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[336]	4	<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM chapter 5.0</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Siegfried Raasch"> <meta name="CREATED" content="20041103;12380720"> <meta name="CHANGED" content="20041123;15532356"> <meta name="KEYWORDS" content="parallel LES model"> <style>
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[404]	8	</style></head><body style="direction: ltr;" lang="en-US"><h2 style="line-height: 100%;"><font size="4">5.0
[62]	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
[290]	20	as a batch job (if a queueing system like NQS, PBS, or LoadLeveler is
	21	available).</font><p style="line-height: 100%;"></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Requirements</span></font></p><p style="line-height: 100%;"><font color="#000000">The
[62]	22	installation and operation of PALM requires at mimimum (on both, the
[290]	23	local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The Korn-shell (AT&T ksh or public
	24	domain ksh) must be
[83]	25	available under<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">/bin/ksh</font><font color="#000000">.<span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-family: Courier New,Courier,monospace;"></span></font><font color="#000000"><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span></font></li><li><font color="#000000">The
[62]	26	NetCDF-library with version number not earlier than 3.6.0-p1 (for
	27	NetCDF, see under <a href="http://www.unidata.ucar.edu/software/netcdf/">www.unidata.ucar.edu</a>).</font></li><li><font color="#000000">A FORTRAN90/95 compiler.</font></li><li><font color="#000000">The Message Passing Interface (MPI), at
	28	least on the remote host, if the parallel version of PALM shall be used.</font></li><li><font color="#000000">On the local host, the revision control
	29	system <span style="font-weight: bold;">subversion</span>
	30	(see <a href="http://subversion.tigris.org/">subversion.tigris.org</a>).
	31	This is already included in many Linux distributions (e.g. SuSe). <span style="font-weight: bold;">subversion requires port 3690 to
	32	be open for tcp/udp.</span> <span style="font-weight: bold;">If
	33	there are firewall restrictions concerning this port, the PALM code
	34	cannot be accessed.</span> The
[40]	35	user needs a permit to access the PALM repository. For getting a permit
	36	please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>)
	37	and define a username under which you like to access the repository.
	38	You will then receive a password which allows the access under this
[62]	39	name.</font></li><li><font color="#000000">A
	40	job queueing system must be available on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle
	41	LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).</font></li><li><font color="#000000">ssh/scp-connections to and from the remote
	42	host must not be blocked by a firewall.<br></font></li></ol><font color="#000000"><span style="font-weight: bold;"></span></font><font color="#000000"> Currently, <span style="font-weight: bold;">mrun</span> is configured
[290]	43	to be used on a limited number of selected machines. These are SGI-ICE
	44	systems at computing center HLRN in Hannover (<span style="font-style: italic;">lcsgih</span>), Berlin (<span style="font-style: italic;">lcsgib</span>),
	45	IBM-Regatta system<span style="font-style: italic;"></span>
[62]	46	at Yonsei University, Seoul (<span style="font-style: italic;">ibms</span>),
	47	on NEC-SX6/8 systems at DKRZ, Hamburg (<span style="font-style: italic;">nech</span>) and RIAM,
[287]	48	Kyushu University, Fukuoka (<span style="font-style: italic;">necriam</span>),
	49	as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>), Tokyo
[290]	50	Institute of Technology (<span style="font-style: italic;">lctit</span>),
	51	and the Bergen Center for Computational Science (<span style="font-style: italic;">lcxt4</span>).
