Changeset 515 for palm/trunk
- Timestamp:
- Mar 18, 2010 2:30:38 AM (15 years ago)
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- palm/trunk
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DOC/app/chapter_5.0.html (modified) (9 diffs)
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INSTALL/MAKE.inc.ifort.imuk (modified) (1 diff)
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SCRIPTS/palm_simple_install (modified) (2 diffs)
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SCRIPTS/palm_simple_run (modified) (4 diffs)
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SOURCE/buoyancy.f90 (modified) (1 diff)
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palm/trunk/DOC/app/chapter_5.0.html
r493 r515 1 1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> 2 2 <html><head> 3 3 4 4 5 … … 8 9 --> 9 10 </style></head><body style="direction: ltr;" lang="en-US"><h2 style="line-height: 100%;"><font size="4">5.0 10 Installation of the 11 model</font></h2>11 Code installation<br> 12 </font></h2> 12 13 <font color="#000000">This chapter 13 describes the installation of PALM on a Linux workstation (local host) 14 and a suitable remote computer, on which the 15 model runs are to be carried out. The local host is used to 16 start batch jobs with <b>mrun</b> and to analyze the 17 results 18 which are produced by the model on the remote host and send backto the14 describes the installation of PALM on a Linux workstation (local host). There are two methods to install and run PALM. With the <span style="font-style: italic;">simple method</span>, you can run PALM interactively on the local computer. This method is using the scripts <span style="font-weight: bold;">palm_simple_install</span> and <span style="font-weight: bold;">palm_simple_run</span>. 15 The simple method cannot create batch jobs itself, and cannot be used 16 to create restart runs. Also file handling and most other features of 17 the <span style="font-style: italic;">advanced method</span> are not available. This method is only recommended for those who like to test PALM quickly.<br> 18 <br> 19 The <span style="font-style: italic;">advanced method</span> is for running PALM in batch mode on a suitable remote computer. The installation procedure is using the script <span style="font-weight: bold;">mbuild</span>. All jobs are started on the local host using the script <b>mrun</b>. The PALM output is automatically sent back from the remote host to the 19 20 local host. Alternatively, <span style="font-weight: bold;">mrun</span> 20 can also be used to start PALM on the local host in interactive mode or 21 as a batch job (if a queueing system like NQS, PBS, or LoadLeveler is 22 available).</font><p style="line-height: 100%;"></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Requirements</span></font></p><p style="line-height: 100%;"><font color="#000000">The 23 installation and operation of PALM requires at mimimum (on both, the 24 local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The Korn-shell (AT&T ksh or public 25 domain ksh) must be 26 available under<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">/bin/ksh</font><font color="#000000">.<span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-family: Courier New,Courier,monospace;"></span></font><font color="#000000"><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span></font></li><li><font color="#000000">The 27 NetCDF-library with version number not earlier than 3.6.0-p1 (for 21 can also be used to start PALM in interactive mode on the local host, or 22 as a batch job on the local host (if a queueing system like NQS, PBS, or LoadLeveler is 23 available).<br> 24 <br> 25 Only the <span style="font-style: italic;">advanced method</span> gives full access to all PALM features.<br> 26 <br> 27 </font><p style="line-height: 100%;"></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Requirements</span></font></p><p style="line-height: 100%;"><font color="#000000">The 28 installation and operation of PALM requires at mimimum (for the <span style="font-style: italic;">advanced method</span> on both, the 29 local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">A Korn-shell (AT&T ksh or public 30 domain ksh); must be 31 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">A NetCDF-library with version number not earlier than 3.6.2 (for 28 32 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 29 33 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 … … 37 41 please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>) 38 42 and define a username under which you like to access the repository. 39 You will then receive a password which allows the access under this 40 name.</font></li><li><font color="#000000">A 41 job queueing system must be available on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle 43 You will then receive a password which allows access under this 44 name.