Mar 2, 2007 6:32:25 AM (17 years ago)

documentation update for the new svn-based version and for 3.1c, update of .mrun.config.default, -u in mbuild only compiles scripts

1 edited


  • palm/trunk/DOC/app/chapter_5.0.html

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    1917<h2 style="line-height: 100%;"><font size="4">5.0 Installation of the
    2119<p style="line-height: 100%;"><font color="#000000">This chapter
    22 describes the installation of PALM on the Linux workstation
    23 cluster of IMUK and a suitable remote computer (host), on which the
    24 model runs are actually carried out. The local cluster is used to
    25 start the batch job with <b>mrun</b> and to analyze the results
    26 produced by the model. In batch mode, runs can be carried on the
    27 IBM-Regatta
    28 system of the HLRN, on an IBM-Regatta at KISTI, Korea </font><font
    29  color="#000000">(via a local
    30 DEC-Alpha-workstation at the Department of Atmospheric Sciences of the
    31 Yonsei University, Seoul)</font><font color="#000000">, and on an
    32 NEC-SX6 at DKRZ. The examples given in this chapter refer to an
    33 installation of PALM on the IMUK cluster, considering the IBM-Regatta
     20describes the installation of PALM on a Linux workstation (local host) and a suitable remote computer, on which the
     21model runs are to be carried out. The local host is used to
     22start batch jobs with <b>mrun</b> and to analyze the results
     23which 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>).
     24This is already included in many Linux distributions (e.g. SuSe). The
     25user needs a permit to access the PALM repository. For getting a permit
     26please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>)
     27and define a username under which you like to access the repository.
     28You will then receive a password which allows the access under this
     29name.</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
     30installation of PALM on an IMUK Linux workstation and the IBM-Regatta
    3431system of
    35 the HLRN as the remote computer. </font>
     32the HLRN used as&nbsp;remote host. They are just called local and remote host from now on. </font>
    3734<p style="line-height: 100%;">The installation process requires a valid
    38 account on the IMUK cluster and on the remote host as well. In the
    39 following the IMUK workstation is called the “local host”. <br>
     35account on the local and on the remote host as well.<br>
    4036&nbsp; </p>
    4945out e.g. on the local host:</p>
    5046  <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
    51 ssh&nbsp; &lt;username on remote host&gt;@&lt;remote IP-address&gt;</span><br>
     47</span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp; &lt;username on remote host&gt;@&lt;remote IP-address&gt;</span><br>
    5248  </p>
    5349  <p style="line-height: 100%;">and on the remote host:<br>
    5450  </p>
    5551  <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
    56 ssh&nbsp; &lt;username on local host&gt;@&lt;local IP-adddress&gt;</span><br>
     52</span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp; &lt;username on local host&gt;@&lt;local IP-adddress&gt;</span><br>
    5753  </p>
    58   <p style="line-height: 100%;">In both cases you should nnot be
     54  <p style="line-height: 100%;">In both cases you should&nbsp;not be
    5955prompted for a password. <b>Before continuing the further installation
    6056process, this must be absolutely guaranteed!</b> This must also be
    6157guaranteed for <b>all</b> other remote hosts, on which PALM shall run.</p>
    63 <p style="line-height: 100%;">In the <b>first installation step</b> a
     59<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
    6460set of directories must be created both on the local and on the
    65 remote host. These directories are: </p>
    66 <ul>
    67   <pre style="line-height: 100%;"><font size="2">~/job_queue</font><br><font
    68  size="2">~/palm</font><br><font size="2">~/palm/current_version</font><br><font
    69  size="2">~/palm/current_version/SOURCE</font><br><font size="2">~/palm/current_version/JOBS</font></pre>
    70 </ul>
    71 <p style="line-height: 100%;">The names of these directories are
     61remote 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
    7262freely selectable (except <tt><font size="2">~/job_queue</font></tt>),
    7363however new users should use them as suggested, since many
    7464examples in this documentation as well as all example files are
    75 assuming these settings. </p>
     65assuming 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>
    7666<p style="line-height: 100%;"><font color="#000000">In the <b>second
    77 step</b> the PALM source code must be copied into directory </font><tt><font
    78  size="2"><font color="#000000">~/palm/current_version/SOURCE</font></font></tt><font
    79  color="#000000"> on the local host by carrying out the following