	52	The strings given in brackets are the systems names (host identifiers)
	53	under which <span style="font-weight: bold;">mrun</span>
	54	identifies the
	55	different hosts.<br><br>You can also use <span style="font-weight: bold;">mrun</span>/PALM on other
	56	Linux-Cluster, IBM-AIX, or NEC-SX machines. See <a href="#configuration_for_other_machines">below</a> on
	57	how to configure <span style="font-weight: bold;">mrun</span>
	58	for other machines. However, these configurations currently (version
	59	3.2a) allow to run PALM in interactive mode only.<br><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span></font><p style="line-height: 100%;"><font color="#000000">The
[62]	60	examples given in this chapter refer to an
[287]	61	installation of PALM on an IMUK Linux workstation and the SGI-ICE
[5]	62	system of
[62]	63	the HLRN used as remote host. They are just called local and
	64	remote host from now on. </font></p><p style="line-height: 100%;">
	65	</p><p style="line-height: 100%;">The installation
	66	process requires a valid
[40]	67	account on the local and on the remote host as well.<br>
[5]	68	</p>
[62]	69	<ul> All hosts (local as well as remote) are
[5]	70	accessed via the secure shell (ssh). The user must establish
	71	passwordless login using the private/public-key mechanism (see e.g. the
[290]	72	<a href="http://www2.hlrn.de/doc/ssh/index.html">HLRN
[62]	73	documentation</a>). <b>To ensure proper function of mrun,
	74	passwordless login must be
[5]	75	established in both directions, from the local to the remote host as
[62]	76	well as from the remote to the local host!</b> Test this by
	77	carrying
	78	out e.g. on the local host: <p style="line-height: 100%;"><span style="font-family: monospace;">
	79	</span><span style="font-family: Courier New,Courier,monospace;">ssh
	80	<username on remote host>@<remote
	81	IP-address></span><br> </p> <p style="line-height: 100%;">and on the remote host:<br>
	82	</p> <p style="line-height: 100%;"><span style="font-family: monospace;">
	83	</span><span style="font-family: Courier New,Courier,monospace;">ssh
	84	<username on local host>@<local IP-adddress></span><br>
	85	</p> In both cases you should not be
	86	prompted for a password. <b>Before continuing the further
	87	installation
	88	process, this must be absolutely guaranteed!</b> This must also
	89	be
	90	guaranteed for <b>all</b> other remote hosts, on which
[290]	91	PALM shall run.<br><br>Please
	92	note that on many remote hosts, passwordless login must also be
	93	established <b>within the remote host</b>, i.e. from the
	94	remote host to itself. Test this by executing on the remote host: <span style="font-family: Courier New,Courier,monospace;">ssh
	95	<remote IP-address></span>. You should not be prompted
	96	for a password.<br><br></ul><p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package
[62]	97	Installation</span></p><p style="line-height: 100%;">In
	98	the <b>first installation step</b> a
[5]	99	set of directories must be created both on the local and on the
[62]	100	remote host. These directories are:</p><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/job_queue<br></div><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm<br></div><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm/current_version<br></div><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS</span><br></div><p style="line-height: 100%;">The names of these directories
	101	are
[290]	102	freely selectable (except <big><tt><font size="2"><big>~/job_queue</big></font></tt></big>),
[5]	103	however new users should use them as suggested, since many
	104	examples in this documentation as well as all example files are
[290]	105	assuming these settings. The directory <big><span style="font-family: monospace;">~/palm/current_version</span></big>
[62]	106	on the local host will be called the working directory from now on. </p>
	107	<p style="line-height: 100%;"><font color="#000000">In
	108	the <b>second
[40]	109	step</b>
	110	a working copy of the recent version of the PALM software package,
[62]	111	including the source code, scripts, documentation, etc.  must
	112	be
[44]	113	copied to the working directory (</font><font color="#000000">local
	114	host!) by executing the following
[62]	115	commands. Replace <your username> by the name that you
	116	chose to
	117	access the repository, and <#> by any of the available
	118	PALM
	119	releases, e.g. "<span style="font-style: italic;">3.1c</span>"
	120	(new releases will be anounced by email to the PALM mailing list).</font></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">cd
	121	~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn
	122	checkout --username <your username>
[404]	123	svn://130.75.105.2/palm/tags/release-<#> trunk</span><br></div><p style="line-height: 100%;"><font color="#000000">You
[62]	124	will then be prompted for your password. After finishing, the
	125	subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">should
[40]	126	appear in your working directory. It contains a number of further
[62]	127	subdirectories which contain e.g. the PALM source code (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SOURCE</font><font color="#000000">)
[404]	128	and the scripts for running PALM (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SCRIPTS</font><font color="#000000">).</font></p><p style="line-height: 100%;">Alternatively, executing</p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username <your username> svn://130.75.105.2/palm/tags/release-<#> abcde</pre><p style="line-height: 100%;">will place your working copy in a
[62]	129	directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span>instead
	130	of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span>.