<br> 45 <br> 46 The <span style="font-style: italic;">advanced method</span> additionally requires:<br> 47 </font></li><li><font color="#000000">A 48 job queueing system on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle 42 49 LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).</font></li><li><font color="#000000">ssh/scp-connections to and from the remote 43 50 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 44 51 to be used on a limited number of selected machines. These are SGI-ICE 45 52 systems at computing center HLRN in Hannover (<span style="font-style: italic;">lcsgih</span>), Berlin (<span style="font-style: italic;">lcsgib</span>), 46 IBM-Regatta system<span style="font-style: italic;"></span> 47 at Yonsei University, Seoul (<span style="font-style: italic;">ibms</span>), 48 on NEC-SX6/8 systems at DKRZ, Hamburg (<span style="font-style: italic;">nech</span>) and RIAM, 53 IBM-Regatta systems<span style="font-style: italic;"></span> 54 at Yonsei University (<span style="font-style: italic;">ibmy</span>), <span style="font-style: italic;"></span> and at DKRZ, Hamburg (<span style="font-style: italic;">ibmh</span>), an NEC-SX8 system at RIAM, 49 55 Kyushu University, Fukuoka (<span style="font-style: italic;">necriam</span>), 50 56 as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>), Tokyo 51 57 Institute of Technology (<span style="font-style: italic;">lctit</span>), 52 and the Bergen Center for Computational Science (<span style="font-style: italic;">lcxt4</span>).58 Kyoto computing center (<span style="font-style: italic;">lckyoto</span>), and Cray-XT4/5 systems at the Bergen Center for Computational Science (<span style="font-style: italic;">lcxt4</span>) and at the Finish Meteorological Institute (<span style="font-style: italic;">lcxt5m</span>). 53 59 The strings given in brackets are the systems names (host identifiers) 54 60 under which <span style="font-weight: bold;">mrun</span> … … 56 62 different hosts.<br><br>You can also use <span style="font-weight: bold;">mrun</span>/PALM on other 57 63 Linux-Cluster, IBM-AIX, or NEC-SX machines. See <a href="#configuration_for_other_machines">below</a> on 58 how to configure <span style="font-weight: bold;">mrun</span> 59 for other machines. However, these configurations currently (version 60 3.2a) allow to run PALM in interactive mode only.<br><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span></font><p style="line-height: 100%;"><font color="#000000">The 64 how to configure <span style="font-weight: bold;">mrun</span>for 65 other machines. However, these configurations currently (version 66 3.7a) allow to run PALM in interactive mode only. Batch mode requires 67 manual adjustments for the respective queing system and MPI 68 installation in scripts <span style="font-weight: bold;">mrun</span>, <span style="font-weight: bold;">mbuild</span>, and <span style="font-weight: bold;">subjob</span>.<br><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span style="font-weight: bold;"></span></font><p style="line-height: 100%;"><font color="#000000">The 61 69 examples given in this chapter refer to an 62 installation of PALM on an IMUK Linux workstation and the SGI-ICE 63 system of 64 the HLRN used as remote host. They are just called local and 70 installation of PALM on an IMUK Linux workstation and (for the <span style="font-style: italic;">advanced method</span>) the SGI-ICE 71 system of HLRN, used as remote host. They are just referred to as local and 65 72 remote host from now on. </font></p><p style="line-height: 100%;"> 66 73 </p><p style="line-height: 100%;">The installation 67 process requires a valid 68 account on the local and on the remote host as well.<br> 74 process for the <span style="font-style: italic;">advanced method</span> requires a valid 75 account on the local and on the remote host as well.</p> 76 <p style="line-height: 100%;">The <span style="font-style: italic;">advanced installation method</span> is described below. For the <span style="font-style: italic;">simple method</span> see the <a href="#simple_installation_method">end of this chapter</a>.<br> 69 77 </p> 70 <ul> All hosts (local as well as remote) are 78 79 <ul> 80 All hosts (local as well as remote) are 71 81 accessed via the secure shell (ssh). The user must establish 72 82 passwordless login using the private/public-key mechanism (see e.g. the … … 87 97 prompted for a password. <b>Before continuing the further 88 98 installation 89 process, this must be absolutely guaranteed!</b> Thismust also99 process, this must be absolutely guaranteed!</b> It must also 90 100 be 91 101 guaranteed for <b>all</b> other remote hosts, on which 92 102 PALM shall run.