Changeset 83 for palm/trunk/DOC/app/chapter_5.0.html
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r62 r83 1 1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> 2 2 <html><head> 3 <meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM 4 chapter 5.0</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Siegfried Raasch"> <meta name="CREATED" content="20041103;12380720"> <meta name="CHANGED" content="20041123;15532356"> <meta name="KEYWORDS" content="parallel LES model"> <style> 3 <meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM chapter 5.0</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Siegfried Raasch"> <meta name="CREATED" content="20041103;12380720"> <meta name="CHANGED" content="20041123;15532356"> <meta name="KEYWORDS" content="parallel LES model"> <style> 5 4 <!-- 6 5 @page { size: 21cm 29.7cm } … … 19 18 local host. Alternatively, <span style="font-weight: bold;">mrun</span> 20 19 can also be used to start PALM on the local host in interactive mode or 21 as a batch job .</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">The20 as a batch job (if a queueing system like NQS, PBS, or LoadLeveler is 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 22 21 installation and operation of PALM requires at mimimum (on both, the 23 local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The AT&T Korn-shell (ksh) must be 24 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">. 25 Most of the current Linux distributions are using the public domain 26 Korn-shell (pdksh). The PALM scripts <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span> do not work 27 with the pdksh! Please replace it by the AT&T ksh. If the 28 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">, 29 please modify the first lines in <span style="font-weight: bold;">mrun</span> 30 and <span style="font-weight: bold;">mbuild</span>, 31 respectively.</font></li><li><font color="#000000">The 22 local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The Korn-shell (AT&T ksh or public domain ksh) must be 23 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 32 24 NetCDF-library with version number not earlier than 3.6.0-p1 (for 33 25 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 … … 55 47 as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>) and Tokyo 56 48 Institute of Technology (<span style="font-style: italic;">lctit</span>). 57 The strings given in brackets are the systems names under which <span style="font-weight: bold;">mrun</span> indentifies the 58 different hosts. mrun should also work on other systems, but this 59 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 60 versions will allow to configure the scripts for different kinds of 61 systems by just using a configuration file.</font><p style="line-height: 100%;"><font color="#000000">The 49 The strings given in brackets are the systems names (host identifiers) under which <span style="font-weight: bold;">mrun</span> identifies the 50 different hosts.<br><br>You can also use <span style="font-weight: bold;">mrun</span>/PALM on other Linux-Cluster, IBM-AIX, or NEC-SX machines. See <a href="#configuration_for_other_machines">below</a> on how to configure <span style="font-weight: bold;">mrun</span> for other machines. However, these configurations currently (version 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 62 51 examples given in this chapter refer to an 63 52 installation of PALM on an IMUK Linux workstation and the IBM-Regatta … … 136 125 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 137 126 Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To 138 use the PALM scripts, the PATHvariable has to be extended and the139 environment variable PALM_BINhas to be set (on local and remote host)127 use the PALM scripts, the <span style="font-family: Courier New,Courier,monospace;">PATH</span>-variable has to be extended and the 128 environment variable<span style="font-family: Courier New,Courier,monospace;"> PALM_BIN </span>has to be set (on local and remote host) 140 129 in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>, 141 130 if<span style="font-family: Courier New,Courier,monospace;"> … … 143 132 PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH</font><font color="#000000"><br><span style="font-family: Courier New,Courier,monospace;">export 144 133 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 145 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 146 small helper/utility programs have to be installed, which are e.g. 147 later used by <span style="font-weight: bold;">mrun</span> 148 or for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script 134 may have to login again in order to activate these settings.</font></p><font color="#000000">On the local and on the remote host, some 135 small helper/utility programs have to be installed, which are later used by <span style="font-weight: bold;">mrun</span> e.g. for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script 149 136 requires a configuration file<span style="font-family: Courier New,Courier,monospace;"> 150 137 .mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the … … 155 142 typical installation parameters 156 143 like compiler name, compiler options, etc. 157 for a set of different remotehosts. Please edit this file, uncomment144 for a set of different (remote) hosts. Please edit this file, uncomment 158 145 lines like</font><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username 159 146 <replace by your ... username> 160 < remote-computer-shortcut></div><p style="line-height: 100%;"><font color="#000000">by147 <host identifier></div><p style="line-height: 100%;"><font color="#000000">by 161 148 removing the first hash (<span style="font-family: Courier New,Courier,monospace;">#</span>) 162 149 character and replace the string "<span style="font-family: Courier New,Courier,monospace;"><replace 163 150 by ...></span>" by your username on the respective host 164 given in the <span style="font-family: Courier New,Courier,monospace;">< remote-computer-shortcut></span>.151 given in the <span style="font-family: Courier New,Courier,monospace;"><host identifier></span>. 165 152 You only have to uncomment lines for those hosts on which you intend to 166 153 use PALM.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the 167 154 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 168 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 remote155 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 169 156 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 170 157 of PALM Code</span></font></p><font color="#000000"> … … 265 252 and time displayed at the top of the file header. <font color="#000000">If 266 253 the file contents are identical, the installation is successfully 267 completed.</font> 254 completed.