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Changeset 41 for palm/trunk/DOC


Ignore:
Timestamp:
Mar 2, 2007 7:25:57 AM (18 years ago)
Author:
raasch
Message:

small changes to documentation

Location:
palm/trunk/DOC
Files:
2 edited

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Removed

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

    r40 r41  
    1313        -->
    1414        </style></head>
    15 
    1615<body dir="ltr" lang="en-US">
    1716<h2 style="line-height: 100%;"><font size="4">5.0 Installation of the
    1817model</font></h2>
    19 <p style="line-height: 100%;"><font color="#000000">This chapter
     18<font color="#000000">This chapter
    2019describes the installation of PALM on a Linux workstation (local host) and a suitable remote computer, on which the
    2120model runs are to be carried out. The local host is used to
    2221start batch jobs with <b>mrun</b> and to analyze the results
    23 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>).
    24 This is already included in many Linux distributions (e.g. SuSe). The
     22which 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>).
     23This 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
    2524user needs a permit to access the PALM repository. For getting a permit
    2625please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>)
    … …  
    3029installation of PALM on an IMUK Linux workstation and the IBM-Regatta
    3130system of
    32 the HLRN used as&nbsp;remote host. They are just called local and remote host from now on. </font>
     31the HLRN used as&nbsp;remote host. They are just called local and remote host from now on. </font></p><p style="line-height: 100%;">
    3332</p>
    3433<p style="line-height: 100%;">The installation process requires a valid
    … …  
    3635&nbsp; </p>
    3736<ul>
    38   <p style="line-height: 100%;">All hosts (local as well as remote) are
     37  All hosts (local as well as remote) are
    3938accessed via the secure shell (ssh). The user must establish
    4039passwordless login using the private/public-key mechanism (see e.g. the
    … …  
    4342established in both directions, from the local to the remote host as
    4443well as from the remote to the local host!</b> Test this by carrying
    45 out e.g. on the local host:</p>
     44out e.g. on the local host:
    4645  <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
    4746</span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp; &lt;username on remote host&gt;@&lt;remote IP-address&gt;</span><br>
    … …  
    5251</span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp; &lt;username on local host&gt;@&lt;local IP-adddress&gt;</span><br>
    5352  </p>
    54   <p style="line-height: 100%;">In both cases you should&nbsp;not be
     53  In both cases you should&nbsp;not be
    5554prompted for a password. <b>Before continuing the further installation
    5655process, this must be absolutely guaranteed!</b> This must also be
    57 guaranteed for <b>all</b> other remote hosts, on which PALM shall run.</p>
     56guaranteed for <b>all</b> other remote hosts, on which PALM shall run.
    5857</ul>
    5958<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
    … …  
    7776use the PALM scripts, the PATH variable has to be extended and the
    7877environment variable PALM_BIN has to be set (on local and remote host)
    79 in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>, if<span style="font-family: Courier New,Courier,monospace;"> ksh </span>is used):</font></p><p style="line-height: 100%; margin-left: 40px;"><font style="font-family: Courier New,Courier,monospace;" color="#000000">export PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH</font><font color="#000000"><br><span style="font-family: Courier New,Courier,monospace;">export PALM_BIN=</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">$HOME/palm/current_version/trunk/SCRIPTS</font></p><p style="line-height: 100%;"><font color="#000000">You may habe to login again in order to activate these settings.</font></p><p style="line-height: 100%;"><font color="#000000">On the local and on the remote host, some small helper/utility programs have to be installed, which are e.g. later used by <span style="font-weight: bold;">mrun</span> or for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script requires a configuration file<span style="font-family: Courier New,Courier,monospace;"> .mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the following. A copy has to be put into the working directory under the name<span style="font-family: Courier New,Courier,monospace;"> .mrun.config </span>by</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">cp trunk/SCRIPTS/.mrun.config.default .mrun.config</span></font></p><p style="line-height: 100%;"><font color="#000000">Beside many other things, this file contains typical installation parameters
     78in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>, if<span style="font-family: Courier New,Courier,monospace;"> ksh </span>is used):</font></p><p style="line-height: 100%; margin-left: 40px;"><font style="font-family: Courier New,Courier,monospace;" color="#000000">export PATH=$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
    8079like compiler name, compiler options, etc.
    81 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">
     80for 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">
    8281</font>
    83 <p style="line-height: 100%;"><font color="#000000">To avoid the
     82<br><font color="#000000">To avoid the
    8483re-compilation of the complete source code for each model run, PALM
    8584willl 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
    … …  
    9190files) are
    9291stored&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
     92</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
    9493pre-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
    9594</span>will prompt some queries<font color="#000000">, which must all be
    … …  
    9897progress at the terminal window, where also error messages
    9998are displayed (hopefully not for this standard installation). By just
    100 entering </font>
     99entering </font></p><p style="line-height: 100%;">
    101100</p>
    102101<blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote>
    … …  
    105104the 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>
    106105</p>
    107 <p style="line-height: 100%;"><font color="#000000"></font></p><p style="line-height: 100%; font-weight: bold; text-decoration: underline;"><font color="#000000">Installation Verification</font></p><p style="line-height: 100%;"><font color="#000000">As a last step,
     106<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,
    108107after the compilation has been finished, the PALM installation has to
    109108be verified. For this
    … …  
    1141134.4</font></a>)<font color="#000000">. The parameter file must be
    115114copied from the PALM working copy by<br>
    116 </font></p>
     115</font>
    117116<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>
    118117<p style="line-height: 100%;"><font color="#000000">The test run can
    … …  
    120119</p>
    121120<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>
    122 <p style="line-height: 100%;"><font color="#000000">This specific run
     121<font color="#000000">This specific run
    123122will be carried out on 8 PEs and is allowed to use up to 500 seconds
    124123CPU time. After pressing &lt;return&gt;, the most important settings of
    … …  
    130129immediately and that all things work as designed, the job protocol of
    131130this 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
    132 file should be carefully examined for any error messages.</font>
     131file should be carefully examined for any error messages.</font><p style="line-height: 100%;">
    133132</p>
    134133
    … …  
    146145</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/MONITORING/ibmh_example_rc</span><br>
    147146</p>
    148 <p style="line-height: 100%;">with those of the example result file which can be found under<span style="font-family: Courier New,Courier,monospace;"> trunk/INSTALL/example_rc</span>., e.g. by using the<span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;"> standard</span> diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff &nbsp;JOBS/example/MONITORING/ibmh_example_rc trunk/INSTALL/example_rc</p><p style="line-height: 100%;">where it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;"> ~/palm/current_version</span>.</p><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
     147<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
    149148the file contents are identical, the installation is successfully
    150 completed.</font> </p>
     149completed.</font>
    151150<p style="line-height: 100%;">If you have any problems with the PALM
    152151installation, the members of the PALM working group are pleased to

