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 </style></head><body style="direction: ltr;" lang="en-US"><h2 style="line-height: 100%;"><font size="4">5.0
-Installation of the
-model</font></h2>
+Code installation<br>
+</font></h2>
 <font color="#000000">This chapter
-describes the installation of PALM on a Linux workstation (local host)
-and a suitable remote computer, on which the
-model runs are to be carried out. The local host is used to
-start batch jobs with <b>mrun</b> and to analyze the
-results
-which are produced by the model on the remote host and send back to the
+describes the installation of PALM on a Linux workstation (local host). There are two methods to install and run PALM. With the <span style="font-style: italic;">simple method</span>, you can run PALM interactively on the local computer. This method is using the scripts <span style="font-weight: bold;">palm_simple_install</span> and <span style="font-weight: bold;">palm_simple_run</span>.&nbsp;
+The simple method cannot create batch jobs itself, and cannot be used
+to create restart runs. Also file handling and most other features of
+the <span style="font-style: italic;">advanced method</span> are not available. This method is only recommended for those who like to test PALM quickly.<br>
+<br>
+The <span style="font-style: italic;">advanced method</span> is for running PALM in batch mode on a suitable remote computer. The installation procedure is using the script <span style="font-weight: bold;">mbuild</span>. All jobs are started on the local host using the script <b>mrun</b>. The PALM output is automatically sent back from the remote host to the
 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 (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
-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 Korn-shell (AT&amp;T ksh or public
-domain 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">.<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
-NetCDF-library with version number not earlier than 3.6.0-p1 (for
+can also be used to start PALM in interactive mode on the local host, or
+as a batch job on the local host (if a queueing system like NQS, PBS, or LoadLeveler is
+available).<br>
+<br>
+Only the <span style="font-style: italic;">advanced method</span> gives full access to all PALM features.<br>
+<br>
+</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
+installation and operation of PALM requires at mimimum (for the <span style="font-style: italic;">advanced method</span> on both, the
+local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">A Korn-shell (AT&amp;T ksh or public
+domain 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">.<span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-family: Courier New,Courier,monospace;"></span></font><font color="#000000"><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span></font></li><li><font color="#000000">A NetCDF-library with version number not earlier than 3.6.2 (for
 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
@@ -37,18 +41,20 @@
 please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>)
 and define a username under which you like to access the repository.
-You will then receive a password which allows the access under this
-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
+You will then receive a password which allows access under this
+name.<br>
+    <br>
+The <span style="font-style: italic;">advanced method</span> additionally requires:<br>
+</font></li><li><font color="#000000">A
+job queueing system 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 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>
-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,
+IBM-Regatta systems<span style="font-style: italic;"></span>
+at Yonsei University (<span style="font-style: italic;">ibmy</span>), <span style="font-style: italic;"></span> and at DKRZ, Hamburg (<span style="font-style: italic;">ibmh</span>), an NEC-SX8 system at RIAM,
 Kyushu University, Fukuoka (<span style="font-style: italic;">necriam</span>),
 as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>), Tokyo
 Institute of Technology (<span style="font-style: italic;">lctit</span>),
-and the Bergen Center for Computational Science (<span style="font-style: italic;">lcxt4</span>).
+Kyoto computing center (<span style="font-style: italic;">lckyoto</span>), and Cray-XT4/5 systems at the Bergen Center for Computational Science (<span style="font-style: italic;">lcxt4</span>) and at the Finish Meteorological Institute (<span style="font-style: italic;">lcxt5m</span>).
