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| 5 | <title>PALM chapter 5.0</title><meta name="GENERATOR" content="StarOffice 7 (Win32)"> |
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| 6 | <meta name="AUTHOR" content="Siegfried Raasch"> |
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| 16 | <h2 style="line-height: 100%;"><font size="4">5.0 Installation of the |
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| 17 | model</font></h2> |
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| 18 | <font color="#000000">This chapter |
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| 19 | describes the installation of PALM on a Linux workstation (local host) and a suitable remote computer, on which the |
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| 20 | model runs are to be carried out. The local host is used to |
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| 21 | start batch jobs with <b>mrun</b> and to analyze the results |
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| 22 | which are produced by the model on the remote host and send back to the local host. Alternatively, <span style="font-weight: bold;">mrun</span> can also be used to start PALM on the local host in interactive mode or as a batch job.</font><p style="line-height: 100%;"><font color="#000000"></font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Requirements</span></font></p><p style="line-height: 100%;"><font color="#000000">The installation and operation of PALM requires at mimimum (on both, the local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The AT&T Korn-shell (ksh) must be available under<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">/bin/ksh</font><font color="#000000">. Most of the current Linux distributions are using the public domain Korn-shell (pdksh). The PALM scripts <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span> do not work with the pdksh! Please replace it by the AT&T ksh. If the AT&T ksh path is different from<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">/bin/ksh</font><font color="#000000">, please modify the first lines in <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span>, respectively.</font></li><li><font color="#000000">The NetCDF-library with version number not earlier than 3.6.0-p1 (for NetCDF, see under <a href="http://www.unidata.ucar.edu/software/netcdf/">www.unidata.ucar.edu</a>).</font></li><li><font color="#000000">A FORTRAN90/95 compiler.</font></li><li><font color="#000000">The Message Passing Interface (MPI), at least on the remote host, if the parallel version of PALM shall be used.</font></li><li><font color="#000000">On the local host, the revision control system <span style="font-weight: bold;">subversion</span> (see <a href="http://subversion.tigris.org/">subversion.tigris.org</a>). |
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| 23 | This is already included in many Linux distributions (e.g. SuSe). <span style="font-weight: bold;">subversion requires port 3690 to be open for tcp/udp.</span> <span style="font-weight: bold;">If there are firewall restrictions concerning this port, the PALM code cannot be accessed.</span> The |
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| 24 | user needs a permit to access the PALM repository. For getting a permit |
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| 25 | please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>) |
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| 26 | and define a username under which you like to access the repository. |
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| 27 | You will then receive a password which allows the access under this |
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| 28 | name.</font></li><li><font color="#000000">A job queueing system must be available on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).</font></li><li><font color="#000000">ssh/scp-connections to and from the remote host must not be blocked by a firewall.<br></font></li></ol><font color="#000000"><span style="font-weight: bold;"></span></font><font color="#000000"> Currently, <span style="font-weight: bold;">mrun</span> is configured to be used on a limited number of selected machines. These are IBM-Regatta at computing center HLRN in Hannover (<span style="font-style: italic;">ibmh</span>), Berlin (<span style="font-style: italic;">ibmb</span>), at KISTI, Korea (<span style="font-style: italic;">ibms</span>), at Yonsei University, Seoul (<span style="font-style: italic;">ibms</span>), on NEC-SX6/8 systems at DKRZ, Hamburg (<span style="font-style: italic;">nech</span>) and RIAM, Kyushu University, Fukuoka (<span style="font-style: italic;">neck</span>), as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>) and Tokyo Institute of Technology (<span style="font-style: italic;">lctit</span>). The strings given in brackets are the systems names under which <span style="font-weight: bold;">mrun</span> indentifies the different hosts. mrun should also work on other systems, but this requires some modifications in the scripts <span style="font-weight: bold;">mrun</span>, <span style="font-weight: bold;">mbuild</span>, and <span style="font-weight: bold;">subjob</span>. Future PALM versions will allow to configure the scripts for different kinds of systems by just using a configuration file.</font><p style="line-height: 100%;"><font color="#000000">The examples given in this chapter refer to an |
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| 29 | installation of PALM on an IMUK Linux workstation and the IBM-Regatta |
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| 30 | system of |
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| 31 | the HLRN used as remote host. They are just called local and remote host from now on. </font></p><p style="line-height: 100%;"> |
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| 32 | </p> |
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| 33 | <p style="line-height: 100%;">The installation process requires a valid |
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| 34 | account on the local and on the remote host as well.<br> |
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| 35 | </p> |
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| 36 | <ul> |
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| 37 | All hosts (local as well as remote) are |
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| 38 | accessed via the secure shell (ssh). The user must establish |
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| 39 | passwordless login using the private/public-key mechanism (see e.g. the |
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| 40 | <a href="http://www.hlrn.de/doc/ssh/index.html">HLRN documentation</a>). |
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| 41 | <b>To ensure proper function of mrun, passwordless login must be |
