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r5 r40 1 1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> 2 <html> 3 <head> 4 <meta http-equiv="CONTENT-TYPE" 5 content="text/html; charset=windows-1252"> 6 <title>PALM chapter 5.0</title> 7 <meta name="GENERATOR" content="StarOffice 7 (Win32)"> 2 <html><head> 3 <meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"> 4 5 <title>PALM chapter 5.0</title><meta name="GENERATOR" content="StarOffice 7 (Win32)"> 8 6 <meta name="AUTHOR" content="Siegfried Raasch"> 9 7 <meta name="CREATED" content="20041103;12380720"> … … 14 12 @page { size: 21cm 29.7cm } 15 13 --> 16 </style> 17 </head> 14 </style></head> 15 18 16 <body dir="ltr" lang="en-US"> 19 17 <h2 style="line-height: 100%;"><font size="4">5.0 Installation of the 20 18 model</font></h2> 21 19 <p style="line-height: 100%;"><font color="#000000">This chapter 22 describes the installation of PALM on the Linux workstation 23 cluster of IMUK and a suitable remote computer (host), on which the 24 model runs are actually carried out. The local cluster is used to 25 start the batch job with <b>mrun</b> and to analyze the results 26 produced by the model. In batch mode, runs can be carried on the 27 IBM-Regatta 28 system of the HLRN, on an IBM-Regatta at KISTI, Korea </font><font 29 color="#000000">(via a local 30 DEC-Alpha-workstation at the Department of Atmospheric Sciences of the 31 Yonsei University, Seoul)</font><font color="#000000">, and on an 32 NEC-SX6 at DKRZ. The examples given in this chapter refer to an 33 installation of PALM on the IMUK cluster, considering the IBM-Regatta 20 describes the installation of PALM on a Linux workstation (local host) and a suitable remote computer, on which the 21 model runs are to be carried out. The local host is used to 22 start batch jobs with <b>mrun</b> and to analyze the results 23 which are produced by the model on the remote host and send back to the local host. Alternatively, <span style="font-weight: bold;">mrun</span> can also be used to start PALM on the local host in interactive mode or as a batch job.</font></p><p style="line-height: 100%;"><font color="#000000"></font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Requirements</span></font></p><p style="line-height: 100%;"><font color="#000000">The installation and operation of PALM requires at mimimum (on both, the local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The AT&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>). 24 This is already included in many Linux distributions (e.g. SuSe). The 25 user needs a permit to access the PALM repository. For getting a permit 26 please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>) 27 and define a username under which you like to access the repository. 28 You will then receive a password which allows the access under this 29 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 30 installation of PALM on an IMUK Linux workstation and the IBM-Regatta 34 31 system of 35 the HLRN as the remote computer. </font>32 the HLRN used as remote host. They are just called local and remote host from now on. </font> 36 33 </p> 37 34 <p style="line-height: 100%;">The installation process requires a valid 38 account on the IMUK cluster and on the remote host as well. In the 39 following the IMUK workstation is called the local host. <br> 35 account on the local and on the remote host as well.<br> 40 36 </p> 41 37 <ul> … … 49 45 out e.g. on the local host:</p> 50 46 <p style="line-height: 100%;"><span style="font-family: monospace;"> 51 ssh <username on remote host>@<remote IP-address></span><br>47 </span><span style="font-family: Courier New,Courier,monospace;">ssh <username on remote host>@<remote IP-address></span><br> 52 48 </p> 53 49 <p style="line-height: 100%;">and on the remote host:<br> 54 50 </p> 55 51 <p style="line-height: 100%;"><span style="font-family: monospace;"> 56 ssh <username on local host>@<local IP-adddress></span><br>52 </span><span style="font-family: Courier New,Courier,monospace;">ssh <username on local host>@<local IP-adddress></span><br> 57 53 </p> 58 <p style="line-height: 100%;">In both cases you should nnot be54 <p style="line-height: 100%;">In both cases you should not be 59 55 prompted for a password. <b>Before continuing the further installation 60 56 process, this must be absolutely guaranteed!</b> This must also be 61 57 guaranteed for <b>all</b> other remote hosts, on which PALM shall run.