Index: trunk/LMDZ.COMMON/libf/evolution/deftank/README =================================================================== --- trunk/LMDZ.COMMON/libf/evolution/deftank/README (revision 3933) +++ trunk/LMDZ.COMMON/libf/evolution/deftank/README (revision 3938) @@ -22,37 +22,48 @@ ------------ To compile the PEM, in "LMDZ.COMMON", do: ./makelmdz_fcm -arch [local] -p [planet] -d [dimensions] -j 8 pem -Options: +Options with example: 1) [local] : root name of arch files, assuming that they have been set up for your configuration; - 2) [planet] : mars to use the planet physics package; - 3) [dimensions]: 64x48x54 to define the grid you want to use. + 2) [planet] : mars to use the Mars planet physics package; + 3) [dimensions]: 64x48x54 to define the grid you want to use (longitude x latitude x atmospheric layers). To run the PEM, you need a dedicated reshaping tool with consistent options. To compile it, in "LMDZ_COMMON", do: ./makelmdz_fcm -arch [local] -p [planet] -d [dimensions] -j 8 reshape_XIOS_output -To run the PEM, you also need a PCM working with XIOS and consistent options. To compile it, in "LMDZ.COMMON", do for example: ./makelmdz_fcm -arch [local] -p [planet] -parallel mpi_omp -io XIOS -d [dimensions] -j 8 gcm +To run the PEM, you also need a PCM working with XIOS and consistent options. To compile it, in "LMDZ.COMMON", do: ./makelmdz_fcm -arch [local] -p [planet] -parallel mpi_omp -io XIOS -d [dimensions] -j 8 gcm After compilation, the executable file can be found in the "bin" sub-directory. Usage: ------ - To run a PEM simulation, do: ./launchPEM.sh [options] - Options: - 1) None: to start a simulation from scratch; - 2) 're': to relaunch a simulation from a starting point (interactive prompt). +To run a PEM simulation, do: ./launchPEM.sh [options] +Options: + 1) None: to start a simulation from scratch; + 2) 're': to relaunch a simulation from a starting point (interactive prompt). + +The Bash file ''launchPEM.sh'' is the master script to launch the PEM chained simulation. It checks if necessary files and required options for your simulation are ok. Requirements: ------------- -To run the PEM, you need the following files: - > your executable files for the PCM, the PEM and the reshaping tool with consistent dimensions; - > the xml files for XIOS ("iodef.xml", "context_lmdz_physics.xml", "file_def_physics_mars.xml" and "field_def_physics_mars.xml") which can be found in the PCM deftank folder; - > the def files you want to run the PCM ("run.def", "callphys.def", "traceur.def", etc). +To run the PEM, you can create a folder in which you need the following files: + > your executable files for the PCM, the PEM and the reshaping tool with consistent options; + > the xml files for XIOS which can be found in the PCM deftank folder: "iodef.xml", "context_lmdz_physics.xml", "file_def_physics_mars.xml" and "field_def_physics_mars.xml"; + > the def files you want to run the PCM: "run.def", "callphys.def", "traceur.def", etc. /!\ Do not forget to rename the PCM "run.def" into "run_PCM.def"; - > the starting files you want to run the PCM ("startfi.nc", "start.nc"/"start1D.txt"/profiles); - > the necessary PEM files ("launchPEM.sh", "lib_launchPEM.sh", "PCMrun.job", "PEMrun.job", "run_PEM.def" and "obl_ecc_lsp.asc"; - > the optional PEM files "diagpem.def" to define the PEM variables to be ouputted and "startpem.nc" to set the initial state of the PEM. + > the starting files you want to run the PCM: "startfi.nc", "start.nc"/"start1D.txt"/profiles; + > the necessary PEM files: "launchPEM.sh", "lib_launchPEM.sh", "PCMrun.job", "PEMrun.job", "run_PEM.def" and "obl_ecc_lsp.asc"; + > the optional PEM files: "diagpem.def" to define the PEM variables to be ouputted and "startpem.nc" to set the initial state of the PEM. + +The PEM files can be found in the deftank folder. + +Before a simulation, you have to set up some parameters/options in: + > "launchPEM.sh"; + > "PCMrun.job"; + > "PEMrun.job"; + > def files, especially for "run_PEM.def", "run_PCM.def", "callphys.def". +In addition, the user has to provide a "startfi.nc" whose orbital parameters are consistent with the initial date set in "run_PEM.def". The script "inipem_orbit.sh" can do it automatically