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[336]	6	<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>
[62]	7	<!--
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[404]	10	</style></head><body style="direction: ltr;" lang="en-US"><h2 style="line-height: 100%;"><font size="4">5.0
[515]	11	Code installation<br>
	12	</font></h2>
[41]	13	<font color="#000000">This chapter
[515]	14	describes the installation of PALM on a Linux workstation (local host). There are two methods to install and run PALM. With the <span style="font-style: italic;">simple method</span>, you can run PALM interactively on the local computer. This method is using the scripts <span style="font-weight: bold;">palm_simple_install</span> and <span style="font-weight: bold;">palm_simple_run</span>.
	15	The simple method cannot create batch jobs itself, and cannot be used
	16	to create restart runs. Also file handling and most other features of
	17	the <span style="font-style: italic;">advanced method</span> are not available. This method is only recommended for those who like to test PALM quickly.<br>
	18	<br>
	19	The <span style="font-style: italic;">advanced method</span> is for running PALM in batch mode on a suitable remote computer. The installation procedure is using the script <span style="font-weight: bold;">mbuild</span>. All jobs are started on the local host using the script <b>mrun</b>. The PALM output is automatically sent back from the remote host to the
[62]	20	local host. Alternatively, <span style="font-weight: bold;">mrun</span>
[515]	21	can also be used to start PALM in interactive mode on the local host, or
	22	as a batch job on the local host (if a queueing system like NQS, PBS, or LoadLeveler is
	23	available).<br>
	24	<br>
	25	Only the <span style="font-style: italic;">advanced method</span> gives full access to all PALM features.<br>
	26	<br>
	27	</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
	28	installation and operation of PALM requires at mimimum (for the <span style="font-style: italic;">advanced method</span> on both, the
	29	local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">A Korn-shell (AT&T ksh or public
	30	domain ksh); must be
	31	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">A NetCDF-library with version number not earlier than 3.6.2 (for
[62]	32	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
	33	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
	34	system <span style="font-weight: bold;">subversion</span>
	35	(see <a href="http://subversion.tigris.org/">subversion.tigris.org</a>).
	36	This is already included in many Linux distributions (e.g. SuSe). <span style="font-weight: bold;">subversion requires port 3690 to
	37	be open for tcp/udp.</span> <span style="font-weight: bold;">If
	38	there are firewall restrictions concerning this port, the PALM code
	39	cannot be accessed.</span> The
[40]	40	user needs a permit to access the PALM repository. For getting a permit
	41	please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>)
	42	and define a username under which you like to access the repository.
[515]	43	You will then receive a password which allows access under this
	44	name.<br>
	45	<br>
	46	The <span style="font-style: italic;">advanced method</span> additionally requires:<br>
	47	</font></li><li><font color="#000000">A
	48	job queueing system on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle
[62]	49	LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).</font></li><li><font color="#000000">ssh/scp-connections to and from the remote
	50	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]	51	to be used on a limited number of selected machines. These are SGI-ICE
	52	systems at computing center HLRN in Hannover (<span style="font-style: italic;">lcsgih</span>), Berlin (<span style="font-style: italic;">lcsgib</span>),
[515]	53	IBM-Regatta systems<span style="font-style: italic;"></span>
	54	at Yonsei University (<span style="font-style: italic;">ibmy</span>), <span style="font-style: italic;"></span> and at DKRZ, Hamburg (<span style="font-style: italic;">ibmh</span>), an NEC-SX8 system at RIAM,
[287]	55	Kyushu University, Fukuoka (<span style="font-style: italic;">necriam</span>),
	56	as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>), Tokyo
[290]	57	Institute of Technology (<span style="font-style: italic;">lctit</span>),
[515]	58	Kyoto computing center (<span style="font-style: italic;">lckyoto</span>), and Cray-XT4/5 systems at the Bergen Center for Computational Science (<span style="font-style: italic;">lcxt4</span>) and at the Finish Meteorological Institute (<span style="font-style: italic;">lcxt5m</span>).
