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| 3 | <meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM |
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| 4 | chapter 5.0</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Siegfried Raasch"> <meta name="CREATED" content="20041103;12380720"> <meta name="CHANGED" content="20041123;15532356"> <meta name="KEYWORDS" content="parallel LES model"> <style> |
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| 9 | <body style="direction: ltr;" lang="en-US"><h2 style="line-height: 100%;"><font size="4">5.0 |
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| 10 | Installation of the |
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| 11 | model</font></h2> |
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| 12 | <font color="#000000">This chapter |
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| 13 | describes the installation of PALM on a Linux workstation (local host) |
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| 14 | and a suitable remote computer, on which the |
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| 15 | model runs are to be carried out. The local host is used to |
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| 16 | start batch jobs with <b>mrun</b> and to analyze the |
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| 17 | results |
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| 18 | which are produced by the model on the remote host and send back to the |
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| 19 | local host. Alternatively, <span style="font-weight: bold;">mrun</span> |
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| 20 | can also be used to start PALM on the local host in interactive mode or |
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| 21 | as a batch job (if a queueing system like NQS, PBS, or LoadLeveler is |
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| 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 |
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| 23 | installation and operation of PALM requires at mimimum (on both, the |
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| 24 | local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The Korn-shell (AT&T ksh or public |
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| 25 | domain ksh) must be |
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| 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 |
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| 27 | NetCDF-library with version number not earlier than 3.6.0-p1 (for |
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| 28 | 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 |
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| 29 | 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 |
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| 30 | system <span style="font-weight: bold;">subversion</span> |
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| 31 | (see <a href="http://subversion.tigris.org/">subversion.tigris.org</a>). |
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| 32 | This is already included in many Linux distributions (e.g. SuSe). <span style="font-weight: bold;">subversion requires port 3690 to |
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| 33 | be open for tcp/udp.</span> <span style="font-weight: bold;">If |
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| 34 | there are firewall restrictions concerning this port, the PALM code |
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| 35 | cannot be accessed.</span> The |
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| 36 | user needs a permit to access the PALM repository. For getting a permit |
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| 37 | please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>) |
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| 38 | and define a username under which you like to access the repository. |
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| 39 | You will then receive a password which allows the access under this |
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| 40 | name.</font></li><li><font color="#000000">A |
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| 41 | job queueing system must be available on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle |
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| 42 | LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).</font></li><li><font color="#000000">ssh/scp-connections to and from the remote |
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| 43 | 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 |
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| 44 | to be used on a limited number of selected machines. These are SGI-ICE |
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| 45 | systems at computing center HLRN in Hannover (<span style="font-style: italic;">lcsgih</span>), Berlin (<span style="font-style: italic;">lcsgib</span>), |
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| 46 | IBM-Regatta system<span style="font-style: italic;"></span> |
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| 47 | at Yonsei University, Seoul (<span style="font-style: italic;">ibms</span>), |
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| 48 | on NEC-SX6/8 systems at DKRZ, Hamburg (<span style="font-style: italic;">nech</span>) and RIAM, |
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| 49 | Kyushu University, Fukuoka (<span style="font-style: italic;">necriam</span>), |
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| 50 | as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>), Tokyo |
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| 51 | Institute of Technology (<span style="font-style: italic;">lctit</span>), |
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| 52 | and the Bergen Center for Computational Science (<span style="font-style: italic;">lcxt4</span>). |
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| 53 | The strings given in brackets are the systems names (host identifiers) |
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| 54 | under which <span style="font-weight: bold;">mrun</span> |
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| 55 | identifies the |
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| 56 | different hosts.<br><br>You can also use <span style="font-weight: bold;">mrun</span>/PALM on other |
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| 57 | Linux-Cluster, IBM-AIX, or NEC-SX machines. See <a href="#configuration_for_other_machines">below</a> on |
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| 58 | how to configure <span style="font-weight: bold;">mrun</span> |
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| 59 | for other machines. However, these configurations currently (version |
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| 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 |
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| 61 | examples given in this chapter refer to an |
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| 62 | installation of PALM on an IMUK Linux workstation and the SGI-ICE |
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| 63 | system of |
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| 64 | the HLRN used as remote host. They are just called local and |
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| 65 | remote host from now on. </font></p><p style="line-height: 100%;"> |
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| 66 | </p><p style="line-height: 100%;">The installation |
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| 67 | process requires a valid |
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| 68 | account on the local and on the remote host as well.<br> |
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| 69 | </p> |