    80 commands: </font>
    81 </p>
    82 <ul>
    83   <pre style="line-height: 100%;"><font color="#000000">cd ~/palm/current_version/SOURCE</font><br><font
    84  color="#000000">ln -s /home/raasch/public_html/PALM_group/INSTALL/RCS .</font><br><font
    85  color="#000000">cp RCS/*,v .</font><br><font color="#000000">co *,v</font><br><font
    86  color="#000000">rm -rf *,v</font></pre>
    87 </ul>
    88 <p style="line-height: 100%;"><font color="#000000">Afterwards, the
    89 directory</font><font color="#000000"> </font><tt><font size="2"><font
    90  color="#000000">~/palm/current_version/SOURCE</font></font></tt><font
    91  color="#000000">
    92 should contain</font><font color="#000000"> all PALM routines as well
    93 as a file with the name </font><tt><font size="2"><font color="#000000">Makefile</font></font></tt><font
    94  color="#000000">. </font><font color="#000000">All files are
    95 write-protected, the source code files end on “</font><tt><font
    96  style="font-size: 11pt;" size="2"><font color="#000000">.f90</font></font></tt><font
    97  color="#000000">”.
    98 The user should never modify these files without further knowledge of
    99 the PALM code. </font>
    100 </p>
     68a working copy of the recent version of the PALM software package,
     69including the source code, scripts, documentation, etc.&nbsp; must be
     70copied to the working directory (</font><font color="#000000">local host!) by executing the following
     71commands. Replace &lt;your username&gt; by the name that you choosed to access the repository.</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://</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
     72appear in your working directory. It contains a number of further
     73subdirectories 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:// 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;">In future PALM releases, repository access to the most recent PALM version will
     74probably be restricted because this is a test version. However, access
     75to the last (and earlier) stable version(s) will still be possible with
     76(e.g.)</p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username &lt;your username&gt; svn:// trunk</pre><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
     77use the PALM scripts, the PATH variable has to be extended and the
     78environment variable PALM_BIN has to be set (on local and remote host)
     79in 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
     80like compiler name, compiler options, etc.
     81for 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">
    10183<p style="line-height: 100%;"><font color="#000000">To avoid the
    10284re-compilation of the complete source code for each model run, PALM
    103 willl be pre-compiled once on the remote host. Due to the use of
     85willl 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
    10486FORTRAN modules in the source code, the subroutines must be compiled
    105 in a certain sequence. Therefore the so-called <i>make</i> mechanism
     87in a certain order. Therefore the so-called <i>make</i> mechanism
    10688is used (see the respective man-page of the Unix operating system),
    107 requiring the file </font><tt><font color="#000000">Makefile</font></tt><font
    108  color="#000000">,
    109 in which the dependencies are described. The compiled sources (object
     89requiring 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">,
     90in 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
    11091files) are
    111 stored on the remote computer in the directory
    112 </font><tt><font color="#000000">~/palm/current_version/SOURCE/MAKE_DEPOSITORY</font></tt><font
    113  color="#000000">.<br>
    114 &nbsp;<br>
    115 For pre-compilation the user has to</font> call <font color="#000000">the
    116 command <b>mbuild</b>, which requires some pre-settings. The path
    117 variable must be extended on <b>both</b> computers, so that the
    118 commands <b>mbuild</b> and <b>mrun</b> as well as further routines
    119 needed by <span style="font-weight: bold;">mrun</span> can be found.
    120 This is achieved on the local computer via:: </font>
    121 </p>
    122 <ul>
    123   <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
    124  color="#000000">PATH=$PATH:/home/raasch/pub,</font></pre>
    125 </ul>
    126 <p style="line-height: 100%;"><font color="#000000">and on the IBM
    127 Regatta
    128 system of the HLRN via</font></p>
    129 <ul>
    130   <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
    131  color="#000000">PATH=$PATH:/home/h/niksiraa/pub.</font></pre>
    132 </ul>
    133 <p style="line-height: 100%;"><font color="#000000">These path
    134 extensions must be automatically set in the profiles of the local and
    135 remote host (file "~/.myprofile" at IMUK, file "~/.profile" at HLRN)</font><font
    136  color="#000000">.