[290]	59	The strings given in brackets are the systems names (host identifiers)
	60	under which <span style="font-weight: bold;">mrun</span>
	61	identifies the
	62	different hosts.<br><br>You can also use <span style="font-weight: bold;">mrun</span>/PALM on other
	63	Linux-Cluster, IBM-AIX, or NEC-SX machines. See <a href="#configuration_for_other_machines">below</a> on
[515]	64	how to configure <span style="font-weight: bold;">mrun</span>for
	65	other machines. However, these configurations currently (version
	66	3.7a) allow to run PALM in interactive mode only. Batch mode requires
	67	manual adjustments for the respective queing system and MPI
	68	installation in scripts <span style="font-weight: bold;">mrun</span>, <span style="font-weight: bold;">mbuild</span>, and <span style="font-weight: bold;">subjob</span>.<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]	69	examples given in this chapter refer to an
[515]	70	installation of PALM on an IMUK Linux workstation and (for the <span style="font-style: italic;">advanced method</span>) the SGI-ICE
	71	system of HLRN, used as remote host. They are just referred to as local and
[62]	72	remote host from now on. </font></p><p style="line-height: 100%;">
	73	</p><p style="line-height: 100%;">The installation
[515]	74	process for the <span style="font-style: italic;">advanced method</span> requires a valid
	75	account on the local and on the remote host as well.</p>
	76	<p style="line-height: 100%;">The <span style="font-style: italic;">advanced installation method</span> is described below. For the <span style="font-style: italic;">simple method</span> see the <a href="#simple_installation_method">end of this chapter</a>.<br>
[5]	77	</p>
[515]	78
	79	<ul>
	80	All hosts (local as well as remote) are
[5]	81	accessed via the secure shell (ssh). The user must establish
	82	passwordless login using the private/public-key mechanism (see e.g. the
[290]	83	<a href="http://www2.hlrn.de/doc/ssh/index.html">HLRN
[62]	84	documentation</a>). <b>To ensure proper function of mrun,
	85	passwordless login must be
[5]	86	established in both directions, from the local to the remote host as
[62]	87	well as from the remote to the local host!</b> Test this by
	88	carrying
	89	out e.g. on the local host: <p style="line-height: 100%;"><span style="font-family: monospace;">
	90	</span><span style="font-family: Courier New,Courier,monospace;">ssh
	91	<username on remote host>@<remote
	92	IP-address></span><br> </p> <p style="line-height: 100%;">and on the remote host:<br>
	93	</p> <p style="line-height: 100%;"><span style="font-family: monospace;">
	94	</span><span style="font-family: Courier New,Courier,monospace;">ssh
	95	<username on local host>@<local IP-adddress></span><br>
	96	</p> In both cases you should not be
	97	prompted for a password. <b>Before continuing the further
	98	installation
[515]	99	process, this must be absolutely guaranteed!</b> It must also
[62]	100	be
	101	guaranteed for <b>all</b> other remote hosts, on which
[290]	102	PALM shall run.<br><br>Please
[515]	103	note that on many remote hosts, passwordless login must also work <b>within the remote host</b>, i.e. for ssh connections from the
	104	remote host to itself. Test this by executing on the remote host:<br>
	105	<br>
	106	<span style="font-family: Courier New,Courier,monospace;">   ssh
	107	<username on remote host>@<remote IP-address></span>     .<br>
	108	<br>
	109	You should not be prompted
	110	for a password.<br><br>
	111	</ul>
	112	<p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package
	113	Installation</span></p><p style="line-height: 100%;">The <b>first installation step</b> requires creating a
	114	set of directories on the local and, for the <span style="font-style: italic;">advanced method</span>, on the
	115	remote host<span style="font-style: italic;"></span>. These 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 can be
	116	freely selected (except <big><tt><font size="2"><big>~/job_queue</big></font></tt></big>),
	117	however new users should choose them as suggested, since many
	118	examples in this documentation as well as all example files are based on these settings. The directory <big><span style="font-family: monospace;">~/palm/current_version</span></big>
[62]	119	on the local host will be called the working directory from now on. </p>
	120	<p style="line-height: 100%;"><font color="#000000">In
	121	the <b>second
[40]	122	step</b>
[515]	123	a working copy of the recent PALM version,
[62]	124	including the source code, scripts, documentation, etc.  must
	125	be
[44]	126	copied to the working directory (</font><font color="#000000">local
	127	host!) by executing the following
[515]	128	commands. Replace <your username> by the name that you have chosen to
[62]	129	access the repository, and <#> by any of the available
	130	PALM
[515]	131	releases, e.g. "<span style="font-style: italic;">3.7a</span>"
	132	(new releases will be announced to members of the PALM mailing list).</font></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">cd
[62]	133	~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn
	134	checkout --username <your username>
[404]	135	svn://130.75.105.2/palm/tags/release-<#> trunk</span><br></div><p style="line-height: 100%;"><font color="#000000">You
[515]	136	will then be prompted for your password. After completion, there should be a subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">in your working directory. It contains a number of further
	137	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]	138	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
[515]	139	directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span>(instead
	140	of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span>).