	131	But keep in mind that you will have to adjust several paths given
	132	below, if you do not use the default directory<span style="font-family: Courier New,Courier,monospace;"> trunk</span>.</p><p style="line-height: 100%;">Please never touch any file in
	133	your working copy of PALM, unless you know exactly what you
	134	are doing.</p><p style="line-height: 100%; font-weight: bold;"><span style="font-weight: normal;">You can also get a copy of the
[404]	135	most recent code by executing</span></p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username <your username> svn://130.75.105.2/palm/trunk trunk</pre>However,
[62]	136	this version may contain bugs and new features may not be documented. <span style="font-weight: bold;">In future PALM releases,
	137	repository access to this most recent version will
	138	probably be restricted to the PALM developers.</span><p style="line-height: 100%;"></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Package
	139	Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To
[290]	140	use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable
	141	has to be extended and the
	142	environment variable<span style="font-family: Courier New,Courier,monospace;">
	143	PALM_BIN </span>has to be set (on local and remote host)
[62]	144	in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>,
	145	if<span style="font-family: Courier New,Courier,monospace;">
	146	ksh </span>is used):</font></p><p style="line-height: 100%; margin-left: 40px;"><font style="font-family: Courier New,Courier,monospace;" color="#000000">export
	147	PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH</font><font color="#000000"><br><span style="font-family: Courier New,Courier,monospace;">export
	148	PALM_BIN=</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">$HOME/palm/current_version/trunk/SCRIPTS</font></p><p style="line-height: 100%;"><font color="#000000">You
[83]	149	may have to login again in order to activate these settings.</font></p><font color="#000000">On the local and on the remote host, some
[290]	150	small helper/utility programs have to be installed, which
	151	are later used by <span style="font-weight: bold;">mrun</span> e.g.
	152	for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script
[62]	153	requires a configuration file<span style="font-family: Courier New,Courier,monospace;">
	154	.mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the
	155	following. A copy has to be put into the working directory under the
	156	name<span style="font-family: Courier New,Courier,monospace;">
	157	.mrun.config </span>by</font><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">cp
	158	trunk/SCRIPTS/.mrun.config.default .mrun.config</span></font></p><font color="#000000">Beside many other things, this file contains
	159	typical installation parameters
[40]	160	like compiler name, compiler options, etc.
[83]	161	for a set of different (remote) hosts. Please edit this file, uncomment
[62]	162	lines like</font><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username
	163	<replace by your ... username>
[83]	164	<host identifier></div><p style="line-height: 100%;"><font color="#000000">by
[62]	165	removing the first hash (<span style="font-family: Courier New,Courier,monospace;">#</span>)
	166	character and replace the string "<span style="font-family: Courier New,Courier,monospace;"><replace
	167	by ...></span>" by your username on the respective host
[290]	168	given in the <span style="font-family: Courier New,Courier,monospace;"><host
	169	identifier></span>.
[62]	170	You only have to uncomment lines for those hosts on which you intend to
[336]	171	use PALM.</font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">Warning:
	172	When editing the configuration file, please NEVER use the TAB key.
	173	Otherwise, very confusing errors in mrun execution may occur.</span></font></p><p style="line-height: 100%;"><font color="#000000">Beside the default configuration file</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> .mrun.config.default</font><font color="#000000">, the directory<span style="font-family: Courier New,Courier,monospace;">
[290]	174	trunk/SCRIPTS </span>contains additional configuration files
	175	which are already adjusted for special hosts:<span style="font-family: Courier New,Courier,monospace;">
	176	.mrun.config.imuk </span>can be used at Hannover University,<span style="font-family: Courier New,Courier,monospace;">
	177	.mrun.config.riam </span>can
[287]	178	be used at the Research Institute of Applied Mechanics, Kyushu
	179	University. These files have to be edited in the same way as described
	180	above.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the
[290]	181	respective executables are generated by executing</font></p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild -u -h lcmuk<br>mbuild -u -h
	182	lcsgih</font></p><p style="line-height: 100%;"><font color="#000000">The
