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[290]	3	<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM
	4	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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	9	<body style="direction: ltr;" lang="en-US"><h2 style="line-height: 100%;"><font size="4">5.0
	10	Installation of the
[5]	11	model</font></h2>
[41]	12	<font color="#000000">This chapter
[62]	13	describes the installation of PALM on a Linux workstation (local host)
	14	and a suitable remote computer, on which the
[40]	15	model runs are to be carried out. The local host is used to
[62]	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
[290]	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
[62]	23	installation and operation of PALM requires at mimimum (on both, the
[290]	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
[83]	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
[62]	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
[40]	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
[62]	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
[290]	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>
[62]	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,
[287]	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
[290]	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
[62]	61	examples given in this chapter refer to an
[287]	62	installation of PALM on an IMUK Linux workstation and the SGI-ICE
[5]	63	system of
[62]	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
[40]	68	account on the local and on the remote host as well.<br>
[5]	69	</p>
[62]	70	<ul> All hosts (local as well as remote) are
[5]	71	accessed via the secure shell (ssh). The user must establish
	72	passwordless login using the private/public-key mechanism (see e.g. the
[290]	73	<a href="http://www2.hlrn.de/doc/ssh/index.html">HLRN
[62]	74	documentation</a>). <b>To ensure proper function of mrun,
	75	passwordless login must be
[5]	76	established in both directions, from the local to the remote host as
[62]	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
[290]	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
[62]	98	Installation</span></p><p style="line-height: 100%;">In
	99	the <b>first installation step</b> a
[5]	100	set of directories must be created both on the local and on the
[62]	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
[290]	103	freely selectable (except <big><tt><font size="2"><big>~/job_queue</big></font></tt></big>),
[5]	104	however new users should use them as suggested, since many
	105	examples in this documentation as well as all example files are
[290]	106	assuming these settings. The directory <big><span style="font-family: monospace;">~/palm/current_version</span></big>
[62]	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
[40]	110	step</b>
	111	a working copy of the recent version of the PALM software package,
[62]	112	including the source code, scripts, documentation, etc.  must
	113	be
[44]	114	copied to the working directory (</font><font color="#000000">local
	115	host!) by executing the following
[62]	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://130.75.105.45/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
[40]	127	appear in your working directory. It contains a number of further
[62]	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://130.75.105.45/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://130.75.105.45/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
[290]	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)
[62]	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
[83]	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
[290]	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
[62]	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
[40]	161	like compiler name, compiler options, etc.
[83]	162	for a set of different (remote) hosts. Please edit this file, uncomment
[62]	163	lines like</font><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username
	164	<replace by your ... username>
[83]	165	<host identifier></div><p style="line-height: 100%;"><font color="#000000">by
[62]	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
[290]	169	given in the <span style="font-family: Courier New,Courier,monospace;"><host
	170	identifier></span>.
[62]	171	You only have to uncomment lines for those hosts on which you intend to
[290]	172	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;">
	173	trunk/SCRIPTS </span>contains additional configuration files
	174	which are already adjusted for special hosts:<span style="font-family: Courier New,Courier,monospace;">
	175	.mrun.config.imuk </span>can be used at Hannover University,<span style="font-family: Courier New,Courier,monospace;">
	176	.mrun.config.riam </span>can
[287]	177	be used at the Research Institute of Applied Mechanics, Kyushu
	178	University. These files have to be edited in the same way as described
	179	above.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the
[290]	180	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
	181	lcsgih</font></p><p style="line-height: 100%;"><font color="#000000">The
	182	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
	183	remote
[62]	184	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
	185	of PALM Code</span></font></p><font color="#000000">
	186	</font><br><font color="#000000">To avoid the
[5]	187	re-compilation of the complete source code for each model run, PALM
[62]	188	willl be pre-compiled once on the remote host by again using the script
	189	<span style="font-weight: bold;">mbuild</span>. Due
	190	to the use of
[5]	191	FORTRAN modules in the source code, the subroutines must be compiled
[62]	192	in a certain order. Therefore the so-called <i>make</i>
	193	mechanism
[5]	194	is used (see the respective man-page of the Unix operating system),
[62]	195	requiring a<span style="font-family: Courier New,Courier,monospace;">
	196	</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">Makefile</font><font color="#000000">,
	197	in which the dependencies are described. This file is found in
[290]	198	subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span></font><font color="#000000">, where
	199	also the PALM code is stored.</font><font color="#000000"> The compiled
[62]	200	sources (object
[5]	201	files) are
[40]	202	stored on the remote computer in the default directory
[41]	203	</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
[290]	204	pre-compilation for the remote host (here the SGI-ICE system of HLRN)
	205	is
[62]	206	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]	207	-h lcsgih  </span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild
[62]	208	</span>will prompt some queries<font color="#000000">,
	209	which must all be
	210	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
	211	the respective compiler calls to the remote
[5]	212	host where they are carried out interactively. You can follow the
	213	progress at the terminal window, where also error messages
	214	are displayed (hopefully not for this standard installation). By just
[41]	215	entering </font></p><p style="line-height: 100%;">
[62]	216	</p><blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote>
	217	<p style="line-height: 100%;"><font color="#000000">PALM
	218	will
[5]	219	be (consecutively) pre-compiled for all remote hosts listed in
[62]	220	the configuration file. If you want to compile for the local host only,
	221	please enter</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">mbuild
	222	-h lcmuk</span> </font>
	223	</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]	224	after the compilation has been finished, the PALM installation has to
	225	be verified. For this
	226	purpose a simple test run is carried out. This once again requires the <b>mrun
[40]	227	</b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter
[62]	228	3.2</font></a><font color="#000000">), as well
[244]	229	as the </font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_cbl_p3d"><font color="#000080">parameter
[62]	230	file</font></a><font color="#000000">
[97]	231	(described in </font><a href="chapter_4.4.1.html"><font color="#000080">chapter
	232	4.4.1</font></a>)<font color="#000000">. The
[62]	233	parameter file must be
[40]	234	copied from the PALM working copy by<br>
[244]	235	</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
	236	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]	237	<p style="line-height: 100%;"><font color="#000000">The
	238	test run can
[40]	239	now be started by executing the command </font>
[290]	240	</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
[5]	241	will be carried out on 8 PEs and is allowed to use up to 500 seconds
[62]	242	CPU time. After pressing <return>, the most important
	243	settings of
[5]	244	the job are displayed at the terminal window
[62]	245	and the user is prompted for o.k. (“</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">y</font><font color="#000000">”).