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| 70 | <ul> All hosts (local as well as remote) are |
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| 71 | accessed via the secure shell (ssh). The user must establish |
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| 72 | passwordless login using the private/public-key mechanism (see e.g. the |
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| 73 | <a href="http://www2.hlrn.de/doc/ssh/index.html">HLRN |
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| 74 | documentation</a>). <b>To ensure proper function of mrun, |
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| 75 | passwordless login must be |
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| 76 | established in both directions, from the local to the remote host as |
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| 77 | well as from the remote to the local host!</b> Test this by |
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| 78 | carrying |
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| 79 | out e.g. on the local host: <p style="line-height: 100%;"><span style="font-family: monospace;"> |
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| 80 | </span><span style="font-family: Courier New,Courier,monospace;">ssh |
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| 81 | <username on remote host>@<remote |
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| 82 | IP-address></span><br> </p> <p style="line-height: 100%;">and on the remote host:<br> |
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| 83 | </p> <p style="line-height: 100%;"><span style="font-family: monospace;"> |
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| 84 | </span><span style="font-family: Courier New,Courier,monospace;">ssh |
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| 85 | <username on local host>@<local IP-adddress></span><br> |
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| 86 | </p> In both cases you should not be |
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| 87 | prompted for a password. <b>Before continuing the further |
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| 88 | installation |
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| 89 | process, this must be absolutely guaranteed!</b> This must also |
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| 90 | be |
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| 91 | guaranteed for <b>all</b> other remote hosts, on which |
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| 92 | PALM shall run.<br><br>Please |
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| 93 | note that on many remote hosts, passwordless login must also be |
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| 94 | established <b>within the remote host</b>, i.e. from the |
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| 95 | remote host to itself. Test this by executing on the remote host: <span style="font-family: Courier New,Courier,monospace;">ssh |
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| 96 | <remote IP-address></span>. You should not be prompted |
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| 97 | for a password.<br><br></ul><p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package |
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| 98 | Installation</span></p><p style="line-height: 100%;">In |
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| 99 | the <b>first installation step</b> a |
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| 100 | set of directories must be created both on the local and on the |
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| 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 |
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| 102 | are |
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| 103 | freely selectable (except <big><tt><font size="2"><big>~/job_queue</big></font></tt></big>), |
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| 104 | however new users should use them as suggested, since many |
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| 105 | examples in this documentation as well as all example files are |
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| 106 | assuming these settings. The directory <big><span style="font-family: monospace;">~/palm/current_version</span></big> |
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| 107 | on the local host will be called the working directory from now on. </p> |
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| 108 | <p style="line-height: 100%;"><font color="#000000">In |
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| 109 | the <b>second |
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| 110 | step</b> |
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| 111 | a working copy of the recent version of the PALM software package, |
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| 112 | including the source code, scripts, documentation, etc. must |
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| 113 | be |
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| 114 | copied to the working directory (</font><font color="#000000">local |
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| 115 | host!) by executing the following |
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| 116 | commands. Replace <your username> by the name that you |
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| 117 | chose to |
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| 118 | access the repository, and <#> by any of the available |
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| 119 | PALM |
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| 120 | releases, e.g. "<span style="font-style: italic;">3.1c</span>" |
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| 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 |
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| 122 | ~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn |
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| 123 | checkout --username <your username> |
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| 124 | svn://130.75.105.45/palm/tags/release-<#> trunk</span><br></div><p style="line-height: 100%;"><font color="#000000">You |
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| 125 | will then be prompted for your password. After finishing, the |
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| 126 | subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">should |
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| 127 | appear in your working directory. It contains a number of further |
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| 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">) |
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| 129 | 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, executing</p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username <your username> svn://130.75.105.45/palm/tags/release-<#> abcde</pre><p style="line-height: 100%;">will place your working copy in a |
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| 130 | directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span>instead |
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| 131 | of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span>. |
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| 132 | But keep in mind that you will have to adjust several paths given |
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| 133 | 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 |
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| 134 | your working copy of PALM, unless you know exactly what you |
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| 135 | are doing.</p><p style="line-height: 100%; font-weight: bold;"><span style="font-weight: normal;">You can also get a copy of the |
