| 42 | |
| 43 | |
| 44 | == Output (problem with combine_plot_fields) == |
| 45 | The 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 | |
| 51 | 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). |
| 52 | |
| 53 | For 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. |