</p> 62 58 </ul> 63 <p style="line-height: 100%;"> In the <b>first installation step</b> a59 <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 64 60 set of directories must be created both on the local and on the 65 remote host. These directories are: </p> 66 <ul> 67 <pre style="line-height: 100%;"><font size="2">~/job_queue</font><br><font 68 size="2">~/palm</font><br><font size="2">~/palm/current_version</font><br><font 69 size="2">~/palm/current_version/SOURCE</font><br><font size="2">~/palm/current_version/JOBS</font></pre> 70 </ul> 71 <p style="line-height: 100%;">The names of these directories are 61 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 72 62 freely selectable (except <tt><font size="2">~/job_queue</font></tt>), 73 63 however new users should use them as suggested, since many 74 64 examples in this documentation as well as all example files are 75 assuming these settings. </p>65 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> 76 66 <p style="line-height: 100%;"><font color="#000000">In the <b>second 77 step</b> the PALM source code must be copied into directory </font><tt><font 78 size="2"><font color="#000000">~/palm/current_version/SOURCE</font></font></tt><font 79 color="#000000"> on the local host by carrying out the following 80 commands: </font> 81 </p> 82 <ul> 83 <pre style="line-height: 100%;"><font color="#000000">cd ~/palm/current_version/SOURCE</font><br><font 84 color="#000000">ln -s /home/raasch/public_html/PALM_group/INSTALL/RCS .</font><br><font 85 color="#000000">cp RCS/*,v .</font><br><font color="#000000">co *,v</font><br><font 86 color="#000000">rm -rf *,v</font></pre> 87 </ul> 88 <p style="line-height: 100%;"><font color="#000000">Afterwards, the 89 directory</font><font color="#000000"> </font><tt><font size="2"><font 90 color="#000000">~/palm/current_version/SOURCE</font></font></tt><font 91 color="#000000"> 92 should contain</font><font color="#000000"> all PALM routines as well 93 as a file with the name </font><tt><font size="2"><font color="#000000">Makefile</font></font></tt><font 94 color="#000000">. </font><font color="#000000">All files are 95 write-protected, the source code files end on </font><tt><font 96 style="font-size: 11pt;" size="2"><font color="#000000">.f90</font></font></tt><font 97 color="#000000">. 98 The user should never modify these files without further knowledge of 99 the PALM code. </font> 100 </p> 67 step</b> 68 a working copy of the recent version of the PALM software package, 69 including the source code, scripts, documentation, etc. must be 70 copied to the working directory (</font><font color="#000000">local host!) by executing the following 71 commands. Replace <your username> by the name that you choosed to access the repository.</font></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">cd ~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn checkout --username <your username> svn://130.75.105.45/palm/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 72 appear in your working directory. It contains a number of further 73 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/trunk 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;">In future PALM releases, repository access to the most recent PALM version will 74 probably be restricted because this is a test version. However, access 75 to the last (and earlier) stable version(s) will still be possible with 76 (e.g.)</p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username <your username> svn://130.75.105.45/palm/tags/release-3.1c trunk</pre><p style="line-height: 100%;"><font color="#000000"></font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Package Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To 77 use the PALM scripts, the PATH variable has to be extended and the 78 environment variable PALM_BIN has to be set (on local and remote host) 79 in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>, if<span style="font-family: Courier New,Courier,monospace;"> ksh </span>is used):</font></p><p style="line-height: 100%; margin-left: 40px;"><font style="font-family: Courier New,Courier,monospace;" color="#000000">export PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH</font><font color="#000000"><br><span style="font-family: Courier New,Courier,monospace;">export PALM_BIN=</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">$HOME/palm/current_version/trunk/SCRIPTS</font></p><p style="line-height: 100%;"><font color="#000000">You may habe to login again in order to activate these settings.