with "obl_ecc_lsp.asc". Outputs: -------- The PEM simulation generates the following files: - > the usual outputs of the PCM ("restartfi.nc", "restart.nc", "diagfi.nc", etc); - > the XIOS outputs of the PCM, then reshaped ("Xdiurnalave.nc"/"data2reshape*.nc"/"data_PCM_Y*.nc"); - > the outputs of the chained simulation ("launchPEM.log", "info_PEM.txt" and possibly "kill_launchPEM.sh"); - > the usual outputs of the PEM ("restartfi.nc", "restart.nc"/"restart1D.txt" and "diagpem.nc"). + > the usual outputs of the PCM: "restartfi.nc", "restart.nc", "diagfi.nc", etc; + > the XIOS outputs of the PCM, then reshaped: "Xdiurnalave.nc"/"data2reshape*.nc"/"data_PCM_Y*.nc"; + > the outputs of the chained simulation: "launchPEM.log", "info_PEM.txt" and possibly "kill_launchPEM.sh"; + > the usual outputs of the PEM: "restartfi.nc", "restart.nc"/"restart1D.txt" and "diagpem.nc". During the simulation, the PCM/PEM run files are renamed conveniently and stored in the sub-directories "logs" (log files), "starts" (starting files) and "diags" (diagnostic files). If you run a simulation by submitting jobs, the script "kill_launchPEM.sh" is automatically generated. It can be used to kill in the queue of the job scheduler the jobs related to your chained simulation. @@ -69,6 +80,6 @@ > mode -> the launching mode (0 = "processing scripts"; any other values = "submitting jobs"). The former option is usually used to process the script on a local machine while the latter is used to submit jobs on a supercomputer with SLURM or PBS/TORQUE. The script can take an argument: - 1) If there is no argument, then the script initiates a PEM simulation from scratch. - 2) If the argument is 're', then the script relaunches an existing PEM simulation. It will ask for parameters to know the starting point that you want to. + 1) None: to start a simulation from scratch; + 2) 're': to relaunch a simulation from a starting point (interactive prompt). # liblaunchPEM.sh: @@ -76,14 +87,18 @@ # PCMrun.job: - Bash script file to submit a PCM job (with SLURM or PBS/TORQUE). The headers correspond to the ADASTRA supercomputer and should be changed for other machines and job schedulers. In case of "processing scripts" launching mode, the headers are naturally omitted. - The path to source the arch file should be adapted to the machine. - The name of the PCM executable file should be adapted. - The execution command should also be adapted according to the set-up. + Bash script file to submit a PCM job (with SLURM or PBS/TORQUE). + The user has to specify: + > The headers correspond to the ADASTRA supercomputer and should be changed for other machines and job schedulers. In case of "processing scripts" launching mode, the headers are naturally omitted. + > The path to source the arch file should be adapted to the machine. + > The name of the PCM executable file should be adapted. + > The execution command should also be adapted according to the set-up. # PEMrun.job: - Bash script file to submit PEM job (with SLURM or PBS/TORQUE).The headers correspond to the ADASTRA supercomputer and should be changed for other machines and job schedulers. In case of "processing scripts" launching mode, the headers are naturally omitted. - The path to source the arch file should be adapted to the machine. - The name of the PEM executable file and Reshaping executable file should be adapted. - The PEM executable can have an optional argument which should be specified according to the set-up. Especially, the value of '--jobid' which is the job ID to make the PEM detect the job time limit. + Bash script file to submit PEM job (with SLURM or PBS/TORQUE). + The user has to specify: + > The headers correspond to the ADASTRA supercomputer and should be changed for other machines and job schedulers. In case of "processing scripts" launching mode, the headers are naturally omitted. + > The path to source the arch file should be adapted to the machine. + > The name of the PEM and Reshaping executable files should be adapted. + > The PEM executable can have an optional argument which should be specified according to the set-up ("--auto-exit" for SLURM and PBS/TORQUE | "" when the script is not run as a job). # run_PEM.def