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| 42 | established in both directions, from the local to the remote host as |
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| 43 | well as from the remote to the local host!</b> Test this by carrying |
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| 44 | out e.g. on the local host: |
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| 45 | <p style="line-height: 100%;"><span style="font-family: monospace;"> |
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| 46 | </span><span style="font-family: Courier New,Courier,monospace;">ssh <username on remote host>@<remote IP-address></span><br> |
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| 47 | </p> |
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| 48 | <p style="line-height: 100%;">and on the remote host:<br> |
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| 49 | </p> |
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| 50 | <p style="line-height: 100%;"><span style="font-family: monospace;"> |
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| 51 | </span><span style="font-family: Courier New,Courier,monospace;">ssh <username on local host>@<local IP-adddress></span><br> |
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| 52 | </p> |
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| 53 | In both cases you should not be |
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| 54 | prompted for a password. <b>Before continuing the further installation |
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| 55 | process, this must be absolutely guaranteed!</b> This must also be |
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| 56 | guaranteed for <b>all</b> other remote hosts, on which PALM shall run. |
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| 57 | </ul> |
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| 58 | <p style="line-height: 100%;"></p><p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package Installation</span></p><p style="line-height: 100%;">In the <b>first installation step</b> a |
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| 59 | set of directories must be created both on the local and on the |
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| 60 | 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 are |
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| 61 | freely selectable (except <tt><font size="2">~/job_queue</font></tt>), |
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| 62 | however new users should use them as suggested, since many |
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| 63 | examples in this documentation as well as all example files are |
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| 64 | assuming these settings. The directory <span style="font-family: monospace;">~/palm/current_version</span> on the local host will be called the working directory from now on. </p> |
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| 65 | <p style="line-height: 100%;"><font color="#000000">In the <b>second |
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| 66 | step</b> |
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| 67 | a working copy of the recent version of the PALM software package, |
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| 68 | including the source code, scripts, documentation, etc. must be |
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| 69 | copied to the working directory (</font><font color="#000000">local |
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| 70 | host!) by executing the following |
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| 71 | commands. Replace <your username> by the name that you choosed to |
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| 72 | access the repository, and <#> by any of the available PALM |
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| 73 | releases, e.g. "<span style="font-style: italic;">3.1c</span>" (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 ~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn checkout --username <your username> svn://130.75.105.45/palm/tags/release-<#> trunk</span><br></div><p style="line-height: 100%;"><font color="#000000">You will then be prompted for your password. After finishing, the subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">should |
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| 74 | appear in your working directory. It contains a number of further |
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| 75 | 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">) 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 directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span>instead of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span>. But keep in mind that you will have to adjust several paths given below, if you do not use the default directory<span style="font-family: Courier New,Courier,monospace;"> trunk</span>.</p><p style="line-height: 100%;">Please never touch any file in your working copy of PALM, unless you know exactly what you are doing.</p><p style="line-height: 100%; font-weight: bold;"><span style="font-weight: normal;">You can also get a copy of the 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, this version may contain bugs and new features may not be documented. <span style="font-weight: bold;">In future PALM releases, repository access to this most recent version will |
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| 76 | probably be restricted to the PALM developers.</span><p style="line-height: 100%;"><font color="#000000"></font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Package Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To |
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| 77 | use the PALM scripts, the PATH variable has to be extended and the |
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| 78 | environment variable PALM_BIN has to be set (on local and remote host) |
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| 79 | in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>, if<span style="font-family: Courier New,Courier,monospace;"> ksh </span>is used):</font></p><p style="line-height: 100%; margin-left: 40px;"><font style="font-family: Courier New,Courier,monospace;" color="#000000">export PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH</font><font color="#000000"><br><span style="font-family: Courier New,Courier,monospace;">export PALM_BIN=</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">$HOME/palm/current_version/trunk/SCRIPTS</font></p><p style="line-height: 100%;"><font color="#000000">You may habe to login again in order to activate these settings.</font></p><font color="#000000">On the local and on the remote host, some small helper/utility programs have to be installed, which are e.g. later used by <span style="font-weight: bold;">mrun</span> or for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script requires a configuration file<span style="font-family: Courier New,Courier,monospace;"> .mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the following. A copy has to be put into the working directory under the name<span style="font-family: Courier New,Courier,monospace;"> .mrun.config </span>by</font><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">cp trunk/SCRIPTS/.mrun.config.default .mrun.config</span></font></p><font color="#000000">Beside many other things, this file contains typical installation parameters |
