Changes between Version 2 and Version 3 of doc/app/machine/hlrnIII

Timestamp:

Dec 12, 2013 4:16:19 PM (12 years ago)

Author:

fricke

Comment:

--

doc/app/machine/hlrnIII

@@ -40 +40 @@
 === Conditional statements (IF-THEN-ELSE) ===
 * It is no longer possible to use {{{==}}} or {{{.EQ.}}} for comparison of variables of type LOGICAL.\\'''Example:'''\\{{{IF ( variable == .TRUE. ) THEN}}} is not supported. You must use {{{IF ( variable ) THEN}}} (or {{{IF ( .NOT. variable ) THEN}}}) instead.
+
+
+== Output (problem with combine_plot_fields) ==
+The output of cross-sections with PALM may cause the following error message in the job protocol:
+{{{
+*** post-processing: now executing "combine_plot_fields_parallel.x" ..../mrun: line 3923: 30156: Memory fault
+}}}
+"/mrun: line 3923:" refers to the line where combine_plot_fields is called in the mrun-script (line number may vary with script version).
+
+The reason for this error is that executables are started on the Cray system managment (MOM) nodes, where the stack size is limited to 8 Mbytes. This value is exceeded if a cross-section has more than 1024 x 1024 grid points. The '''stack size should not be increased''', otherwise the system may crash (see the HLRN site for more information).
+
+For the moment we recommend to carry out the following steps:
+   1. If you start the job, save the temporary directory by using the following option:
+      {{{
+      mrun ... -B
+      }}}
+   2. After the job has finished, the executable file 'combine_plot_fields_<block>.x' has to be copied from trunk/SCRIPTS/ to the temporary directory. 
+      <block> is given in the .mrun.config in column five (and six), e.g. parallel. The location of the temporary directory is given by
+      %tmp_user_catalog in the .mrun.config.
+
+   3. Create a batch script which is using '''aprun''' to start the executable file, e.g. like this:
+      {{{
+      #!/bin/bash
+      #PBS -l nodes=1:ppn=1
+      #PBS -q mpp1q
+      #PBS -l walltime=00:30:00
+      #PBS -l partition=berlin
+
+      cd <%tmp_user_catalog>
+      aprun -n 1 -N 1 ./combine_plot_fields_<block>.x
+      }}} 
+      '''Attention''': Use only the batch queues mmp1q or testq, otherwise it may not be working so far.
+
+   4. After running the batch script, the following files should be available in the temporary directory (depending on the chosen output during the simulation):
+      DATA_2D_XY_NETCDF, DATA_2D_XZ_NETCDF, DATA_2D_YZ_NETCDF, DATA_2D_XY_AV_NETCDF, DATA_2D_XZ_AV_NETCDF and DATA_2D_YZ_AV_NETCDF. You can copy these files to the 
+      standard output directory and you can rename them, e.g. DATA_2D_XY_NETCDF to <job_name>_xy.nc.