MOSAIK

Timestamp:

Aug 24, 2017 11:15:05 AM (8 years ago)

Author:

kanani

Comment:

--

idefix

@@ -4 +4 @@
 = idefix user documentation =
 
-[[Image(idefix.png,nolink,400px,right)]]
-
 == System overview ==
+{{{#!table align=left style="border: none; text-align:left"
+   {{{#!tr 
+      {{{#!td style="border: none; width:50%"
 || hostname ||idefix ||
 || CPU architecture ||Intel Xeon Haswell || 
@@ -21 +22 @@
 ||          ||0.5 TB SSD SATA (/) ||
 ||          ||2.0 TB SAS 7.2K (/data) ||
+      }}}
+      {{{#!td align=left style="border: none; vertical-align:top; width: 50%"
+         [[Image(idefix.png,nolink,100%,left)]]\\
+      }}}
+   }}}
+}}}
+
+
 
 
@@ -35 +44 @@
 }}}
 
-In your $HOME directory, add lines
+Add this user login script file [attachment:.myprofile .myprofile] to your $HOME directory on '''idefix'''. The file contains the following lines:
 {{{
-export LD_LIBRARY_PATH=/opt/netcdf4_hdf5parallel/4411c_443f/intel/lib:$LD_LIBRARY_PATH
+#Required software modules for running PALM
+module load intel-compiler/2017.1.132
+module load mvapich2/2.2/intel
+module load fftw/3.3.6-pl1/mvapich2-intel
+module load hdf5-parallel/1.10.0-patch1/intel
+module load netcdf4_hdf5parallel/4411c_443f/intel
+
+#To use the PALM scripts, the PATH variable has to be extended and the environment variable PALM_BIN has to be set
+export PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH
+export PALM_BIN=$HOME/palm/current_version/trunk/SCRIPTS
+
+#Increase stack size to unlimited, otherwise large runs may abort
 ulimit -s unlimited
 }}}
-to file {{{.myprofile}}} (create if it doesn't exist).
+You may have to login again in order to activate these settings.
 
 
 \\
 == Installation of PALM ==
-To download and install the latest PALM version, follow the first steps of the [https://palm.muk.uni-hannover.de/trac/wiki/doc/install/advanced#Packageinstallation advanced installation procedure] as described on the PALM website. The [https://palm.muk.uni-hannover.de/trac/wiki/doc/install/automatic automatic installer] will be available soon. Following steps also need to be carried out and are slightly different to those described on the PALM website. With the automatic installer, the following steps will be carried out automatically. The [https://palm.muk.uni-hannover.de/trac/wiki/doc/app/mrungui mrungui] does not run on idefix at the moment.
+To download and install the latest PALM version, follow the first steps of the [https://palm.muk.uni-hannover.de/trac/wiki/doc/install/advanced#Packageinstallation advanced installation procedure] as described on the PALM website. The [https://palm.muk.uni-hannover.de/trac/wiki/doc/install/automatic automatic installer] will be available soon. Following steps also need to be carried out and are slightly different to those described on the PALM website. With the automatic installer, the following steps will be carried out automatically. The graphical user interface [https://palm.muk.uni-hannover.de/trac/wiki/doc/app/mrungui mrungui] can be used to create an mrun command line for starting a selected PALM simulation.
 
-(1) To use the PALM scripts, the {{{PATH}}}-variable has to be extended and the environment variable {{{PALM_BIN}}} has to be set in the respective profile of the users default shell (e.g. {{{.myprofile}}}:
-{{{
-  export PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH
-  export PALM_BIN=$HOME/palm/current_version/trunk/SCRIPTS
-}}}
-You may have to login again in order to activate these settings.\\\\
-
-(2) Copy '''idefix'''-specific mbuild/mrun configuration file (available from r2202) to your working directory:
+(1) Copy '''idefix'''-specific mbuild/mrun configuration file (available from r2202) to your working directory:
 {{{
 cp $HOME/palm/current_version/trunk/SCRIPTS/.mrun.config.idefix $HOME/palm/current_version/.mrun.config
@@ -61 +74 @@
 '''Warning: When editing the configuration file, please NEVER use the TAB key. Otherwise, very confusing errors may occur when mrun is executing.'''\\\\
 
-(3) Compilation of utilities and source code:
+(2) Compilation of utilities and source code:
 After modifying the configuration file, the respective executables are generated by executing
 {{{
@@ -71 +84 @@
 }}}
 
-(4) Installation verification: Follow the steps of the [https://palm.muk.uni-hannover.de/trac/wiki/doc/install/advanced#Installationverification verification procedure] as described on the PALM website.
+(3) Installation verification: Follow the steps of the [https://palm.muk.uni-hannover.de/trac/wiki/doc/install/advanced#Installationverification verification procedure] as described on the PALM website.
 
 == Batch system (not yet available) ==