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| 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 <your username> svn://130.75.105.45/palm/trunk trunk</pre>However, |
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| 137 | this version may contain bugs and new features may not be documented. <span style="font-weight: bold;">In future PALM releases, |
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| 138 | repository access to this most recent version will |
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| 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 |
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| 140 | Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To |
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| 141 | use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable |
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| 142 | has to be extended and the |
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| 143 | environment variable<span style="font-family: Courier New,Courier,monospace;"> |
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| 144 | PALM_BIN </span>has to be set (on local and remote host) |
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| 145 | in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>, |
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| 146 | if<span style="font-family: Courier New,Courier,monospace;"> |
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| 147 | 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 |
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| 148 | PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH</font><font color="#000000"><br><span style="font-family: Courier New,Courier,monospace;">export |
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| 149 | 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 |
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| 150 | may have to login again in order to activate these settings.</font></p><font color="#000000">On the local and on the remote host, some |
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| 151 | small helper/utility programs have to be installed, which |
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| 152 | are later used by <span style="font-weight: bold;">mrun</span> e.g. |
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| 153 | for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script |
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| 154 | requires a configuration file<span style="font-family: Courier New,Courier,monospace;"> |
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| 155 | .mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the |
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| 156 | following. A copy has to be put into the working directory under the |
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| 157 | name<span style="font-family: Courier New,Courier,monospace;"> |
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| 158 | .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 |
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| 159 | trunk/SCRIPTS/.mrun.config.default .mrun.config</span></font></p><font color="#000000">Beside many other things, this file contains |
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| 160 | typical installation parameters |
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| 161 | like compiler name, compiler options, etc. |
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| 162 | for a set of different (remote) hosts. Please edit this file, uncomment |
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| 163 | lines like</font><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username |
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| 164 | <replace by your ... username> |
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| 165 | <host identifier></div><p style="line-height: 100%;"><font color="#000000">by |
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| 166 | removing the first hash (<span style="font-family: Courier New,Courier,monospace;">#</span>) |
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| 167 | character and replace the string "<span style="font-family: Courier New,Courier,monospace;"><replace |
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| 168 | by ...></span>" by your username on the respective host |
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| 169 | given in the <span style="font-family: Courier New,Courier,monospace;"><host |
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| 170 | identifier></span>. |
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| 171 | You only have to uncomment lines for those hosts on which you intend to |
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| 172 | use PALM.</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;"> |
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| 173 | trunk/SCRIPTS </span>contains additional configuration files |
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| 174 | which are already adjusted for special hosts:<span style="font-family: Courier New,Courier,monospace;"> |
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| 175 | .mrun.config.imuk </span>can be used at Hannover University,<span style="font-family: Courier New,Courier,monospace;"> |
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| 176 | .mrun.config.riam </span>can |
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| 177 | be used at the Research Institute of Applied Mechanics, Kyushu |
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| 178 | University. These files have to be edited in the same way as described |
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| 179 | above.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the |
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| 180 | 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 |
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| 181 | lcsgih</font></p><p style="line-height: 100%;"><font color="#000000">The |
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| 182 | 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 |
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| 183 | remote |
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| 184 | 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 |
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| 185 | of PALM Code</span></font></p><font color="#000000"> |
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| 186 | </font><br><font color="#000000">To avoid the |
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| 187 | re-compilation of the complete source code for each model run, PALM |
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| 188 | willl be pre-compiled once on the remote host by again using the script |
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| 189 | <span style="font-weight: bold;">mbuild</span>. Due |
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| 190 | to the use of |
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| 191 | FORTRAN modules in the source code, the subroutines must be compiled |
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| 192 | in a certain order. Therefore the so-called <i>make</i> |
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| 193 | mechanism |
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| 194 | is used (see the respective man-page of the Unix operating system), |
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| 195 | requiring a<span style="font-family: Courier New,Courier,monospace;"> |
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| 196 | </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">Makefile</font><font color="#000000">, |
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| 197 | in which the dependencies are described. This file is found in |
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| 198 | subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span></font><font color="#000000">, where |