[62]	141	But keep in mind that you will have to adjust several paths given
	142	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
[515]	143	your working copy of PALM, unless you know what you
[62]	144	are doing.</p><p style="line-height: 100%; font-weight: bold;"><span style="font-weight: normal;">You can also get a copy of the
[515]	145	most recent developer 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>This version may contain new features (they might not be documented well), but it may also contain bugs.<span style="font-weight: bold;"><br>
	146	</span><br>
	147	<p style="line-height: 100%;"></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Package
[62]	148	Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To
[290]	149	use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable
	150	has to be extended and the
	151	environment variable<span style="font-family: Courier New,Courier,monospace;">
	152	PALM_BIN </span>has to be set (on local and remote host)
[62]	153	in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>,
	154	if<span style="font-family: Courier New,Courier,monospace;">
	155	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
	156	PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH</font><font color="#000000"><br><span style="font-family: Courier New,Courier,monospace;">export
	157	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]	158	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]	159	small helper/utility programs have to be installed, which
	160	are later used by <span style="font-weight: bold;">mrun</span> e.g.
	161	for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script
[62]	162	requires a configuration file<span style="font-family: Courier New,Courier,monospace;">
	163	.mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the
	164	following. A copy has to be put into the working directory under the
	165	name<span style="font-family: Courier New,Courier,monospace;">
	166	.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
	167	trunk/SCRIPTS/.mrun.config.default .mrun.config</span></font></p><font color="#000000">Beside many other things, this file contains
	168	typical installation parameters
[40]	169	like compiler name, compiler options, etc.
[83]	170	for a set of different (remote) hosts. Please edit this file, uncomment
[62]	171	lines like</font><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username
	172	<replace by your ... username>
[83]	173	<host identifier></div><p style="line-height: 100%;"><font color="#000000">by
[62]	174	removing the first hash (<span style="font-family: Courier New,Courier,monospace;">#</span>)
	175	character and replace the string "<span style="font-family: Courier New,Courier,monospace;"><replace
	176	by ...></span>" by your username on the respective host
[290]	177	given in the <span style="font-family: Courier New,Courier,monospace;"><host
	178	identifier></span>.
[62]	179	You only have to uncomment lines for those hosts on which you intend to
[336]	180	use PALM.</font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">Warning:
	181	When editing the configuration file, please NEVER use the TAB key.
[515]	182	Otherwise, very confusing errors may occur when mrun is executing.</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]	183	trunk/SCRIPTS </span>contains additional configuration files
[515]	184	which are already adjusted for special hosts</font><font color="#000000">, e.g.</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">
	185	.mrun.config.imuk </span>can be used at Hannover University</font><font color="#000000">, etc.. </font><font color="#000000">These files have to be edited in the same way as described
[287]	186	above.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the
[290]	187	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
	188	lcsgih</font></p><p style="line-height: 100%;"><font color="#000000">The
	189	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
	190	remote
[515]	191	host.<br>
	192	<br>
	193	</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
[62]	194	of PALM Code</span></font></p><font color="#000000">
	195	</font><br><font color="#000000">To avoid the
[5]	196	re-compilation of the complete source code for each model run, PALM
[62]	197	willl be pre-compiled once on the remote host by again using the script
	198	<span style="font-weight: bold;">mbuild</span>. Due
	199	to the use of
[5]	200	FORTRAN modules in the source code, the subroutines must be compiled
[62]	201	in a certain order. Therefore the so-called <i>make</i>
	202	mechanism
[5]	203	is used (see the respective man-page of the Unix operating system),
[62]	204	requiring a<span style="font-family: Courier New,Courier,monospace;">
	205	</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">Makefile</font><font color="#000000">,
	206	in which the dependencies are described. This file is found in
[290]	207	subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span></font><font color="#000000">, where
	208	also the PALM code is stored.</font><font color="#000000"> The compiled
[62]	209	sources (object
[5]	210	files) are
[40]	211	stored on the remote computer in the default directory
[515]	212	</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">~/palm/current_version/MAKE_DEPOSITORY</font>_<span style="font-family: Courier New,Courier,monospace;"><block_descriptor></span>, where<font color="#000000"> <span style="font-family: Courier New,Courier,monospace;"><block_descriptor></span> is composed of the third (and fourth, if existing) column of the respective block in the configuration file (e.g. <span style="font-family: Courier New,Courier,monospace;">lcsgih_parallel</span> for HLRN).<span style="font-weight: bold;"></span></font><p style="line-height: 100%;"><font color="#000000">The
[290]	213	pre-compilation for the remote host (here the SGI-ICE system of HLRN)
	214	is
[62]	215	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]	216	-h lcsgih  </span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild
[62]	217	</span>will prompt some queries<font color="#000000">,
	218	which must all be
	219	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
	220	the respective compiler calls to the remote
[5]	221	host where they are carried out interactively. You can follow the
	222	progress at the terminal window, where also error messages
	223	are displayed (hopefully not for this standard installation). By just
[41]	224	entering </font></p><p style="line-height: 100%;">
[62]	225	</p><blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote>
	226	<p style="line-height: 100%;"><font color="#000000">PALM
	227	will
[5]	228	be (consecutively) pre-compiled for all remote hosts listed in
[62]	229	the configuration file. If you want to compile for the local host only,
	230	please enter</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">mbuild
	231	-h lcmuk</span> </font>
	232	</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]	233	after the compilation has been finished, the PALM installation has to
	234	be verified. For this
	235	purpose a simple test run is carried out. This once again requires the <b>mrun
[40]	236	</b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter
[62]	237	3.2</font></a><font color="#000000">), as well
[244]	238	as the </font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_cbl_p3d"><font color="#000080">parameter
[62]	239	file</font></a><font color="#000000">
[97]	240	(described in </font><a href="chapter_4.4.1.html"><font color="#000080">chapter
	241	4.4.1</font></a>)<font color="#000000">. The
[62]	242	parameter file must be
[40]	243	copied from the PALM working copy by<br>
[244]	244	</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
	245	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]	246	<p style="line-height: 100%;"><font color="#000000">The
	247	test run can
[40]	248	now be started by executing the command </font>
[404]	249	</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]	250	will be carried out on 8 PEs and is allowed to use up to 500 seconds
[62]	251	CPU time. After pressing <return>, the most important
	252	settings of
[5]	253	the job are displayed at the terminal window
[404]	254	and the user is prompted for o.k. (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">y</font><font color="#000000">).