<br><br>Please 93 note that on many remote hosts, passwordless login must also be 94 established <b>within the remote host</b>, i.e. from the 95 remote host to itself. Test this by executing on the remote host: <span style="font-family: Courier New,Courier,monospace;">ssh 96 <remote IP-address></span>. You should not be prompted 97 for a password.<br><br></ul><p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package 98 Installation</span></p><p style="line-height: 100%;">In 99 the <b>first installation step</b> a 100 set of directories must be created both on the local and on the 101 remote host. These directories are:</p><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/job_queue<br></div><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm<br></div><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm/current_version<br></div><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS</span><br></div><p style="line-height: 100%;">The names of these directories 102 are 103 freely selectable (except <big><tt><font size="2"><big>~/job_queue</big></font></tt></big>), 104 however new users should use them as suggested, since many 105 examples in this documentation as well as all example files are 106 assuming these settings. The directory <big><span style="font-family: monospace;">~/palm/current_version</span></big> 103 note that on many remote hosts, passwordless login must also work <b>within the remote host</b>, i.e. for ssh connections from the 104 remote host to itself. Test this by executing on the remote host:<br> 105 <br> 106 <span style="font-family: Courier New,Courier,monospace;"> ssh 107 <username on remote host>@<remote IP-address></span> .<br> 108 <br> 109 You should not be prompted 110 for a password.<br><br> 111 </ul> 112 <p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package 113 Installation</span></p><p style="line-height: 100%;">The <b>first installation step</b> requires creating a 114 set of directories on the local and, for the <span style="font-style: italic;">advanced method</span>, on the 115 remote host<span style="font-style: italic;"></span>. These are:</p><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/job_queue<br></div><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm<br></div><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm/current_version<br></div><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS</span><br></div><p style="line-height: 100%;">The names of these directories can be 116 freely selected (except <big><tt><font size="2"><big>~/job_queue</big></font></tt></big>), 117 however new users should choose them as suggested, since many 118 examples in this documentation as well as all example files are based on these settings. The directory <big><span style="font-family: monospace;">~/palm/current_version</span></big> 107 119 on the local host will be called the working directory from now on. </p> 108 120 <p style="line-height: 100%;"><font color="#000000">In 109 121 the <b>second 110 122 step</b> 111 a working copy of the recent version of the PALM software package,123 a working copy of the recent PALM version, 112 124 including the source code, scripts, documentation, etc. must 113 125 be 114 126 copied to the working directory (</font><font color="#000000">local 115 127 host!) by executing the following 116 commands. Replace <your username> by the name that you 117 chose to 128 commands. Replace <your username> by the name that you have chosen to 118 129 access the repository, and <#> by any of the available 119 130 PALM 120 releases, e.g. "<span style="font-style: italic;">3. 1c</span>"121 (new releases will be an ounced by email tothe PALM mailing list).</font></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">cd131 releases, e.g. "<span style="font-style: italic;">3.7a</span>" 132 (new releases will be announced to members of the PALM mailing list).</font></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">cd 122 133 ~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn 123 134 checkout --username <your username> 124 135 svn://130.75.105.2/palm/tags/release-<#> trunk</span><br></div><p style="line-height: 100%;"><font color="#000000">You 125 will then be prompted for your password. After finishing, the 126 subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">should 127 appear in your working directory. It contains a number of further 128 subdirectories which contain e.g. the PALM source code (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SOURCE</font><font color="#000000">) 136 will then be prompted for your password. After completion, there should be a subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">in your working directory. It contains a number of further 137 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">) 129 138 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://130.75.105.2/palm/tags/release-<#> abcde</pre><p style="line-height: 100%;">will place your working copy in a 130 directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span> instead131 of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span> .139 directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span>(instead 140 of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span>). 