Changeset 515


Ignore:
Timestamp:
Mar 18, 2010 2:30:38 AM (12 years ago)
Author:
raasch
Message:

simple installation method documented and updated; bugfix for PGI compiler in buoyancy

Location:
palm/trunk
Files:
5 edited

Legend:

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

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    910</style></head><body style="direction: ltr;" lang="en-US"><h2 style="line-height: 100%;"><font size="4">5.0
    10 Installation of the
    11 model</font></h2>
     11Code installation<br>
     12</font></h2>
    1213<font color="#000000">This chapter
    13 describes the installation of PALM on a Linux workstation (local host)
    14 and a suitable remote computer, on which the
    15 model runs are to be carried out. The local host is used to
    16 start batch jobs with <b>mrun</b> and to analyze the
    17 results
    18 which are produced by the model on the remote host and send back to the
     14describes 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;
     15The simple method cannot create batch jobs itself, and cannot be used
     16to create restart runs. Also file handling and most other features of
     17the <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>
     18<br>
     19The <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
    1920local host. Alternatively, <span style="font-weight: bold;">mrun</span>
    20 can also be used to start PALM on the local host in interactive mode or
    21 as a batch job (if a queueing system like NQS, PBS, or LoadLeveler is
    22 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
    23 installation and operation of PALM requires at mimimum (on both, the
    24 local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The Korn-shell (AT&amp;T ksh or public
    25 domain ksh) must be
    26 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
    27 NetCDF-library with version number not earlier than 3.6.0-p1 (for
     21can also be used to start PALM in interactive mode on the local host, or
     22as a batch job on the local host (if a queueing system like NQS, PBS, or LoadLeveler is
     23available).<br>
     24<br>
     25Only the <span style="font-style: italic;">advanced method</span> gives full access to all PALM features.<br>
     26<br>
     27</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
     28installation and operation of PALM requires at mimimum (for the <span style="font-style: italic;">advanced method</span> on both, the
     29local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">A Korn-shell (AT&amp;T ksh or public
     30domain ksh); must be
     31available 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
    2832NetCDF, 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
    2933least 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
     
    3741please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>)
    3842and define a username under which you like to access the repository.
    39 You will then receive a password which allows the access under this
    40 name.</font></li><li><font color="#000000">A
    41 job queueing system must be available on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle
     43You will then receive a password which allows access under this
     44name.<br>
     45    <br>
     46The <span style="font-style: italic;">advanced method</span> additionally requires:<br>
     47</font></li><li><font color="#000000">A
     48job queueing system on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle
    4249LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).</font></li><li><font color="#000000">ssh/scp-connections to and from the remote
    4350host 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
    4451to be used on a limited number of selected machines. These are SGI-ICE
    4552systems at computing center HLRN in Hannover (<span style="font-style: italic;">lcsgih</span>), Berlin (<span style="font-style: italic;">lcsgib</span>),
    46 IBM-Regatta system<span style="font-style: italic;"></span>
    47 at Yonsei University, Seoul (<span style="font-style: italic;">ibms</span>),
    48 on NEC-SX6/8 systems at DKRZ, Hamburg (<span style="font-style: italic;">nech</span>) and RIAM,
     53IBM-Regatta systems<span style="font-style: italic;"></span>
     54at 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,
    4955Kyushu University, Fukuoka (<span style="font-style: italic;">necriam</span>),
    5056as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>), Tokyo
    5157Institute of Technology (<span style="font-style: italic;">lctit</span>),
    52 and the Bergen Center for Computational Science (<span style="font-style: italic;">lcxt4</span>).
     58Kyoto 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>).
    5359The strings given in brackets are the systems names (host identifiers)
    5460under which <span style="font-weight: bold;">mrun</span>
     
    5662different hosts.<br><br>You can also use <span style="font-weight: bold;">mrun</span>/PALM on other
    5763Linux-Cluster, IBM-AIX, or NEC-SX machines. See <a href="#configuration_for_other_machines">below</a> on
    58 how to configure <span style="font-weight: bold;">mrun</span>
    59 for other machines. However, these configurations currently (version
    60 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
     64how to configure <span style="font-weight: bold;">mrun</span>for
     65other machines. However, these configurations currently (version
     663.7a) allow to run PALM in interactive mode only. Batch mode requires
     67manual adjustments for the respective queing system and MPI
     68installation 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
    6169examples given in this chapter refer to an
    62 installation of PALM on an IMUK Linux workstation and the SGI-ICE
    63 system of
    64 the HLRN used as&nbsp;remote host. They are just called local and
     70installation of PALM on an IMUK Linux workstation and (for the <span style="font-style: italic;">advanced method</span>) the SGI-ICE
     71system of HLRN, used as&nbsp;remote host. They are just referred to as local and
    6572remote host from now on. </font></p><p style="line-height: 100%;">
    6673</p><p style="line-height: 100%;">The installation
    67 process requires a valid
    68 account on the local and on the remote host as well.<br>
     74process for the <span style="font-style: italic;">advanced method</span> requires a valid
     75account on the local and on the remote host as well.</p>
     76<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>
    6977&nbsp; </p>
    70 <ul> All hosts (local as well as remote) are
     78
     79<ul>
     80 All hosts (local as well as remote) are
    7181accessed via the secure shell (ssh). The user must establish
    7282passwordless login using the private/public-key mechanism (see e.g. the
     