	255	Next, a message of the queuing system like <i>Request</i>
	256
	257	<i>Submitted to queue by </i>should
[62]	258	be displayed. Now the job is
	259	queued and either started immediately or at a later time, depending on
	260	the
[5]	261	current workload of the remote host. Provided that it is executed
	262	immediately and that all things work as designed, the job protocol of
[287]	263	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]	264	more than a few minutes later. The content of this
[41]	265	file should be carefully examined for any error messages.</font><p style="line-height: 100%;">
[62]	266	</p><p style="line-height: 100%;">Beside the job
	267	protocol and according to
[5]	268	the configuration file and arguments given for <b>mrun</b>
[62]	269	options<span style="font-family: Courier New,Courier,monospace;">
	270	-d </span>and<span style="font-family: Courier New,Courier,monospace;"> -r</span><tt>,</tt>further
	271	files should be found in
[5]	272	the
[244]	273	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]	274	<p style="line-height: 100%;"><span style="font-family: monospace;">
[244]	275	</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]	276	</p><p style="line-height: 100%;">Please compare the
	277	contents of file</p>
[5]	278	<p style="line-height: 100%;"><span style="font-family: monospace;">
[287]	279	</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/MONITORING/lcsgih_example_rc</span><br>
[62]	280	</p><p style="line-height: 100%;">with those of the
	281	example result file which can be found under<span style="font-family: Courier New,Courier,monospace;">
[244]	282	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]	283	diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff
[287]	284	JOBS/example_cbl/MONITORING/lcsgih_example_cbl_rc
[244]	285	trunk/INSTALL/example_cbl_rc</p><p style="line-height: 100%;">where
[62]	286	it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;">
	287	~/palm/current_version</span>.</p><span style="font-weight: bold;">You should not find any
	288	difference between these two files</span>, except of the run date
	289	and time displayed at the top of the file header. <font color="#000000">If
[5]	290	the file contents are identical, the installation is successfully
[290]	291	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
	292	for other machines</font></p><font color="#000000">Starting
[83]	293	from version 3.2a, beside the default hosts (HLRN, etc.), PALM can also
	294	be installed and run on other Linux-Cluster-, IBM-AIX, or
	295	NEC-SX-systems. To configure PALM for a non-default host only requires
[290]	296	to add some lines to the configuration file<span style="font-family: Courier New,Courier,monospace;">
	297	.mrun.config</span>.<br><br>First,
[83]	298	you have to define the host identifier (a string of arbitrary length)
[290]	299	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
	300	<hostname>  <host
	301	identifier></span><br></div><br>to the
	302	configuration file (best to do this in the section where the other
	303	default host identifiers are defined). Here<span style="font-family: Courier New,Courier,monospace;">
	304	<hostname> </span>must be the name of your local
	305	host as provided by the unix-command "<span style="font-family: Courier New,Courier,monospace;">hostname</span>".
	306	The first characters of<span style="font-family: Courier New,Courier,monospace;">
	307	<host identifier> </span>have to be "<span style="font-family: Courier New,Courier,monospace;">lc</span>",
	308	if your system is (part of) a linux-cluster, "<span style="font-family: Courier New,Courier,monospace;">ibm</span>",
	309	or "<span style="font-family: Courier New,Courier,monospace;">nec</span>"
[83]	310	in case of an IBM-AIX- or NEC-SX-system, respectively. For example, if
[290]	311	you want to install on a linux-cluster, the line may read as<br><br><div style="margin-left: 40px;">%host_identifier  foo
	312	lc_bar<br></div><br>In
[83]	313	the second step, you have to give all informations neccessary to
	314	compile and run PALM on your local host by adding an additional section
[290]	315	to the configuration file:<br><br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username
	316	<1>      <host
	317	identifier> parallel<br>%tmp_user_catalog
	318	<2>      <host
	319	identifier> parallel<br>%compiler_name
	320	<3>      <host
	321	identifier> parallel<br>%compiler_name_ser
	322	<4>      <host
	323	identifier> parallel<br>%cpp_options
	324	<5>      <host
	325	identifier> parallel<br>%netcdf_inc
	326	<6>      <host
	327	identifier> parallel<br>%netcdf_lib
	328	<7>      <host
	329	identifier> parallel<br>%fopts
	330	<8>      <host
	331	identifier> parallel<br>%lopts
	332	<9>
	333	<host identifier> parallel<br></div><br>The
[83]	334	section consists of four columns each separated by one or more blanks.
	335	The first column gives the name of the respective environment variable
[290]	336	used by <span style="font-weight: bold;">mrun</span>
	337	and <span style="font-weight: bold;">mbuild</span>,
[83]	338	while the second column defines its value. The third column has to be
	339	the host identifier as defined above, and the last column in each line
	340	must contain the string "<span style="font-family: Courier New,Courier,monospace;">parallel</span>".
