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palmrun

Timestamp:: Apr 26, 2018 12:15:05 PM (7 years ago)
Author:: raasch
Comment:: --

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doc/app/palmrun

-                      v19
+                      v20
 PALM can be run in three different modes: interactive mode, batch mode, and batch mode on a remote computer. Here we explain how to run PALM in interactive mode, which means that PALM executes (almost) immediately within your terminal session after you entered the {{{palmrun}}} command. You can follow the progress of the simulation on the terminal where a lot of informative messages will be output. You can also stop the simulation at any time by typing {{{CTRL C}}}. Running PALM in batch mode requires additional manual settings in the configuration file, which will be explained here (add link).
 The following instructions assume, that the automatic installer has run without any problems. Please switch to your working directory and check if the default configuration file has been generated
+The following instructions assume, that the automatic installer has run without any problems. Please switch to your working directory and check if the default configuration and parameter files have been generated
 {{{
    cd ~/palm/current_version
 …
 You should see the default configuration file {{{.palm.config.default}}}. Furthermore, the parameter file {{{JOBS/example_cbl/INPUT/example_cbl_p3d}}} should also exist. This is a FORTRAN-NAMELIST file to define the simulation setup and to steer the PALM simulation. You should now be able to start the first PALM simulation yourself. Please enter
 {{{
    palmrun  -d example_cbl  -h default  -a "d3#"  -X4  -T4
+   palmrun  -d example_cbl  -h default  -a "d3#"  -X4
 }}}
 {{{example_cbl}}} is the so-called ''run identifier'' and tells {{{palmrun}}} to use the NAMELIST file {{{example_cbl_p3d}}} from {{{JOBS/example_cbl/INPUT}}}. It also determines folders and names of output files generated by PALM using informations from the default file configuration file {{{..../trunk/SCRIPTS/.palm.iofiles}}}. Chapter .... explains the format of this file and how you can modify or extend it. As a new user, you should not need to care about this file because the default settings should do the job for you.
 …
 Option {{{-h}}} specifies the so-called host identifier. It tells {{{palmrun}}} which configuration file should be used. {{{-h default}}} means to use the configuration file {{{.palm.config.default}}}. The configuration file contains all the computer (host) specific settings, e.g. which compiler and compiler options should be used, the pathnames of libraries (e.g. NetCDF or MPI), or the name of the execution command (e.g. {{{mpirun}}} or {{{mpiexec}}}), as well as many other important settings. If the automatic installer worked correctly, it created this file for you with settings based on your responses during the installation process. You may create additional configuration files with different settings for other computers (hosts), or for the same computer, e.g. if you like to compile and run PALM with debug compiler options (see "creating configuration files manually").
+Option {{{-a}}} is used for steering the handling of input and output files that are required / generated by PALM. Its argument is called the file activation string. The file configuration file {{{..../trunk/SCRIPTS/.palm.iofiles}}} contains a complete list of PALM's I/O files, one line per file. .....
+Option {{{-X}}} specifies on how many cores the simulation shall run. The argument should not be larger than the maximum number of cores available on your computer (except in case of hyperthreading), because that usually slows down the performance significantly.
+-T:  really required ??
+Option {{{-a}}} is used for steering the handling of input and output files that are required / generated by PALM. Its argument is called the file activation string(s). The file configuration file {{{..../trunk/SCRIPTS/.palm.iofiles}}} contains a complete list of PALM's I/O files, one line per file. PALM expects its input files in a temporary working directory that is created by each call of {{{palmrun}}} and it outputs data to this temporary directory too. The file configuration file tells {{{palmrun}}} where to find your input files and where to copy the output files (because the temporary working directory is automatically deleted before {{{palmrun}}} has finished). The default setting is that all these files are in subdirectory {{{$HOME/palm/current_version/JOBS/<run_identifier>}}}, where {{{<run_identifier>}}} is the one given with option {{{-d}}}. The argument of option {{{-a}}} tells {{{palmrun}}} which of these files need to be copied. If the option is omitted, no I/O files will be copied at all. Argument {{{"d3#"}}} means that the parameter/NAMELIST file for steering PALM shall be provided as input file. This is the minimum setting for option {{{-a}}}, because PALM cannot run without this parameter file. Multiple activation strings can be given. See ... for handling PALM I/O files.