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| 199 | also the PALM code is stored.</font><font color="#000000"> The compiled |
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| 200 | sources (object |
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| 201 | files) are |
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| 202 | stored on the remote computer in the default directory |
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| 203 | </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 |
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| 204 | pre-compilation for the remote host (here the SGI-ICE system of HLRN) |
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| 205 | is |
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| 206 | done by</font><span style="font-family: monospace;"></span></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">mbuild |
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| 207 | -h lcsgih </span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild |
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| 208 | </span>will prompt some queries<font color="#000000">, |
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| 209 | which must all be |
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| 210 | answered "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 |
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| 211 | the respective compiler calls to the remote |
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| 212 | host where they are carried out interactively. You can follow the |
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| 213 | progress at the terminal window, where also error messages |
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| 214 | are displayed (hopefully not for this standard installation). By just |
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| 215 | entering </font></p><p style="line-height: 100%;"> |
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| 216 | </p><blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote> |
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| 217 | <p style="line-height: 100%;"><font color="#000000">PALM |
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| 218 | will |
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| 219 | be (consecutively) pre-compiled for all remote hosts listed in |
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| 220 | the configuration file. If you want to compile for the local host only, |
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| 221 | please enter</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">mbuild |
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| 222 | -h lcmuk</span> </font> |
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| 223 | </p><p style="line-height: 100%;"></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, |
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| 224 | after the compilation has been finished, the PALM installation has to |
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| 225 | be verified. For this |
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| 226 | purpose a simple test run is carried out. This once again requires the <b>mrun |
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| 227 | </b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter |
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| 228 | 3.2</font></a><font color="#000000">), as well |
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| 229 | as the </font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_cbl_p3d"><font color="#000080">parameter |
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| 230 | file</font></a><font color="#000000"> |
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| 231 | (described in </font><a href="chapter_4.4.1.html"><font color="#000080">chapter |
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| 232 | 4.4.1</font></a>)<font color="#000000">. The |
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| 233 | parameter file must be |
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| 234 | copied from the PALM working copy by<br> |
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| 235 | </font><div style="margin-left: 40px;"><span style="font-family: monospace;"></span><font style="font-family: Courier New,Courier,monospace;" color="#000000">mkdir -p JOBS/example_cbl/INPUT<br>cp |
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| 236 | trunk/INSTALL/example_cbl_p3d JOBS/example_cbl/INPUT/example_cbl_p3d</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"></span></font></div> |
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| 237 | <p style="line-height: 100%;"><font color="#000000">The |
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| 238 | test run can |
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| 239 | now be started by executing the command </font> |
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| 240 | </p><pre style="margin-left: 1cm; margin-right: 1cm; margin-bottom: 0.5cm; line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mrun -d example_cbl -h lcsgih -K parallel -X 8 -T 8 -t 500 -q testq -r “d3# pr#”</font></pre><font color="#000000">This specific run |
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| 241 | will be carried out on 8 PEs and is allowed to use up to 500 seconds |
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| 242 | CPU time. After pressing <return>, the most important |
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| 243 | settings of |
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| 244 | the job are displayed at the terminal window |
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| 245 | and the user is prompted for o.k. (“</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">y</font><font color="#000000">”). |
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| 246 | Next, a message of the queuing system like “<i>Request</i> |
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| 247 | … |
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| 248 | <i>Submitted to queue… by…” </i>should |
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| 249 | be displayed. Now the job is |
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| 250 | queued and either started immediately or at a later time, depending on |
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| 251 | the |
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| 252 | current workload of the remote host. Provided that it is executed |
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| 253 | immediately and that all things work as designed, the job protocol of |
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| 254 | this run will appear under the file name<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">~/job_queue/lcsgih_example</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"> </span>no |
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| 255 | more than a few minutes later. The content of this |
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| 256 | file should be carefully examined for any error messages.</font><p style="line-height: 100%;"> |
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| 257 | </p><p style="line-height: 100%;">Beside the job |
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| 258 | protocol and according to |
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| 259 | the configuration file and arguments given for <b>mrun</b> |
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| 260 | options<span style="font-family: Courier New,Courier,monospace;"> |
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| 261 | -d </span>and<span style="font-family: Courier New,Courier,monospace;"> -r</span><tt>,</tt>further |
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| 262 | files should be found in |