132 141 But keep in mind that you will have to adjust several paths given 133 142 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 134 your working copy of PALM, unless you know exactlywhat you143 your working copy of PALM, unless you know what you 135 144 are doing.</p><p style="line-height: 100%; font-weight: bold;"><span style="font-weight: normal;">You can also get a copy of the 136 most recent code by executing</span></p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username <your username> svn://130.75.105.2/palm/trunk trunk</pre>However, 137 this version may contain bugs and new features may not be documented. <span style="font-weight: bold;">In future PALM releases, 138 repository access to this most recent version will 139 probably be restricted to the PALM developers.</span><p style="line-height: 100%;"></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Package 145 most recent developer 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://130.75.105.2/palm/trunk trunk</pre>This version may contain new features (they might not be documented well), but it may also contain bugs.<span style="font-weight: bold;"><br> 146 </span><br> 147 <p style="line-height: 100%;"></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Package 140 148 Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To 141 149 use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable … … 172 180 use PALM.</font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">Warning: 173 181 When editing the configuration file, please NEVER use the TAB key. 174 Otherwise, very confusing errors in mrun execution may occur.</span></font></p><p style="line-height: 100%;"><font color="#000000">Beside the default configuration file</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> .mrun.config.default</font><font color="#000000">, the directory<span style="font-family: Courier New,Courier,monospace;">182 Otherwise, very confusing errors may occur when mrun is executing.</span></font></p><p style="line-height: 100%;"><font color="#000000">Beside the default configuration file</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> .mrun.config.default</font><font color="#000000">, the directory<span style="font-family: Courier New,Courier,monospace;"> 175 183 trunk/SCRIPTS </span>contains additional configuration files 176 which are already adjusted for special hosts:<span style="font-family: Courier New,Courier,monospace;"> 177 .mrun.config.imuk </span>can be used at Hannover University,<span style="font-family: Courier New,Courier,monospace;"> 178 .mrun.config.riam </span>can 179 be used at the Research Institute of Applied Mechanics, Kyushu 180 University. These files have to be edited in the same way as described 184 which are already adjusted for special hosts</font><font color="#000000">, e.g.</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"> 185 .mrun.config.imuk </span>can be used at Hannover University</font><font color="#000000">, etc.. </font><font color="#000000">These files have to be edited in the same way as described 181 186 above.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the 182 187 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 … … 184 189 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 185 190 remote 186 host.</font></p><p style="line-height: 100%;"></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Pre-Compilation 191 host.<br> 192 <br> 193 </font></p><p style="line-height: 100%;"></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Pre-Compilation 187 194 of PALM Code</span></font></p><font color="#000000"> 188 195 </font><br><font color="#000000">To avoid the … … 203 210 files) are 204 211 stored on the remote computer in the default directory 205 </font><font style="font-family: Courier New,Courier,monospace;" color="#000000">~/palm/current_version/MAKE_DEPOSITORY</font> .<font color="#000000"><span style="font-weight: bold;"></span></font><p style="line-height: 100%;"><font color="#000000">The212 </font><font style="font-family: Courier New,Courier,monospace;" color="#000000">~/palm/current_version/MAKE_DEPOSITORY</font>_<span style="font-family: Courier New,Courier,monospace;"><block_descriptor></span>, where<font color="#000000"> <span style="font-family: Courier New,Courier,monospace;"><block_descriptor></span> is composed of the third (and fourth, if existing) column of the respective block in the configuration file (e.g. <span style="font-family: Courier New,Courier,monospace;">lcsgih_parallel</span> for HLRN).