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Last change on this file since 231 was 97, checked in by raasch, 17 years ago

New:
---
ocean version including prognostic equation for salinity and equation of state for seawater. Routine buoyancy can be used with both temperature and density.
+ inipar-parameters bc_sa_t, bottom_salinityflux, ocean, sa_surface, sa_vertical_gradient, sa_vertical_gradient_level, top_salinityflux

advec_s_bc, average_3d_data, boundary_conds, buoyancy, check_parameters, data_output_2d, data_output_3d, diffusion_e, flow_statistics, header, init_grid, init_3d_model, modules, netcdf, parin, production_e, prognostic_equations, read_var_list, sum_up_3d_data, swap_timelevel, time_integration, user_interface, write_var_list, write_3d_binary

New:
eqn_state_seawater, init_ocean

Changed:

inipar-parameter use_pt_reference renamed use_reference

hydro_press renamed hyp, routine calc_mean_pt_profile renamed calc_mean_profile

format adjustments for the ocean version (run_control)

advec_particles, buoyancy, calc_liquid_water_content, check_parameters, diffusion_e, diffusivities, header, init_cloud_physics, modules, production_e, prognostic_equations, run_control

Errors:

Bugfix: height above topography instead of height above level k=0 is used for calculating the mixing length (diffusion_e and diffusivities).

Bugfix: error in boundary condition for TKE removed (advec_s_bc)