	183	second call also copies the PALM scripts (like <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span>) to the
	184	remote
[62]	185	host.</font></p><p style="line-height: 100%;"></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Pre-Compilation
	186	of PALM Code</span></font></p><font color="#000000">
	187	</font><br><font color="#000000">To avoid the
[5]	188	re-compilation of the complete source code for each model run, PALM
[62]	189	willl be pre-compiled once on the remote host by again using the script
	190	<span style="font-weight: bold;">mbuild</span>. Due
	191	to the use of
[5]	192	FORTRAN modules in the source code, the subroutines must be compiled
[62]	193	in a certain order. Therefore the so-called <i>make</i>
	194	mechanism
[5]	195	is used (see the respective man-page of the Unix operating system),
[62]	196	requiring a<span style="font-family: Courier New,Courier,monospace;">
	197	</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">Makefile</font><font color="#000000">,
	198	in which the dependencies are described. This file is found in
[290]	199	subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span></font><font color="#000000">, where
	200	also the PALM code is stored.</font><font color="#000000"> The compiled
[62]	201	sources (object
[5]	202	files) are
[40]	203	stored on the remote computer in the default directory
[41]	204	</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">~/palm/current_version/MAKE_DEPOSITORY</font>.<font color="#000000"><span style="font-weight: bold;"></span></font><p style="line-height: 100%;"><font color="#000000">The
[290]	205	pre-compilation for the remote host (here the SGI-ICE system of HLRN)
	206	is
[62]	207	done by</font><span style="font-family: monospace;"></span></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">mbuild
[287]	208	-h lcsgih  </span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild
[62]	209	</span>will prompt some queries<font color="#000000">,
	210	which must all be
	211	answered "y" by the user. The compiling process </font><font color="#000000">will take some time.<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">mbuild</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"> </span>transfers
	212	the respective compiler calls to the remote
[5]	213	host where they are carried out interactively. You can follow the
	214	progress at the terminal window, where also error messages
	215	are displayed (hopefully not for this standard installation). By just
[41]	216	entering </font></p><p style="line-height: 100%;">
[62]	217	</p><blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote>
	218	<p style="line-height: 100%;"><font color="#000000">PALM
	219	will
[5]	220	be (consecutively) pre-compiled for all remote hosts listed in
[62]	221	the configuration file. If you want to compile for the local host only,
	222	please enter</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">mbuild
	223	-h lcmuk</span> </font>
	224	</p><p style="line-height: 100%;"></p><p style="line-height: 100%; font-weight: bold; text-decoration: underline;"><font color="#000000">Installation Verification</font></p><font color="#000000">As a last step,
[5]	225	after the compilation has been finished, the PALM installation has to
	226	be verified. For this
	227	purpose a simple test run is carried out. This once again requires the <b>mrun
[40]	228	</b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter
[62]	229	3.2</font></a><font color="#000000">), as well
[244]	230	as the </font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_cbl_p3d"><font color="#000080">parameter
[62]	231	file</font></a><font color="#000000">
[97]	232	(described in </font><a href="chapter_4.4.1.html"><font color="#000080">chapter
	233	4.4.1</font></a>)<font color="#000000">. The
[62]	234	parameter file must be
[40]	235	copied from the PALM working copy by<br>
[244]	236	</font><div style="margin-left: 40px;"><span style="font-family: monospace;"></span><font style="font-family: Courier New,Courier,monospace;" color="#000000">mkdir -p JOBS/example_cbl/INPUT<br>cp
	237	trunk/INSTALL/example_cbl_p3d JOBS/example_cbl/INPUT/example_cbl_p3d</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"></span></font></div>
[62]	238	<p style="line-height: 100%;"><font color="#000000">The
	239	test run can
[40]	240	now be started by executing the command </font>
[404]	241	</p><pre style="margin-left: 1cm; margin-right: 1cm; margin-bottom: 0.5cm; line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mrun -d example_cbl -h lcsgih -K parallel -X 8 -T 8 -t 500 -q testq -r d3# pr#</font></pre><font color="#000000">This specific run
[5]	242	will be carried out on 8 PEs and is allowed to use up to 500 seconds
[62]	243	CPU time. After pressing <return>, the most important
	244	settings of
[5]	245	the job are displayed at the terminal window
[404]	246	and the user is prompted for o.k. (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">y</font><font color="#000000">).
