Changeset 290 for palm/trunk/DOC


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Apr 15, 2009 1:24:04 PM (13 years ago)
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letzel
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  • updated trunk/DOC/app/chapter_5.0.html
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    11<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
    22<html><head>
    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>
     3<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM
     4chapter 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>
    45<!--
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    1819local host. Alternatively, <span style="font-weight: bold;">mrun</span>
    1920can also be used to start PALM on the local host in interactive mode or
    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
     21as a batch job (if a queueing system like NQS, PBS, or LoadLeveler is
     22available).</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
    2123installation and operation of PALM requires at mimimum (on both, the
    22 local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The Korn-shell (AT&amp;T ksh or public domain ksh) must be
     24local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The Korn-shell (AT&amp;T ksh or public
     25domain ksh) must be
    2326available 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
    2427NetCDF-library with version number not earlier than 3.6.0-p1 (for
     
    3942LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).</font></li><li><font color="#000000">ssh/scp-connections to and from the remote
    4043host 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 SGI-ICE systems at computing center HLRN in Hannover (<span style="font-style: italic;">lcsgih</span>), Berlin (<span style="font-style: italic;">lcsgib</span>), IBM-Regatta system<span style="font-style: italic;"></span>
     44to be used on a limited number of selected machines. These are SGI-ICE
     45systems at computing center HLRN in Hannover (<span style="font-style: italic;">lcsgih</span>), Berlin (<span style="font-style: italic;">lcsgib</span>),
     46IBM-Regatta system<span style="font-style: italic;"></span>
    4247at Yonsei University, Seoul (<span style="font-style: italic;">ibms</span>),
    4348on NEC-SX6/8 systems at DKRZ, Hamburg (<span style="font-style: italic;">nech</span>) and RIAM,
    4449Kyushu University, Fukuoka (<span style="font-style: italic;">necriam</span>),
    4550as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>), Tokyo
    46 Institute of Technology (<span style="font-style: italic;">lctit</span>), and the Bergen Center for Computational Science (<span style="font-style: italic;">lcxt4</span>).
    47 The strings given in brackets are the systems names (host identifiers) under which <span style="font-weight: bold;">mrun</span> identifies the
    48 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
     51Institute of Technology (<span style="font-style: italic;">lctit</span>),
     52and the Bergen Center for Computational Science (<span style="font-style: italic;">lcxt4</span>).
     53The strings given in brackets are the systems names (host identifiers)
     54under which <span style="font-weight: bold;">mrun</span>
     55identifies the
     56different hosts.<br><br>You can also use <span style="font-weight: bold;">mrun</span>/PALM on other
     57Linux-Cluster, IBM-AIX, or NEC-SX machines. See <a href="#configuration_for_other_machines">below</a> on
     58how to configure <span style="font-weight: bold;">mrun</span>
     59for other machines. However, these configurations currently (version
     603.2a) 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
    4961examples given in this chapter refer to an
    5062installation of PALM on an IMUK Linux workstation and the SGI-ICE
     
    5971accessed via the secure shell (ssh). The user must establish
    6072passwordless login using the private/public-key mechanism (see e.g. the
    61 <a href="http://www.hlrn.de/doc/ssh/index.html">HLRN
     73<a href="http://www2.hlrn.de/doc/ssh/index.html">HLRN
    6274documentation</a>). <b>To ensure proper function of mrun,
    6375passwordless login must be
     
    7890be
    7991guaranteed for <b>all</b> other remote hosts, on which
    80 PALM shall run.
    81 </ul><p style="line-height: 100%;"></p><p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package
     92PALM shall run.<br><br>Please
     93note that on many remote hosts, passwordless login must also be
     94established <b>within the remote host</b>, i.e. from the
     95remote host to itself. Test this by executing on the remote host: <span style="font-family: Courier New,Courier,monospace;">ssh
     96&lt;remote IP-address&gt;</span>. You should not be prompted
     97for a password.<br><br></ul><p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package
    8298Installation</span></p><p style="line-height: 100%;">In
    8399the <b>first installation step</b> a
     
    85101remote 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
    86102are
    87 freely selectable (except <tt><font size="2">~/job_queue</font></tt>),
     103freely selectable (except <big><tt><font size="2"><big>~/job_queue</big></font></tt></big>),
    88104however new users should use them as suggested, since many
    89105examples in this documentation as well as all example files are
    90 assuming these settings. The directory <span style="font-family: monospace;">~/palm/current_version</span>
     106assuming these settings. The directory <big><span style="font-family: monospace;">~/palm/current_version</span></big>
    91107on the local host will be called the working directory from now on. </p>
    92108<p style="line-height: 100%;"><font color="#000000">In
     