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| 80 | like compiler name, compiler options, etc. |
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| 81 | for a set of different remote hosts. Please edit this file, uncomment lines like</font><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username <replace by your ... username> <remote-computer-shortcut></div><p style="line-height: 100%;"><font color="#000000">by removing the first hash (<span style="font-family: Courier New,Courier,monospace;">#</span>) character and replace the string "<span style="font-family: Courier New,Courier,monospace;"><replace by ...></span>" by your username on the respective host given in the <span style="font-family: Courier New,Courier,monospace;"><remote-computer-shortcut></span>. You only have to uncomment lines for those hosts on which you intend to use PALM.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the respective executables are generated by executing</font></p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild -u -h lcmuk<br>mbuild -u -h ibmh</font></p><p style="line-height: 100%;"><font color="#000000">The second call also copies the PALM scripts like <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span> to the remote host.</font></p><p style="line-height: 100%;"><font color="#000000"></font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Pre-Compilation of PALM Code</span></font></p><font color="#000000"> |
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| 82 | </font> |
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| 83 | <br><font color="#000000">To avoid the |
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| 84 | re-compilation of the complete source code for each model run, PALM |
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| 85 | willl be pre-compiled once on the remote host by again using the script <span style="font-weight: bold;">mbuild</span>. Due to the use of |
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| 86 | FORTRAN modules in the source code, the subroutines must be compiled |
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| 87 | in a certain order. Therefore the so-called <i>make</i> mechanism |
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| 88 | is used (see the respective man-page of the Unix operating system), |
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| 89 | requiring a<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">Makefile</font><font color="#000000">, |
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| 90 | in which the dependencies are described. This file is found in subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE<span style="font-family: Times New Roman,Times,serif;">, where also the PALM code is stored</span></span>. The compiled sources (object |
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| 91 | files) are |
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| 92 | stored on the remote computer in the default directory |
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| 93 | </font><font style="font-family: Courier New,Courier,monospace;" color="#000000">~/palm/current_version/MAKE_DEPOSITORY</font>.<font color="#000000"><span style="font-weight: bold;"></span></font><p style="line-height: 100%;"><font color="#000000">The |
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| 94 | pre-compilation for the remote host (here the IBM-Regatta of HLRN) is done by</font><span style="font-family: monospace;"></span></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">mbuild -h ibmh </span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild |
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| 95 | </span>will prompt some queries<font color="#000000">, which must all be |
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| 96 | 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 the respective compiler calls to the remote |
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| 97 | host where they are carried out interactively. You can follow the |
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| 98 | progress at the terminal window, where also error messages |
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| 99 | are displayed (hopefully not for this standard installation). By just |
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| 100 | entering </font></p><p style="line-height: 100%;"> |
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| 101 | </p> |
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| 102 | <blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote> |
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| 103 | <p style="line-height: 100%;"><font color="#000000">PALM will |
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| 104 | be (consecutively) pre-compiled for all remote hosts listed in |
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| 105 | the configuration file. If you want to compile for the local host only, please enter</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">mbuild -h lcmuk</span> </font> |
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| 106 | </p> |
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| 107 | <p style="line-height: 100%;"><font color="#000000"></font></p><p style="line-height: 100%; font-weight: bold; text-decoration: underline;"><font color="#000000">Installation Verification</font></p><font color="#000000">As a last step, |
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| 108 | after the compilation has been finished, the PALM installation has to |
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| 109 | be verified. For this |
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| 110 | purpose a simple test run is carried out. This once again requires the <b>mrun |
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| 111 | </b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter |
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| 112 | 3.2</font></a><font color="#000000">), as well as the </font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d"><font color="#000080">parameter |
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| 113 | file</font></a><font color="#000000"> (described in </font><a href="chapter_4.4.html"><font color="#000080">chapter |
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| 114 | 4.4</font></a>)<font color="#000000">. The parameter file must be |