    8797prompted for a password. <b>Before continuing the further
    8898installation
    89 process, this must be absolutely guaranteed!</b> This must also
     99process, this must be absolutely guaranteed!</b> It must also
    90100be
    91101guaranteed for <b>all</b> other remote hosts, on which
    92102PALM shall run.<br><br>Please
    93 note that on many remote hosts, passwordless login must also be
    94 established <b>within the remote host</b>, i.e. from the
    95 remote host to itself. Test this by executing on the remote host: <span style="font-family: Courier New,Courier,monospace;">ssh
    96 &lt;remote IP-address&gt;</span>. You should not be prompted
    97 for a password.<br><br></ul><p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package
    98 Installation</span></p><p style="line-height: 100%;">In
    99 the <b>first installation step</b> a
    100 set of directories must be created both on the local and on the
    101 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
    102 are
    103 freely selectable (except <big><tt><font size="2"><big>~/job_queue</big></font></tt></big>),
    104 however new users should use them as suggested, since many
    105 examples in this documentation as well as all example files are
    106 assuming these settings. The directory <big><span style="font-family: monospace;">~/palm/current_version</span></big>
     103note that on many remote hosts, passwordless login must also work <b>within the remote host</b>, i.e. for ssh connections from the
     104remote host to itself. Test this by executing on the remote host:<br>
     105  <br>
     106  <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; ssh
     107&lt;username on remote host&gt;@&lt;remote IP-address&gt;</span>&nbsp;&nbsp;&nbsp;&nbsp; .<br>
     108  <br>
     109You should not be prompted
     110for a password.<br><br>
     111</ul>
     112<p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package
     113Installation</span></p><p style="line-height: 100%;">The <b>first installation step</b> requires creating a
     114set of directories on the local and, for the <span style="font-style: italic;">advanced method</span>, on the
     115remote 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
     116freely selected (except <big><tt><font size="2"><big>~/job_queue</big></font></tt></big>),
     117however new users should choose them as suggested, since many
     118examples 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>
    107119on the local host will be called the working directory from now on. </p>
    108120<p style="line-height: 100%;"><font color="#000000">In
    109121the <b>second
    110122step</b>
    111 a working copy of the recent version of the PALM software package,
     123a working copy of the recent PALM version,
    112124including the source code, scripts, documentation, etc.&nbsp; must
    113125be
    114126copied to the working directory (</font><font color="#000000">local
    115127host!) by executing the following
    116 commands. Replace &lt;your username&gt; by the name that you
    117 chose to
     128commands. Replace &lt;your username&gt; by the name that you have chosen to
    118129access the repository, and &lt;#&gt; by any of the available
    119130PALM
    120 releases, e.g. "<span style="font-style: italic;">3.1c</span>"
    121 (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
     131releases, e.g. "<span style="font-style: italic;">3.7a</span>"
     132(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
    122133~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn
    123134checkout --username &lt;your username&gt;
    124135svn://130.75.105.2/palm/tags/release-&lt;#&gt; trunk</span><br></div><p style="line-height: 100%;"><font color="#000000">You
    125 will then be prompted for your password. After finishing, the
    126 subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">should
    127 appear in your working directory. It contains a number of further
    128 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">)
     136will 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
     137subdirectories, which contain e.g. the PALM source code (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SOURCE</font><font color="#000000">)
    129138and 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
    130 directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span>instead
    131 of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span>.
     139directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span>(instead
     140of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span>).
    132141But keep in mind that you will have to adjust several paths given
    133142below, 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
    134 your working copy of PALM, unless you&nbsp;know exactly what you
     143your working copy of PALM, unless you&nbsp;know what you
    135144are doing.</p><p style="line-height: 100%; font-weight: bold;"><span style="font-weight: normal;">You can also get a copy of the
    136 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,
    137 this version may contain bugs and new features may not be documented. <span style="font-weight: bold;">In future PALM releases,
    138 repository access to this most recent&nbsp;version will
    139 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
     145most 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>
     146</span><br>
     147<p style="line-height: 100%;"></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Package
    140148Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To
    141149use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable
     
