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Mar 13, 2007 2:52:40 AM (17 years ago)
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    16 <h2 style="line-height: 100%;"><font size="4">5.0 Installation of the
     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>
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     9<body style="direction: ltr;" lang="en-US"><h2 style="line-height: 100%;"><font size="4">5.0
     10Installation of the
    1711model</font></h2>
    1812<font color="#000000">This chapter
    19 describes the installation of PALM on a Linux workstation (local host) and a suitable remote computer, on which the
     13describes the installation of PALM on a Linux workstation (local host)
     14and a suitable remote computer, on which the
    2015model runs are to be carried out. The local host is used to
    21 start batch jobs with <b>mrun</b> and to analyze the results
    22 which are produced by the model on the remote host and send back to the local host. Alternatively, <span style="font-weight: bold;">mrun</span> can also be used to start PALM on the local host in interactive mode or as a batch job.</font><p style="line-height: 100%;"><font color="#000000"></font></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 installation and operation of PALM requires at mimimum (on both, the local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The AT&amp;T Korn-shell (ksh) must be 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">. Most of the current Linux distributions are using the public domain Korn-shell (pdksh). The PALM scripts <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span> do not work with the pdksh! Please replace it by the AT&amp;T ksh. If the AT&amp;T ksh path is different from<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">, please modify the first lines in <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span>, respectively.</font></li><li><font color="#000000">The NetCDF-library with version number not earlier than 3.6.0-p1 (for 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 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 system <span style="font-weight: bold;">subversion</span> (see <a href="http://subversion.tigris.org/">subversion.tigris.org</a>).
    23 This is already included in many Linux distributions (e.g. SuSe). <span style="font-weight: bold;">subversion requires port 3690 to be open for tcp/udp.</span> <span style="font-weight: bold;">If there are firewall restrictions concerning this port, the PALM code cannot be accessed.</span> The
     16start batch jobs with <b>mrun</b> and to analyze the
     17results
     18which are produced by the model on the remote host and send back to the
     19local host. Alternatively, <span style="font-weight: bold;">mrun</span>
     20can also be used to start PALM on the local host in interactive mode or
     21as a batch job.</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
     22installation and operation of PALM requires at mimimum (on both, the
     23local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The AT&amp;T Korn-shell (ksh) must be
     24available 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">.
     25Most of the current Linux distributions are using the public domain
     26Korn-shell (pdksh). The PALM scripts <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span> do not work
     27with the pdksh! Please replace it by the AT&amp;T ksh. If the
     28AT&amp;T ksh path is different from<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">,
     29please modify the first lines in <span style="font-weight: bold;">mrun</span>
     30and <span style="font-weight: bold;">mbuild</span>,
     31respectively.</font></li><li><font color="#000000">The
     32NetCDF-library with version number not earlier than 3.6.0-p1 (for
     33NetCDF, 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
     34least 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
     35system <span style="font-weight: bold;">subversion</span>
     36(see <a href="http://subversion.tigris.org/">subversion.tigris.org</a>).
     37This is already included in many Linux distributions (e.g. SuSe). <span style="font-weight: bold;">subversion requires port 3690 to
     38be open for tcp/udp.</span> <span style="font-weight: bold;">If
     39there are firewall restrictions concerning this port, the PALM code
     40cannot be accessed.</span> The
    2441user needs a permit to access the PALM repository. For getting a permit
    2542please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>)
    2643and define a username under which you like to access the repository.
