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Last change on this file since 494 was 493, checked in by raasch, 15 years ago

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

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

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

%modules ifort/11.0.069:netcdf lcsgih parallel

This method replaces the (undocumented) mpilib-variable.

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

Changed:

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

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

Errors:

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

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

Property svn:keywords set to Id

File size: 32.7 KB

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[336]	5	<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM chapter 5.0</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Siegfried Raasch"> <meta name="CREATED" content="20041103;12380720"> <meta name="CHANGED" content="20041123;15532356"> <meta name="KEYWORDS" content="parallel LES model"> <style>
[62]	6	<!--
	7	@page { size: 21cm 29.7cm }
	8	-->
[404]	9	</style></head><body style="direction: ltr;" lang="en-US"><h2 style="line-height: 100%;"><font size="4">5.0
[62]	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>
[404]	124	svn://130.75.105.2/palm/tags/release-<#> trunk</span><br></div><p style="line-height: 100%;"><font color="#000000">You
[62]	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">)
[404]	129	and the scripts for running PALM (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SCRIPTS</font><font color="#000000">).</font></p><p style="line-height: 100%;">Alternatively, executing</p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username <your username> svn://130.75.105.2/palm/tags/release-<#> abcde</pre><p style="line-height: 100%;">will place your working copy in a
[62]	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
[404]	136	most recent code by executing</span></p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username <your username> svn://130.75.105.2/palm/trunk trunk</pre>However,
[62]	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
[336]	172	use PALM.</font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">Warning:
	173	When editing the configuration file, please NEVER use the TAB key.
	174	Otherwise, very confusing errors in mrun execution may occur.</span></font></p><p style="line-height: 100%;"><font color="#000000">Beside the default configuration file</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> .mrun.config.default</font><font color="#000000">, the directory<span style="font-family: Courier New,Courier,monospace;">
[290]	175	trunk/SCRIPTS </span>contains additional configuration files
	176	which are already adjusted for special hosts:<span style="font-family: Courier New,Courier,monospace;">
	177	.mrun.config.imuk </span>can be used at Hannover University,<span style="font-family: Courier New,Courier,monospace;">
	178	.mrun.config.riam </span>can
[287]	179	be used at the Research Institute of Applied Mechanics, Kyushu
	180	University. These files have to be edited in the same way as described
	181	above.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the
[290]	182	respective executables are generated by executing</font></p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild -u -h lcmuk<br>mbuild -u -h
	183	lcsgih</font></p><p style="line-height: 100%;"><font color="#000000">The
	184	second call also copies the PALM scripts (like <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span>) to the
	185	remote
[62]	186	host.</font></p><p style="line-height: 100%;"></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Pre-Compilation
	187	of PALM Code</span></font></p><font color="#000000">
	188	</font><br><font color="#000000">To avoid the
[5]	189	re-compilation of the complete source code for each model run, PALM
[62]	190	willl be pre-compiled once on the remote host by again using the script
	191	<span style="font-weight: bold;">mbuild</span>. Due
	192	to the use of
[5]	193	FORTRAN modules in the source code, the subroutines must be compiled
[62]	194	in a certain order. Therefore the so-called <i>make</i>
	195	mechanism
[5]	196	is used (see the respective man-page of the Unix operating system),
[62]	197	requiring a<span style="font-family: Courier New,Courier,monospace;">
	198	</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">Makefile</font><font color="#000000">,
	199	in which the dependencies are described. This file is found in
[290]	200	subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span></font><font color="#000000">, where
	201	also the PALM code is stored.</font><font color="#000000"> The compiled
[62]	202	sources (object
[5]	203	files) are
[40]	204	stored on the remote computer in the default directory
[41]	205	</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">~/palm/current_version/MAKE_DEPOSITORY</font>.<font color="#000000"><span style="font-weight: bold;"></span></font><p style="line-height: 100%;"><font color="#000000">The
[290]	206	pre-compilation for the remote host (here the SGI-ICE system of HLRN)
	207	is
[62]	208	done by</font><span style="font-family: monospace;"></span></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">mbuild
[287]	209	-h lcsgih  </span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild
[62]	210	</span>will prompt some queries<font color="#000000">,
	211	which must all be
	212	answered "y" by the user. The compiling process </font><font color="#000000">will take some time.<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">mbuild</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"> </span>transfers
	213	the respective compiler calls to the remote
[5]	214	host where they are carried out interactively. You can follow the