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| 263 | the |
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| 264 | directories</p><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/MONITORING</div><p style="line-height: 100%;">and</p> |
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| 265 | <p style="line-height: 100%;"><span style="font-family: monospace;"> |
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| 266 | </span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/OUTPUT</span><span style="font-family: monospace;"></span><br> |
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| 267 | </p><p style="line-height: 100%;">Please compare the |
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| 268 | contents of file</p> |
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| 269 | <p style="line-height: 100%;"><span style="font-family: monospace;"> |
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| 270 | </span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example_cbl/MONITORING/lcsgih_example_rc</span><br> |
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| 271 | </p><p style="line-height: 100%;">with those of the |
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| 272 | example result file which can be found under<span style="font-family: Courier New,Courier,monospace;"> |
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| 273 | trunk/INSTALL/example_cbl_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> |
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| 274 | diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff |
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| 275 | JOBS/example_cbl/MONITORING/lcsgih_example_cbl_rc |
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| 276 | trunk/INSTALL/example_cbl_rc</p><p style="line-height: 100%;">where |
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| 277 | it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;"> |
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| 278 | ~/palm/current_version</span>.</p><span style="font-weight: bold;">You should not find any |
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| 279 | difference between these two files</span>, except of the run date |
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| 280 | and time displayed at the top of the file header. <font color="#000000">If |
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| 281 | the file contents are identical, the installation is successfully |
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| 282 | completed.<br><br></font><p style="line-height: 100%;"></p><p style="line-height: 100%; font-weight: bold; text-decoration: underline;"><font color="#000000"><a name="configuration_for_other_machines"></a>Configuration |
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| 283 | for other machines</font></p><font color="#000000">Starting |
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| 284 | from version 3.2a, beside the default hosts (HLRN, etc.), PALM can also |
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| 285 | be installed and run on other Linux-Cluster-, IBM-AIX, or |
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| 286 | NEC-SX-systems. To configure PALM for a non-default host only requires |
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| 287 | to add some lines to the configuration file<span style="font-family: Courier New,Courier,monospace;"> |
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| 288 | .mrun.config</span>.<br><br>First, |
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| 289 | you have to define the host identifier (a string of arbitrary length) |
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| 290 | under which your local host shall be identified by adding a line<br><br></font><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">%host_identifier |
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| 291 | <hostname> <host |
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| 292 | identifier></span><br></div><br>to the |
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| 293 | configuration file (best to do this in the section where the other |
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| 294 | default host identifiers are defined). Here<span style="font-family: Courier New,Courier,monospace;"> |
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| 295 | <hostname> </span>must be the name of your local |
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| 296 | host as provided by the unix-command "<span style="font-family: Courier New,Courier,monospace;">hostname</span>". |
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| 297 | The first characters of<span style="font-family: Courier New,Courier,monospace;"> |
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| 298 | <host identifier> </span>have to be "<span style="font-family: Courier New,Courier,monospace;">lc</span>", |
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| 299 | if your system is (part of) a linux-cluster, "<span style="font-family: Courier New,Courier,monospace;">ibm</span>", |
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| 300 | or "<span style="font-family: Courier New,Courier,monospace;">nec</span>" |
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| 301 | in case of an IBM-AIX- or NEC-SX-system, respectively. For example, if |
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| 302 | you want to install on a linux-cluster, the line may read as<br><br><div style="margin-left: 40px;">%host_identifier foo |
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| 303 | lc_bar<br></div><br>In |
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| 304 | the second step, you have to give all informations neccessary to |
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| 305 | compile and run PALM on your local host by adding an additional section |
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| 306 | to the configuration file:<br><br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username |
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| 307 | <1> <host |
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| 308 | identifier> parallel<br>%tmp_user_catalog |
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| 309 | <2> <host |
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| 310 | identifier> parallel<br>%compiler_name |
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| 311 | <3> <host |
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| 312 | identifier> parallel<br>%compiler_name_ser |
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| 313 | <4> <host |
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| 314 | identifier> parallel<br>%cpp_options |
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| 315 | <5> <host |
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| 316 | identifier> parallel<br>%netcdf_inc |
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| 317 | <6> <host |
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| 318 | identifier> parallel<br>%netcdf_lib |
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| 319 | <7> <host |
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| 320 | identifier> parallel<br>%fopts |
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| 321 | <8> <host |
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| 322 | identifier> parallel<br>%lopts |
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| 323 | <9> |
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| 324 | <host identifier> parallel<br></div><br>The |
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| 325 | section consists of four columns each separated by one or more blanks. |
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| 326 | The first column gives the name of the respective environment variable |
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| 327 | used by <span style="font-weight: bold;">mrun</span> |