    2744You will then receive a password which allows the access under this
    28 name.</font></li><li><font color="#000000">A job queueing system must be available on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).</font></li><li><font color="#000000">ssh/scp-connections to and from the remote 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 to be used on a limited number of selected machines. These are 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, Korea (<span style="font-style: italic;">ibms</span>), at Yonsei University, Seoul (<span style="font-style: italic;">ibms</span>), on NEC-SX6/8 systems at DKRZ, Hamburg (<span style="font-style: italic;">nech</span>) and RIAM, Kyushu University, Fukuoka (<span style="font-style: italic;">neck</span>), as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>) and Tokyo Institute of Technology (<span style="font-style: italic;">lctit</span>). The strings given in brackets are the systems names under which <span style="font-weight: bold;">mrun</span> indentifies the different hosts. mrun should also work on other systems, but this requires some modifications in the scripts <span style="font-weight: bold;">mrun</span>, <span style="font-weight: bold;">mbuild</span>, and <span style="font-weight: bold;">subjob</span>. Future PALM versions will allow to configure the scripts for different kinds of systems by just using a configuration file.</font><p style="line-height: 100%;"><font color="#000000">The examples given in this chapter refer to an
     45name.</font></li><li><font color="#000000">A
     46job queueing system must be available on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle
     47LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).</font></li><li><font color="#000000">ssh/scp-connections to and from the remote
     48host 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
     49to be used on a limited number of selected machines. These are
     50IBM-Regatta at computing center HLRN in Hannover (<span style="font-style: italic;">ibmh</span>), Berlin (<span style="font-style: italic;">ibmb</span>), at KISTI,
     51Korea (<span style="font-style: italic;">ibms</span>),
     52at Yonsei University, Seoul (<span style="font-style: italic;">ibms</span>),
     53on NEC-SX6/8 systems at DKRZ, Hamburg (<span style="font-style: italic;">nech</span>) and RIAM,
     54Kyushu University, Fukuoka (<span style="font-style: italic;">neck</span>),
     55as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>) and Tokyo
     56Institute of Technology (<span style="font-style: italic;">lctit</span>).
     57The strings given in brackets are the systems names under which <span style="font-weight: bold;">mrun</span> indentifies the
     58different hosts. mrun should also work on other systems, but this
     59requires some modifications in the scripts <span style="font-weight: bold;">mrun</span>, <span style="font-weight: bold;">mbuild</span>, and <span style="font-weight: bold;">subjob</span>. Future PALM
     60versions will allow to configure the scripts for different kinds of
     61systems by just using a configuration file.</font><p style="line-height: 100%;"><font color="#000000">The
     62examples given in this chapter refer to an
    2963installation of PALM on an IMUK Linux workstation and the IBM-Regatta
    3064system of
    31 the HLRN used as&nbsp;remote host. They are just called local and remote host from now on. </font></p><p style="line-height: 100%;">
    32 </p>
    33 <p style="line-height: 100%;">The installation process requires a valid
     65the HLRN used as&nbsp;remote host. They are just called local and
     66remote host from now on. </font></p><p style="line-height: 100%;">
     67</p><p style="line-height: 100%;">The installation
     68process requires a valid
    3469account on the local and on the remote host as well.<br>
    3570&nbsp; </p>
    36 <ul>
    37   All hosts (local as well as remote) are
     71<ul> All hosts (local as well as remote) are
    3872accessed via the secure shell (ssh). The user must establish
    3973passwordless login using the private/public-key mechanism (see e.g. the
    40   <a href="http://www.hlrn.de/doc/ssh/index.html">HLRN documentation</a>).
    41   <b>To ensure proper function of mrun, passwordless login must be
     74<a href="http://www.hlrn.de/doc/ssh/index.html">HLRN
     75documentation</a>). <b>To ensure proper function of mrun,
     76passwordless login must be
    4277established in both directions, from the local to the remote host as
    43 well as from the remote to the local host!</b> Test this by carrying
    44 out e.g. on the local host:
    45   <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
    46 </span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp; &lt;username on remote host&gt;@&lt;remote IP-address&gt;</span><br>
    47   </p>
    48   <p style="line-height: 100%;">and on the remote host:<br>
    49   </p>
    50   <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
    51 </span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp; &lt;username on local host&gt;@&lt;local IP-adddress&gt;</span><br>
    52   </p>
    53   In both cases you should&nbsp;not be
    54 prompted for a password. <b>Before continuing the further installation
    55 process, this must be absolutely guaranteed!</b> This must also be
    56 guaranteed for <b>all</b> other remote hosts, on which PALM shall run.
    57 </ul>
    58 <p style="line-height: 100%;"></p><p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package Installation</span></p><p style="line-height: 100%;">In the <b>first installation step</b> a
     78well as from the remote to the local host!</b> Test this by
     79carrying
     80out e.g. on the local host: <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
     81</span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp;
     82&lt;username on remote host&gt;@&lt;remote
     83IP-address&gt;</span><br> </p> <p style="line-height: 100%;">and on the remote host:<br>
     84</p> <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
     85</span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp;
     86&lt;username on local host&gt;@&lt;local IP-adddress&gt;</span><br>
     87</p> In both cases you should&nbsp;not be
     88prompted for a password. <b>Before continuing the further
     89installation
     90process, this must be absolutely guaranteed!</b> This must also
     91be
     92guaranteed for <b>all</b> other remote hosts, on which
     93PALM shall run.