advec_s_bc, diffusion_e, prognostic_equations

Property svn:keywords set to Id

File size: 31.2 KB

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[83]	3	<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM chapter 5.0</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Siegfried Raasch"> <meta name="CREATED" content="20041103;12380720"> <meta name="CHANGED" content="20041123;15532356"> <meta name="KEYWORDS" content="parallel LES model"> <style>
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	8	<body style="direction: ltr;" lang="en-US"><h2 style="line-height: 100%;"><font size="4">5.0
	9	Installation of the
[5]	10	model</font></h2>
[41]	11	<font color="#000000">This chapter
[62]	12	describes the installation of PALM on a Linux workstation (local host)
	13	and a suitable remote computer, on which the
[40]	14	model runs are to be carried out. The local host is used to
[62]	15	start batch jobs with <b>mrun</b> and to analyze the
	16	results
	17	which are produced by the model on the remote host and send back to the
	18	local host. Alternatively, <span style="font-weight: bold;">mrun</span>
	19	can also be used to start PALM on the local host in interactive mode or
[83]	20	as a batch job (if a queueing system like NQS, PBS, or LoadLeveler is available).</font><p style="line-height: 100%;"></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Requirements</span></font></p><p style="line-height: 100%;"><font color="#000000">The
[62]	21	installation and operation of PALM requires at mimimum (on both, the
[83]	22	local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The Korn-shell (AT&T ksh or public domain ksh) must be
	23	available under<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">/bin/ksh</font><font color="#000000">.<span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-family: Courier New,Courier,monospace;"></span></font><font color="#000000"><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span></font></li><li><font color="#000000">The
[62]	24	NetCDF-library with version number not earlier than 3.6.0-p1 (for
	25	NetCDF, see under <a href="http://www.unidata.ucar.edu/software/netcdf/">www.unidata.ucar.edu</a>).</font></li><li><font color="#000000">A FORTRAN90/95 compiler.</font></li><li><font color="#000000">The Message Passing Interface (MPI), at
	26	least on the remote host, if the parallel version of PALM shall be used.</font></li><li><font color="#000000">On the local host, the revision control
	27	system <span style="font-weight: bold;">subversion</span>
	28	(see <a href="http://subversion.tigris.org/">subversion.tigris.org</a>).
	29	This is already included in many Linux distributions (e.g. SuSe). <span style="font-weight: bold;">subversion requires port 3690 to
	30	be open for tcp/udp.</span> <span style="font-weight: bold;">If
	31	there are firewall restrictions concerning this port, the PALM code
	32	cannot be accessed.</span> The
[40]	33	user needs a permit to access the PALM repository. For getting a permit
	34	please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>)
	35	and define a username under which you like to access the repository.
	36	You will then receive a password which allows the access under this
[62]	37	name.</font></li><li><font color="#000000">A
	38	job queueing system must be available on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle
	39	LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).</font></li><li><font color="#000000">ssh/scp-connections to and from the remote
	40	host must not be blocked by a firewall.<br></font></li></ol><font color="#000000"><span style="font-weight: bold;"></span></font><font color="#000000"> Currently, <span style="font-weight: bold;">mrun</span> is configured
	41	to be used on a limited number of selected machines. These are
	42	IBM-Regatta at computing center HLRN in Hannover (<span style="font-style: italic;">ibmh</span>), Berlin (<span style="font-style: italic;">ibmb</span>), at KISTI,
	43	Korea (<span style="font-style: italic;">ibms</span>),
	44	at Yonsei University, Seoul (<span style="font-style: italic;">ibms</span>),
	45	on NEC-SX6/8 systems at DKRZ, Hamburg (<span style="font-style: italic;">nech</span>) and RIAM,
	46	Kyushu University, Fukuoka (<span style="font-style: italic;">neck</span>),
	47	as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>) and Tokyo
	48	Institute of Technology (<span style="font-style: italic;">lctit</span>).
[83]	49	The strings given in brackets are the systems names (host identifiers) under which <span style="font-weight: bold;">mrun</span> identifies the
	50	different hosts.<br><br>You can also use <span style="font-weight: bold;">mrun</span>/PALM on other Linux-Cluster, IBM-AIX, or NEC-SX machines. See <a href="#configuration_for_other_machines">below</a> on how to configure <span style="font-weight: bold;">mrun</span> for other machines. However, these configurations currently (version 3.2a) allow to run PALM in interactive mode only.<br><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span></font><p style="line-height: 100%;"><font color="#000000">The
[62]	51	examples given in this chapter refer to an
[40]	52	installation of PALM on an IMUK Linux workstation and the IBM-Regatta
[5]	53	system of
[62]	54	the HLRN used as remote host. They are just called local and