    137 </font></p>
    138 <p style="line-height: 100%;"><font color="#000000">It is now assumed
    139 that the working directory is
    140 </font><tt><font color="#000000">~/palm/current_version/SOURCE</font></tt><font
    141  color="#000000">
    142 on the local host. Compilation of the PALM code via <b>mbuild </b>needs
    143 a </font><a
    144  href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/.mrun.config"><font
    145  color="#000080">configuration
    146 file</font></a><font color="#000080">,</font><font color="#000000">
    147 which must be copied to the working directory under name
    148 </font><tt><font color="#000000">.mrun.config</font></tt><font
    149  color="#000000">
    150 (please click on the link with &lt;SHIFT&gt; + left mouse button)</font><font
    151  color="#000000">. This file contains typical installation parameters
    152 like compiler name, compiler options, etc.
    153 for a set of different remote hosts. This file is also needed later on
    154 for starting the model runs. </font>
    155 </p>
    156 <p style="line-height: 100%;"><font color="#000000">In the
    157 configuration file </font><tt><font color="#000000">.mrun.config</font></tt><font
    158  color="#000000">
    159 the user name on the respective remote host must be entered. In lines
    160 like</font>
    161 </p>
    162 <ul>
    163   <p style="line-height: 100%;"><tt><font color="#000000">%
    164 remote_username &lt;username&gt; &lt;remote-computer-shortcut&gt;</font></tt></p>
    165 </ul>
    166 the string "<span style="font-family: monospace;">&lt;username&gt;</span>"
    167 has to be replaced by the actual name of the user on the respective
    168 remote host (e.g. "nik....." on HLRN).<font color="#000000">
    169 </font>
    170 <p style="line-height: 100%;"><font color="#000000">After this, the
    171 pre-compilation for the IBM-Regatta of HLRN can be started by entering</font><font
    172  color="#000000"> </font>
    173 </p>
    174 <ul>
    175   <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
    176  color="#000000">mbuild - h ibmh  .</font></pre>
    177 </ul>
    178 <p style="line-height: 100%;"><span style="font-family: monospace;">mbuild</span>
    179 will prompt some queries<font color="#000000">, which must all be
    180 answered "y" by the user. The compiling process </font><font
    181  color="#000000">will take some time. </font><font color="#000000"><span
    182  style="font-family: monospace;">mbuild</span></font><font
    183  color="#000000"> transfers the respective compiler calls to the remote
     92stored&nbsp;on the remote computer in the default directory
     93</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
     94pre-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
     96answered "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
    18497host where they are carried out interactively. You can follow the
    18598progress at the terminal window, where also error messages
    187100entering </font>
    189 <blockquote style="line-height: 100%;"><tt><font color="#000000">mbuild</font></tt></blockquote>
     102<blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote>
    190103<p style="line-height: 100%;"><font color="#000000">PALM will
    191104be (consecutively) pre-compiled for all remote hosts listed in
    192 the configuration file. </font>
     105the 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>
    194 <p style="line-height: 100%;"><font color="#000000">As a last step,
     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><p style="line-height: 100%;"><font color="#000000">As a last step,
    195108after the compilation has been finished, the PALM installation has to
    196109be verified. For this
    197110purpose a simple test run is carried out. This once again requires the <b>mrun
    198 </b>configuration file (described in </font><a href="chapter_3.2.html"><font
    199  color="#000080">chapter
    200 3.2</font></a><font color="#000000">), as well as the </font><a
    201  href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d"><font
    202  color="#000080">parameter
    203 file</font></a><font color="#000000"> (described in </font><a
    204  href="chapter_4.4.html"><font color="#000080">chapter
    205 4.4</font></a>)<font color="#000000">. The parameter file must be&nbsp;
    206 copied to<br>
     111</b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter
     1123.2</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
     113file</font></a><font color="#000000"> (described in </font><a href="chapter_4.4.html"><font color="#000080">chapter
     1144.4</font></a>)<font color="#000000">. The parameter file must be
     115copied from the PALM working copy by<br>
    208 <p style="line-height: 100%;"><tt><font color="#000000">&nbsp;&nbsp;&nbsp;
    209 ~/palm/current_version/JOBS/example/INPUT/example_p3d</font></tt><font
    210  color="#000000">&nbsp;&nbsp; .