	246	Next, a message of the queuing system like “<i>Request</i>
	247	…
	248	<i>Submitted to queue… by…” </i>should
	249	be displayed. Now the job is
	250	queued and either started immediately or at a later time, depending on
	251	the
[5]	252	current workload of the remote host. Provided that it is executed
	253	immediately and that all things work as designed, the job protocol of
[287]	254	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]	255	more than a few minutes later. The content of this
[41]	256	file should be carefully examined for any error messages.</font><p style="line-height: 100%;">
[62]	257	</p><p style="line-height: 100%;">Beside the job
	258	protocol and according to
[5]	259	the configuration file and arguments given for <b>mrun</b>
[62]	260	options<span style="font-family: Courier New,Courier,monospace;">
	261	-d </span>and<span style="font-family: Courier New,Courier,monospace;"> -r</span><tt>,</tt>further
	262	files should be found in
[5]	263	the
[244]	264	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]	265	<p style="line-height: 100%;"><span style="font-family: monospace;">
[244]	266	</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]	267	</p><p style="line-height: 100%;">Please compare the
	268	contents of file</p>
[5]	269	<p style="line-height: 100%;"><span style="font-family: monospace;">
[287]	270	</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/MONITORING/lcsgih_example_rc</span><br>
[62]	271	</p><p style="line-height: 100%;">with those of the
	272	example result file which can be found under<span style="font-family: Courier New,Courier,monospace;">
[244]	273	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]	274	diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff
[287]	275	JOBS/example_cbl/MONITORING/lcsgih_example_cbl_rc
[244]	276	trunk/INSTALL/example_cbl_rc</p><p style="line-height: 100%;">where
[62]	277	it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;">
	278	~/palm/current_version</span>.</p><span style="font-weight: bold;">You should not find any
	279	difference between these two files</span>, except of the run date
	280	and time displayed at the top of the file header. <font color="#000000">If
[5]	281	the file contents are identical, the installation is successfully
[290]	282	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
	283	for other machines</font></p><font color="#000000">Starting
[83]	284	from version 3.2a, beside the default hosts (HLRN, etc.), PALM can also
	285	be installed and run on other Linux-Cluster-, IBM-AIX, or
	286	NEC-SX-systems. To configure PALM for a non-default host only requires
[290]	287	to add some lines to the configuration file<span style="font-family: Courier New,Courier,monospace;">
	288	.mrun.config</span>.<br><br>First,
[83]	289	you have to define the host identifier (a string of arbitrary length)
[290]	290	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
	291	<hostname>  <host
	292	identifier></span><br></div><br>to the
	293	configuration file (best to do this in the section where the other
	294	default host identifiers are defined). Here<span style="font-family: Courier New,Courier,monospace;">
	295	<hostname> </span>must be the name of your local
	296	host as provided by the unix-command "<span style="font-family: Courier New,Courier,monospace;">hostname</span>".
	297	The first characters of<span style="font-family: Courier New,Courier,monospace;">
	298	<host identifier> </span>have to be "<span style="font-family: Courier New,Courier,monospace;">lc</span>",
	299	if your system is (part of) a linux-cluster, "<span style="font-family: Courier New,Courier,monospace;">ibm</span>",
	300	or "<span style="font-family: Courier New,Courier,monospace;">nec</span>"
[83]	301	in case of an IBM-AIX- or NEC-SX-system, respectively. For example, if
[290]	302	you want to install on a linux-cluster, the line may read as<br><br><div style="margin-left: 40px;">%host_identifier  foo
	303	lc_bar<br></div><br>In
[83]	304	the second step, you have to give all informations neccessary to
	305	compile and run PALM on your local host by adding an additional section
[290]	306	to the configuration file:<br><br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username
	307	<1>      <host
	308	identifier> parallel<br>%tmp_user_catalog
	309	<2>      <host
	310	identifier> parallel<br>%compiler_name
	311	<3>      <host
	312	identifier> parallel<br>%compiler_name_ser
	313	<4>      <host
	314	identifier> parallel<br>%cpp_options
	315	<5>      <host
	316	identifier> parallel<br>%netcdf_inc
	317	<6>      <host
	318	identifier> parallel<br>%netcdf_lib
	319	<7>      <host
	320	identifier> parallel<br>%fopts
	321	<8>      <host
	322	identifier> parallel<br>%lopts
	323	<9>
	324	<host identifier> parallel<br></div><br>The
[83]	325	section consists of four columns each separated by one or more blanks.