	55	remote host from now on. </font></p><p style="line-height: 100%;">
	56	</p><p style="line-height: 100%;">The installation
	57	process requires a valid
[40]	58	account on the local and on the remote host as well.<br>
[5]	59	</p>
[62]	60	<ul> All hosts (local as well as remote) are
[5]	61	accessed via the secure shell (ssh). The user must establish
	62	passwordless login using the private/public-key mechanism (see e.g. the
[62]	63	<a href="http://www.hlrn.de/doc/ssh/index.html">HLRN
	64	documentation</a>). <b>To ensure proper function of mrun,
	65	passwordless login must be
[5]	66	established in both directions, from the local to the remote host as
[62]	67	well as from the remote to the local host!</b> Test this by
	68	carrying
	69	out e.g. on the local host: <p style="line-height: 100%;"><span style="font-family: monospace;">
	70	</span><span style="font-family: Courier New,Courier,monospace;">ssh
	71	<username on remote host>@<remote
	72	IP-address></span><br> </p> <p style="line-height: 100%;">and on the remote host:<br>
	73	</p> <p style="line-height: 100%;"><span style="font-family: monospace;">
	74	</span><span style="font-family: Courier New,Courier,monospace;">ssh
	75	<username on local host>@<local IP-adddress></span><br>
	76	</p> In both cases you should not be
	77	prompted for a password. <b>Before continuing the further
	78	installation
	79	process, this must be absolutely guaranteed!</b> This must also
	80	be
	81	guaranteed for <b>all</b> other remote hosts, on which
	82	PALM shall run.
	83	</ul><p style="line-height: 100%;"></p><p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package
	84	Installation</span></p><p style="line-height: 100%;">In
	85	the <b>first installation step</b> a
[5]	86	set of directories must be created both on the local and on the
[62]	87	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
	88	are
[5]	89	freely selectable (except <tt><font size="2">~/job_queue</font></tt>),
	90	however new users should use them as suggested, since many
	91	examples in this documentation as well as all example files are
[62]	92	assuming these settings. The directory <span style="font-family: monospace;">~/palm/current_version</span>
	93	on the local host will be called the working directory from now on. </p>
	94	<p style="line-height: 100%;"><font color="#000000">In
	95	the <b>second
[40]	96	step</b>
	97	a working copy of the recent version of the PALM software package,
[62]	98	including the source code, scripts, documentation, etc.  must
	99	be
[44]	100	copied to the working directory (</font><font color="#000000">local
	101	host!) by executing the following
[62]	102	commands. Replace <your username> by the name that you
	103	chose to
	104	access the repository, and <#> by any of the available
	105	PALM
	106	releases, e.g. "<span style="font-style: italic;">3.1c</span>"
	107	(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
	108	~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn
	109	checkout --username <your username>
	110	svn://130.75.105.45/palm/tags/release-<#> trunk</span><br></div><p style="line-height: 100%;"><font color="#000000">You
	111	will then be prompted for your password. After finishing, the
	112	subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">should
[40]	113	appear in your working directory. It contains a number of further
[62]	114	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">)
	115	and the scripts for running PALM (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SCRIPTS</font><font color="#000000">).</font></p><p style="line-height: 100%;">Alternatively, executing</p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username <your username> svn://130.75.105.45/palm/tags/release-<#> abcde</pre><p style="line-height: 100%;">will place your working copy in a
	116	directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span>instead
	117	of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span>.
	118	But keep in mind that you will have to adjust several paths given
	119	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
	120	your working copy of PALM, unless you know exactly what you
	121	are doing.</p><p style="line-height: 100%; font-weight: bold;"><span style="font-weight: normal;">You can also get a copy of the
	122	most recent code by executing</span></p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username <your username> svn://130.75.105.45/palm/trunk trunk</pre>However,
	123	this version may contain bugs and new features may not be documented. <span style="font-weight: bold;">In future PALM releases,
	124	repository access to this most recent version will
	125	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
	126	Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To
[83]	127	use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable has to be extended and the
	128	environment variable<span style="font-family: Courier New,Courier,monospace;"> PALM_BIN </span>has to be set (on local and remote host)
[62]	129	in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>,
	130	if<span style="font-family: Courier New,Courier,monospace;">
	131	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
	132	PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH</font><font color="#000000"><br><span style="font-family: Courier New,Courier,monospace;">export