    211 </font></p>
     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>
    212118<p style="line-height: 100%;"><font color="#000000">The test run can
    213 now be started by entering the command: </font>
     119now be started by executing the command </font>
    215 <pre
    216  style="margin-left: 1cm; margin-right: 1cm; margin-bottom: 0.5cm; line-height: 100%;"><font
    217  color="#000000">mrun -d example -h ibmh -K parallel -X 8 -T 8 -t 500 -q cdev -r “d3# pr#”</font></pre>
     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>
    218122<p style="line-height: 100%;"><font color="#000000">This specific run
    219123will be carried out on 8 PEs and is allowed to use up to 500 seconds
    220124CPU time. After pressing &lt;return&gt;, the most important settings of
    221125the job are displayed at the terminal window
    222 and the user is prompted for o.k. (“</font><tt><font color="#000000">y</font></tt><font
    223  color="#000000">”).
    224 Afterwards a message of the queuing system like “<i>Request</i>
    226 <i>Submitted to queue
    227  by
    228 ” </i>should be displayed. Now the job is
    229 queued either started immediately or at a later time, depending on the
     126and 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
     128queued and either started immediately or at a later time, depending on the
    230129current workload of the remote host. Provided that it is executed
    231130immediately and that all things work as designed, the job protocol of
    232 this run will appear under the file name </font><tt><font
    233  color="#000000">~/job_queue/ibmh_example</font></tt><font
    234  color="#000000"> no more than 3 minutes later. The content of this
     131this 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
    235132file should be carefully examined for any error messages.</font>
    237136<p style="line-height: 100%;">Beside the job protocol and according to
    238137the configuration file and arguments given for <b>mrun</b>
    239 options <tt>-d</tt> and <tt>-r,</tt>further files should be found in
     138options<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
    241 directories<br>
    242 </p>
    243 <p style="line-height: 100%; font-family: monospace;">&nbsp;&nbsp;&nbsp;
    244 ~/palm/current_version/JOBS/example/MONITORING
    245 <br>
    246 </p>
    247 <p style="line-height: 100%;">and</p>
     140directories</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>
    248141<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
    249 ~/palm/current_version/JOBS/example/OUTPUT&nbsp; .
    250 </span><br>
     142</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/OUTPUT</span><span style="font-family: monospace;"></span><br>
    252144<p style="line-height: 100%;">Please compare the contents of file</p>
    253145<p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
    254 ~/palm/current_version/JOBS/example/MONITORING/ibmh_example_rc</span><br>
     146</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/MONITORING/ibmh_example_rc</span><br>
    256 <p style="line-height: 100%;">with those of the <a
    257  href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_rc">result
    258 example file</a> (e.g. with the help of the UNIX-command <span
    259  style="font-family: monospace;">diff</span>). There should be not a
    260 single difference between these two files. <font color="#000000">If
     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><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
    261149the file contents are identical, the installation is successfully
    262150completed.</font> </p>
    265153help you. &nbsp; </p>
    267 <p style="line-height: 100%;"><font color="#000080"><font
    268  color="#000080"><a href="chapter_4.6.html"><font color="#000080"><img
    269  src="left.gif" name="Grafik1" align="bottom" border="2" height="32"
    270  width="32"></font></a><a href="Inhaltsverzeichnis.html"><font
    271  color="#000080"><img src="up.gif" name="Grafik2" align="bottom"
    272  border="2" height="32" width="32"></font></a><a href="chapter_5.1.html"><font
    273  color="#000080"><img src="right.gif" name="Grafik3" align="bottom"
    274  border="2" height="32" width="32"></font></a></font></font></p>
    275 <p style="line-height: 100%;"><i>Last change:&nbsp;</i> 20/04/05 (SR) </p>
    276 </body>
    277 </html>
     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>
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