 The strings given in brackets are the systems names (host identifiers)
 under which <span style="font-weight: bold;">mrun</span>
@@ -56,17 +62,21 @@
 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
+how to configure <span style="font-weight: bold;">mrun</span>for
+other machines. However, these configurations currently (version
+3.7a) allow to run PALM in interactive mode only. Batch mode requires
+manual adjustments for the respective queing system and MPI
+installation in scripts <span style="font-weight: bold;">mrun</span>, <span style="font-weight: bold;">mbuild</span>, and <span style="font-weight: bold;">subjob</span>.<br><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span></font><p style="line-height: 100%;"><font color="#000000">The
 examples given in this chapter refer to an
-installation of PALM on an IMUK Linux workstation and the SGI-ICE
-system of
-the HLRN used as&nbsp;remote host. They are just called local and
+installation of PALM on an IMUK Linux workstation and (for the <span style="font-style: italic;">advanced method</span>) the SGI-ICE
+system of HLRN, used as&nbsp;remote host. They are just referred to as local and
 remote host from now on. </font></p><p style="line-height: 100%;">
 </p><p style="line-height: 100%;">The installation
-process requires a valid
-account on the local and on the remote host as well.<br>
+process for the <span style="font-style: italic;">advanced method</span> requires a valid
+account on the local and on the remote host as well.</p>
+<p style="line-height: 100%;">The <span style="font-style: italic;">advanced installation method</span> is described below. For the <span style="font-style: italic;">simple  method</span> see the <a href="#simple_installation_method">end of this chapter</a>.<br>
 &nbsp; </p>
-<ul> All hosts (local as well as remote) are
+
+<ul>
+ All hosts (local as well as remote) are
 accessed via the secure shell (ssh). The user must establish
 passwordless login using the private/public-key mechanism (see e.g. the
@@ -87,55 +97,53 @@
 prompted for a password. <b>Before continuing the further
 installation
-process, this must be absolutely guaranteed!</b> This must also
+process, this must be absolutely guaranteed!</b> It must also
 be
 guaranteed for <b>all</b> other remote hosts, on which
 PALM shall run.<br><br>Please
-note that on many remote hosts, passwordless login must also be
-established <b>within the remote host</b>, i.e. from the
-remote host to itself. Test this by executing on the remote host: <span style="font-family: Courier New,Courier,monospace;">ssh
-&lt;remote IP-address&gt;</span>. You should not be prompted
-for a password.<br><br></ul><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
-set of directories must be created both on the local and on the
-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
-freely selectable (except <big><tt><font size="2"><big>~/job_queue</big></font></tt></big>),
-however new users should use them as suggested, since many
-examples in this documentation as well as all example files are
-assuming these settings. The directory <big><span style="font-family: monospace;">~/palm/current_version</span></big>
+note that on many remote hosts, passwordless login must also work <b>within the remote host</b>, i.e. for ssh connections from the
+remote host to itself. Test this by executing on the remote host:<br>
+  <br>
+  <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; ssh
+&lt;username on remote host&gt;@&lt;remote IP-address&gt;</span>&nbsp;&nbsp;&nbsp;&nbsp; .<br>
+  <br>
+You should not be prompted
+for a password.<br><br>
+</ul>
+<p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package
+Installation</span></p><p style="line-height: 100%;">The <b>first installation step</b> requires creating a
+set of directories on the local and, for the <span style="font-style: italic;">advanced method</span>, on the
+remote host<span style="font-style: italic;"></span>. These are:</p><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/job_queue<br></div><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm<br></div><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm/current_version<br></div><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS</span><br></div><p style="line-height: 100%;">The names of these directories can be
+freely selected (except <big><tt><font size="2"><big>~/job_queue</big></font></tt></big>),
+however new users should choose them as suggested, since many
+examples in this documentation as well as all example files are based on these settings. The directory <big><span style="font-family: monospace;">~/palm/current_version</span></big>
 on the local host will be called the working directory from now on. </p>
 <p style="line-height: 100%;"><font color="#000000">In
 the <b>second
 step</b>
-a working copy of the recent version of the PALM software package,
+a working copy of the recent PALM version,
 including the source code, scripts, documentation, etc.&nbsp; must
 be
 copied to the working directory (</font><font color="#000000">local
 host!) by executing the following
-commands. Replace &lt;your username&gt; by the name that you
-chose to
+commands. Replace &lt;your username&gt; by the name that you have chosen to
 access the repository, and &lt;#&gt; by any of the available
 PALM
-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
+releases, e.g. "<span style="font-style: italic;">3.7a</span>"
+(new releases will be announced to members of the PALM mailing list).</font></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">cd
 ~/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://130.75.105.2/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
-appear in your working directory. It contains a number of further
-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">)
+will then be prompted for your password. After completion, there should be a subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">in your working directory. It contains a number of further
+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://130.75.105.2/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>.