	215	progress at the terminal window, where also error messages
	216	are displayed (hopefully not for this standard installation). By just
[41]	217	entering </font></p><p style="line-height: 100%;">
[62]	218	</p><blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote>
	219	<p style="line-height: 100%;"><font color="#000000">PALM
	220	will
[5]	221	be (consecutively) pre-compiled for all remote hosts listed in
[62]	222	the configuration file. If you want to compile for the local host only,
	223	please enter</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">mbuild
	224	-h lcmuk</span> </font>
	225	</p><p style="line-height: 100%;"></p><p style="line-height: 100%; font-weight: bold; text-decoration: underline;"><font color="#000000">Installation Verification</font></p><font color="#000000">As a last step,
[5]	226	after the compilation has been finished, the PALM installation has to
	227	be verified. For this
	228	purpose a simple test run is carried out. This once again requires the <b>mrun
[40]	229	</b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter
[62]	230	3.2</font></a><font color="#000000">), as well
[244]	231	as the </font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_cbl_p3d"><font color="#000080">parameter
[62]	232	file</font></a><font color="#000000">
[97]	233	(described in </font><a href="chapter_4.4.1.html"><font color="#000080">chapter
	234	4.4.1</font></a>)<font color="#000000">. The
[62]	235	parameter file must be
[40]	236	copied from the PALM working copy by<br>
[244]	237	</font><div style="margin-left: 40px;"><span style="font-family: monospace;"></span><font style="font-family: Courier New,Courier,monospace;" color="#000000">mkdir -p JOBS/example_cbl/INPUT<br>cp
	238	trunk/INSTALL/example_cbl_p3d JOBS/example_cbl/INPUT/example_cbl_p3d</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"></span></font></div>
[62]	239	<p style="line-height: 100%;"><font color="#000000">The
	240	test run can
[40]	241	now be started by executing the command </font>
[404]	242	</p><pre style="margin-left: 1cm; margin-right: 1cm; margin-bottom: 0.5cm; line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mrun -d example_cbl -h lcsgih -K parallel -X 8 -T 8 -t 500 -q testq -r d3# pr#</font></pre><font color="#000000">This specific run
[5]	243	will be carried out on 8 PEs and is allowed to use up to 500 seconds
[62]	244	CPU time. After pressing <return>, the most important
	245	settings of
[5]	246	the job are displayed at the terminal window
[404]	247	and the user is prompted for o.k. (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">y</font><font color="#000000">).
	248	Next, a message of the queuing system like <i>Request</i>
	249
	250	<i>Submitted to queue by </i>should
[62]	251	be displayed. Now the job is
	252	queued and either started immediately or at a later time, depending on
	253	the
[5]	254	current workload of the remote host. Provided that it is executed
	255	immediately and that all things work as designed, the job protocol of
[287]	256	this run will appear under the file name<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">~/job_queue/lcsgih_example</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"> </span>no
[62]	257	more than a few minutes later. The content of this
[41]	258	file should be carefully examined for any error messages.</font><p style="line-height: 100%;">
[62]	259	</p><p style="line-height: 100%;">Beside the job
	260	protocol and according to
[5]	261	the configuration file and arguments given for <b>mrun</b>
[62]	262	options<span style="font-family: Courier New,Courier,monospace;">
	263	-d </span>and<span style="font-family: Courier New,Courier,monospace;"> -r</span><tt>,</tt>further
	264	files should be found in
[5]	265	the
[244]	266	directories</p><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/MONITORING</div><p style="line-height: 100%;">and</p>
[5]	267	<p style="line-height: 100%;"><span style="font-family: monospace;">
[244]	268	</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/OUTPUT</span><span style="font-family: monospace;"></span><br>
[62]	269	</p><p style="line-height: 100%;">Please compare the
	270	contents of file</p>
[5]	271	<p style="line-height: 100%;"><span style="font-family: monospace;">
[287]	272	</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/MONITORING/lcsgih_example_rc</span><br>
[62]	273	</p><p style="line-height: 100%;">with those of the
	274	example result file which can be found under<span style="font-family: Courier New,Courier,monospace;">
[244]	275	trunk/INSTALL/example_cbl_rc</span>., e.g. by using the<span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;"> standard</span>
[62]	276	diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff
[287]	277	JOBS/example_cbl/MONITORING/lcsgih_example_cbl_rc
[244]	278	trunk/INSTALL/example_cbl_rc</p><p style="line-height: 100%;">where
[62]	279	it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;">
	280	~/palm/current_version</span>.</p><span style="font-weight: bold;">You should not find any
	281	difference between these two files</span>, except of the run date
	282	and time displayed at the top of the file header. <font color="#000000">If
[5]	283	the file contents are identical, the installation is successfully
[290]	284	completed.<br><br></font><p style="line-height: 100%;"></p><p style="line-height: 100%; font-weight: bold; text-decoration: underline;"><font color="#000000"><a name="configuration_for_other_machines"></a>Configuration
	285	for other machines</font></p><font color="#000000">Starting
[83]	286	from version 3.2a, beside the default hosts (HLRN, etc.), PALM can also
	287	be installed and run on other Linux-Cluster-, IBM-AIX, or
	288	NEC-SX-systems. To configure PALM for a non-default host only requires
[290]	289	to add some lines to the configuration file<span style="font-family: Courier New,Courier,monospace;">