<br><br></font><p style="line-height: 100%;"></p><p style="line-height: 100%; font-weight: bold; text-decoration: underline;"><font color="#000000"><a name="configuration_for_other_machines"></a>Configuration for other machines</font></p><font color="#000000">Starting 255 from version 3.2a, beside the default hosts (HLRN, etc.), PALM can also 256 be installed and run on other Linux-Cluster-, IBM-AIX, or 257 NEC-SX-systems. To configure PALM for a non-default host only requires 258 to add some lines to the configuration file<span style="font-family: Courier New,Courier,monospace;"> .mrun.config</span>.<br><br>First, 259 you have to define the host identifier (a string of arbitrary length) 260 under which your local host shall be identified by adding a line<br><br></font><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">%host_identifier <hostname> <host identifier></span><br></div><br>to the configuration file (best to do this in the section where the other default host identifiers are defined). Here<span style="font-family: Courier New,Courier,monospace;"> <hostname> </span>must be the name of your local host as provided by the unix-command "<span style="font-family: Courier New,Courier,monospace;">hostname</span>". The first characters of<span style="font-family: Courier New,Courier,monospace;"> <host identifier> </span>have to be "<span style="font-family: Courier New,Courier,monospace;">lc</span>", if your system is (part of) a linux-cluster, "<span style="font-family: Courier New,Courier,monospace;">ibm</span>", or "<span style="font-family: Courier New,Courier,monospace;">nec</span>" 261 in case of an IBM-AIX- or NEC-SX-system, respectively. For example, if 262 you want to install on a linux-cluster, the line may read as<br><br><div style="margin-left: 40px;">%host_identifier foo lc_bar<br></div><br>In 263 the second step, you have to give all informations neccessary to 264 compile and run PALM on your local host by adding an additional section 265 to the configuration file:<br><br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username <1> <host identifier> parallel<br>%tmp_user_catalog <2> <host identifier> parallel<br>%compiler_name <3> <host identifier> parallel<br>%compiler_name_ser <4> <host identifier> parallel<br>%cpp_options 266 <5> <host identifier> parallel<br>%netcdf_inc <6> <host identifier> parallel<br>%netcdf_lib <7> <host identifier> parallel<br>%fopts 267 <8> <host identifier> parallel<br>%lopts 268 <9> <host identifier> parallel<br></div><br>The 269 section consists of four columns each separated by one or more blanks. 270 The first column gives the name of the respective environment variable 271 used by <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span>, 272 while the second column defines its value. The third column has to be 273 the host identifier as defined above, and the last column in each line 274 must contain the string "<span style="font-family: Courier New,Courier,monospace;">parallel</span>". 275 Otherwise, the respective line(s) will be interpreted as belonging to 276 the setup for compiling and running a serial (non-parallel) version of 277 PALM.<br><br>All brackets have to be replaced by the appropriate settings for your local host:<br><ul><li><span style="font-family: Courier New,Courier,monospace;"><1> </span>is the username on your LOCAL host</li><li><span style="font-family: Courier New,Courier,monospace;"><2> </span>is the temporary directory in which PALM runs will be carried out</li><li><span style="font-family: Courier New,Courier,monospace;"><3> </span>is the compiler name which generates parallel code</li><li><span style="font-family: Courier New,Courier,monospace;"><4> </span>is the compiler name for generating serial code</li><li><span style="font-family: Courier New,Courier,monospace;"><5> </span>are 278 the preprocessor options to be invoked. In most of the cases, it will 279 be neccessary to adjust the MPI data types to double precision by 280 giving <span style="font-family: Courier New,Courier,monospace;">-DMPI_REAL=MPI_DOUBLE_PRECISION -DMPI_2REAL=MPI_2DOUBLE_PRECISION</span>. To switch on the NetCDF support, you also have to give <span style="font-family: Courier New,Courier,monospace;">-D__netcdf</span> and <span style="font-family: Courier New,Courier,monospace;">-D__netcdf_64bit</span> (if you like to have 64bit NetCDF output).</li><li><span style="font-family: Courier New,Courier,monospace;"><6> </span>is the compiler option for specifying the include path to search for the NetCDF module/include files</li><li><span style="font-family: Courier New,Courier,monospace;"><7> </span>are the linker options to search for the NetCDF library</li><li><span style="font-family: Courier New,Courier,monospace;"><8> </span>are the general compiler options to be used. You should allways switch on double precision (e.g. <span style="font-family: Courier New,Courier,monospace;">-r8</span>) and code optimization (e.g. <span style="font-family: Courier New,Courier,monospace;">-O2</span>).</li><li><span style="font-family: Courier New,Courier,monospace;"><9> </span>are the linker options</li><li><span style="font-family: Courier New,Courier,monospace;"><host identifier> </span>is the host identifier as defined before</li></ul><br>A typical example may be:<br><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">%remote_username 281 raasch 282 lc_bar parallel<br>%tmp_user_catalog 283 /tmp lc_bar 284 parallel<br>%compiler_name 285 mpif90 lc_bar 286 parallel<br>%compiler_name_ser 287 ifort lc_bar 288 parallel<br>%cpp_options 289 -DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__netcdf_64bit 290 lc_bar parallel<br>%netcdf_inc 291 -I:/usr/local/netcdf/include 292 lc_bar parallel<br>%netcdf_lib 293 -L/usr/local/netcdf/lib:-lnetcdf 294 lc_bar parallel<br>%fopts 295 -axW:-cpp:-openmp:-r8:-nbs 296 lc_bar parallel<br>%lopts 297 -axW:-cpp:-openmp:-r8:-nbs:-Vaxlib lc_bar 298 parallel<br></div><br>Currently (version 3.2a), depending on the MPI 299 version which is running on your local host, the options for the 300 execution command (which may be <span style="font-family: Courier New,Courier,monospace;">mpirun</span> or <span style="font-family: Courier New,Courier,monospace;">mpiexec</span>) 301 may have to be adjusted manually in the mrun-script. A future version 302 will allow to give the respective settings in the configuration file. 268 303 <p style="line-height: 100%;">If you have any problems 269 304 with the PALM 270 305 installation, the members of the PALM working group are pleased to 271 306 help you. </p> 272 <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=" 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>307 <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> 273 308 <p style="line-height: 100%;"><i>Last 274 309 change: </i> $Id$</p>
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