     94</ul><p style="line-height: 100%;"></p><p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package
     95Installation</span></p><p style="line-height: 100%;">In
     96the <b>first installation step</b> a
    5997set of directories must be created both on the local and on the
    60 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 are
     98remote 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
     99are
    61100freely selectable (except <tt><font size="2">~/job_queue</font></tt>),
    62101however new users should use them as suggested, since many
    63102examples in this documentation as well as all example files are
    64 assuming these settings. The directory <span style="font-family: monospace;">~/palm/current_version</span> on the local host will be called the working directory from now on. </p>
    65 <p style="line-height: 100%;"><font color="#000000">In the <b>second
     103assuming these settings. The directory <span style="font-family: monospace;">~/palm/current_version</span>
     104on the local host will be called the working directory from now on. </p>
     105<p style="line-height: 100%;"><font color="#000000">In
     106the <b>second
    66107step</b>
    67108a working copy of the recent version of the PALM software package,
    68 including the source code, scripts, documentation, etc.&nbsp; must be
     109including the source code, scripts, documentation, etc.&nbsp; must
     110be
    69111copied to the working directory (</font><font color="#000000">local
    70112host!) by executing the following
    71 commands. Replace &lt;your username&gt; by the name that you chose to
    72 access the repository, and &lt;#&gt; by any of the available PALM
    73 releases, e.g. "<span style="font-style: italic;">3.1c</span>" (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 ~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn checkout --username &lt;your username&gt; svn://130.75.105.45/palm/tags/release-&lt;#&gt; trunk</span><br></div><p style="line-height: 100%;"><font color="#000000">You will then be prompted for your password. After finishing, the subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">should
     113commands. Replace &lt;your username&gt; by the name that you
     114chose to
     115access the repository, and &lt;#&gt; by any of the available
     116PALM
     117releases, e.g. "<span style="font-style: italic;">3.1c</span>"
     118(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
     119~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn
     120checkout --username &lt;your username&gt;
     121svn://130.75.105.45/palm/tags/release-&lt;#&gt; trunk</span><br></div><p style="line-height: 100%;"><font color="#000000">You
     122will then be prompted for your password. After finishing, the
     123subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">should
    74124appear in your working directory. It contains a number of further
    75 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">) 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,&nbsp;executing</p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username &lt;your username&gt; svn://130.75.105.45/palm/tags/release-&lt;#&gt; abcde</pre><p style="line-height: 100%;">will place your working copy in a directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span>instead of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span>. But keep in mind that you will have to adjust several paths given 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 your working copy of PALM, unless you&nbsp;know exactly what you are doing.</p><p style="line-height: 100%; font-weight: bold;"><span style="font-weight: normal;">You can also get a copy of the most recent code by executing</span></p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username &lt;your username&gt; svn://130.75.105.45/palm/trunk trunk</pre>However, this version may contain bugs and new features may not be documented. <span style="font-weight: bold;">In future PALM releases, repository access to this most recent&nbsp;version will
    76 probably be restricted to the PALM developers.</span><p style="line-height: 100%;"><font color="#000000"></font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Package Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To
     125subdirectories which contain e.g. the PALM source code (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SOURCE</font><font color="#000000">)
     126and 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,&nbsp;executing</p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username &lt;your username&gt; svn://130.75.105.45/palm/tags/release-&lt;#&gt; abcde</pre><p style="line-height: 100%;">will place your working copy in a
     127directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span>instead
     128of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span>.