+Option {{{-X}}} specifies on how many cores the simulation shall run. The argument should not be larger than the maximum number of cores available on your computer (except in case of hyperthreading), because that would usually slow down the performance significantly.
+After entering the {{{palmrun}}} command, some general settings will be listed on the terminal and the user is prompted for confirmation:
+{{{
+*** palmrun  1.0 Rev: 2993 $
+    will be executed.     Please wait ...
+    Reading the configuration file...
+    Reading the I/O files...
+  *** INFORMATIVE: additional source code directory
+      "/home/raasch/palm/current_version/JOBS/example_cbl/USER_CODE"
+      does not exist or is not a directory.
+      No source code will be used from this directory!
+#------------------------------------------------------------------------#
+| palmrun  1.0 Rev: 2993 $                 Thu Apr 26 12:59:34 CEST 2018 |
+|                                                                        |
+| called on:               bora                                          |
+| host identifier:         default (execute on IP: 111.11.111.111)       |
+| running in:              interactive run mode                          |
+| number of cores:         4                                             |
+| tasks per node:          4 (number of nodes: 1)                        |
+|                                                                        |
+| cpp directives:          -cpp -D__parallel -DMPI_REAL=MPI_DOUBLE_PRECI |
+|                          SION -DMPI_2REAL=MPI_2DOUBLE_PRECISION -D__ff |
+|                          tw -D__netcdf                                 |
+| compiler options:        -openmp -fpe0 -O3 -xHost -fp-model source -ft |
+|                          z -fno-alias -no-prec-div -no-prec-sqrt -ip - |
+|                          nbs -I /muksoft/packages/fftw/3.3.4/include - |
+|                          L/muksoft/packages/fftw/3.3.4/lib64 -lfftw3 - |
+|                          I /muksoft/packages/netcdf/4_intel/include -L |
+|                          /muksoft/packages/netcdf/4_intel/lib -lnetcdf |
+|                           -lnetcdff                                    |
+| linker options:          -openmp -fpe0 -O3 -xHost -fp-model source -ft |
+|                          z -fno-alias -no-prec-div -no-prec-sqrt -ip - |
+|                          nbs -I /muksoft/packages/fftw/3.3.4/include - |
+|                          L/muksoft/packages/fftw/3.3.4/lib64 -lfftw3 - |
+|                          I /muksoft/packages/netcdf/4_intel/include -L |
+|                          /muksoft/packages/netcdf/4_intel/lib -lnetcdf |
+|                           -lnetcdff                                    |
+|                                                                        |
+| run identifier:          example_cbl                                   |
+| activation string list:  d3#                                           |
+#------------------------------------------------------------------------#
+ >>> everything o.k. (y/n) ?
+}}}
+Listed settings are determined by the {{{palmrun}}} options and settings in the configuration file (here {{{.palm.config.default}}}). Entering {{{n}}} will abort {{{palmrun}}}. Entering {{{y}}} will finally start execution of PALM and a larger number of informative messages will appear on the terminal:
+{{{
+ ***  PALMRUN will now continue to execute on this machine
+  *** creating executable and other sources for the local host
+  *** nothing to compile for this run
+  *** executable and other sources created
+  *** changed to temporary directory: /localdata/......./example_cbl.23751
+  *** providing INPUT-files:
+  ----------------------------------------------------------------------------
+  >>> INPUT: /home/....../palm/current_version/JOBS/example_cbl/INPUT/example_cbl_p3d  to  PARIN
+  *** INFORMATIVE: some optional INPUT-files are not present
+  ----------------------------------------------------------------------------
+  *** all INPUT-files provided
+  *** execution of INPUT-commands:
+  ----------------------------------------------------------------------------
+  >>> ulimit -s unlimited
+  ----------------------------------------------------------------------------
+  *** execution starts in directory
+      "/localdata/....../example_cbl.23751"
+  ----------------------------------------------------------------------------
+  *** running on: bora bora bora bora
+  *** execute command:
+      "mpiexec -machinefile hostfile -n 4 palm"
+      ... reading environment parameters from ENVPAR      --- finished
+      ... reading NAMELIST parameters from PARIN      --- finished
+      ... creating virtual PE grids + MPI derived data types      --- finished
+      ... checking parameters      --- finished
+      ... allocating arrays      --- finished
+      ... initializing with constant profiles      --- finished
+      ... initializing statistics, boundary conditions, etc.      --- finished
+      ... creating initial disturbances      --- finished
+      ... calling pressure solver      --- finished
+      ... initializing surface layer      --- finished
+      --- leaving init_3d_model
+      --- starting timestep-sequence
+      [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX]   0.0 left
+      --- finished time-stepping
+      ... calculating cpu statistics      --- finished
+  ----------------------------------------------------------------------------
+  *** execution finished
+}}}
+In case that {{{palmrun}}} has proceeded to this point ({{{finished time stepping}}} and {{{execution finished}}}) without giving warning- or error-messages, the PALM simulation has finished successfully. The displayed progress bar ({{{xxxxx}}}}) allows you to estimate how long the run still needs to finish.