    123139probably 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
    124140Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To
    125 use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable has to be extended and the
    126 environment variable<span style="font-family: Courier New,Courier,monospace;"> PALM_BIN </span>has to be set (on local and remote host)
     141use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable
     142has to be extended and the
     143environment variable<span style="font-family: Courier New,Courier,monospace;">
     144PALM_BIN </span>has to be set (on local and remote host)
    127145in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>,
    128146if<span style="font-family: Courier New,Courier,monospace;">
     
    131149PALM_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
    132150may have to login again in order to activate these settings.</font></p><font color="#000000">On the local and on the remote host, some
    133 small helper/utility programs have to be installed, which are&nbsp;later used by <span style="font-weight: bold;">mrun</span>&nbsp;e.g. for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script
     151small helper/utility programs have to be installed, which
     152are&nbsp;later used by <span style="font-weight: bold;">mrun</span>&nbsp;e.g.
     153for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script
    134154requires a configuration file<span style="font-family: Courier New,Courier,monospace;">
    135155.mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the
     
    147167character and replace the string "<span style="font-family: Courier New,Courier,monospace;">&lt;replace
    148168by ...&gt;</span>" by your username on the respective host
    149 given in the <span style="font-family: Courier New,Courier,monospace;">&lt;host identifier&gt;</span>.
     169given in the <span style="font-family: Courier New,Courier,monospace;">&lt;host
     170identifier&gt;</span>.
    150171You only have to uncomment lines for those hosts on which you intend to
    151 use PALM.</font></p><p style="line-height: 100%;"><font color="#000000">Beside the default configuration file</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> .mrun.config.default</font><font color="#000000">, the directory<span style="font-family: Courier New,Courier,monospace;"> trunk/SCRIPTS </span>contains additional configuration files which are already adjusted for special hosts:<span style="font-family: Courier New,Courier,monospace;"> .mrun.config.imuk </span>can be used at Hannover University,<span style="font-family: Courier New,Courier,monospace;"> .mrun.config.riam </span>can
     172use PALM.</font></p><p style="line-height: 100%;"><font color="#000000">Beside the default configuration file</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> .mrun.config.default</font><font color="#000000">, the directory<span style="font-family: Courier New,Courier,monospace;">
     173trunk/SCRIPTS </span>contains additional configuration files
     174which are already adjusted for special hosts:<span style="font-family: Courier New,Courier,monospace;">
     175.mrun.config.imuk </span>can be used at Hannover University,<span style="font-family: Courier New,Courier,monospace;">
     176.mrun.config.riam </span>can
    152177be used at the Research Institute of Applied Mechanics, Kyushu
    153178University. These files have to be edited in the same way as described
    154179above.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the
    155 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 lcsgih</font></p><p style="line-height: 100%;"><font color="#000000">The
    156 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
     180respective 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
     181lcsgih</font></p><p style="line-height: 100%;"><font color="#000000">The
     182second call also copies the PALM scripts (like <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span>) to the
     183remote
    157184host.</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
    158185of PALM Code</span></font></p><font color="#000000">
     
    169196</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">Makefile</font><font color="#000000">,
    170197in which the dependencies are described. This file is found in
    171 subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE<span style="font-family: Times New Roman,Times,serif;">, where
    172 also the PALM code is stored</span></span>. The compiled
     198subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span></font><font color="#000000">, where
     199also the PALM code is stored.</font><font color="#000000"> The compiled
    173200sources (object
    174201files) are
    175202stored&nbsp;on the remote computer in the default directory
    176203</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
    177 pre-compilation for the remote host (here the SGI-ICE system of HLRN) is
     204pre-compilation for the remote host (here the SGI-ICE system of HLRN)
     205is
    178206done by</font><span style="font-family: monospace;"></span></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">mbuild
    179207-h lcsgih &nbsp;</span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild
     
    210238test run can
    211239now be started by executing the command </font>
    212 </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 &ldquo;d3# pr#&rdquo;</font></pre>
    213 <font color="#000000">This specific run
     240</p><pre style="margin-left: 1cm; margin-right: 1cm; margin-bottom: 0.5cm; line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mrun -d example_cbl -h lcsgih -K parallel -X 8 -T 8 -t 500 -q testq -r &ldquo;d3# pr#&rdquo;</font></pre><font color="#000000">This specific run
    214241will be carried out on 8 PEs and is allowed to use up to 500 seconds
    215242CPU time. After pressing &lt;return&gt;, the most important
     