+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
+your working copy of PALM, unless you&nbsp;know 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://130.75.105.2/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
-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
+most recent developer code by executing</span></p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username &lt;your username&gt; svn://130.75.105.2/palm/trunk trunk</pre>This version may contain new features (they might not be documented well), but it may also contain bugs.<span style="font-weight: bold;"><br>
+</span><br>
+<p style="line-height: 100%;"></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
 use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable
@@ -172,11 +180,8 @@
 use PALM.</font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">Warning:
 When editing the configuration file, please NEVER use the TAB key.
-Otherwise, very confusing errors in mrun execution may occur.</span></font></p><p style="line-height: 100%;"><font color="#000000">Beside the default configuration file</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> .mrun.config.default</font><font color="#000000">, the directory<span style="font-family: Courier New,Courier,monospace;">
+Otherwise, very confusing errors may occur when mrun is executing.</span></font></p><p style="line-height: 100%;"><font color="#000000">Beside the default configuration file</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> .mrun.config.default</font><font color="#000000">, the directory<span style="font-family: Courier New,Courier,monospace;">
 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
-be used at the Research Institute of Applied Mechanics, Kyushu
-University. These files have to be edited in the same way as described
+which are already adjusted for special hosts</font><font color="#000000">, e.g.</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">
+.mrun.config.imuk </span>can be used at Hannover University</font><font color="#000000">, etc.. </font><font color="#000000">These files have to be edited in the same way as described
 above.</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
@@ -184,5 +189,7 @@
 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%;"></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Pre-Compilation
+host.<br>
+<br>
+</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
 of PALM Code</span></font></p><font color="#000000">
 </font><br><font color="#000000">To avoid the
@@ -203,5 +210,5 @@
 files) are
 stored&nbsp;on the remote computer in the default directory
-</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
+</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">~/palm/current_version/MAKE_DEPOSITORY</font>_<span style="font-family: Courier New,Courier,monospace;">&lt;block_descriptor&gt;</span>, where<font color="#000000"> <span style="font-family: Courier New,Courier,monospace;">&lt;block_descriptor&gt;</span> is composed of the third (and fourth, if existing) column of the respective block in the configuration file (e.g. <span style="font-family: Courier New,Courier,monospace;">lcsgih_parallel</span> for HLRN).<span style="font-weight: bold;"></span></font><p style="line-height: 100%;"><font color="#000000">The
 pre-compilation for the remote host (here the SGI-ICE system of HLRN)
 is
@@ -385,11 +392,114 @@
 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>)
-may have to be adjusted manually in the mrun-script. A future version
+may have to be adjusted manually in the <span style="font-weight: bold;">mrun</span>-script. A future version
 will allow to give the respective settings in the configuration file.