	247	Next, a message of the queuing system like <i>Request</i>
	248
	249	<i>Submitted to queue by </i>should
[62]	250	be displayed. Now the job is
	251	queued and either started immediately or at a later time, depending on
	252	the
[5]	253	current workload of the remote host. Provided that it is executed
	254	immediately and that all things work as designed, the job protocol of
[287]	255	this run will appear under the file name<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">~/job_queue/lcsgih_example</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"> </span>no
[62]	256	more than a few minutes later. The content of this
[41]	257	file should be carefully examined for any error messages.</font><p style="line-height: 100%;">
[62]	258	</p><p style="line-height: 100%;">Beside the job
	259	protocol and according to
[5]	260	the configuration file and arguments given for <b>mrun</b>
[62]	261	options<span style="font-family: Courier New,Courier,monospace;">
	262	-d </span>and<span style="font-family: Courier New,Courier,monospace;"> -r</span><tt>,</tt>further
	263	files should be found in
[5]	264	the
[244]	265	directories</p><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/MONITORING</div><p style="line-height: 100%;">and</p>
[5]	266	<p style="line-height: 100%;"><span style="font-family: monospace;">
[244]	267	</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/OUTPUT</span><span style="font-family: monospace;"></span><br>
[62]	268	</p><p style="line-height: 100%;">Please compare the
	269	contents of file</p>
[5]	270	<p style="line-height: 100%;"><span style="font-family: monospace;">
[287]	271	</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/MONITORING/lcsgih_example_rc</span><br>
[62]	272	</p><p style="line-height: 100%;">with those of the
	273	example result file which can be found under<span style="font-family: Courier New,Courier,monospace;">
[244]	274	trunk/INSTALL/example_cbl_rc</span>., e.g. by using the<span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;"> standard</span>
[62]	275	diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff
[287]	276	JOBS/example_cbl/MONITORING/lcsgih_example_cbl_rc
[244]	277	trunk/INSTALL/example_cbl_rc</p><p style="line-height: 100%;">where
[62]	278	it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;">
	279	~/palm/current_version</span>.</p><span style="font-weight: bold;">You should not find any
	280	difference between these two files</span>, except of the run date
	281	and time displayed at the top of the file header. <font color="#000000">If
[5]	282	the file contents are identical, the installation is successfully
[290]	283	completed.<br><br></font><p style="line-height: 100%;"></p><p style="line-height: 100%; font-weight: bold; text-decoration: underline;"><font color="#000000"><a name="configuration_for_other_machines"></a>Configuration
	284	for other machines</font></p><font color="#000000">Starting
[83]	285	from version 3.2a, beside the default hosts (HLRN, etc.), PALM can also
	286	be installed and run on other Linux-Cluster-, IBM-AIX, or
	287	NEC-SX-systems. To configure PALM for a non-default host only requires
[290]	288	to add some lines to the configuration file<span style="font-family: Courier New,Courier,monospace;">
	289	.mrun.config</span>.<br><br>First,
[83]	290	you have to define the host identifier (a string of arbitrary length)
[290]	291	under which your local host shall be identified by adding a line<br><br></font><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">%host_identifier
	292	<hostname>  <host
	293	identifier></span><br></div><br>to the
	294	configuration file (best to do this in the section where the other
	295	default host identifiers are defined). Here<span style="font-family: Courier New,Courier,monospace;">
	296	<hostname> </span>must be the name of your local
	297	host as provided by the unix-command "<span style="font-family: Courier New,Courier,monospace;">hostname</span>".
	298	The first characters of<span style="font-family: Courier New,Courier,monospace;">
	299	<host identifier> </span>have to be "<span style="font-family: Courier New,Courier,monospace;">lc</span>",
	300	if your system is (part of) a linux-cluster, "<span style="font-family: Courier New,Courier,monospace;">ibm</span>",
	301	or "<span style="font-family: Courier New,Courier,monospace;">nec</span>"
[83]	302	in case of an IBM-AIX- or NEC-SX-system, respectively. For example, if
[290]	303	you want to install on a linux-cluster, the line may read as<br><br><div style="margin-left: 40px;">%host_identifier  foo
	304	lc_bar<br></div><br>In
[83]	305	the second step, you have to give all informations neccessary to
	306	compile and run PALM on your local host by adding an additional section
[290]	307	to the configuration file:<br><br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username
	308	<1>      <host
	309	identifier> parallel<br>%tmp_user_catalog
	310	<2>      <host
	311	identifier> parallel<br>%compiler_name
	312	<3>      <host
	313	identifier> parallel<br>%compiler_name_ser
	314	<4>      <host
	315	identifier> parallel<br>%cpp_options
	316	<5>      <host
	317	identifier> parallel<br>%netcdf_inc
	318	<6>      <host
	319	identifier> parallel<br>%netcdf_lib
	320	<7>      <host
	321	identifier> parallel<br>%fopts
	322	<8>      <host
	323	identifier> parallel<br>%lopts
	324	<9>
	325	<host identifier> parallel<br></div><br>The
[83]	326	section consists of four columns each separated by one or more blanks.