	133	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]	134	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
	135	small helper/utility programs have to be installed, which are later used by <span style="font-weight: bold;">mrun</span> e.g. for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script
[62]	136	requires a configuration file<span style="font-family: Courier New,Courier,monospace;">
	137	.mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the
	138	following. A copy has to be put into the working directory under the
	139	name<span style="font-family: Courier New,Courier,monospace;">
	140	.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
	141	trunk/SCRIPTS/.mrun.config.default .mrun.config</span></font></p><font color="#000000">Beside many other things, this file contains
	142	typical installation parameters
[40]	143	like compiler name, compiler options, etc.
[83]	144	for a set of different (remote) hosts. Please edit this file, uncomment
[62]	145	lines like</font><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username
	146	<replace by your ... username>
[83]	147	<host identifier></div><p style="line-height: 100%;"><font color="#000000">by
[62]	148	removing the first hash (<span style="font-family: Courier New,Courier,monospace;">#</span>)
	149	character and replace the string "<span style="font-family: Courier New,Courier,monospace;"><replace
	150	by ...></span>" by your username on the respective host
[83]	151	given in the <span style="font-family: Courier New,Courier,monospace;"><host identifier></span>.
[62]	152	You only have to uncomment lines for those hosts on which you intend to
	153	use PALM.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the
	154	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 ibmh</font></p><p style="line-height: 100%;"><font color="#000000">The
[83]	155	second call also copies the PALM scripts (like <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span>) to the remote
[62]	156	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
	157	of PALM Code</span></font></p><font color="#000000">
	158	</font><br><font color="#000000">To avoid the
[5]	159	re-compilation of the complete source code for each model run, PALM
[62]	160	willl be pre-compiled once on the remote host by again using the script
	161	<span style="font-weight: bold;">mbuild</span>. Due
	162	to the use of
[5]	163	FORTRAN modules in the source code, the subroutines must be compiled
[62]	164	in a certain order. Therefore the so-called <i>make</i>
	165	mechanism
[5]	166	is used (see the respective man-page of the Unix operating system),
[62]	167	requiring a<span style="font-family: Courier New,Courier,monospace;">
	168	</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">Makefile</font><font color="#000000">,
	169	in which the dependencies are described. This file is found in
	170	subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE<span style="font-family: Times New Roman,Times,serif;">, where
	171	also the PALM code is stored</span></span>. The compiled
	172	sources (object
[5]	173	files) are
[40]	174	stored on the remote computer in the default directory
[41]	175	</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
[62]	176	pre-compilation for the remote host (here the IBM-Regatta of HLRN) is
	177	done by</font><span style="font-family: monospace;"></span></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">mbuild
	178	-h ibmh  </span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild
	179	</span>will prompt some queries<font color="#000000">,
	180	which must all be
	181	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
	182	the respective compiler calls to the remote
[5]	183	host where they are carried out interactively. You can follow the
	184	progress at the terminal window, where also error messages
	185	are displayed (hopefully not for this standard installation). By just
[41]	186	entering </font></p><p style="line-height: 100%;">
[62]	187	</p><blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote>
	188	<p style="line-height: 100%;"><font color="#000000">PALM
	189	will
[5]	190	be (consecutively) pre-compiled for all remote hosts listed in
[62]	191	the configuration file. If you want to compile for the local host only,
	192	please enter</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">mbuild
	193	-h lcmuk</span> </font>
	194	</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]	195	after the compilation has been finished, the PALM installation has to
	196	be verified. For this
	197	purpose a simple test run is carried out. This once again requires the <b>mrun
[40]	198	</b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter
[62]	199	3.2</font></a><font color="#000000">), as well
	200	as the </font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d"><font color="#000080">parameter
	201	file</font></a><font color="#000000">
[97]	202	(described in </font><a href="chapter_4.4.1.html"><font color="#000080">chapter
	203	4.4.1</font></a>)<font color="#000000">. The
[62]	204	parameter file must be
[40]	205	copied from the PALM working copy by<br>
[62]	206	</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/INPUT<br>cp
	207	trunk/INSTALL/example_p3d JOBS/example/INPUT/example_p3d</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"></span></font></div>