<span style="font-weight: bold;"></span></font><p style="line-height: 100%;"><font color="#000000">The 206 213 pre-compilation for the remote host (here the SGI-ICE system of HLRN) 207 214 is … … 385 392 execution command (which may be <span style="font-family: Courier New,Courier,monospace;">mpirun</span> 386 393 or <span style="font-family: Courier New,Courier,monospace;">mpiexec</span>) 387 may have to be adjusted manually in the mrun-script. A future version394 may have to be adjusted manually in the <span style="font-weight: bold;">mrun</span>-script. A future version 388 395 will allow to give the respective settings in the configuration file. 389 396 <p style="line-height: 100%;">If you have any problems 390 397 with the PALM 391 398 installation, the members of the PALM working group are pleased to 392 help you. </p> 393 <hr><p style="line-height: 100%;"><font color="#000080"><font color="#000080"><a href="chapter_4.6.html"><font color="#000080"><img src="left.gif" name="Grafik1" align="bottom" border="2" height="32" width="32"></font></a><a href="index.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="up" src="up.gif" name="Grafik2"></font></a><a href="chapter_5.1.html"><font color="#000080"><img src="right.gif" name="Grafik3" align="bottom" border="2" height="32" width="32"></font></a></font></font></p><p style="line-height: 100%;"><i>Last 399 help you.<br> 400 </p> 401 <p style="line-height: 100%;"><br> 402 <span style="font-weight: bold; text-decoration: underline;"><a name="simple_installation_method"></a>Simple installation method</span><br> 403 </p> 404 <p style="line-height: 100%;">The simple installation method is using the scripts <span style="font-weight: bold;">palm_simple_install</span> and <span style="font-weight: bold;">palm_simple_run</span> for installing and running PALM.<br> 405 <br> 406 <span style="font-weight: bold; text-decoration: underline;">Package 407 Installation</span></p> 408 <p style="line-height: 100%;"><span style="font-weight: bold;">First step:</span> Create a directory<span style="font-style: italic;"></span>:</p> 409 <div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">mkdir -p ~/palm/current_version/</div> 410 <p style="line-height: 100%;">You can freely choose the directory name, but if you intend to switch to the <span style="font-style: italic;">advanced method</span> of running PALM later, you should use<span style="font-family: Courier New,Courier,monospace;"> ~/palm/current_version</span>. This directory <big><span style="font-family: monospace;"></span></big>will be called working directory from now on. </p> 411 412 <p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">S</span><b>econd 413 step</b>: 414 Check out a working copy of the recent PALM version from the svn-repository</font><font color="#000000">. Replace<span style="font-family: Courier New,Courier,monospace;"> <your username> </span>by your valid repository username, and<span style="font-family: Courier New,Courier,monospace;"> <#> </span>by any of the available 415 PALM 416 releases, e.g. "<span style="font-style: italic;">3.7a</span>" 417 (new releases will be announced to members of the PALM mailing list).</font></p> 418 <div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">cd 419 ~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn 420 checkout --username <your username> 421 svn://130.75.105.2/palm/tags/release-<#> trunk</span><br></div> 422 <p style="line-height: 100%;"><font color="#000000">You 423 will be prompted for your password. After completion, a subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk <span style="font-family: Times New Roman,Times,serif;">will appear </span></font><font color="#000000">in your working directory. It contains a number of further 424 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">) 425 and the scripts for running PALM (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SCRIPTS</font><font color="#000000">). For checking out the most recent PALM version (developer version), see the <span style="font-style: italic;">advanced installation method</span> described above.<br> 426 </font></p> 427 <p style="line-height: 100%;">Please never touch any file in 428 your working copy of PALM, unless you really know what you 429 are doing.