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@@ -13,14 +13,13 @@
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 <h2 style="line-height: 100%;"><font size="4">5.0 Installation of the
 model</font></h2>
-<p style="line-height: 100%;"><font color="#000000">This chapter
+<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 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><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>).
-This is already included in many Linux distributions (e.g. SuSe). The
+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>).
+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
 user needs a permit to access the PALM repository. For getting a permit
 please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>)
@@ -30,5 +29,5 @@
 installation of PALM on an IMUK Linux workstation and the IBM-Regatta
 system of
-the HLRN used as&nbsp;remote host. They are just called local and remote host from now on. </font>
+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%;">
 </p>
 <p style="line-height: 100%;">The installation process requires a valid
@@ -36,5 +35,5 @@
 &nbsp; </p>
 <ul>
-  <p style="line-height: 100%;">All hosts (local as well as remote) are
+  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
@@ -43,5 +42,5 @@
 established in both directions, from the local to the remote host as
 well as from the remote to the local host!</b> Test this by carrying
-out e.g. on the local host:</p>
+out e.g. on the local host:
   <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
 </span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp; &lt;username on remote host&gt;@&lt;remote IP-address&gt;</span><br>
@@ -52,8 +51,8 @@
 </span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp; &lt;username on local host&gt;@&lt;local IP-adddress&gt;</span><br>
   </p>
-  <p style="line-height: 100%;">In both cases you should&nbsp;not be
+  In both cases you should&nbsp;not be
 prompted for a password. <b>Before continuing the further installation
 process, this must be absolutely guaranteed!</b> This must also be
-guaranteed for <b>all</b> other remote hosts, on which PALM shall run.</p>
+guaranteed for <b>all</b> other remote hosts, on which PALM shall run.
 </ul>
 <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
@@ -77,9 +76,9 @@
 use the PALM scripts, the PATH variable has to be extended and the
 environment variable PALM_BIN has to be set (on local and remote host)
-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">$HOME/palm/current_version/trunk/SCRIPTS</font></p><p style="line-height: 100%;"><font color="#000000">You may habe to login again in order to activate these settings.</font></p><p style="line-height: 100%;"><font color="#000000">On the local and on the remote host, some small helper/utility programs have to be installed, which are e.g. later used by <span style="font-weight: bold;">mrun</span> or for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script requires a configuration file<span style="font-family: Courier New,Courier,monospace;"> .mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the following. A copy has to be put into the working directory under the name<span style="font-family: Courier New,Courier,monospace;"> .mrun.config </span>by</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">cp trunk/SCRIPTS/.mrun.config.default .mrun.config</span></font></p><p style="line-height: 100%;"><font color="#000000">Beside many other things, this file contains typical installation parameters
+in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>, if<span style="font-family: Courier New,Courier,monospace;"> ksh </span>is used):</font></p><p style="line-height: 100%; margin-left: 40px;"><font style="font-family: Courier New,Courier,monospace;" color="#000000">export PATH=$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
 like compiler name, compiler options, etc.
-for a set of different remote hosts. Please edit this file, uncomment lines like</font></p><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">
+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">
 </font>
-<p style="line-height: 100%;"><font color="#000000">To avoid the
+<br><font color="#000000">To avoid the
 re-compilation of the complete source code for each model run, PALM
 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
@@ -91,5 +90,5 @@
 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><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>.<font color="#000000"><span style="font-weight: bold;"></span></font><p style="line-height: 100%;"><font color="#000000">The
 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
 </span>will prompt some queries<font color="#000000">, which must all be
@@ -98,5 +97,5 @@
 progress at the terminal window, where also error messages
 are displayed (hopefully not for this standard installation). By just
-entering </font>
+entering </font></p><p style="line-height: 100%;">
 </p>
 <blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote>
@@ -105,5 +104,5 @@
 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>
 </p>
-<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><p style="line-height: 100%;"><font color="#000000">As a last step,
+<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,
 after the compilation has been finished, the PALM installation has to
 be verified. For this
@@ -114,5 +113,5 @@
 4.4</font></a>)<font color="#000000">. The parameter file must be
 copied from the PALM working copy by<br>
-</font></p>
+</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 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>
 <p style="line-height: 100%;"><font color="#000000">The test run can
@@ -120,5 +119,5 @@
 </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>
-<p style="line-height: 100%;"><font color="#000000">This specific run
+<font color="#000000">This specific run
 will be carried out on 8 PEs and is allowed to use up to 500 seconds
 CPU time. After pressing &lt;return&gt;, the most important settings of
@@ -130,5 +129,5 @@
 immediately and that all things work as designed, the job protocol of
 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
-file should be carefully examined for any error messages.</font>
+file should be carefully examined for any error messages.</font><p style="line-height: 100%;">
 </p>
 
@@ -146,7 +145,7 @@
 </span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/MONITORING/ibmh_example_rc</span><br>
 </p>
-<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><p style="line-height: 100%;"><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
+<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
 the file contents are identical, the installation is successfully
-completed.</font> </p>
+completed.</font>
 <p style="line-height: 100%;">If you have any problems with the PALM
 installation, the members of the PALM working group are pleased to