	290	.mrun.config</span>.<br><br>First,
[83]	291	you have to define the host identifier (a string of arbitrary length)
[290]	292	under which your local host shall be identified by adding a line<br><br></font><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">%host_identifier
	293	<hostname>  <host
	294	identifier></span><br></div><br>to the
	295	configuration file (best to do this in the section where the other
	296	default host identifiers are defined). Here<span style="font-family: Courier New,Courier,monospace;">
	297	<hostname> </span>must be the name of your local
	298	host as provided by the unix-command "<span style="font-family: Courier New,Courier,monospace;">hostname</span>".
	299	The first characters of<span style="font-family: Courier New,Courier,monospace;">
	300	<host identifier> </span>have to be "<span style="font-family: Courier New,Courier,monospace;">lc</span>",
	301	if your system is (part of) a linux-cluster, "<span style="font-family: Courier New,Courier,monospace;">ibm</span>",
	302	or "<span style="font-family: Courier New,Courier,monospace;">nec</span>"
[83]	303	in case of an IBM-AIX- or NEC-SX-system, respectively. For example, if
[290]	304	you want to install on a linux-cluster, the line may read as<br><br><div style="margin-left: 40px;">%host_identifier  foo
	305	lc_bar<br></div><br>In
[83]	306	the second step, you have to give all informations neccessary to
	307	compile and run PALM on your local host by adding an additional section
[290]	308	to the configuration file:<br><br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username
	309	<1>      <host
	310	identifier> parallel<br>%tmp_user_catalog
	311	<2>      <host
	312	identifier> parallel<br>%compiler_name
	313	<3>      <host
	314	identifier> parallel<br>%compiler_name_ser
	315	<4>      <host
	316	identifier> parallel<br>%cpp_options
	317	<5>      <host
	318	identifier> parallel<br>%netcdf_inc
	319	<6>      <host
	320	identifier> parallel<br>%netcdf_lib
	321	<7>      <host
	322	identifier> parallel<br>%fopts
	323	<8>      <host
	324	identifier> parallel<br>%lopts
	325	<9>
	326	<host identifier> parallel<br></div><br>The
[83]	327	section consists of four columns each separated by one or more blanks.
	328	The first column gives the name of the respective environment variable
[290]	329	used by <span style="font-weight: bold;">mrun</span>
	330	and <span style="font-weight: bold;">mbuild</span>,
[83]	331	while the second column defines its value. The third column has to be
	332	the host identifier as defined above, and the last column in each line
	333	must contain the string "<span style="font-family: Courier New,Courier,monospace;">parallel</span>".
	334	Otherwise, the respective line(s) will be interpreted as belonging to
	335	the setup for compiling and running a serial (non-parallel) version of
[290]	336	PALM.<br><br>All brackets have to be replaced by the
	337	appropriate settings for your local host:<br><ul><li><span style="font-family: Courier New,Courier,monospace;"><1>
	338	</span>is the username on your LOCAL host</li><li><span style="font-family: Courier New,Courier,monospace;"><2>
	339	</span>is the temporary directory in which PALM runs will be
	340	carried out</li><li><span style="font-family: Courier New,Courier,monospace;"><3>
	341	</span>is the compiler name which generates parallel code</li><li><span style="font-family: Courier New,Courier,monospace;"><4>
	342	</span>is the compiler name for generating serial code</li><li><span style="font-family: Courier New,Courier,monospace;"><5>
	343	</span>are
[83]	344	the preprocessor options to be invoked. In most of the cases, it will
	345	be neccessary to adjust the MPI data types to double precision by
[290]	346	giving <span style="font-family: Courier New,Courier,monospace;">-DMPI_REAL=MPI_DOUBLE_PRECISION
	347	-DMPI_2REAL=MPI_2DOUBLE_PRECISION</span>. To switch on the NetCDF
	348	support, you also have to give <span style="font-family: Courier New,Courier,monospace;">-D__netcdf</span>
[493]	349	and <span style="font-family: Courier New,Courier,monospace;">-D__netcdf4</span>
	350	(if you like to have NetCDF4/HDF5 data format; this requires a NetCDF4 library!).</li><li><span style="font-family: Courier New,Courier,monospace;"><6>
[290]	351	</span>is the compiler option for specifying the include path to
	352	search for the NetCDF module/include files</li><li><span style="font-family: Courier New,Courier,monospace;"><7>
	353	</span>are the linker options to search for the NetCDF library</li><li><span style="font-family: Courier New,Courier,monospace;"><8>
	354	</span>are the general compiler options to be used. You should
	355	allways switch on double precision (e.g. <span style="font-family: Courier New,Courier,monospace;">-r8</span>)
	356	and code optimization (e.g. <span style="font-family: Courier New,Courier,monospace;">-O2</span>).</li><li><span style="font-family: Courier New,Courier,monospace;"><9>
	357	</span>are the linker options</li><li><span style="font-family: Courier New,Courier,monospace;"><host
	358	identifier> </span>is the host identifier as defined
	359	before</li></ul><br>A typical example may be:<br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username
	360	raasch
	361
	362
	363	lc_bar parallel<br>%tmp_user_catalog
[83]	364	/tmp                                    lc_bar
	365	parallel<br>%compiler_name
	366	mpif90                                  lc_bar
	367	parallel<br>%compiler_name_ser
	368	ifort                                   lc_bar
	369	parallel<br>%cpp_options
[493]	370	-DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf  lc_bar parallel<br>%netcdf_inc
[83]	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
[493]	379	parallel<br></div><br>Currently (version 3.7a),
[290]	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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