	341	Otherwise, the respective line(s) will be interpreted as belonging to
	342	the setup for compiling and running a serial (non-parallel) version of
[290]	343	PALM.<br><br>All brackets have to be replaced by the
	344	appropriate settings for your local host:<br><ul><li><span style="font-family: Courier New,Courier,monospace;"><1>
	345	</span>is the username on your LOCAL host</li><li><span style="font-family: Courier New,Courier,monospace;"><2>
	346	</span>is the temporary directory in which PALM runs will be
	347	carried out</li><li><span style="font-family: Courier New,Courier,monospace;"><3>
	348	</span>is the compiler name which generates parallel code</li><li><span style="font-family: Courier New,Courier,monospace;"><4>
	349	</span>is the compiler name for generating serial code</li><li><span style="font-family: Courier New,Courier,monospace;"><5>
	350	</span>are
[83]	351	the preprocessor options to be invoked. In most of the cases, it will
	352	be neccessary to adjust the MPI data types to double precision by
[290]	353	giving <span style="font-family: Courier New,Courier,monospace;">-DMPI_REAL=MPI_DOUBLE_PRECISION
	354	-DMPI_2REAL=MPI_2DOUBLE_PRECISION</span>. To switch on the NetCDF
	355	support, you also have to give <span style="font-family: Courier New,Courier,monospace;">-D__netcdf</span>
[493]	356	and <span style="font-family: Courier New,Courier,monospace;">-D__netcdf4</span>
	357	(if you like to have NetCDF4/HDF5 data format; this requires a NetCDF4 library!).</li><li><span style="font-family: Courier New,Courier,monospace;"><6>
[290]	358	</span>is the compiler option for specifying the include path to
	359	search for the NetCDF module/include files</li><li><span style="font-family: Courier New,Courier,monospace;"><7>
	360	</span>are the linker options to search for the NetCDF library</li><li><span style="font-family: Courier New,Courier,monospace;"><8>
	361	</span>are the general compiler options to be used. You should
	362	allways switch on double precision (e.g. <span style="font-family: Courier New,Courier,monospace;">-r8</span>)
	363	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>
	364	</span>are the linker options</li><li><span style="font-family: Courier New,Courier,monospace;"><host
	365	identifier> </span>is the host identifier as defined
	366	before</li></ul><br>A typical example may be:<br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username
	367	raasch
	368
	369
	370	lc_bar parallel<br>%tmp_user_catalog
[83]	371	/tmp                                    lc_bar
	372	parallel<br>%compiler_name
	373	mpif90                                  lc_bar
	374	parallel<br>%compiler_name_ser
	375	ifort                                   lc_bar
	376	parallel<br>%cpp_options
[493]	377	-DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf  lc_bar parallel<br>%netcdf_inc
[83]	378	-I:/usr/local/netcdf/include
	379	lc_bar parallel<br>%netcdf_lib
	380	-L/usr/local/netcdf/lib:-lnetcdf
	381	lc_bar parallel<br>%fopts
[290]	382	-axW:-cpp:-openmp:-r8:-nbs
	383
[83]	384	lc_bar parallel<br>%lopts
	385	-axW:-cpp:-openmp:-r8:-nbs:-Vaxlib      lc_bar
[493]	386	parallel<br></div><br>Currently (version 3.7a),
[290]	387	depending on the MPI
[83]	388	version which is running on your local host, the options for the
[290]	389	execution command (which may be <span style="font-family: Courier New,Courier,monospace;">mpirun</span>
	390	or <span style="font-family: Courier New,Courier,monospace;">mpiexec</span>)
[515]	391	may have to be adjusted manually in the <span style="font-weight: bold;">mrun</span>-script. A future version
[83]	392	will allow to give the respective settings in the configuration file.