 <p style="line-height: 100%;">If you have any problems
 with the PALM
 installation, the members of the PALM working group are pleased to
-help you. &nbsp; </p>
-<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
+help you.<br>
+</p>
+<p style="line-height: 100%;"><br>
+<span style="font-weight: bold; text-decoration: underline;"><a name="simple_installation_method"></a>Simple installation method</span><br>
+</p>
+<p style="line-height: 100%;">The simple installation method is using the scripts <span style="font-weight: bold;">palm_simple_install</span> and <span style="font-weight: bold;">palm_simple_run</span> for installing and running PALM.<br>
+<br>
+<span style="font-weight: bold; text-decoration: underline;">Package
+Installation</span></p>
+<p style="line-height: 100%;"><span style="font-weight: bold;">First step:</span> Create a directory<span style="font-style: italic;"></span>:</p>
+<div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">mkdir -p ~/palm/current_version/</div>
+<p style="line-height: 100%;">You can freely choose the directory name, but if you intend to switch to the <span style="font-style: italic;">advanced method</span> of running PALM later, you should use<span style="font-family: Courier New,Courier,monospace;"> ~/palm/current_version</span>. This directory <big><span style="font-family: monospace;"></span></big>will be called working directory from now on. </p>
+
+<p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">S</span><b>econd
+step</b>:
+Check out a working copy of the recent PALM version from the svn-repository</font><font color="#000000">. Replace<span style="font-family: Courier New,Courier,monospace;"> &lt;your username&gt; </span>by your valid repository username, and<span style="font-family: Courier New,Courier,monospace;"> &lt;#&gt; </span>by any of the available
+PALM
+releases, e.g. "<span style="font-style: italic;">3.7a</span>"
+(new releases will be announced to members of the PALM mailing list).</font></p>
+<div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">cd
+~/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://130.75.105.2/palm/tags/release-&lt;#&gt; trunk</span><br></div>
+<p style="line-height: 100%;"><font color="#000000">You
+will be prompted for your password. After completion, a subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk <span style="font-family: Times New Roman,Times,serif;">will appear </span></font><font color="#000000">in your working directory. It contains a number of further
+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">). For checking out the most recent PALM version (developer version), see the <span style="font-style: italic;">advanced installation method</span> described above.<br>
+</font></p>
+<p style="line-height: 100%;">Please never touch any file in
+your working copy of PALM, unless you really know what you
+are doing.</p>
+<br>
+
+<p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Configuration and compilation<br>
+</span></font></p>
+<p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">Third step:</span> To
+use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable
+has to be extended and the
+environment variable<span style="font-family: Courier New,Courier,monospace;">
+PALM_BIN </span>has to be set. For convenience, setting should be done
+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 color="#000000"><span style="font-family: Courier New,Courier,monospace;">export
+PALM_BIN=</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">$HOME/palm/current_version/trunk/SCRIPTS<br>
+</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">export
+PATH=$PALM_BIN:$PATH</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"><br>
+</span></font></p>
+<p style="line-height: 100%;"><font color="#000000">You
+may have to login again in order to activate the profile settings.<br>
+</font></p>
+<p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">Fourth step:</span> Call the installation script:<br>
+</font></p>
+<p style="line-height: 100%; margin-left: 40px;"><font style="font-family: Courier New,Courier,monospace;" color="#000000">palm_simple_install -i MAKE.inc.ifort.imuk</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"><br>
+</span></font></p>
+
+<p style="line-height: 100%;"><font color="#000000">The script copies the PALM source code into a new subdirectory <span style="font-family: Courier New,Courier,monospace;">MAKE_DEPOSITORY_simple</span>. This directory also will contain a <span style="font-family: Courier New,Courier,monospace;">Makefile</span> and an include file <span style="font-family: Courier New,Courier,monospace;">MAKE.inc</span>
+to be used for compiling the code in the next step. The include file
+contains compiler name, compiler options, library path for NetCDF, etc.
+<span style="font-weight: bold;">Please adjust these settings as required by your system, before you proceed with the next step.</span> The default settings in <span style="font-family: Courier New,Courier,monospace;">MAKE.inc</span>
+are for the Intel-FORTRAN compiler in the IMUK environment. You may
+find default settings for other compilers and environments in <span style="font-family: Courier New,Courier,monospace;">.../trunk/INSTALL/</span> See for files<span style="font-family: Courier New,Courier,monospace;"> MAKE.inc.*</span>.<br>
+</font></p>
+<p style="line-height: 100%; margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">cd MAKE_DEPOSITORY_simple<br>
+</span><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">make<br>
+cd ..<br>
+</span></font></p>
+
+
+<p style="line-height: 100%;">In order to shorten compilation time, you can run make in parallel, e.g.<span style="font-family: Courier New,Courier,monospace;"> make -j 4 </span>runs 4 compile threads simultaneously.<br>
+<br>
+<span style="font-weight: bold;">Fifth step:</span> Carry out a test
+run in order to check the installation. The test run (as every PALM
+run) requires a parameter file for steering PALM, which is in
+FORTRAN-NAMELIST format. This file has been already generated by the
+installation script <span style="font-family: Courier New,Courier,monospace;">palm_simple_install</span> under <span style="font-family: Courier New,Courier,monospace;">JOBS/example_cbl/INPUT/example_cbl_p3d</span><span style="font-family: Courier New,Courier,monospace;"></span>. PALM is started with script <span style="font-family: Courier New,Courier,monospace;">palm_simple_run</span>. <span style="font-weight: bold;">Before</span> the first run, it may be necessary to change the MPI-execution command (<span style="font-family: Courier New,Courier,monospace;">mpiexec</span>, <span style="font-family: Courier New,Courier,monospace;">mpirun</span>, etc.) and options in this script, depending on the MPI-library that you are using. The script can be found in directory <span style="font-family: Courier New,Courier,monospace;">.../trunk/SCRIPTS</span>.
