Changes between Version 3 and Version 4 of doc/app/machine/hlrnIII

Timestamp:

Dec 12, 2013 4:45:42 PM (11 years ago)

Author:

fricke

Comment:

--

doc/app/machine/hlrnIII

@@ -3 +3 @@
 * Running remote jobs 
 * Fortran issues
+* Output (problem with combine_plot_fields)
 
 == Running remote jobs ==
@@ -43 +44 @@
 
 == Output (problem with combine_plot_fields) ==
-The output of cross-sections with PALM may cause the following error message in the job protocol:
+The output of 2D or 3D data 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
@@ -49 +50 @@
 "/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).
+Since each processor opens its own output file and writes 2D- or 3D-binary data into it, the routine combine_plot_fields combines these output files into one single file. Output format is netcdf.
+The reason for this error is that combine_plot_fields is started on the Cray system managment (MOM) nodes, where the stack size is limited to 8 Mbytes. This value is exceeded e.g. 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). To start combine_plot_fields on the computing nodes, '''aprun''' is required (so far, combine_plot_fields is not started with aprun in PALM).
 
 For the moment we recommend to carry out the following steps:
@@ -71 +73 @@
       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.
+      '''Attention''': Use only the batch queues mmp1q or testq, otherwise it may not be working.
 
    4. After running the batch script, the following files should be available in the temporary directory (depending on the chosen output during the simulation):