	326	The first column gives the name of the respective environment variable
[290]	327	used by <span style="font-weight: bold;">mrun</span>
	328	and <span style="font-weight: bold;">mbuild</span>,
[83]	329	while the second column defines its value. The third column has to be
	330	the host identifier as defined above, and the last column in each line
	331	must contain the string "<span style="font-family: Courier New,Courier,monospace;">parallel</span>".
	332	Otherwise, the respective line(s) will be interpreted as belonging to
	333	the setup for compiling and running a serial (non-parallel) version of
[290]	334	PALM.<br><br>All brackets have to be replaced by the
	335	appropriate settings for your local host:<br><ul><li><span style="font-family: Courier New,Courier,monospace;"><1>
	336	</span>is the username on your LOCAL host</li><li><span style="font-family: Courier New,Courier,monospace;"><2>
	337	</span>is the temporary directory in which PALM runs will be
	338	carried out</li><li><span style="font-family: Courier New,Courier,monospace;"><3>
	339	</span>is the compiler name which generates parallel code</li><li><span style="font-family: Courier New,Courier,monospace;"><4>
	340	</span>is the compiler name for generating serial code</li><li><span style="font-family: Courier New,Courier,monospace;"><5>
	341	</span>are
[83]	342	the preprocessor options to be invoked. In most of the cases, it will
	343	be neccessary to adjust the MPI data types to double precision by
[290]	344	giving <span style="font-family: Courier New,Courier,monospace;">-DMPI_REAL=MPI_DOUBLE_PRECISION
	345	-DMPI_2REAL=MPI_2DOUBLE_PRECISION</span>. To switch on the NetCDF
	346	support, you also have to give <span style="font-family: Courier New,Courier,monospace;">-D__netcdf</span>
	347	and <span style="font-family: Courier New,Courier,monospace;">-D__netcdf_64bit</span>
	348	(if you like to have 64bit NetCDF output).</li><li><span style="font-family: Courier New,Courier,monospace;"><6>
	349	</span>is the compiler option for specifying the include path to
	350	search for the NetCDF module/include files</li><li><span style="font-family: Courier New,Courier,monospace;"><7>
	351	</span>are the linker options to search for the NetCDF library</li><li><span style="font-family: Courier New,Courier,monospace;"><8>
	352	</span>are the general compiler options to be used. You should
	353	allways switch on double precision (e.g. <span style="font-family: Courier New,Courier,monospace;">-r8</span>)
	354	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>
	355	</span>are the linker options</li><li><span style="font-family: Courier New,Courier,monospace;"><host
	356	identifier> </span>is the host identifier as defined
	357	before</li></ul><br>A typical example may be:<br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username
	358	raasch
	359
	360
	361	lc_bar parallel<br>%tmp_user_catalog
[83]	362	/tmp                                    lc_bar
	363	parallel<br>%compiler_name
	364	mpif90                                  lc_bar
	365	parallel<br>%compiler_name_ser
	366	ifort                                   lc_bar
	367	parallel<br>%cpp_options
	368	-DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__netcdf_64bit
	369	lc_bar parallel<br>%netcdf_inc
	370	-I:/usr/local/netcdf/include
	371	lc_bar parallel<br>%netcdf_lib
	372	-L/usr/local/netcdf/lib:-lnetcdf
	373	lc_bar parallel<br>%fopts
[290]	374	-axW:-cpp:-openmp:-r8:-nbs
	375
[83]	376	lc_bar parallel<br>%lopts
	377	-axW:-cpp:-openmp:-r8:-nbs:-Vaxlib      lc_bar
[290]	378	parallel<br></div><br>Currently (version 3.2a),
	379	depending on the MPI
[83]	380	version which is running on your local host, the options for the
[290]	381	execution command (which may be <span style="font-family: Courier New,Courier,monospace;">mpirun</span>
	382	or <span style="font-family: Courier New,Courier,monospace;">mpiexec</span>)
[83]	383	may have to be adjusted manually in the mrun-script. A future version
	384	will allow to give the respective settings in the configuration file.
[62]	385	<p style="line-height: 100%;">If you have any problems
	386	with the PALM
[5]	387	installation, the members of the PALM working group are pleased to
	388	help you.   </p>
[290]	389	<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
	390	change: </i> $Id: chapter_5.0.html 287 2009-04-09
	391	08:59:36Z raasch $</p>
[40]	392	</body></html>

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