the terminal window
247	and the user is prompted for o.k. (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">y</font><font color="#000000">).
248	Next, a message of the queuing system like <i>Request</i>
249
250	<i>Submitted to queue by </i>should
251	be displayed. Now the job is
252	queued and either started immediately or at a later time, depending on
253	the
254	current workload of the remote host. Provided that it is executed
255	immediately and that all things work as designed, the job protocol of
256	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
257	more than a few minutes later. The content of this
258	file should be carefully examined for any error messages.</font><p style="line-height: 100%;">
259	</p><p style="line-height: 100%;">Beside the job
260	protocol and according to
261	the configuration file and arguments given for <b>mrun</b>
262	options<span style="font-family: Courier New,Courier,monospace;">
263	-d </span>and<span style="font-family: Courier New,Courier,monospace;"> -r</span><tt>,</tt>further
264	files should be found in
265	the
266	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>
267	<p style="line-height: 100%;"><span style="font-family: monospace;">
268	</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/OUTPUT</span><span style="font-family: monospace;"></span><br>
269	</p><p style="line-height: 100%;">Please compare the
270	contents of file</p>
271	<p style="line-height: 100%;"><span style="font-family: monospace;">
272	</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/MONITORING/lcsgih_example_rc</span><br>
273	</p><p style="line-height: 100%;">with those of the
274	example result file which can be found under<span style="font-family: Courier New,Courier,monospace;">
275	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>
276	diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff
277	JOBS/example_cbl/MONITORING/lcsgih_example_cbl_rc
278	trunk/INSTALL/example_cbl_rc</p><p style="line-height: 100%;">where
279	it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;">
280	~/palm/current_version</span>.</p><span style="font-weight: bold;">You should not find any
281	difference between these two files</span>, except of the run date
282	and time displayed at the top of the file header. <font color="#000000">If
283	the file contents are identical, the installation is successfully
284	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
285	for other machines</font></p><font color="#000000">Starting
286	from version 3.2a, beside the default hosts (HLRN, etc.), PALM can also
287	be installed and run on other Linux-Cluster-, IBM-AIX, or
288	NEC-SX-systems. To configure PALM for a non-default host only requires
289	to add some lines to the configuration file<span style="font-family: Courier New,Courier,monospace;">
290	.mrun.config</span>.<br><br>First,
291	you have to define the host identifier (a string of arbitrary length)
292	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
293	<hostname>  <host
294	identifier></span><br></div><br>to the
295	configuration file (best to do this in the section where the other
296	default host identifiers are defined). Here<span style="font-family: Courier New,Courier,monospace;">
297	<hostname> </span>must be the name of your local
298	host as provided by the unix-command "<span style="font-family: Courier New,Courier,monospace;">hostname</span>".
299	The first characters of<span style="font-family: Courier New,Courier,monospace;">
300	<host identifier> </span>have to be "<span style="font-family: Courier New,Courier,monospace;">lc</span>",
301	if your system is (part of) a linux-cluster, "<span style="font-family: Courier New,Courier,monospace;">ibm</span>",
302	or "<span style="font-family: Courier New,Courier,monospace;">nec</span>"
303	in case of an IBM-AIX- or NEC-SX-system, respectively. For example, if
304	you want to install on a linux-cluster, the line may read as<br><br><div style="margin-left: 40px;">%host_identifier  foo
305	lc_bar<br></div><br>In
306	the second step, you have to give all informations neccessary to
307	compile and run PALM on your local host by adding an additional section
308	to the configuration file:<br><br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username
309	<1>      <host
310	identifier> parallel<br>%tmp_user_catalog
311	<2>      <host
312	identifier> parallel<br>%compiler_name
313	<3>      <host
314	identifier> parallel<br>%compiler_name_ser
315	<4>      <host
316	identifier> parallel<br>%cpp_options
317	<5>      <host
318	identifier> parallel<br>%netcdf_inc
319	<6>      <host
320	identifier> parallel<br>%netcdf_lib
321	<7>      <host
322	identifier> parallel<br>%fopts
323	<8>      <host
324	identifier> parallel<br>%lopts
325	<9>
326	<host identifier> parallel<br></div><br>The
327	section consists of four columns each separated by one or more blanks.
328	The first column gives the name of the respective environment variable
329	used by <span style="font-weight: bold;">mrun</span>
330	and <span style="font-weight: bold;">mbuild</span>,
331	while the second column defines its value. The third column has to be
332	the host identifier as defined above, and the last column in each line
333	must contain the string "<span style="font-family: Courier New,Courier,monospace;">parallel</span>".
334	Otherwise, the respective line(s) will be interpreted as belonging to
335	the setup for compiling and running a serial (non-parallel) version of
336	PALM.<br><br>All brackets have to be replaced by the
337	appropriate settings for your local host:<br><ul><li><span style="font-family: Courier New,Courier,monospace;"><1>
338	</span>is the username on your LOCAL host</li><li><span style="font-family: Courier New,Courier,monospace;"><2>
339	</span>is the temporary directory in which PALM runs will be
340	carried out</li><li><span style="font-family: Courier New,Courier,monospace;"><3>
341	</span>is the compiler name which generates parallel code</li><li><span style="font-family: Courier New,Courier,monospace;"><4>
342	</span>is the compiler name for generating serial code</li><li><span style="font-family: Courier New,Courier,monospace;"><5>
343	</span>are
344	the preprocessor options to be invoked. In most of the cases, it will
345	be neccessary to adjust the MPI data types to double precision by
346	giving <span style="font-family: Courier New,Courier,monospace;">-DMPI_REAL=MPI_DOUBLE_PRECISION
347	-DMPI_2REAL=MPI_2DOUBLE_PRECISION</span>. To switch on the NetCDF
348	support, you also have to give <span style="font-family: Courier New,Courier,monospace;">-D__netcdf</span>
349	and <span style="font-family: Courier New,Courier,monospace;">-D__netcdf4</span>
350	(if you like to have NetCDF4/HDF5 data format; this requires a NetCDF4 library!).</li><li><span style="font-family: Courier New,Courier,monospace;"><6>
351	</span>is the compiler option for specifying the include path to
352	search for the NetCDF module/include files</li><li><span style="font-family: Courier New,Courier,monospace;"><7>
353	</span>are the linker options to search for the NetCDF library</li><li><span style="font-family: Courier New,Courier,monospace;"><8>
354	</span>are the general compiler options to be used. You should
355	allways switch on double precision (e.g. <span style="font-family: Courier New,Courier,monospace;">-r8</span>)
356	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>
357	</span>are the linker options</li><li><span style="font-family: Courier New,Courier,monospace;"><host
358	identifier> </span>is the host identifier as defined
359	before</li></ul><br>A typical example may be:<br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username
360	raasch
361
362
363	lc_bar parallel<br>%tmp_user_catalog
364	/tmp                                    lc_bar
365	parallel<br>%compiler_name
366	mpif90                                  lc_bar
367	parallel<br>%compiler_name_ser
368	ifort                                   lc_bar
369	parallel<br>%cpp_options
370	-DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf  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 3.7a),
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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