    172180use PALM.</font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">Warning:
    173181When editing the configuration file, please NEVER use the TAB key.
    174 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;">
     182Otherwise, 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;">
    175183trunk/SCRIPTS </span>contains additional configuration files
    176 which are already adjusted for special hosts:<span style="font-family: Courier New,Courier,monospace;">
    177 .mrun.config.imuk </span>can be used at Hannover University,<span style="font-family: Courier New,Courier,monospace;">
    178 .mrun.config.riam </span>can
    179 be used at the Research Institute of Applied Mechanics, Kyushu
    180 University. These files have to be edited in the same way as described
     184which are already adjusted for special hosts</font><font color="#000000">, e.g.</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">
     185.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
    181186above.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the
    182187respective 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
     
    184189second call also copies the PALM scripts (like <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span>) to the
    185190remote
    186 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
     191host.<br>
     192<br>
     193</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
    187194of PALM Code</span></font></p><font color="#000000">
    188195</font><br><font color="#000000">To avoid the
     
    203210files) are
    204211stored&nbsp;on the remote computer in the default directory
    205 </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
     212</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
    206213pre-compilation for the remote host (here the SGI-ICE system of HLRN)
    207214is
     
    385392execution command (which may be <span style="font-family: Courier New,Courier,monospace;">mpirun</span>
    386393or <span style="font-family: Courier New,Courier,monospace;">mpiexec</span>)
    387 may have to be adjusted manually in the mrun-script. A future version
     394may have to be adjusted manually in the <span style="font-weight: bold;">mrun</span>-script. A future version
    388395will allow to give the respective settings in the configuration file.
    389396<p style="line-height: 100%;">If you have any problems
    390397with the PALM
    391398installation, the members of the PALM working group are pleased to
    392 help you. &nbsp; </p>
    393 <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
     399help you.<br>
     400</p>
     401<p style="line-height: 100%;"><br>
     402<span style="font-weight: bold; text-decoration: underline;"><a name="simple_installation_method"></a>Simple installation method</span><br>
     403</p>
     404<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>
     405<br>
     406<span style="font-weight: bold; text-decoration: underline;">Package
     407Installation</span></p>
     408<p style="line-height: 100%;"><span style="font-weight: bold;">First step:</span> Create a directory<span style="font-style: italic;"></span>:</p>
     409<div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">mkdir -p ~/palm/current_version/</div>
     410<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>
     411
     412<p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">S</span><b>econd
     413step</b>:
     414Check 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
     415PALM
     416releases, e.g. "<span style="font-style: italic;">3.7a</span>"
     417(new releases will be announced to members of the PALM mailing list).</font></p>
     418<div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">cd
     419~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn
     420checkout --username &lt;your username&gt;
     421svn://130.75.105.2/palm/tags/release-&lt;#&gt; trunk</span><br></div>
     422<p style="line-height: 100%;"><font color="#000000">You
     423will 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
     424subdirectories, which contain e.g. the PALM source code (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SOURCE</font><font color="#000000">)
     425and 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>
     426</font></p>
     427<p style="line-height: 100%;">Please never touch any file in
     428your working copy of PALM, unless you really know what you
     429are doing.</p>
     430<br>
     431
     432<p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Configuration and compilation<br>
     433</span></font></p>
     434<p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">Third step:</span> To
     435use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable
     436has to be extended and the
     437environment variable<span style="font-family: Courier New,Courier,monospace;">
     438PALM_BIN </span>has to be set. For convenience, setting should be done
     439in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>,
     440if<span style="font-family: Courier New,Courier,monospace;">
     441ksh </span>is used):</font></p>
     442<p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">export
     443PALM_BIN=</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">$HOME/palm/current_version/trunk/SCRIPTS<br>
     444</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">export
     445PATH=$PALM_BIN:$PATH</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"><br>
     446</span></font></p>
     447<p style="line-height: 100%;"><font color="#000000">You
     448may have to login again in order to activate the profile settings.<br>
     449</font></p>
     450<p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">Fourth step:</span> Call the installation script:<br>
     451</font></p>
     452<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>
     453</span></font></p>
     454
     455<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>
     456to be used for compiling the code in the next step. The include file
     457contains compiler name, compiler options, library path for NetCDF, etc.
     458<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>
     459are for the Intel-FORTRAN compiler in the IMUK environment. You may
     460find 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>
     461</font></p>
     462<p style="line-height: 100%; margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">cd MAKE_DEPOSITORY_simple<br>
     463</span><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">make<br>
     464cd ..<br>
     465</span></font></p>
     466
     467
     468<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>
     469<br>
     470<span style="font-weight: bold;">Fifth step:</span> Carry out a test
     471run in order to check the installation. The test run (as every PALM
     472run) requires a parameter file for steering PALM, which is in
     473FORTRAN-NAMELIST format. This file has been already generated by the
     474installation 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>.
     475Default settings in this script are for the SGI-mpt-library installed
     476on HLRN. You will find the execution command almost at the end of this
     477script. After having adjusted the MPI-execution command, start the run
     478with:<br>
     479</p>
     480<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>
     481</span></font></p>
     482
     483
     484
     485<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>
     486After 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>.
     487The directory name is composed of the parameter file name, the number
     488of cores that have been used, and the current data and time. For every
     489run a unique directory is created.<br>
     490</p>
     491<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>
     492<span style="font-weight: bold;"></span></p>
     493<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>
     494</span></font></p>
     495
     496
     497
     498
     499<span style="font-weight: bold;">You should not find any
     500difference between these two files</span>, except of the run date
     501and time displayed at the top of the file header, and, maybe, the number of cores that have been used. <font color="#000000">If
     502the file contents are identical, the installation is successfully
     503completed.</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
    394504change:&nbsp;</i> $Id: chapter_5.0.html 287 2009-04-09
    39550508:59:36Z raasch $</p>
  • palm/trunk/INSTALL/MAKE.inc.ifort.imuk