</font></p><p style="line-height: 100%;"><font color="#000000">On the local and on the remote host, some small helper/utility programs have to be installed, which are e.g. later used by <span style="font-weight: bold;">mrun</span> or for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script requires a configuration file<span style="font-family: Courier New,Courier,monospace;"> .mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the following. A copy has to be put into the working directory under the name<span style="font-family: Courier New,Courier,monospace;"> .mrun.config </span>by</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">cp trunk/SCRIPTS/.mrun.config.default .mrun.config</span></font></p><p style="line-height: 100%;"><font color="#000000">Beside many other things, this file contains typical installation parameters 80 like compiler name, compiler options, etc. 81 for a set of different remote hosts. Please edit this file, uncomment lines like</font></p><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username <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"> 82 </font> 101 83 <p style="line-height: 100%;"><font color="#000000">To avoid the 102 84 re-compilation of the complete source code for each model run, PALM 103 willl be pre-compiled once on the remote host . Due to the use of85 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 104 86 FORTRAN modules in the source code, the subroutines must be compiled 105 in a certain sequence. Therefore the so-called <i>make</i> mechanism87 in a certain order. Therefore the so-called <i>make</i> mechanism 106 88 is used (see the respective man-page of the Unix operating system), 107 requiring the file </font><tt><font color="#000000">Makefile</font></tt><font 108 color="#000000">, 109 in which the dependencies are described. The compiled sources (object 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">, 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 110 91 files) are 111 stored on the remote computer in the directory 112 </font><tt><font color="#000000">~/palm/current_version/SOURCE/MAKE_DEPOSITORY</font></tt><font 113 color="#000000">.<br> 114 <br> 115 For pre-compilation the user has to</font> call <font color="#000000">the 116 command <b>mbuild</b>, which requires some pre-settings. The path 117 variable must be extended on <b>both</b> computers, so that the 118 commands <b>mbuild</b> and <b>mrun</b> as well as further routines 119 needed by <span style="font-weight: bold;">mrun</span> can be found. 120 This is achieved on the local computer via:: </font> 121 </p> 122 <ul> 123 <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font 124 color="#000000">PATH=$PATH:/home/raasch/pub,</font></pre> 125 </ul> 126 <p style="line-height: 100%;"><font color="#000000">and on the IBM 127 Regatta 128 system of the HLRN via</font></p> 129 <ul> 130 <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font 131 color="#000000">PATH=$PATH:/home/h/niksiraa/pub.</font></pre> 132 </ul> 133 <p style="line-height: 100%;"><font color="#000000">These path 134 extensions must be automatically set in the profiles of the local and 135 remote host (file "~/.myprofile" at IMUK, file "~/.profile" at HLRN)</font><font 136 color="#000000">. 137 </font></p> 138 <p style="line-height: 100%;"><font color="#000000">It is now assumed 139 that the working directory is 140 </font><tt><font color="#000000">~/palm/current_version/SOURCE</font></tt><font 141 color="#000000"> 142 on the local host. Compilation of the PALM code via <b>mbuild </b>needs 143 a </font><a 144 href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/.mrun.config"><font 145 color="#000080">configuration 146 file</font></a><font color="#000080">,</font><font color="#000000"> 147 which must be copied to the working directory under name 148 </font><tt><font color="#000000">.mrun.config</font></tt><font 149 color="#000000"> 150 (please click on the link with <SHIFT> + left mouse button)</font><font 151 color="#000000">. This file contains typical installation parameters 152 like compiler name, compiler options, etc. 153 for a set of different remote hosts. This file is also needed later on 154 for starting the model runs. </font> 155 </p> 156 <p style="line-height: 100%;"><font color="#000000">In the 157 configuration file </font><tt><font color="#000000">.mrun.config</font></tt><font 158 color="#000000"> 159 the user name on the respective remote host must be entered. In lines 160 like</font> 161 </p> 162 <ul> 163 <p style="line-height: 100%;"><tt><font color="#000000">% 164 remote_username <username> <remote-computer-shortcut></font></tt></p> 165 </ul> 166 the string "<span style="font-family: monospace;"><username></span>" 167 has to be replaced by the actual name of the user on the respective 168 remote host (e.g. "nik....." on HLRN).