  • palm/trunk/DOC/tec/technical_documentation.html

    r40 r41  
    43294329
    43304330The content of the testresult-file (run control output) has changed
    4331 due to this modification.<br><br>Output of xz and yz cross sections now up to gridpoint nzt+1.<br><br>Default settings of particle start positions changed.</td><td style="vertical-align: top;">check_open, close_file, data_output_2d, init_particles, netcdf, time_integration</td></tr><tr><td style="vertical-align: top;">&nbsp;</td><td style="vertical-align: top;">&nbsp;</td><td style="vertical-align: top;">&nbsp;</td><td style="vertical-align: top;">E</td><td style="vertical-align: top;">Initialisation of all tendency arrays (t.._m) needed for the Runge-Kutta schemes.<br><br>Bugfix in index array initialization for line- or point-like topography structures.<br><br>Bugfix: yv coordinates are now used for yz cross sections, where neccessary.</td><td style="vertical-align: top;">init_3d_model, init_grid, netcdf</td></tr><tr><td style="vertical-align: top;">12/02/07</td><td style="vertical-align: top;">SR</td><td style="vertical-align: top;">3.1b</td><td style="vertical-align: top;">&nbsp;N</td><td style="vertical-align: top;"><span style="font-weight: bold;">Attention:</span><br>This is the last revision before switching to the subversion revison control system!<br><br>Informative output to the job protocoll in case of restarts.</td><td style="vertical-align: top;">check_for_restart</td></tr><tr><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td style="vertical-align: top;">C</td><td style="vertical-align: top;">Values of environment variables are now read from local file <span style="font-family: monospace;">ENVPAR</span> instead of getting them by a system call.<br><br>For interpolation in <span style="font-family: monospace;">advec_particles</span>, allways level k is used.</td><td style="vertical-align: top;">advec_particles, local_tremain_ini, parin</td></tr><tr><td></td><td></td><td></td><td style="vertical-align: top;">E</td><td style="vertical-align: top;">Several bugfixes in <span style="font-family: monospace;">advec_particles</span>: new particles are released only if <span style="font-family: monospace;">end_time_prel</span> &gt; <span style="font-family: monospace;">simulated_time</span>,&nbsp;transfer
     4331due to this modification.<br><br>Output of xz and yz cross sections now up to gridpoint nzt+1.<br><br>Default settings of particle start positions changed.</td><td style="vertical-align: top;">check_open, close_file, data_output_2d, init_particles, netcdf, time_integration</td></tr><tr><td style="vertical-align: top;">&nbsp;</td><td style="vertical-align: top;">&nbsp;</td><td style="vertical-align: top;">&nbsp;</td><td style="vertical-align: top;">E</td><td style="vertical-align: top;">Initialisation of all tendency arrays (t.._m) needed for the Runge-Kutta schemes.<br><br>Bugfix in index array initialization for line- or point-like topography structures.<br><br>Bugfix: yv coordinates are now used for yz cross sections, where neccessary.</td><td style="vertical-align: top;">init_3d_model, init_grid, netcdf</td></tr><tr><td style="vertical-align: top;">12/02/07</td><td style="vertical-align: top;">SR</td><td style="vertical-align: top;">3.1b</td><td style="vertical-align: top;">&nbsp;N</td><td style="vertical-align: top;"><span style="font-weight: bold;">Attention:</span><br>This is the last revision before switching to the subversion revison control system!<br><br>Informative output to the job protocoll in case of restarts.</td><td style="vertical-align: top;">check_for_restart</td></tr><tr><td>&nbsp;&nbsp;</td><td>&nbsp;&nbsp;</td><td>&nbsp;&nbsp;</td><td style="vertical-align: top;">C</td><td style="vertical-align: top;">Values of environment variables are now read from local file <span style="font-family: monospace;">ENVPAR</span> instead of getting them by a system call.<br><br>For interpolation in <span style="font-family: monospace;">advec_particles</span>, allways level k is used.</td><td style="vertical-align: top;">advec_particles, local_tremain_ini, parin</td></tr><tr><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td style="vertical-align: top;">E</td><td style="vertical-align: top;">Several bugfixes in <span style="font-family: monospace;">advec_particles</span>: new particles are released only if <span style="font-family: monospace;">end_time_prel</span> &gt; <span style="font-family: monospace;">simulated_time</span>,&nbsp;transfer
    43324332of particles when x &lt; -0.5*dx (0.0 before), etc., index i,j used
    43334333instead of cartesian (x,y) coordinate to check for transfer because
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