</p> 430 <br> 431 432 <p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Configuration and compilation<br> 433 </span></font></p> 434 <p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">Third step:</span> To 435 use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable 436 has to be extended and the 437 environment variable<span style="font-family: Courier New,Courier,monospace;"> 438 PALM_BIN </span>has to be set. For convenience, setting should be done 439 in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>, 440 if<span style="font-family: Courier New,Courier,monospace;"> 441 ksh </span>is used):</font></p> 442 <p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">export 443 PALM_BIN=</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">$HOME/palm/current_version/trunk/SCRIPTS<br> 444 </font><font style="font-family: Courier New,Courier,monospace;" color="#000000">export 445 PATH=$PALM_BIN:$PATH</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"><br> 446 </span></font></p> 447 <p style="line-height: 100%;"><font color="#000000">You 448 may have to login again in order to activate the profile settings.<br> 449 </font></p> 450 <p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">Fourth step:</span> Call the installation script:<br> 451 </font></p> 452 <p style="line-height: 100%; margin-left: 40px;"><font style="font-family: Courier New,Courier,monospace;" color="#000000">palm_simple_install -i MAKE.inc.ifort.imuk</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"><br> 453 </span></font></p> 454 455 <p style="line-height: 100%;"><font color="#000000">The script copies the PALM source code into a new subdirectory <span style="font-family: Courier New,Courier,monospace;">MAKE_DEPOSITORY_simple</span>. This directory also will contain a <span style="font-family: Courier New,Courier,monospace;">Makefile</span> and an include file <span style="font-family: Courier New,Courier,monospace;">MAKE.inc</span> 456 to be used for compiling the code in the next step. The include file 457 contains compiler name, compiler options, library path for NetCDF, etc. 458 <span style="font-weight: bold;">Please adjust these settings as required by your system, before you proceed with the next step.</span> The default settings in <span style="font-family: Courier New,Courier,monospace;">MAKE.inc</span> 459 are for the Intel-FORTRAN compiler in the IMUK environment. You may 460 find default settings for other compilers and environments in <span style="font-family: Courier New,Courier,monospace;">.../trunk/INSTALL/</span> See for files<span style="font-family: Courier New,Courier,monospace;"> MAKE.inc.*</span>.<br> 461 </font></p> 462 <p style="line-height: 100%; margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">cd MAKE_DEPOSITORY_simple<br> 463 </span><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">make<br> 464 cd ..<br> 465 </span></font></p> 466 467 468 <p style="line-height: 100%;">In order to shorten compilation time, you can run make in parallel, e.g.<span style="font-family: Courier New,Courier,monospace;"> make -j 4 </span>runs 4 compile threads simultaneously.<br> 469 <br> 470 <span style="font-weight: bold;">Fifth step:</span> Carry out a test 471 run in order to check the installation. The test run (as every PALM 472 run) requires a parameter file for steering PALM, which is in 473 FORTRAN-NAMELIST format. This file has been already generated by the 474 installation script <span style="font-family: Courier New,Courier,monospace;">palm_simple_install</span> under <span style="font-family: Courier New,Courier,monospace;">JOBS/example_cbl/INPUT/example_cbl_p3d</span><span style="font-family: Courier New,Courier,monospace;"></span>. PALM is started with script <span style="font-family: Courier New,Courier,monospace;">palm_simple_run</span>. <span style="font-weight: bold;">Before</span> the first run, it may be necessary to change the MPI-execution command (<span style="font-family: Courier New,Courier,monospace;">mpiexec</span>, <span style="font-family: Courier New,Courier,monospace;">mpirun</span>, etc.) and options in this script, depending on the MPI-library that you are using. The script can be found in directory <span style="font-family: Courier New,Courier,monospace;">.../trunk/SCRIPTS</span>. 475 Default settings in this script are for the SGI-mpt-library installed 476 on HLRN. You will find the execution command almost at the end of this 477 script. After having adjusted the MPI-execution command, start the run 478 with:<br> 479 </p> 480 <p style="line-height: 100%; margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">palm_simple_run -p 4 -n 4 -c example_cbl</span><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"><br> 481 </span></font></p> 482 483 484 485 <p style="line-height: 100%;">where option <span style="font-family: Courier New,Courier,monospace;">-p</span> gives the total number of MPI tasks, <span style="font-family: Courier New,Courier,monospace;">-n</span> gives the number of MPI tasks per node, and <span style="font-family: Courier New,Courier,monospace;">-c</span> gives the parameter file to be used.<br> 486 After the run has finished, all OUTPUT files can be found in directory <span style="font-family: Courier New,Courier,monospace;">OUTPUT....</span> Names and contents of PALM output files are described in <a href="chapter_3.4.html">chapter 3.4</a>. 