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| 328 | and <span style="font-weight: bold;">mbuild</span>, |
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| 329 | while the second column defines its value. The third column has to be |
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| 330 | the host identifier as defined above, and the last column in each line |
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| 331 | must contain the string "<span style="font-family: Courier New,Courier,monospace;">parallel</span>". |
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| 332 | Otherwise, the respective line(s) will be interpreted as belonging to |
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| 333 | the setup for compiling and running a serial (non-parallel) version of |
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| 334 | PALM.<br><br>All brackets have to be replaced by the |
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| 335 | appropriate settings for your local host:<br><ul><li><span style="font-family: Courier New,Courier,monospace;"><1> |
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| 336 | </span>is the username on your LOCAL host</li><li><span style="font-family: Courier New,Courier,monospace;"><2> |
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| 337 | </span>is the temporary directory in which PALM runs will be |
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| 338 | carried out</li><li><span style="font-family: Courier New,Courier,monospace;"><3> |
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| 339 | </span>is the compiler name which generates parallel code</li><li><span style="font-family: Courier New,Courier,monospace;"><4> |
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| 340 | </span>is the compiler name for generating serial code</li><li><span style="font-family: Courier New,Courier,monospace;"><5> |
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| 341 | </span>are |
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| 342 | the preprocessor options to be invoked. In most of the cases, it will |
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| 343 | be neccessary to adjust the MPI data types to double precision by |
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| 344 | giving <span style="font-family: Courier New,Courier,monospace;">-DMPI_REAL=MPI_DOUBLE_PRECISION |
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| 345 | -DMPI_2REAL=MPI_2DOUBLE_PRECISION</span>. To switch on the NetCDF |
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| 346 | support, you also have to give <span style="font-family: Courier New,Courier,monospace;">-D__netcdf</span> |
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| 347 | and <span style="font-family: Courier New,Courier,monospace;">-D__netcdf_64bit</span> |
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| 348 | (if you like to have 64bit NetCDF output).</li><li><span style="font-family: Courier New,Courier,monospace;"><6> |
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| 349 | </span>is the compiler option for specifying the include path to |
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| 350 | search for the NetCDF module/include files</li><li><span style="font-family: Courier New,Courier,monospace;"><7> |
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| 351 | </span>are the linker options to search for the NetCDF library</li><li><span style="font-family: Courier New,Courier,monospace;"><8> |
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| 352 | </span>are the general compiler options to be used. You should |
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| 353 | allways switch on double precision (e.g. <span style="font-family: Courier New,Courier,monospace;">-r8</span>) |
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| 354 | and code optimization (e.g. <span style="font-family: Courier New,Courier,monospace;">-O2</span>).</li><li><span style="font-family: Courier New,Courier,monospace;"><9> |
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| 355 | </span>are the linker options</li><li><span style="font-family: Courier New,Courier,monospace;"><host |
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| 356 | identifier> </span>is the host identifier as defined |
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| 357 | before</li></ul><br>A typical example may be:<br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username |
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| 358 | raasch |
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| 359 | |
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| 360 | |
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| 361 | lc_bar parallel<br>%tmp_user_catalog |
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| 362 | /tmp lc_bar |
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| 363 | parallel<br>%compiler_name |
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| 364 | mpif90 lc_bar |
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| 365 | parallel<br>%compiler_name_ser |
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| 366 | ifort lc_bar |
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| 367 | parallel<br>%cpp_options |
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| 368 | -DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__netcdf_64bit |
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| 369 | lc_bar parallel<br>%netcdf_inc |
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| 370 | -I:/usr/local/netcdf/include |
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| 371 | lc_bar parallel<br>%netcdf_lib |
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| 372 | -L/usr/local/netcdf/lib:-lnetcdf |
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| 373 | lc_bar parallel<br>%fopts |
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| 374 | -axW:-cpp:-openmp:-r8:-nbs |
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| 375 | |
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| 376 | lc_bar parallel<br>%lopts |
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| 377 | -axW:-cpp:-openmp:-r8:-nbs:-Vaxlib lc_bar |
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| 378 | parallel<br></div><br>Currently (version 3.2a), |
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| 379 | depending on the MPI |
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| 380 | version which is running on your local host, the options for the |
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| 381 | execution command (which may be <span style="font-family: Courier New,Courier,monospace;">mpirun</span> |
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| 382 | or <span style="font-family: Courier New,Courier,monospace;">mpiexec</span>) |
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| 383 | may have to be adjusted manually in the mrun-script. A future version |
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| 384 | will allow to give the respective settings in the configuration file. |
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| 385 | <p style="line-height: 100%;">If you have any problems |
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| 386 | with the PALM |
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| 387 | installation, the members of the PALM working group are pleased to |
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| 388 | help you. </p> |
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| 389 | <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 |
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| 390 | change: </i> $Id: chapter_5.0.html 287 2009-04-09 |
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| 391 | 08:59:36Z raasch $</p> |
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| 392 | </body></html> |
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