    253280and time displayed at the top of the file header. <font color="#000000">If
    254281the file contents are identical, the installation is successfully
    255 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
     282completed.<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
     283for other machines</font></p><font color="#000000">Starting
    256284from version 3.2a, beside the default hosts (HLRN, etc.), PALM can also
    257285be installed and run on other Linux-Cluster-, IBM-AIX, or
    258286NEC-SX-systems. To configure PALM for a non-default host only requires
    259 to add some lines to the configuration file<span style="font-family: Courier New,Courier,monospace;"> .mrun.config</span>.<br><br>First,
     287to add some lines to the configuration file<span style="font-family: Courier New,Courier,monospace;">
     288.mrun.config</span>.<br><br>First,
    260289you have to define the host identifier (a string of arbitrary length)
    261 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 &nbsp;&lt;hostname&gt; &nbsp;&lt;host identifier&gt;</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;"> &lt;hostname&gt; </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;"> &lt;host identifier&gt; </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>"
     290under which your local host shall be identified by adding a line<br><br></font><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">%host_identifier
     291&nbsp;&lt;hostname&gt; &nbsp;&lt;host
     292identifier&gt;</span><br></div><br>to the
     293configuration file (best to do this in the section where the other
     294default host identifiers are defined). Here<span style="font-family: Courier New,Courier,monospace;">
     295&lt;hostname&gt; </span>must be the name of your local
     296host as provided by the unix-command "<span style="font-family: Courier New,Courier,monospace;">hostname</span>".
     297The first characters of<span style="font-family: Courier New,Courier,monospace;">
     298&lt;host identifier&gt; </span>have to be "<span style="font-family: Courier New,Courier,monospace;">lc</span>",
     299if your system is (part of) a linux-cluster, "<span style="font-family: Courier New,Courier,monospace;">ibm</span>",
     300or "<span style="font-family: Courier New,Courier,monospace;">nec</span>"
    262301in case of an IBM-AIX- or NEC-SX-system, respectively. For example, if
    263 you want to install on a linux-cluster, the line may read as<br><br><div style="margin-left: 40px;">%host_identifier &nbsp;foo &nbsp;lc_bar<br></div><br>In
     302you want to install on a linux-cluster, the line may read as<br><br><div style="margin-left: 40px;">%host_identifier &nbsp;foo
     303&nbsp;lc_bar<br></div><br>In
    264304the second step, you have to give all informations neccessary to
    265305compile and run PALM on your local host by adding an additional section
    266 to the configuration file:<br><br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username&nbsp;&nbsp; &lt;1&gt;&nbsp; &nbsp; &nbsp; &lt;host identifier&gt; parallel<br>%tmp_user_catalog&nbsp; &lt;2&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host identifier&gt; parallel<br>%compiler_name&nbsp;&nbsp;&nbsp;&nbsp; &lt;3&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host identifier&gt; parallel<br>%compiler_name_ser &lt;4&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host identifier&gt; parallel<br>%cpp_options&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    267 &lt;5&gt; &nbsp; &nbsp; &nbsp;&lt;host identifier&gt;&nbsp;parallel<br>%netcdf_inc&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;6&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host identifier&gt; parallel<br>%netcdf_lib&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;7&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host identifier&gt; parallel<br>%fopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    268 &lt;8&gt; &nbsp;&nbsp;&nbsp; &nbsp;&lt;host identifier&gt; parallel<br>%lopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    269 &nbsp;&lt;9&gt; &nbsp; &nbsp; &nbsp;&lt;host identifier&gt; parallel<br></div><br>The
     306to the configuration file:<br><br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username&nbsp;&nbsp;
     307&lt;1&gt;&nbsp; &nbsp; &nbsp; &lt;host
     308identifier&gt; parallel<br>%tmp_user_catalog&nbsp;
     309&lt;2&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host
     310identifier&gt; parallel<br>%compiler_name&nbsp;&nbsp;&nbsp;&nbsp;
     311&lt;3&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host
     312identifier&gt; parallel<br>%compiler_name_ser
     313&lt;4&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host
     314identifier&gt; parallel<br>%cpp_options&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     315&lt;5&gt; &nbsp; &nbsp; &nbsp;&lt;host
     316identifier&gt;&nbsp;parallel<br>%netcdf_inc&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     317&lt;6&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host
     318identifier&gt; parallel<br>%netcdf_lib&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     319&lt;7&gt; &nbsp;&nbsp;&nbsp;&nbsp; &lt;host
     320identifier&gt; parallel<br>%fopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     321&lt;8&gt; &nbsp;&nbsp;&nbsp; &nbsp;&lt;host
     322identifier&gt; parallel<br>%lopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     323&nbsp;&lt;9&gt; &nbsp; &nbsp;
     324&nbsp;&lt;host identifier&gt; parallel<br></div><br>The
    270325section consists of four columns each separated by one or more blanks.
    271326The first column gives the name of the respective environment variable
    272 used by <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span>,
     327used by <span style="font-weight: bold;">mrun</span>
     328and <span style="font-weight: bold;">mbuild</span>,
    273329while the second column defines its value. The third column has to be
    274330the host identifier as defined above, and the last column in each line
     