487 The directory name is composed of the parameter file name, the number 488 of cores that have been used, and the current data and time. For every 489 run a unique directory is created.<br> 490 </p> 491 <p style="line-height: 100%;"><span style="font-weight: bold;">Sixth step:</span> To verify the results of this example run, compare it with the default result:<br> 492 <span style="font-weight: bold;"></span></p> 493 <p style="line-height: 100%; margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">diff OUTPUT..../RUN_CONTROL trunk/INSTALL/example_cbl_rc</span><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"><br> 494 </span></font></p> 495 496 497 498 499 <span style="font-weight: bold;">You should not find any 500 difference between these two files</span>, except of the run date 501 and time displayed at the top of the file header, and, maybe, the number of cores that have been used. <font color="#000000">If 502 the file contents are identical, the installation is successfully 503 completed.</font><hr><p style="line-height: 100%;"><font color="#000080"><font color="#000080"><a href="chapter_4.6.html"><font color="#000080"><img src="left.gif" name="Grafik1" align="bottom" border="2" height="32" width="32"></font></a><a href="index.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="up" src="up.gif" name="Grafik2"></font></a><a href="chapter_5.1.html"><font color="#000080"><img src="right.gif" name="Grafik3" align="bottom" border="2" height="32" width="32"></font></a></font></font></p><p style="line-height: 100%;"><i>Last 394 504 change: </i> $Id: chapter_5.0.html 287 2009-04-09 395 505 08:59:36Z raasch $</p> -
palm/trunk/INSTALL/MAKE.inc.ifort.imuk
r421 r515 1 # contents of this file are includein palm's makefile if the simple install1 # Contents of this file are included in palm's makefile if the simple install 2 2 # process (palm_simple_install) is used. 3 # Please adjust compiling parameters as required for your system 3 # Please adjust compiling parameters as required for your system. 4 4 5 5 PROG=palm 6 6 F90=mpif90 7 COPT= -cpp -DMPI_REAL=MPI_DOUBLE_PRECISION -DMPI_2REAL=MPI_2DOUBLE_PRECISION -D__netcdf -D__ netcdf_64bit -D__intel_openmp_bug -D__lc -D__parallel8 F90FLAGS= -axW - openmp-r8 -nbs -convert little_endian -I /muksoft_64/packages/netcdf/3.6.3/include9 LDFLAGS= -axW - openmp-r8 -nbs -Vaxlib -L/muksoft_64/packages/netcdf/3.6.3/lib -lnetcdf7 COPT= -cpp -DMPI_REAL=MPI_DOUBLE_PRECISION -DMPI_2REAL=MPI_2DOUBLE_PRECISION -D__netcdf -D__lc -D__parallel 8 F90FLAGS= -axW -O3 -r8 -nbs -convert little_endian -I /muksoft_64/packages/netcdf/3.6.3/include 9 LDFLAGS= -axW -O3 -r8 -nbs -Vaxlib -L/muksoft_64/packages/netcdf/3.6.3/lib -lnetcdf -
palm/trunk/SCRIPTS/palm_simple_install
r421 r515 14 14 # Last changes: 15 15 # 25/01/10 - Siggi - Generating the first version 16 # 18/03/10 - Siggi - switch to palm/current_version removed: working 17 # copy can be in any directory 16 18 17 19 … … 31 33 done 32 34 33 34 35 # Switch to default working directory36 cd ~/palm/current_version37 35 38 36 -
palm/trunk/SCRIPTS/palm_simple_run
r426 r515 9 9 # It requires that palm has been installed with command 10 10 # palm_simple_install and that the executable palm has been created 11 # with make in directory ~/palm/current_version/MAKE_DEPOSITORY_simple11 # with make in directory ...../MAKE_DEPOSITORY_simple 12 12 13 13 # Last changes: 14 14 # 25/01/10 - Siggi - Generating the first version 15 # 18/03/10 - Siggi - Some comments changed 15 16 16 17 … … 23 24 mpi_procs_per_node=1 24 25 openmp_threads=1 25 # palm_dir=~/palm/current_version/26 26 27 27 typeset -i ii … … 51 51 # Generate unique directory/files for this run 52 52 timedate="`date +%d.%b_%H:%M:%S`" 53 suffix=$case+$ nnodes+$timedate53 suffix=$case+$mpi_procs+$timedate 54 54 RUNDIR=OUTPUT.$suffix/ 55 55 … … 125 125 echo "*** palm will be run: MPI tasks: $mpi_procs OpenMP thread: $OMP_NUM_THREADS" 126 126 127 # mpiexec -machinefile hostfile -n $mpi_procs ./palm < runfile_atmos 128 mpiexec_mpt -np $mpi_procs ./palm < runfile_atmos 127 # IMUK: 128 mpiexec -machinefile hostfile -n $mpi_procs ./palm < runfile_atmos 129 130 # SGI-MPT HLRN 131 # mpiexec_mpt -np $mpi_procs ./palm < runfile_atmos 129 132 130 133 -
palm/trunk/SOURCE/buoyancy.f90
r392 r515 154 154 !------------------------------------------------------------------------------! 155 155 ! Call for grid point i,j 156 !------------------------------------------------------------------------------! 156 ! ATTENTION: PGI-compiler creates SIGFPE if opt>1 is used! Therefore, opt=1 is 157 ! forced by compiler-directive. 158 !------------------------------------------------------------------------------! 159 !pgi$r opt=1 157 160 SUBROUTINE buoyancy_ij( i, j, var, var_reference, wind_component, pr ) 158 161
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