<font color="#000000"> 169 </font> 170 <p style="line-height: 100%;"><font color="#000000">After this, the 171 pre-compilation for the IBM-Regatta of HLRN can be started by entering</font><font 172 color="#000000"> </font> 173 </p> 174 <ul> 175 <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font 176 color="#000000">mbuild - h ibmh .</font></pre> 177 </ul> 178 <p style="line-height: 100%;"><span style="font-family: monospace;">mbuild</span> 179 will prompt some queries<font color="#000000">, which must all be 180 answered "y" by the user. The compiling process </font><font 181 color="#000000">will take some time. </font><font color="#000000"><span 182 style="font-family: monospace;">mbuild</span></font><font 183 color="#000000"> transfers the respective compiler calls to the remote 92 stored on the remote computer in the default directory 93 </font><font style="font-family: Courier New,Courier,monospace;" color="#000000">~/palm/current_version/MAKE_DEPOSITORY</font>.<font color="#000000"><span style="font-weight: bold;"></span></font></p><p style="line-height: 100%;"><font color="#000000">The 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 95 </span>will prompt some queries<font color="#000000">, which must all be 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 184 97 host where they are carried out interactively. You can follow the 185 98 progress at the terminal window, where also error messages … … 187 100 entering </font> 188 101 </p> 189 <blockquote style="line-height: 100%; "><tt><font color="#000000">mbuild</font></tt></blockquote>102 <blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote> 190 103 <p style="line-height: 100%;"><font color="#000000">PALM will 191 104 be (consecutively) pre-compiled for all remote hosts listed in 192 the configuration file. </font>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> 193 106 </p> 194 <p style="line-height: 100%;"><font color="#000000"> As a last step,107 <p style="line-height: 100%;"><font color="#000000"></font></p><p style="line-height: 100%; font-weight: bold; text-decoration: underline;"><font color="#000000">Installation Verification</font></p><p style="line-height: 100%;"><font color="#000000">As a last step, 195 108 after the compilation has been finished, the PALM installation has to 196 109 be verified. For this 197 110 purpose a simple test run is carried out. This once again requires the <b>mrun 198 </b>configuration file (described in </font><a href="chapter_3.2.html"><font 199 color="#000080">chapter 200 3.2</font></a><font color="#000000">), as well as the </font><a 201 href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d"><font 202 color="#000080">parameter 203 file</font></a><font color="#000000"> (described in </font><a 204 href="chapter_4.4.html"><font color="#000080">chapter 205 4.4</font></a>)<font color="#000000">. The parameter file must be 206 copied to<br> 111 </b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter 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 113 file</font></a><font color="#000000"> (described in </font><a href="chapter_4.4.html"><font color="#000080">chapter 114 4.4</font></a>)<font color="#000000">. The parameter file must be 115 copied from the PALM working copy by<br> 207 116 </font></p> 208 <p style="line-height: 100%;"><tt><font color="#000000"> 209 ~/palm/current_version/JOBS/example/INPUT/example_p3d</font></tt><font 210 color="#000000"> . 211 </font></p> 117 <div style="margin-left: 40px;"><span style="font-family: monospace;"></span><font style="font-family: Courier New,Courier,monospace;" color="#000000">mkdir -p JOBS/example/INPUT<br>cp trunk/INSTALL/example_p3d JOBS/example/INPUT/example_p3d</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"></span></font></div> 212 118 <p style="line-height: 100%;"><font color="#000000">The test run can 213 now be started by e ntering the command:</font>119 now be started by executing the command </font> 214 120 </p> 215 <pre 216 style="margin-left: 1cm; margin-right: 1cm; margin-bottom: 0.5cm; line-height: 100%;"><font 217 color="#000000">mrun -d example -h ibmh -K parallel -X 8 -T 8 -t 500 -q cdev -r d3# pr#</font></pre> 121 <pre style="margin-left: 1cm; margin-right: 1cm; margin-bottom: 0.5cm; line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mrun -d example -h ibmh -K parallel -X 8 -T 8 -t 500 -q cdev -r “d3# pr#”</font></pre> 218 122 <p style="line-height: 100%;"><font color="#000000">This specific run 219 123 will be carried out on 8 PEs and is allowed to use up to 500 seconds 220 124 CPU time. After pressing <return>, the most important settings of 221 125 the job are displayed at the terminal window 222 and the user is prompted for o.k. (</font><tt><font color="#000000">y</font></tt><font 223 color="#000000">). 