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[83]	3	<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM chapter 5.0</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Siegfried Raasch"> <meta name="CREATED" content="20041103;12380720"> <meta name="CHANGED" content="20041123;15532356"> <meta name="KEYWORDS" content="parallel LES model"> <style>
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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
[5]	10	model</font></h2>
[41]	11	<font color="#000000">This chapter
[62]	12	describes the installation of PALM on a Linux workstation (local host)
	13	and a suitable remote computer, on which the
[40]	14	model runs are to be carried out. The local host is used to
[62]	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
[83]	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
[62]	21	installation and operation of PALM requires at mimimum (on both, the
[83]	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
[62]	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
[40]	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
[62]	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
[287]	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>
[62]	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,
[287]	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>).
[83]	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
[62]	49	examples given in this chapter refer to an
[287]	50	installation of PALM on an IMUK Linux workstation and the SGI-ICE
[5]	51	system of
[62]	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
[40]	56	account on the local and on the remote host as well.<br>
[5]	57	</p>
[62]	58	<ul> All hosts (local as well as remote) are
[5]	59	accessed via the secure shell (ssh). The user must establish
	60	passwordless login using the private/public-key mechanism (see e.g. the
[62]	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
[5]	64	established in both directions, from the local to the remote host as
[62]	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
[5]	84	set of directories must be created both on the local and on the
[62]	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
[5]	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
[62]	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
[40]	94	step</b>
	95	a working copy of the recent version of the PALM software package,
[62]	96	including the source code, scripts, documentation, etc.  must
	97	be
[44]	98	copied to the working directory (</font><font color="#000000">local
	99	host!) by executing the following
[62]	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
[40]	111	appear in your working directory. It contains a number of further
[62]	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
[83]	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)
[62]	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
[83]	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
[62]	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
[40]	141	like compiler name, compiler options, etc.
[83]	142	for a set of different (remote) hosts. Please edit this file, uncomment
[62]	143	lines like</font><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username
	144	<replace by your ... username>
[83]	145	<host identifier></div><p style="line-height: 100%;"><font color="#000000">by
[62]	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
[83]	149	given in the <span style="font-family: Courier New,Courier,monospace;"><host identifier></span>.
[62]	150	You only have to uncomment lines for those hosts on which you intend to
[287]	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
[83]	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
[62]	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
[5]	160	re-compilation of the complete source code for each model run, PALM
[62]	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
[5]	164	FORTRAN modules in the source code, the subroutines must be compiled
[62]	165	in a certain order. Therefore the so-called <i>make</i>
	166	mechanism
[5]	167	is used (see the respective man-page of the Unix operating system),
[62]	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
[5]	174	files) are
[40]	175	stored on the remote computer in the default directory
[41]	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
[287]	177	pre-compilation for the remote host (here the SGI-ICE system of HLRN) is
[62]	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
[287]	179	-h lcsgih  </span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild
[62]	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
[5]	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
[41]	187	entering </font></p><p style="line-height: 100%;">
[62]	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
[5]	191	be (consecutively) pre-compiled for all remote hosts listed in
[62]	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,
[5]	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
[40]	199	</b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter
[62]	200	3.2</font></a><font color="#000000">), as well
[244]	201	as the </font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_cbl_p3d"><font color="#000080">parameter
[62]	202	file</font></a><font color="#000000">
[97]	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
[62]	205	parameter file must be
[40]	206	copied from the PALM working copy by<br>
[244]	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>
[62]	209	<p style="line-height: 100%;"><font color="#000000">The
	210	test run can
[40]	211	now be started by executing the command </font>
[287]	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>
[41]	213	<font color="#000000">This specific run
[5]	214	will be carried out on 8 PEs and is allowed to use up to 500 seconds
[62]	215	CPU time. After pressing <return>, the most important
	216	settings of
[5]	217	the job are displayed at the terminal window
[62]	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
[5]	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
[287]	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
[62]	228	more than a few minutes later. The content of this
[41]	229	file should be carefully examined for any error messages.</font><p style="line-height: 100%;">
[62]	230	</p><p style="line-height: 100%;">Beside the job
	231	protocol and according to
[5]	232	the configuration file and arguments given for <b>mrun</b>
[62]	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
[5]	236	the
[244]	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>
[5]	238	<p style="line-height: 100%;"><span style="font-family: monospace;">
[244]	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>
[62]	240	</p><p style="line-height: 100%;">Please compare the
	241	contents of file</p>
[5]	242	<p style="line-height: 100%;"><span style="font-family: monospace;">
[287]	243	</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/MONITORING/lcsgih_example_rc</span><br>
[62]	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;">
[244]	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>
[62]	247	diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff
[287]	248	JOBS/example_cbl/MONITORING/lcsgih_example_cbl_rc
[244]	249	trunk/INSTALL/example_cbl_rc</p><p style="line-height: 100%;">where
[62]	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
[5]	254	the file contents are identical, the installation is successfully
[83]	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.
[62]	304	<p style="line-height: 100%;">If you have any problems
	305	with the PALM
[5]	306	installation, the members of the PALM working group are pleased to
	307	help you.   </p>
[83]	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>
[62]	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>
[40]	311	</body></html>

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