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| 115 | copied from the PALM working copy by<br> |
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| 116 | </font> |
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| 117 | <div style="margin-left: 40px;"><span style="font-family: monospace;"></span><font style="font-family: Courier New,Courier,monospace;" color="#000000">mkdir -p JOBS/example/INPUT<br>cp trunk/INSTALL/example_p3d JOBS/example/INPUT/example_p3d</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"></span></font></div> |
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| 118 | <p style="line-height: 100%;"><font color="#000000">The test run can |
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| 119 | now be started by executing the command </font> |
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| 120 | </p> |
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| 121 | <pre style="margin-left: 1cm; margin-right: 1cm; margin-bottom: 0.5cm; line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mrun -d example -h ibmh -K parallel -X 8 -T 8 -t 500 -q cdev -r “d3# pr#”</font></pre> |
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| 122 | <font color="#000000">This specific run |
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| 123 | will be carried out on 8 PEs and is allowed to use up to 500 seconds |
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| 124 | CPU time. After pressing <return>, the most important settings of |
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| 125 | the job are displayed at the terminal window |
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| 126 | and the user is prompted for o.k. (“</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">y</font><font color="#000000">”). Next, a message of the queuing system like “<i>Request</i> … |
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| 127 | <i>Submitted to queue… by…” </i>should be displayed. Now the job is |
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| 128 | queued and either started immediately or at a later time, depending on the |
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| 129 | current workload of the remote host. Provided that it is executed |
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| 130 | immediately and that all things work as designed, the job protocol of |
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| 131 | this run will appear under the file name<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">~/job_queue/ibmh_example</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"> </span>no more than a few minutes later. The content of this |
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| 132 | file should be carefully examined for any error messages.</font><p style="line-height: 100%;"> |
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| 133 | </p> |
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| 134 | |
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| 135 | |
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| 136 | <p style="line-height: 100%;">Beside the job protocol and according to |
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| 137 | the configuration file and arguments given for <b>mrun</b> |
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| 138 | options<span style="font-family: Courier New,Courier,monospace;"> -d </span>and<span style="font-family: Courier New,Courier,monospace;"> -r</span><tt>,</tt>further files should be found in |
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| 139 | the |
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| 140 | directories</p><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/MONITORING</div><p style="line-height: 100%;">and</p> |
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| 141 | <p style="line-height: 100%;"><span style="font-family: monospace;"> |
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| 142 | </span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/OUTPUT</span><span style="font-family: monospace;"></span><br> |
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| 143 | </p> |
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| 144 | <p style="line-height: 100%;">Please compare the contents of file</p> |
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| 145 | <p style="line-height: 100%;"><span style="font-family: monospace;"> |
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| 146 | </span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/MONITORING/ibmh_example_rc</span><br> |
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| 147 | </p> |
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| 148 | <p style="line-height: 100%;">with those of the example result file which can be found under<span style="font-family: Courier New,Courier,monospace;"> trunk/INSTALL/example_rc</span>., e.g. by using the<span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;"> standard</span> diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff JOBS/example/MONITORING/ibmh_example_rc trunk/INSTALL/example_rc</p><p style="line-height: 100%;">where it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;"> ~/palm/current_version</span>.</p><span style="font-weight: bold;">You should not find any difference between these two files</span>, except of the run date and time displayed at the top of the file header. <font color="#000000">If |
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| 149 | the file contents are identical, the installation is successfully |
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| 150 | completed.</font> |
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| 151 | <p style="line-height: 100%;">If you have any problems with the PALM |
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| 152 | installation, the members of the PALM working group are pleased to |
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| 153 | help you. </p> |
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| 154 | <hr> |
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| 155 | <p style="line-height: 100%;"><font color="#000080"><font color="#000080"><a href="chapter_4.6.html"><font color="#000080"><img src="left.gif" name="Grafik1" align="bottom" border="2" height="32" width="32"></font></a><a href="Inhaltsverzeichnis.html"><font color="#000080"><img src="up.gif" name="Grafik2" align="bottom" border="2" height="32" width="32"></font></a><a href="chapter_5.1.html"><font color="#000080"><img src="right.gif" name="Grafik3" align="bottom" border="2" height="32" width="32"></font></a></font></font></p> |
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| 156 | <p style="line-height: 100%;"><i>Last change: </i> 02/03/07 (SR) </p> |
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| 157 | </body></html> |
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