[62]	393	<p style="line-height: 100%;">If you have any problems
	394	with the PALM
[5]	395	installation, the members of the PALM working group are pleased to
[515]	396	help you.<br>
	397	</p>
	398	<p style="line-height: 100%;"><br>
	399	<span style="font-weight: bold; text-decoration: underline;"><a name="simple_installation_method"></a>Simple installation method</span><br>
	400	</p>
	401	<p style="line-height: 100%;">The simple installation method is using the scripts <span style="font-weight: bold;">palm_simple_install</span> and <span style="font-weight: bold;">palm_simple_run</span> for installing and running PALM.<br>
	402	<br>
	403	<span style="font-weight: bold; text-decoration: underline;">Package
	404	Installation</span></p>
	405	<p style="line-height: 100%;"><span style="font-weight: bold;">First step:</span> Create a directory<span style="font-style: italic;"></span>:</p>
	406	<div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">mkdir -p ~/palm/current_version/</div>
	407	<p style="line-height: 100%;">You can freely choose the directory name, but if you intend to switch to the <span style="font-style: italic;">advanced method</span> of running PALM later, you should use<span style="font-family: Courier New,Courier,monospace;"> ~/palm/current_version</span>. This directory <big><span style="font-family: monospace;"></span></big>will be called working directory from now on. </p>
	408
	409	<p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">S</span><b>econd
	410	step</b>:
	411	Check out a working copy of the recent PALM version from the svn-repository</font><font color="#000000">. Replace<span style="font-family: Courier New,Courier,monospace;"> <your username> </span>by your valid repository username, and<span style="font-family: Courier New,Courier,monospace;"> <#> </span>by any of the available
	412	PALM
	413	releases, e.g. "<span style="font-style: italic;">3.7a</span>"
	414	(new releases will be announced to members of the PALM mailing list).</font></p>
	415	<div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">cd
	416	~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn
	417	checkout --username <your username>
	418	svn://130.75.105.2/palm/tags/release-<#> trunk</span><br></div>
	419	<p style="line-height: 100%;"><font color="#000000">You
	420	will be prompted for your password. After completion, a subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk <span style="font-family: Times New Roman,Times,serif;">will appear </span></font><font color="#000000">in your working directory. It contains a number of further
	421	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">)
	422	and the scripts for running PALM (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SCRIPTS</font><font color="#000000">). For checking out the most recent PALM version (developer version), see the <span style="font-style: italic;">advanced installation method</span> described above.<br>
	423	</font></p>
	424	<p style="line-height: 100%;">Please never touch any file in
	425	your working copy of PALM, unless you really know what you
	426	are doing.</p>
	427	<br>
	428
	429	<p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Configuration and compilation<br>
	430	</span></font></p>
	431	<p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">Third step:</span> To
	432	use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable
	433	has to be extended and the
	434	environment variable<span style="font-family: Courier New,Courier,monospace;">
	435	PALM_BIN </span>has to be set. For convenience, setting should be done
	436	in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>,
	437	if<span style="font-family: Courier New,Courier,monospace;">
	438	ksh </span>is used):</font></p>
	439	<p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">export
	440	PALM_BIN=</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">$HOME/palm/current_version/trunk/SCRIPTS<br>
	441	</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">export
	442	PATH=$PALM_BIN:$PATH</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"><br>
	443	</span></font></p>
	444	<p style="line-height: 100%;"><font color="#000000">You
	445	may have to login again in order to activate the profile settings.<br>
	446	</font></p>
	447	<p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">Fourth step:</span> Call the installation script:<br>
	448	</font></p>
	449	<p style="line-height: 100%; margin-left: 40px;"><font style="font-family: Courier New,Courier,monospace;" color="#000000">palm_simple_install -i MAKE.inc.ifort.imuk</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"><br>
	450	</span></font></p>
	451
	452	<p style="line-height: 100%;"><font color="#000000">The script copies the PALM source code into a new subdirectory <span style="font-family: Courier New,Courier,monospace;">MAKE_DEPOSITORY_simple</span>. This directory also will contain a <span style="font-family: Courier New,Courier,monospace;">Makefile</span> and an include file <span style="font-family: Courier New,Courier,monospace;">MAKE.inc</span>
	453	to be used for compiling the code in the next step. The include file
	454	contains compiler name, compiler options, library path for NetCDF, etc.