     129But keep in mind that you will have to adjust several paths given
     130below, 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
     131your working copy of PALM, unless you&nbsp;know exactly what you
     132are doing.</p><p style="line-height: 100%; font-weight: bold;"><span style="font-weight: normal;">You can also get a copy of the
     133most recent code by executing</span></p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username &lt;your username&gt; svn://130.75.105.45/palm/trunk trunk</pre>However,
     134this version may contain bugs and new features may not be documented. <span style="font-weight: bold;">In future PALM releases,
     135repository access to this most recent&nbsp;version will
     136probably 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
     137Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To
    77138use the PALM scripts, the PATH variable has to be extended and the
    78139environment variable PALM_BIN has to be set (on local and remote host)
    79 in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>, if<span style="font-family: Courier New,Courier,monospace;"> 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 PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH</font><font color="#000000"><br><span style="font-family: Courier New,Courier,monospace;">export PALM_BIN=</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">$HOME/palm/current_version/trunk/SCRIPTS</font></p><p style="line-height: 100%;"><font color="#000000">You may habe to login again in order to activate these settings.</font></p><font color="#000000">On the local and on the remote host, some small helper/utility programs have to be installed, which are e.g. later used by <span style="font-weight: bold;">mrun</span> or for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script requires a configuration file<span style="font-family: Courier New,Courier,monospace;"> .mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the following. A copy has to be put into the working directory under the name<span style="font-family: Courier New,Courier,monospace;"> .mrun.config </span>by</font><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">cp trunk/SCRIPTS/.mrun.config.default .mrun.config</span></font></p><font color="#000000">Beside many other things, this file contains typical installation parameters
     140in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>,
     141if<span style="font-family: Courier New,Courier,monospace;">
     142ksh </span>is used):</font></p><p style="line-height: 100%; margin-left: 40px;"><font style="font-family: Courier New,Courier,monospace;" color="#000000">export
     143PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH</font><font color="#000000"><br><span style="font-family: Courier New,Courier,monospace;">export
     144PALM_BIN=</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">$HOME/palm/current_version/trunk/SCRIPTS</font></p><p style="line-height: 100%;"><font color="#000000">You
     145may habe to login again in order to activate these settings.</font></p><font color="#000000">On the local and on the remote host, some
     146small helper/utility programs have to be installed, which are e.g.
     147later used by <span style="font-weight: bold;">mrun</span>
     148or for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script
     149requires a configuration file<span style="font-family: Courier New,Courier,monospace;">
     150.mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the
     151following. A copy has to be put into the working directory under the
     152name<span style="font-family: Courier New,Courier,monospace;">
     153.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
     154trunk/SCRIPTS/.mrun.config.default .mrun.config</span></font></p><font color="#000000">Beside many other things, this file contains
     155typical installation parameters
    80156like compiler name, compiler options, etc.
    81 for a set of different remote hosts. Please edit this file, uncomment lines like</font><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username &nbsp;&lt;replace by your ... username&gt; &nbsp; &lt;remote-computer-shortcut&gt;</div><p style="line-height: 100%;"><font color="#000000">by removing the first hash (<span style="font-family: Courier New,Courier,monospace;">#</span>) character and replace the string "<span style="font-family: Courier New,Courier,monospace;">&lt;replace by ...&gt;</span>" by your username on the respective host given in the <span style="font-family: Courier New,Courier,monospace;">&lt;remote-computer-shortcut&gt;</span>. You only have to uncomment lines for those hosts on which you intend to use PALM.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the 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 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 host.</font></p><p style="line-height: 100%;"><font color="#000000"></font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Pre-Compilation of PALM Code</span></font></p><font color="#000000">
    82 </font>
    83 <br><font color="#000000">To avoid the
     157for a set of different remote hosts. Please edit this file, uncomment
     158lines like</font><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username
     159&nbsp;&lt;replace by your ... username&gt; &nbsp;
     160&lt;remote-computer-shortcut&gt;</div><p style="line-height: 100%;"><font color="#000000">by
     161removing the first hash (<span style="font-family: Courier New,Courier,monospace;">#</span>)
     162character and replace the string "<span style="font-family: Courier New,Courier,monospace;">&lt;replace
     163by ...&gt;</span>" by your username on the respective host
     164given in the <span style="font-family: Courier New,Courier,monospace;">&lt;remote-computer-shortcut&gt;</span>.