    r421 r515  
    1 # contents of this file are include in palm's makefile if the simple install
     1# Contents of this file are included in palm's makefile if the simple install
    22# process (palm_simple_install) is used.
    3 # Please adjust compiling parameters as required for your system
     3# Please adjust compiling parameters as required for your system.
    44
    55PROG=palm
    66F90=mpif90
    7 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
    8 F90FLAGS= -axW -openmp -r8 -nbs -convert little_endian -I /muksoft_64/packages/netcdf/3.6.3/include
    9 LDFLAGS= -axW -openmp -r8 -nbs -Vaxlib -L/muksoft_64/packages/netcdf/3.6.3/lib -lnetcdf
     7COPT= -cpp -DMPI_REAL=MPI_DOUBLE_PRECISION -DMPI_2REAL=MPI_2DOUBLE_PRECISION -D__netcdf -D__lc -D__parallel
     8F90FLAGS= -axW -O3 -r8 -nbs -convert little_endian -I /muksoft_64/packages/netcdf/3.6.3/include
     9LDFLAGS= -axW -O3 -r8 -nbs -Vaxlib -L/muksoft_64/packages/netcdf/3.6.3/lib -lnetcdf
  • palm/trunk/SCRIPTS/palm_simple_install

    r421 r515  
    1414     # Last changes:
    1515     # 25/01/10 - Siggi - Generating the first version
     16     # 18/03/10 - Siggi - switch to palm/current_version removed: working
     17     #                    copy can be in any directory
    1618
    1719
     
    3133 done
    3234
    33 
    34 
    35     # Switch to default working directory
    36  cd  ~/palm/current_version
    3735
    3836
  • palm/trunk/SCRIPTS/palm_simple_run

    r426 r515  
    99     # It requires that palm has been installed with command
    1010     # palm_simple_install and that the executable palm has been created
    11      # with make in directory ~/palm/current_version/MAKE_DEPOSITORY_simple
     11     # with make in directory  ...../MAKE_DEPOSITORY_simple
    1212
    1313     # Last changes:
    1414     # 25/01/10 - Siggi - Generating the first version
     15     # 18/03/10 - Siggi - Some comments changed
    1516
    1617
     
    2324 mpi_procs_per_node=1
    2425 openmp_threads=1
    25  # palm_dir=~/palm/current_version/
    2626
    2727 typeset -i  ii
     
    5151    # Generate unique directory/files for this run
    5252 timedate="`date +%d.%b_%H:%M:%S`"
    53  suffix=$case+$nnodes+$timedate
     53 suffix=$case+$mpi_procs+$timedate
    5454 RUNDIR=OUTPUT.$suffix/
    5555
     
    125125 echo "*** palm will be run:  MPI tasks: $mpi_procs   OpenMP thread: $OMP_NUM_THREADS"
    126126
    127 # mpiexec  -machinefile hostfile  -n $mpi_procs  ./palm  < runfile_atmos
    128  mpiexec_mpt  -np $mpi_procs  ./palm  < runfile_atmos
     127# IMUK:
     128 mpiexec  -machinefile hostfile  -n $mpi_procs  ./palm  < runfile_atmos
     129
     130# SGI-MPT HLRN
     131# mpiexec_mpt  -np $mpi_procs  ./palm  < runfile_atmos
    129132
    130133
  • palm/trunk/SOURCE/buoyancy.f90

    r392 r515  
    154154!------------------------------------------------------------------------------!
    155155! Call for grid point i,j
    156 !------------------------------------------------------------------------------!
     156! ATTENTION: PGI-compiler creates SIGFPE if opt>1 is used! Therefore, opt=1 is
     157!            forced by compiler-directive.
     158!------------------------------------------------------------------------------!
     159!pgi$r opt=1
    157160    SUBROUTINE buoyancy_ij( i, j, var, var_reference, wind_component, pr )
    158161
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