	455	<span style="font-weight: bold;">Please adjust these settings as required by your system, before you proceed with the next step.</span> The default settings in <span style="font-family: Courier New,Courier,monospace;">MAKE.inc</span>
	456	are for the Intel-FORTRAN compiler in the IMUK environment. You may
	457	find default settings for other compilers and environments in <span style="font-family: Courier New,Courier,monospace;">.../trunk/INSTALL/</span> See for files<span style="font-family: Courier New,Courier,monospace;"> MAKE.inc.*</span>.<br>
	458	</font></p>
	459	<p style="line-height: 100%; margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">cd MAKE_DEPOSITORY_simple<br>
	460	</span><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">make<br>
	461	cd ..<br>
	462	</span></font></p>
	463
	464
	465	<p style="line-height: 100%;">In order to shorten compilation time, you can run make in parallel, e.g.<span style="font-family: Courier New,Courier,monospace;"> make -j 4 </span>runs 4 compile threads simultaneously.<br>
	466	<br>
	467	<span style="font-weight: bold;">Fifth step:</span> Carry out a test
	468	run in order to check the installation. The test run (as every PALM
	469	run) requires a parameter file for steering PALM, which is in
	470	FORTRAN-NAMELIST format. This file has been already generated by the
	471	installation script <span style="font-family: Courier New,Courier,monospace;">palm_simple_install</span> under <span style="font-family: Courier New,Courier,monospace;">JOBS/example_cbl/INPUT/example_cbl_p3d</span><span style="font-family: Courier New,Courier,monospace;"></span>. PALM is started with script <span style="font-family: Courier New,Courier,monospace;">palm_simple_run</span>. <span style="font-weight: bold;">Before</span> the first run, it may be necessary to change the MPI-execution command (<span style="font-family: Courier New,Courier,monospace;">mpiexec</span>, <span style="font-family: Courier New,Courier,monospace;">mpirun</span>, etc.) and options in this script, depending on the MPI-library that you are using. The script can be found in directory <span style="font-family: Courier New,Courier,monospace;">.../trunk/SCRIPTS</span>.
	472	Default settings in this script are for the SGI-mpt-library installed
	473	on HLRN. You will find the execution command almost at the end of this
	474	script. After having adjusted the MPI-execution command, start the run
	475	with:<br>
	476	</p>
	477	<p style="line-height: 100%; margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">palm_simple_run -p 4 -n 4 -c example_cbl</span><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"><br>
	478	</span></font></p>
	479
	480
	481
	482	<p style="line-height: 100%;">where option <span style="font-family: Courier New,Courier,monospace;">-p</span> gives the total number of MPI tasks, <span style="font-family: Courier New,Courier,monospace;">-n</span> gives the number of MPI tasks per node, and <span style="font-family: Courier New,Courier,monospace;">-c</span> gives the parameter file to be used.<br>
	483	After the run has finished, all OUTPUT files can be found in directory <span style="font-family: Courier New,Courier,monospace;">OUTPUT....</span> Names and contents of PALM output files are described in <a href="chapter_3.4.html">chapter 3.4</a>.
	484	The directory name is composed of the parameter file name, the number
	485	of cores that have been used, and the current data and time. For every
	486	run a unique directory is created.<br>
	487	</p>
	488	<p style="line-height: 100%;"><span style="font-weight: bold;">Sixth step:</span> To verify the results of this example run, compare it with the default result:<br>
	489	<span style="font-weight: bold;"></span></p>
	490	<p style="line-height: 100%; margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">diff  OUTPUT..../RUN_CONTROL   trunk/INSTALL/example_cbl_rc</span><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"><br>
	491	</span></font></p>
	492
	493
	494
	495
	496	<span style="font-weight: bold;">You should not find any
	497	difference between these two files</span>, except of the run date
	498	and time displayed at the top of the file header, and, maybe, the number of cores that have been used. <font color="#000000">If
	499	the file contents are identical, the installation is successfully
	500	completed.</font><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
[290]	501	change: </i> $Id: chapter_5.0.html 287 2009-04-09
	502	08:59:36Z raasch $</p>
[40]	503	</body></html>

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