     165You only have to uncomment lines for those hosts on which you intend to
     166use PALM.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the
     167respective 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
     168second 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
     169host.</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
     170of PALM Code</span></font></p><font color="#000000">
     171</font><br><font color="#000000">To avoid the
    84172re-compilation of the complete source code for each model run, PALM
    85 willl be pre-compiled once on the remote host by again using the script <span style="font-weight: bold;">mbuild</span>. Due to the use of
     173willl be pre-compiled once on the remote host by again using the script
     174<span style="font-weight: bold;">mbuild</span>. Due
     175to the use of
    86176FORTRAN modules in the source code, the subroutines must be compiled
    87 in a certain order. Therefore the so-called <i>make</i> mechanism
     177in a certain order. Therefore the so-called <i>make</i>
     178mechanism
    88179is used (see the respective man-page of the Unix operating system),
    89 requiring a<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">Makefile</font><font color="#000000">,
    90 in which the dependencies are described. This file is found in subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE<span style="font-family: Times New Roman,Times,serif;">, where also the PALM code is stored</span></span>. The compiled sources (object
     180requiring a<span style="font-family: Courier New,Courier,monospace;">
     181</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">Makefile</font><font color="#000000">,
     182in which the dependencies are described. This file is found in
     183subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE<span style="font-family: Times New Roman,Times,serif;">, where
     184also the PALM code is stored</span></span>. The compiled
     185sources (object
    91186files) are
    92187stored&nbsp;on the remote computer in the default directory
    93188</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
    94 pre-compilation for the remote host (here the IBM-Regatta of HLRN) is done by</font><span style="font-family: monospace;"></span></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">mbuild -h ibmh&nbsp;&nbsp;</span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild
    95 </span>will prompt some queries<font color="#000000">, which must all be
    96 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 the respective compiler calls to the remote
     189pre-compilation for the remote host (here the IBM-Regatta of HLRN) is
     190done by</font><span style="font-family: monospace;"></span></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">mbuild
     191-h ibmh&nbsp;&nbsp;</span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild
     192</span>will prompt some queries<font color="#000000">,
     193which must all be
     194answered "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
     195the respective compiler calls to the remote
    97196host where they are carried out interactively. You can follow the
    98197progress at the terminal window, where also error messages
    99198are displayed (hopefully not for this standard installation). By just
    100199entering </font></p><p style="line-height: 100%;">
    101 </p>
    102 <blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote>
    103 <p style="line-height: 100%;"><font color="#000000">PALM will
     200</p><blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote>
     201<p style="line-height: 100%;"><font color="#000000">PALM
     202will
    104203be (consecutively) pre-compiled for all remote hosts listed in
    105 the configuration file. If you want to compile for the local host only, please enter</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">mbuild -h lcmuk</span> </font>
    106 </p>
    107 <p style="line-height: 100%;"><font color="#000000"></font></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,
     204the configuration file. If you want to compile for the local host only,
     205please enter</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">mbuild
     206-h lcmuk</span> </font>
     207</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,
    108208after the compilation has been finished, the PALM installation has to
    109209be verified. For this
    110210purpose a simple test run is carried out. This once again requires the <b>mrun
    111211</b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter
    112 3.2</font></a><font color="#000000">), as well as the </font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d"><font color="#000080">parameter
    113 file</font></a><font color="#000000"> (described in </font><a href="chapter_4.4.html"><font color="#000080">chapter
    114 4.4</font></a>)<font color="#000000">. The parameter file must be
     2123.2</font></a><font color="#000000">), as well
     213as the </font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d"><font color="#000080">parameter
     214file</font></a><font color="#000000">
     215(described in </font><a href="chapter_4.4.html"><font color="#000080">chapter
     2164.4</font></a>)<font color="#000000">. The
     217parameter file must be
    115218copied from the PALM working copy by<br>
    116 </font>
    117 <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 trunk/INSTALL/example_p3d&nbsp;JOBS/example/INPUT/example_p3d</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"></span></font></div>
    118 <p style="line-height: 100%;"><font color="#000000">The test run can
     219</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
     220trunk/INSTALL/example_p3d&nbsp;JOBS/example/INPUT/example_p3d</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"></span></font></div>
     221<p style="line-height: 100%;"><font color="#000000">The
     222test run can
    119223now be started by executing the command </font>
    120 </p>
    121 <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 &ldquo;d3# pr#&rdquo;</font></pre>
     224</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 &ldquo;d3# pr#&rdquo;</font></pre>
    122225<font color="#000000">This specific run
    123226will be carried out on 8 PEs and is allowed to use up to 500 seconds
    124 CPU time. After pressing &lt;return&gt;, the most important settings of
     227CPU time. After pressing &lt;return&gt;, the most important
     228settings of
    125229the job are displayed at the terminal window
    126 and the user is prompted for o.k. (&ldquo;</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">y</font><font color="#000000">&rdquo;). Next, a message of the queuing system like &ldquo;<i>Request</i> &hellip;
    127 <i>Submitted to queue&hellip; by&hellip;&rdquo; </i>should be displayed. Now the job is
    128 queued and either started immediately or at a later time, depending on the
     230and the user is prompted for o.k. (&ldquo;</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">y</font><font color="#000000">&rdquo;).