	208	<p style="line-height: 100%;"><font color="#000000">The
	209	test run can
[40]	210	now be started by executing the command </font>
[62]	211	</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 -h ibmh -K parallel -X 8 -T 8 -t 500 -q cdev -r “d3# pr#”</font></pre>
[41]	212	<font color="#000000">This specific run
[5]	213	will be carried out on 8 PEs and is allowed to use up to 500 seconds
[62]	214	CPU time. After pressing <return>, the most important
	215	settings of
[5]	216	the job are displayed at the terminal window
[62]	217	and the user is prompted for o.k. (“</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">y</font><font color="#000000">”).
	218	Next, a message of the queuing system like “<i>Request</i>
	219	…
	220	<i>Submitted to queue… by…” </i>should
	221	be displayed. Now the job is
	222	queued and either started immediately or at a later time, depending on
	223	the
[5]	224	current workload of the remote host. Provided that it is executed
	225	immediately and that all things work as designed, the job protocol of
[62]	226	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/ibmh_example</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"> </span>no
	227	more than a few minutes later. The content of this
[41]	228	file should be carefully examined for any error messages.</font><p style="line-height: 100%;">
[62]	229	</p><p style="line-height: 100%;">Beside the job
	230	protocol and according to
[5]	231	the configuration file and arguments given for <b>mrun</b>
[62]	232	options<span style="font-family: Courier New,Courier,monospace;">
	233	-d </span>and<span style="font-family: Courier New,Courier,monospace;"> -r</span><tt>,</tt>further
	234	files should be found in
[5]	235	the
[40]	236	directories</p><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/MONITORING</div><p style="line-height: 100%;">and</p>
[5]	237	<p style="line-height: 100%;"><span style="font-family: monospace;">
[40]	238	</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/OUTPUT</span><span style="font-family: monospace;"></span><br>
[62]	239	</p><p style="line-height: 100%;">Please compare the
	240	contents of file</p>
[5]	241	<p style="line-height: 100%;"><span style="font-family: monospace;">
[40]	242	</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/MONITORING/ibmh_example_rc</span><br>
[62]	243	</p><p style="line-height: 100%;">with those of the
	244	example result file which can be found under<span style="font-family: Courier New,Courier,monospace;">
	245	trunk/INSTALL/example_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>
	246	diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff
	247	JOBS/example/MONITORING/ibmh_example_rc
	248	trunk/INSTALL/example_rc</p><p style="line-height: 100%;">where
	249	it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;">
	250	~/palm/current_version</span>.</p><span style="font-weight: bold;">You should not find any
	251	difference between these two files</span>, except of the run date
	252	and time displayed at the top of the file header. <font color="#000000">If
[5]	253	the file contents are identical, the installation is successfully
[83]	254	completed.<br><br></font><p style="line-height: 100%;"></p><p style="line-height: 100%; font-weight: bold; text-decoration: underline;"><font color="#000000"><a name="configuration_for_other_machines"></a>Configuration for other machines</font></p><font color="#000000">Starting
	255	from version 3.2a, beside the default hosts (HLRN, etc.), PALM can also
	256	be installed and run on other Linux-Cluster-, IBM-AIX, or
	257	NEC-SX-systems. To configure PALM for a non-default host only requires
	258	to add some lines to the configuration file<span style="font-family: Courier New,Courier,monospace;"> .mrun.config</span>.<br><br>First,
	259	you have to define the host identifier (a string of arbitrary length)
	260	under which your local host shall be identified by adding a line<br><br></font><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">%host_identifier  <hostname>  <host identifier></span><br></div><br>to the configuration file (best to do this in the section where the other default host identifiers are defined). Here<span style="font-family: Courier New,Courier,monospace;"> <hostname> </span>must be the name of your local host as provided by the unix-command "<span style="font-family: Courier New,Courier,monospace;">hostname</span>". The first characters of<span style="font-family: Courier New,Courier,monospace;"> <host identifier> </span>have to be "<span style="font-family: Courier New,Courier,monospace;">lc</span>", if your system is (part of) a linux-cluster, "<span style="font-family: Courier New,Courier,monospace;">ibm</span>", or "<span style="font-family: Courier New,Courier,monospace;">nec</span>"
	261	in case of an IBM-AIX- or NEC-SX-system, respectively. For example, if
	262	you want to install on a linux-cluster, the line may read as<br><br><div style="margin-left: 40px;">%host_identifier  foo  lc_bar<br></div><br>In
	263	the second step, you have to give all informations neccessary to
	264	compile and run PALM on your local host by adding an additional section