224 Afterwards a message of the queuing system like <i>Request</i> 225 226 <i>Submitted to queue 227 by 228 </i>should be displayed. Now the job is 229 queued either started immediately or at a later time, depending on the 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> … 127 <i>Submitted to queue… by…” </i>should be displayed. Now the job is 128 queued and either started immediately or at a later time, depending on the 230 129 current workload of the remote host. Provided that it is executed 231 130 immediately and that all things work as designed, the job protocol of 232 this run will appear under the file name </font><tt><font 233 color="#000000">~/job_queue/ibmh_example</font></tt><font 234 color="#000000"> no more than 3 minutes later. The content of this 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 235 132 file should be carefully examined for any error messages.</font> 236 133 </p> 134 135 237 136 <p style="line-height: 100%;">Beside the job protocol and according to 238 137 the configuration file and arguments given for <b>mrun</b> 239 options <tt>-d</tt> and <tt>-r,</tt>further files should be found in138 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 240 139 the 241 directories<br> 242 </p> 243 <p style="line-height: 100%; font-family: monospace;"> 244 ~/palm/current_version/JOBS/example/MONITORING 245 <br> 246 </p> 247 <p style="line-height: 100%;">and</p> 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> 248 141 <p style="line-height: 100%;"><span style="font-family: monospace;"> 249 ~/palm/current_version/JOBS/example/OUTPUT . 250 </span><br> 142 </span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/OUTPUT</span><span style="font-family: monospace;"></span><br> 251 143 </p> 252 144 <p style="line-height: 100%;">Please compare the contents of file</p> 253 145 <p style="line-height: 100%;"><span style="font-family: monospace;"> 254 ~/palm/current_version/JOBS/example/MONITORING/ibmh_example_rc</span><br>146 </span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/MONITORING/ibmh_example_rc</span><br> 255 147 </p> 256 <p style="line-height: 100%;">with those of the <a 257 href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_rc">result 258 example file</a> (e.g. with the help of the UNIX-command <span 259 style="font-family: monospace;">diff</span>). There should be not a 260 single difference between these two files. <font color="#000000">If 148 <p style="line-height: 100%;">with those of the example result file which can be found under<span style="font-family: Courier New,Courier,monospace;"> trunk/INSTALL/example_rc</span>., e.g. by using the<span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;"> standard</span> diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff JOBS/example/MONITORING/ibmh_example_rc trunk/INSTALL/example_rc</p><p style="line-height: 100%;">where it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;"> ~/palm/current_version</span>.</p><p style="line-height: 100%;"><span style="font-weight: bold;">You should not find any difference between these two files</span>, except of the run date and time displayed at the top of the file header. <font color="#000000">If 261 149 the file contents are identical, the installation is successfully 262 150 completed.</font> </p> … … 265 153 help you. </p> 266 154 <hr> 267 <p style="line-height: 100%;"><font color="#000080"><font 268 color="#000080"><a href="chapter_4.6.html"><font color="#000080"><img 269 src="left.gif" name="Grafik1" align="bottom" border="2" height="32" 270 width="32"></font></a><a href="Inhaltsverzeichnis.html"><font 271 color="#000080"><img src="up.gif" name="Grafik2" align="bottom" 272 border="2" height="32" width="32"></font></a><a href="chapter_5.1.html"><font 273 color="#000080"><img src="right.gif" name="Grafik3" align="bottom" 274 border="2" height="32" width="32"></font></a></font></font></p> 275 <p style="line-height: 100%;"><i>Last change: </i> 20/04/05 (SR) </p> 276 </body> 277 </html> 155 <p style="line-height: 100%;"><font color="#000080"><font color="#000080"><a href="chapter_4.6.html"><font color="#000080"><img src="left.gif" name="Grafik1" align="bottom" border="2" height="32" width="32"></font></a><a href="Inhaltsverzeichnis.html"><font color="#000080"><img src="up.gif" name="Grafik2" align="bottom" border="2" height="32" width="32"></font></a><a href="chapter_5.1.html"><font color="#000080"><img src="right.gif" name="Grafik3" align="bottom" border="2" height="32" width="32"></font></a></font></font></p> 156 <p style="line-height: 100%;"><i>Last change: </i> 02/03/07 (SR) </p> 157 </body></html>
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