     231Next, a message of the queuing system like &ldquo;<i>Request</i>
     232&hellip;
     233<i>Submitted to queue&hellip; by&hellip;&rdquo; </i>should
     234be displayed. Now the job is
     235queued and either started immediately or at a later time, depending on
     236the
    129237current workload of the remote host. Provided that it is executed
    130238immediately and that all things work as designed, the job protocol of
    131 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 more than a few minutes later. The content of this
     239this 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
     240more than a few minutes later. The content of this
    132241file should be carefully examined for any error messages.</font><p style="line-height: 100%;">
    133 </p>
    134 
    135 
    136 <p style="line-height: 100%;">Beside the job protocol and according to
     242</p><p style="line-height: 100%;">Beside the job
     243protocol and according to
    137244the configuration file and arguments given for <b>mrun</b>
    138 options<span style="font-family: Courier New,Courier,monospace;"> -d </span>and<span style="font-family: Courier New,Courier,monospace;"> -r</span><tt>,</tt>further files should be found in
     245options<span style="font-family: Courier New,Courier,monospace;">
     246-d </span>and<span style="font-family: Courier New,Courier,monospace;"> -r</span><tt>,</tt>further
     247files should be found in
    139248the
    140249directories</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>
    141250<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
    142251</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/OUTPUT</span><span style="font-family: monospace;"></span><br>
    143 </p>
    144 <p style="line-height: 100%;">Please compare the contents of file</p>
     252</p><p style="line-height: 100%;">Please compare the
     253contents of file</p>
    145254<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
    146255</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/MONITORING/ibmh_example_rc</span><br>
    147 </p>
    148 <p style="line-height: 100%;">with those of the example result file which can be found under<span style="font-family: Courier New,Courier,monospace;"> 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> diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff &nbsp;JOBS/example/MONITORING/ibmh_example_rc trunk/INSTALL/example_rc</p><p style="line-height: 100%;">where it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;"> ~/palm/current_version</span>.</p><span style="font-weight: bold;">You should not find any difference between these two files</span>, except of the run date and time displayed at the top of the file header. <font color="#000000">If
     256</p><p style="line-height: 100%;">with those of the
     257example result file which can be found under<span style="font-family: Courier New,Courier,monospace;">
     258trunk/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>
     259diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff
     260&nbsp;JOBS/example/MONITORING/ibmh_example_rc
     261trunk/INSTALL/example_rc</p><p style="line-height: 100%;">where
     262it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;">
     263~/palm/current_version</span>.</p><span style="font-weight: bold;">You should not find any
     264difference between these two files</span>, except of the run date
     265and time displayed at the top of the file header. <font color="#000000">If
    149266the file contents are identical, the installation is successfully
    150267completed.</font>
    151 <p style="line-height: 100%;">If you have any problems with the PALM
     268<p style="line-height: 100%;">If you have any problems
     269with the PALM
    152270installation, the members of the PALM working group are pleased to
    153271help you. &nbsp; </p>
    154 <hr>
    155 <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="Inhaltsverzeichnis.html"><font color="#000080"><img src="up.gif" name="Grafik2" align="bottom" border="2" height="32" width="32"></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>
    156 <p style="line-height: 100%;"><i>Last change:&nbsp;</i> 02/03/07 (SR) </p>
     272<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="Inhaltsverzeichnis.html"><font color="#000080"><img src="up.gif" name="Grafik2" align="bottom" border="2" height="32" width="32"></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>
     273<p style="line-height: 100%;"><i>Last
     274change:&nbsp;</i> $Id$</p>
    157275</body></html>
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