+Subsequent messages give information about post processing and copying of output data:
+{{{
+ *** post-processing: now executing "mpiexec -machinefile hostfile -n 1 combine_plot_fields.x" ...
+ *** combine_plot_fields ***
+     uncoupled run
+     NetCDF output enabled
+     no XY-section data available
+     NetCDF output enabled
+     no XZ-section data available
+     no YZ-section data available
+     no 3D-data file available
+  *** execution of OUTPUT-commands:
+  ----------------------------------------------------------------------------
+  >>> [[ -f LIST_PROFIL_1D ]] && cat LIST_PROFIL_1D >> LIST_PROFILE
+  >>> [[ -f LIST_PROFIL ]] && cat LIST_PROFIL >> LIST_PROFILE
+  >>> [[ -f PARTICLE_INFOS/_0000 ]] && cat PARTICLE_INFOS/* >> PARTICLE_INFO
+  ----------------------------------------------------------------------------
+  *** saving OUTPUT-files:
+  ----------------------------------------------------------------------------
+  >>> OUTPUT: RUN_CONTROL  to
+              /home/raasch/palm/current_version/JOBS/example_cbl/MONITORING/example_cbl_rc
+  >>> OUTPUT: HEADER  to
+              /home/raasch/palm/current_version/JOBS/example_cbl/MONITORING/example_cbl_header
+  >>> OUTPUT: CPU_MEASURES  to
+              /home/raasch/palm/current_version/JOBS/example_cbl/MONITORING/example_cbl_cpu
+  >>> OUTPUT: DATA_1D_PR_NETCDF  to
+              /home/raasch/palm/current_version/JOBS/example_cbl/OUTPUT/example_cbl_pr.nc
+  >>> OUTPUT: DATA_1D_TS_NETCDF  to
+              /home/raasch/palm/current_version/JOBS/example_cbl/OUTPUT/example_cbl_ts.nc
+  >>> OUTPUT: DATA_2D_XY_NETCDF  to
+              /home/raasch/palm/current_version/JOBS/example_cbl/OUTPUT/example_cbl_xy.nc
+  >>> OUTPUT: DATA_2D_XZ_NETCDF  to
+              /home/raasch/palm/current_version/JOBS/example_cbl/OUTPUT/example_cbl_xz.nc
+  >>> OUTPUT: DATA_2D_XZ_AV_NETCDF  to
+              /home/raasch/palm/current_version/JOBS/example_cbl/OUTPUT/example_cbl_xz_av.nc
+  ----------------------------------------------------------------------------
+  *** all OUTPUT-files saved
+ --> palmrun finished
+}}}
+You should find the output files at their respective positions as listed in the terminal output. Most of PALM's output files are written in NetCDF format. Please see here (add link) for a complete list of different output data/files that PALM offers. Section ..... describes how to steer PALM's output (e.g. output quantities, output intervals, etc.).
+You are now at the point where you can define and run your own simulation set-up for the first time.
 \\\\\\