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


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Timestamp:
Dec 12, 2013 4:16:19 PM (11 years ago)
Author:
fricke
Comment:

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  • doc/app/machine/hlrnIII

    v2 v3  
    4040=== Conditional statements (IF-THEN-ELSE) ===
    4141* 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.
     42
     43
     44== Output (problem with combine_plot_fields) ==
     45The output of cross-sections with PALM may cause the following error message in the job protocol:
     46{{{
     47*** post-processing: now executing "combine_plot_fields_parallel.x" ..../mrun: line 3923: 30156: Memory fault
     48}}}
     49"/mrun: line 3923:" refers to the line where combine_plot_fields is called in the mrun-script (line number may vary with script version).
     50
     51The 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).
     52
     53For the moment we recommend to carry out the following steps:
     54   1. If you start the job, save the temporary directory by using the following option:
     55      {{{
     56      mrun ... -B
     57      }}}
     58   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.
     59      <block> is given in the .mrun.config in column five (and six), e.g. parallel. The location of the temporary directory is given by
     60      %tmp_user_catalog in the .mrun.config.
     61
     62   3. Create a batch script which is using '''aprun''' to start the executable file, e.g. like this:
     63      {{{
     64      #!/bin/bash
     65      #PBS -l nodes=1:ppn=1
     66      #PBS -q mpp1q
     67      #PBS -l walltime=00:30:00
     68      #PBS -l partition=berlin
     69
     70      cd <%tmp_user_catalog>
     71      aprun -n 1 -N 1 ./combine_plot_fields_<block>.x
     72      }}}
     73      '''Attention''': Use only the batch queues mmp1q or testq, otherwise it may not be working so far.
     74
     75   4. After running the batch script, the following files should be available in the temporary directory (depending on the chosen output during the simulation):
     76      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
     77      standard output directory and you can rename them, e.g. DATA_2D_XY_NETCDF to <job_name>_xy.nc.