Changes between Version 23 and Version 24 of doc/app/runs

Timestamp:

Apr 21, 2021 4:15:39 AM (4 years ago)

Author:

motisi

Comment:

--

doc/app/runs

@@ -26 +26 @@
       palmrun -c default -r abcde  -t 900 -X 96 -T 48  -a “d3# restart” -b -q queue_name
 }}}
-Giving the activation string {{{restart}}} as argument of option {{{-a}}} is essential. Only for that case the model writes binary data for a restart run to the local file [../iofiles#BINOUT BINOUT] (in case of running on more than 1 core, BINOUT is a folder). The local output file is then saved to a permanent file as defined in the file connection statement for BINOUT. The last line of the example above shows that savinf of the file is only be done of the activation string {{{restart}}} has been set.
+Giving the activation string {{{restart}}} as argument of option {{{-a}}} is essential. Only for that case the model writes binary data for a restart run to the local file [../iofiles#BINOUT BINOUT] (in case of running on more than 1 core, BINOUT is a folder). The local output file is then saved to a permanent file as defined in the file connection statement for BINOUT. The last line of the example above shows that saving of the file is only be done of the activation string {{{restart}}} has been set.
 
 Only by specifying {{{restart}}} as activation string, PALM is instructed to compute the remaining CPU time after each time step and to stop, if the run is not going to be completed and finished briefly before expiration of this time. Actually the stop takes place when the difference between the available job time (determined by the '''palmrun''' option {{{-t}}}) and the time used by the job so far becomes smaller than the time given by the runtime parameter [../runtime_parameters#termination_time_needed termination_time_needed]. The runtime parameter '''termination_time_needed''' can be used to inform PALM, how much time is required for copying the binary data for restart runs, as well as for other pre- or post-processing steps that are done within the job. Thus, as soon as the remaining job time is less than '''termination_time_needed''', PALM interrupts the time stepping and outputs the restart data to local file/folder [../iofiles#BINOUT BINOUT]. The [../initialization_parameters initialization parameters] are also added to that file. In a last step, PALM creates a flag file with local name {{{CONTINUE_RUN}}}. The presence of this file signals '''palmrun''' that a restart run needs to be generated and initiates and starts a respective job.
 
-Within PALM, the initial phase of a restart run requires different actions than during during an initial run. In case of a restart, PALM first needs to read the data written by the preceding run and also reads the initialization parameters from the same file. Therefore, these parameters do not need to be provided in the parameter file (local name [../iofiles#PARIN PARIN]). Anyhow, if they are provided and if their value differ from the respective value of the initial run, these settings are ignored. There is exactly one exception to this rule: the initialization parameter [../initialization_parameters#initializing_actions initializing_actions] determines whether the job is a restart run or an initial run. If '''initializing_actions''' = '' 'read_restart_data','' then it is a restart run, otherwise an initial run. The previous explanation make it clear that the model obviously needs two different parameter files (local name PARIN) for the case of job chains. One is required for the initial run and contains all initialization parameters and the other one is needed for restart runs. The last one only contains the initialization parameter '''initializing_actions''' (any other initialization parameters may appear in this file, but they will be ignored), which needs to be set to '' 'read_restart_data'.'' So you need to provide two different parameter files if you like to carry out restart runs. Since PALM always expects the parameters to be in the local file PARIN, regardless if it is an initial or a restart run, two different file connection statements must be given for that file in the file-connection file. One is active for the initial run only, the other one only for restart runs. The '''palmrun''' call for the initial run shown above activates the first of the two specified file connection statements for PARIN, because the activation string {{{d3#}}} with the option {{{-r}}} coincides with the string in the third column of the file connection statement. Obviously the next statement
+Within PALM, the initial phase of a restart run requires different actions than during an initial run. In case of a restart, PALM first needs to read the data written by the preceding run and also reads the initialization parameters from the same file. Therefore, these parameters do not need to be provided in the parameter file (local name [../iofiles#PARIN PARIN]). Anyhow, if they are provided and if their value differ from the respective value of the initial run, these settings are ignored. There is exactly one exception to this rule: the initialization parameter [../initialization_parameters#initializing_actions initializing_actions] determines whether the job is a restart run or an initial run. If '''initializing_actions''' = '' 'read_restart_data','' then it is a restart run, otherwise an initial run. The previous explanation make it clear that the model obviously needs two different parameter files (local name PARIN) for the case of job chains. One is required for the initial run and contains all initialization parameters and the other one is needed for restart runs. The last one only contains the initialization parameter '''initializing_actions''' (any other initialization parameters may appear in this file, but they will be ignored), which needs to be set to '' 'read_restart_data'.'' So you need to provide two different parameter files if you like to carry out restart runs. Since PALM always expects the parameters to be in the local file PARIN, regardless if it is an initial or a restart run, two different file connection statements must be given for that file in the file-connection file. One is active for the initial run only, the other one only for restart runs. The '''palmrun''' call for the initial run shown above activates the first of the two specified file connection statements for PARIN, because the activation string {{{d3#}}} with the option {{{-r}}} coincides with the string in the third column of the file connection statement. Obviously the next statement
 {{{
       PARIN in:tr     d3r   $base_data/$run_identifier/INPUT _p3dr*
@@ -36 +36 @@
 must be active for the restart runs. Given that this statement only becomes active with option {{{-r "d3r"}}}, and that the '''palmrun''' call for this restart run is generated automatically (thus not yourself), '''palmrun''' obviously needs to replace {{{"d3#"}}} of the initial run with {{{"d3r"}}} for the restart run. Actually, with restart runs all {{{"#"}}} characters within the arguments given for options {{{-r}}} are replaced by {{{"r"}}}.
 
-This way, folling the above palmrun example, the initial run will use the permanent file
+This way, following the above palmrun example, the initial run will use the permanent file
 {{{
       ~/palm/current_version/JOBS/abcde/INPUT/abcde_p3d