+Default settings in this script are for the SGI-mpt-library installed
+on HLRN. You will find the execution command almost at the end of this
+script. After having adjusted the MPI-execution command, start the run
+with:<br>
+</p>
+<p style="line-height: 100%; margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">palm_simple_run -p 4 -n 4 -c example_cbl</span><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"><br>
+</span></font></p>
+
+
+
+<p style="line-height: 100%;">where option <span style="font-family: Courier New,Courier,monospace;">-p</span> gives the total number of MPI tasks, <span style="font-family: Courier New,Courier,monospace;">-n</span> gives the number of MPI tasks per node, and <span style="font-family: Courier New,Courier,monospace;">-c</span> gives the parameter file to be used.<br>
+After the run has finished, all OUTPUT files can be found in directory <span style="font-family: Courier New,Courier,monospace;">OUTPUT....</span> Names and contents of PALM output files are described in <a href="chapter_3.4.html">chapter 3.4</a>.
+The directory name is composed of the parameter file name, the number
+of cores that have been used, and the current data and time. For every
+run a unique directory is created.<br>
+</p>
+<p style="line-height: 100%;"><span style="font-weight: bold;">Sixth step:</span> To verify the results of this example run, compare it with the default result:<br>
+<span style="font-weight: bold;"></span></p>
+<p style="line-height: 100%; margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">diff&nbsp; OUTPUT..../RUN_CONTROL&nbsp;&nbsp; trunk/INSTALL/example_cbl_rc</span><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"><br>
+</span></font></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, and, maybe, the number of cores that have been used. <font color="#000000">If
+the file contents are identical, the installation is successfully
+completed.</font><hr><p style="line-height: 100%;"><font color="#000080"><font color="#000080"><a href="chapter_4.6.html"><font color="#000080"><img src="left.gif" name="Grafik1" align="bottom" border="2" height="32" width="32"></font></a><a href="index.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="up" src="up.gif" name="Grafik2"></font></a><a href="chapter_5.1.html"><font color="#000080"><img src="right.gif" name="Grafik3" align="bottom" border="2" height="32" width="32"></font></a></font></font></p><p style="line-height: 100%;"><i>Last
 change:&nbsp;</i> $Id: chapter_5.0.html 287 2009-04-09
 08:59:36Z raasch $</p>
Index: /palm/trunk/INSTALL/MAKE.inc.ifort.imuk
===================================================================
--- /palm/trunk/INSTALL/MAKE.inc.ifort.imuk	(revision 514)
+++ /palm/trunk/INSTALL/MAKE.inc.ifort.imuk	(revision 515)
@@ -1,9 +1,9 @@
-# contents of this file are include in palm's makefile if the simple install
+# Contents of this file are included in palm's makefile if the simple install
 # process (palm_simple_install) is used.
-# Please adjust compiling parameters as required for your system
+# Please adjust compiling parameters as required for your system.