	265	to the configuration file:<br><br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username   <1>      <host identifier> parallel<br>%tmp_user_catalog  <2>      <host identifier> parallel<br>%compiler_name     <3>      <host identifier> parallel<br>%compiler_name_ser <4>      <host identifier> parallel<br>%cpp_options
	266	<5>      <host identifier> parallel<br>%netcdf_inc        <6>      <host identifier> parallel<br>%netcdf_lib        <7>      <host identifier> parallel<br>%fopts
	267	<8>      <host identifier> parallel<br>%lopts
	268	<9>      <host identifier> parallel<br></div><br>The
	269	section consists of four columns each separated by one or more blanks.
	270	The first column gives the name of the respective environment variable
	271	used by <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span>,
	272	while the second column defines its value. The third column has to be
	273	the host identifier as defined above, and the last column in each line
	274	must contain the string "<span style="font-family: Courier New,Courier,monospace;">parallel</span>".
	275	Otherwise, the respective line(s) will be interpreted as belonging to
	276	the setup for compiling and running a serial (non-parallel) version of
	277	PALM.<br><br>All brackets have to be replaced by the appropriate settings for your local host:<br><ul><li><span style="font-family: Courier New,Courier,monospace;"><1> </span>is the username on your LOCAL host</li><li><span style="font-family: Courier New,Courier,monospace;"><2> </span>is the temporary directory in which PALM runs will be carried out</li><li><span style="font-family: Courier New,Courier,monospace;"><3> </span>is the compiler name which generates parallel code</li><li><span style="font-family: Courier New,Courier,monospace;"><4> </span>is the compiler name for generating serial code</li><li><span style="font-family: Courier New,Courier,monospace;"><5> </span>are
	278	the preprocessor options to be invoked. In most of the cases, it will
	279	be neccessary to adjust the MPI data types to double precision by
	280	giving <span style="font-family: Courier New,Courier,monospace;">-DMPI_REAL=MPI_DOUBLE_PRECISION -DMPI_2REAL=MPI_2DOUBLE_PRECISION</span>. To switch on the NetCDF support, you also have to give <span style="font-family: Courier New,Courier,monospace;">-D__netcdf</span> and <span style="font-family: Courier New,Courier,monospace;">-D__netcdf_64bit</span> (if you like to have 64bit NetCDF output).</li><li><span style="font-family: Courier New,Courier,monospace;"><6> </span>is the compiler option for specifying the include path to search for the NetCDF module/include files</li><li><span style="font-family: Courier New,Courier,monospace;"><7> </span>are the linker options to search for the NetCDF library</li><li><span style="font-family: Courier New,Courier,monospace;"><8> </span>are the general compiler options to be used. You should allways switch on double precision (e.g. <span style="font-family: Courier New,Courier,monospace;">-r8</span>) and code optimization (e.g. <span style="font-family: Courier New,Courier,monospace;">-O2</span>).</li><li><span style="font-family: Courier New,Courier,monospace;"><9> </span>are the linker options</li><li><span style="font-family: Courier New,Courier,monospace;"><host identifier> </span>is the host identifier as defined before</li></ul><br>A typical example may be:<br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username
	281	raasch
	282	lc_bar parallel<br>%tmp_user_catalog
	283	/tmp                                    lc_bar
	284	parallel<br>%compiler_name
	285	mpif90                                  lc_bar
	286	parallel<br>%compiler_name_ser
	287	ifort                                   lc_bar
	288	parallel<br>%cpp_options
	289	-DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__netcdf_64bit
	290	lc_bar parallel<br>%netcdf_inc
	291	-I:/usr/local/netcdf/include
	292	lc_bar parallel<br>%netcdf_lib
	293	-L/usr/local/netcdf/lib:-lnetcdf
	294	lc_bar parallel<br>%fopts
	295	-axW:-cpp:-openmp:-r8:-nbs
	296	lc_bar parallel<br>%lopts
	297	-axW:-cpp:-openmp:-r8:-nbs:-Vaxlib      lc_bar
	298	parallel<br></div><br>Currently (version 3.2a), depending on the MPI
	299	version which is running on your local host, the options for the
	300	execution command (which may be <span style="font-family: Courier New,Courier,monospace;">mpirun</span> or <span style="font-family: Courier New,Courier,monospace;">mpiexec</span>)
	301	may have to be adjusted manually in the mrun-script. A future version
	302	will allow to give the respective settings in the configuration file.
[62]	303	<p style="line-height: 100%;">If you have any problems
	304	with the PALM
[5]	305	installation, the members of the PALM working group are pleased to
	306	help you.   </p>
[83]	307	<hr><p style="line-height: 100%;"><font color="#000080"><font color="#000080"><a href="chapter_4.6.html"><font color="#000080"><img src="left.gif" name="Grafik1" align="bottom" border="2" height="32" width="32"></font></a><a href="index.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="up" src="up.gif" name="Grafik2"></font></a><a href="chapter_5.1.html"><font color="#000080"><img src="right.gif" name="Grafik3" align="bottom" border="2" height="32" width="32"></font></a></font></font></p>
[62]	308	<p style="line-height: 100%;"><i>Last
	309	change: </i> $Id: chapter_5.0.html 97 2007-06-21 08:23:15Z raasch $</p>
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