    276332Otherwise, the respective line(s) will be interpreted as belonging to
    277333the setup for compiling and running a serial (non-parallel) version of
    278 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;">&lt;1&gt; </span>is the username on your LOCAL host</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;2&gt; </span>is the temporary directory in which PALM runs will be carried out</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;3&gt; </span>is the compiler name which generates parallel code</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;4&gt; </span>is the compiler name for generating serial code</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;5&gt; </span>are
     334PALM.<br><br>All brackets have to be replaced by the
     335appropriate settings for your local host:<br><ul><li><span style="font-family: Courier New,Courier,monospace;">&lt;1&gt;
     336</span>is the username on your LOCAL host</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;2&gt;
     337</span>is the temporary directory in which PALM runs will be
     338carried out</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;3&gt;
     339</span>is the compiler name which generates parallel code</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;4&gt;
     340</span>is the compiler name for generating serial code</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;5&gt;
     341</span>are
    279342the preprocessor options to be invoked. In most of the cases, it will
    280343be neccessary to adjust the MPI data types to double precision by
    281 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;">&lt;6&gt; </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;">&lt;7&gt; </span>are the linker options to search for the NetCDF library</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;8&gt; </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;">&lt;9&gt; </span>are the linker options</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;host identifier&gt; </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&nbsp;&nbsp;
    282 raasch &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
    283 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;lc_bar parallel<br>%tmp_user_catalog&nbsp;
     344giving <span style="font-family: Courier New,Courier,monospace;">-DMPI_REAL=MPI_DOUBLE_PRECISION
     345-DMPI_2REAL=MPI_2DOUBLE_PRECISION</span>. To switch on the NetCDF
     346support, you also have to give <span style="font-family: Courier New,Courier,monospace;">-D__netcdf</span>
     347and <span style="font-family: Courier New,Courier,monospace;">-D__netcdf_64bit</span>
     348(if you like to have 64bit NetCDF output).</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;6&gt;
     349</span>is the compiler option for specifying the include path to
     350search for the NetCDF module/include files</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;7&gt;
     351</span>are the linker options to search for the NetCDF library</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;8&gt;
     352</span>are the general compiler options to be used. You should
     353allways switch on double precision (e.g. <span style="font-family: Courier New,Courier,monospace;">-r8</span>)
     354and code optimization (e.g. <span style="font-family: Courier New,Courier,monospace;">-O2</span>).</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;9&gt;
     355</span>are the linker options</li><li><span style="font-family: Courier New,Courier,monospace;">&lt;host
     356identifier&gt; </span>is the host identifier as defined
     357before</li></ul><br>A typical example may be:<br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username&nbsp;&nbsp;
     358raasch &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
     359&nbsp; &nbsp; &nbsp; &nbsp;
     360&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
     361&nbsp; &nbsp;lc_bar parallel<br>%tmp_user_catalog&nbsp;
    284362/tmp&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;lc_bar
    285363parallel<br>%compiler_name&nbsp;&nbsp;&nbsp;&nbsp;
     
    294372-L/usr/local/netcdf/lib:-lnetcdf&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    295373lc_bar parallel<br>%fopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    296 -axW:-cpp:-openmp:-r8:-nbs &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;
     374-axW:-cpp:-openmp:-r8:-nbs &nbsp; &nbsp; &nbsp;
     375&nbsp;&nbsp;
    297376&nbsp;&nbsp;&nbsp; lc_bar parallel<br>%lopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    298377-axW:-cpp:-openmp:-r8:-nbs:-Vaxlib&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;lc_bar
    299 parallel<br></div><br>Currently (version 3.2a), depending on the MPI
     378parallel<br></div><br>Currently (version 3.2a),
     379depending on the MPI
    300380version which is running on your local host, the options for the
    301 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>)
     381execution command (which may be <span style="font-family: Courier New,Courier,monospace;">mpirun</span>
     382or <span style="font-family: Courier New,Courier,monospace;">mpiexec</span>)
    302383may have to be adjusted manually in the mrun-script. A future version
    303384will allow to give the respective settings in the configuration file.
     
    306387installation, the members of the PALM working group are pleased to
    307388help you. &nbsp; </p>
    308 <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>
    309 <p style="line-height: 100%;"><i>Last
    310 change:&nbsp;</i> $Id$</p>
     389<hr><p style="line-height: 100%;"><font color="#000080"><font color="#000080"><a href="chapter_4.6.html"><font color="#000080"><img src="left.gif" name="Grafik1" align="bottom" border="2" height="32" width="32"></font></a><a href="index.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="up" src="up.gif" name="Grafik2"></font></a><a href="chapter_5.1.html"><font color="#000080"><img src="right.gif" name="Grafik3" align="bottom" border="2" height="32" width="32"></font></a></font></font></p><p style="line-height: 100%;"><i>Last
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