	327	The first column gives the name of the respective environment variable
[290]	328	used by <span style="font-weight: bold;">mrun</span>
	329	and <span style="font-weight: bold;">mbuild</span>,
[83]	330	while the second column defines its value. The third column has to be
	331	the host identifier as defined above, and the last column in each line
	332	must contain the string "<span style="font-family: Courier New,Courier,monospace;">parallel</span>".
	333	Otherwise, the respective line(s) will be interpreted as belonging to
	334	the setup for compiling and running a serial (non-parallel) version of
[290]	335	PALM.<br><br>All brackets have to be replaced by the
	336	appropriate settings for your local host:<br><ul><li><span style="font-family: Courier New,Courier,monospace;"><1>
	337	</span>is the username on your LOCAL host</li><li><span style="font-family: Courier New,Courier,monospace;"><2>
	338	</span>is the temporary directory in which PALM runs will be
	339	carried out</li><li><span style="font-family: Courier New,Courier,monospace;"><3>
	340	</span>is the compiler name which generates parallel code</li><li><span style="font-family: Courier New,Courier,monospace;"><4>
	341	</span>is the compiler name for generating serial code</li><li><span style="font-family: Courier New,Courier,monospace;"><5>
	342	</span>are
[83]	343	the preprocessor options to be invoked. In most of the cases, it will
	344	be neccessary to adjust the MPI data types to double precision by
[290]	345	giving <span style="font-family: Courier New,Courier,monospace;">-DMPI_REAL=MPI_DOUBLE_PRECISION
	346	-DMPI_2REAL=MPI_2DOUBLE_PRECISION</span>. To switch on the NetCDF
	347	support, you also have to give <span style="font-family: Courier New,Courier,monospace;">-D__netcdf</span>
	348	and <span style="font-family: Courier New,Courier,monospace;">-D__netcdf_64bit</span>
	349	(if you like to have 64bit NetCDF output).</li><li><span style="font-family: Courier New,Courier,monospace;"><6>
	350	</span>is the compiler option for specifying the include path to
	351	search for the NetCDF module/include files</li><li><span style="font-family: Courier New,Courier,monospace;"><7>
	352	</span>are the linker options to search for the NetCDF library</li><li><span style="font-family: Courier New,Courier,monospace;"><8>
	353	</span>are the general compiler options to be used. You should
	354	allways switch on double precision (e.g. <span style="font-family: Courier New,Courier,monospace;">-r8</span>)
	355	and code optimization (e.g. <span style="font-family: Courier New,Courier,monospace;">-O2</span>).</li><li><span style="font-family: Courier New,Courier,monospace;"><9>
	356	</span>are the linker options</li><li><span style="font-family: Courier New,Courier,monospace;"><host
	357	identifier> </span>is the host identifier as defined
	358	before</li></ul><br>A typical example may be:<br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username
	359	raasch
	360
	361
	362	lc_bar parallel<br>%tmp_user_catalog
[83]	363	/tmp                                    lc_bar
	364	parallel<br>%compiler_name
	365	mpif90                                  lc_bar
	366	parallel<br>%compiler_name_ser
	367	ifort                                   lc_bar
	368	parallel<br>%cpp_options
	369	-DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__netcdf_64bit
	370	lc_bar parallel<br>%netcdf_inc
	371	-I:/usr/local/netcdf/include
	372	lc_bar parallel<br>%netcdf_lib
	373	-L/usr/local/netcdf/lib:-lnetcdf
	374	lc_bar parallel<br>%fopts
[290]	375	-axW:-cpp:-openmp:-r8:-nbs
	376
[83]	377	lc_bar parallel<br>%lopts
	378	-axW:-cpp:-openmp:-r8:-nbs:-Vaxlib      lc_bar
[290]	379	parallel<br></div><br>Currently (version 3.2a),
	380	depending on the MPI
[83]	381	version which is running on your local host, the options for the
[290]	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>)
[83]	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.
[62]	386	<p style="line-height: 100%;">If you have any problems
	387	with the PALM
[5]	388	installation, the members of the PALM working group are pleased to
	389	help you.   </p>
[290]	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>
[40]	393	</body></html>

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