 
 PROG=palm 
 F90=mpif90
-COPT= -cpp -DMPI_REAL=MPI_DOUBLE_PRECISION -DMPI_2REAL=MPI_2DOUBLE_PRECISION -D__netcdf -D__netcdf_64bit -D__intel_openmp_bug -D__lc -D__parallel
-F90FLAGS= -axW -openmp -r8 -nbs -convert little_endian -I /muksoft_64/packages/netcdf/3.6.3/include
-LDFLAGS= -axW -openmp -r8 -nbs -Vaxlib -L/muksoft_64/packages/netcdf/3.6.3/lib -lnetcdf
+COPT= -cpp -DMPI_REAL=MPI_DOUBLE_PRECISION -DMPI_2REAL=MPI_2DOUBLE_PRECISION -D__netcdf -D__lc -D__parallel
+F90FLAGS= -axW -O3 -r8 -nbs -convert little_endian -I /muksoft_64/packages/netcdf/3.6.3/include
+LDFLAGS= -axW -O3 -r8 -nbs -Vaxlib -L/muksoft_64/packages/netcdf/3.6.3/lib -lnetcdf
Index: /palm/trunk/SCRIPTS/palm_simple_install
===================================================================
--- /palm/trunk/SCRIPTS/palm_simple_install	(revision 514)
+++ /palm/trunk/SCRIPTS/palm_simple_install	(revision 515)
@@ -14,4 +14,6 @@
      # Last changes:
      # 25/01/10 - Siggi - Generating the first version
+     # 18/03/10 - Siggi - switch to palm/current_version removed: working
+     #                    copy can be in any directory
 
 
@@ -31,8 +33,4 @@
  done
 
-
-
-    # Switch to default working directory
- cd  ~/palm/current_version
 
 
Index: /palm/trunk/SCRIPTS/palm_simple_run
===================================================================
--- /palm/trunk/SCRIPTS/palm_simple_run	(revision 514)
+++ /palm/trunk/SCRIPTS/palm_simple_run	(revision 515)
@@ -9,8 +9,9 @@
      # It requires that palm has been installed with command
      # palm_simple_install and that the executable palm has been created
-     # with make in directory ~/palm/current_version/MAKE_DEPOSITORY_simple
+     # with make in directory  ...../MAKE_DEPOSITORY_simple
 
      # Last changes:
      # 25/01/10 - Siggi - Generating the first version
+     # 18/03/10 - Siggi - Some comments changed
 
 
@@ -23,5 +24,4 @@
  mpi_procs_per_node=1
  openmp_threads=1
- # palm_dir=~/palm/current_version/
 
  typeset -i  ii
@@ -51,5 +51,5 @@
     # Generate unique directory/files for this run
  timedate="`date +%d.%b_%H:%M:%S`"
- suffix=$case+$nnodes+$timedate
+ suffix=$case+$mpi_procs+$timedate
  RUNDIR=OUTPUT.$suffix/
 
@@ -125,6 +125,9 @@
  echo "*** palm will be run:  MPI tasks: $mpi_procs   OpenMP thread: $OMP_NUM_THREADS"
 
-# mpiexec  -machinefile hostfile  -n $mpi_procs  ./palm  < runfile_atmos
- mpiexec_mpt  -np $mpi_procs  ./palm  < runfile_atmos
+# IMUK:
+ mpiexec  -machinefile hostfile  -n $mpi_procs  ./palm  < runfile_atmos
+
+# SGI-MPT HLRN
+# mpiexec_mpt  -np $mpi_procs  ./palm  < runfile_atmos
 
 
Index: /palm/trunk/SOURCE/buoyancy.f90
===================================================================
--- /palm/trunk/SOURCE/buoyancy.f90	(revision 514)
+++ /palm/trunk/SOURCE/buoyancy.f90	(revision 515)
@@ -154,5 +154,8 @@
 !------------------------------------------------------------------------------!
 ! Call for grid point i,j
-!------------------------------------------------------------------------------!
+! ATTENTION: PGI-compiler creates SIGFPE if opt>1 is used! Therefore, opt=1 is
+!            forced by compiler-directive.
+!------------------------------------------------------------------------------!
+!pgi$r opt=1
     SUBROUTINE buoyancy_ij( i, j, var, var_reference, wind_component, pr )
 
