A job started by mrun will - according to its requested computing time, its memory size requirement and the number of necessary processing elements (on parallel computers) - be queued by the queuing-system of the remote computer into a suitable job class which fulfills these requirements. Each job class permits only jobs with certain maximum requirements (e.g. the job class cdev on the IBM Regatta "hanni" of the HLRN permits only jobs with no more than 7200 seconds required computing time and with using no more than 32 processing elements). The job classes are important for the scheduling process of the computer. Jobs with small requirements usually come to execution very fast, jobs with higher requirements must wait longer (sometimes several days).
Before the start of a model
run the user
must estimate how much CPU time the model will need for the simulation.
The necessary time in seconds has to be indicated with the mrun
and has an influence on the job class into which the job is queued. Due
to the fact that the model usually uses a variable
time step and thus the number of time steps to be executed and
consequently the time needed by the model is not
known at the beginning, this can be measured only very roughly in
many cases. So it may happen that the model needs more time than
indicated for the option -t,
which normally leads to an abort of the job as soon as the available
CPU time is consumed. In principle one could solve this problem by
setting a very generously estimated value for -t,
but this will possibly lead to the disadvantage that the queued job has
to wait longer for execution.
To avoid this problem mrun offers the possibility of so-called restart runs. During the model run PALM continuously examines how much time is left for the execution of the job. If the run is not completed and finished shortly before expiration of this time, the model stops and writes down the values of (nearly) all model variables in binary form to a file (local name BINOUT). After copying the output files required by the user, mrun automatically starts a restart run. For this purpose a new mrun call is set off automatically on the local computer of the user; mrun thus calls itself. The options with this call correspond to a large extent to those which the user had selected with his initial call of mrun. The model restarts and this time at the beginning it reads in the binary data written before and continues the run with them. If in this job the CPU time is not sufficient either, in order to terminate the run, at the end of the job another restart run is started, etc., until the time which shall be simulated by the model, is reached. Thus a set of restart runs can develop - a so-called job chain. The first run of this chain (model start at t=0) is called initial run.
Working with restart runs and their generation through mrun requires certain entries in the mrun-configuration file and in the parameter file, which are described and explained in the following. The configuration file must contain the following entries (example for the IBM Regatta of the HLRN):
%write_binary true restart
PARIN in:job:npe d3# ~/palm/current_version/JOBS/$fname/INPUT _p3d
PARIN in:job:npe d3f ~/palm/current_version/JOBS/$fname/INPUT _p3df
BININ in:loc d3f ~/palm/current_version/JOBS/$fname/OUTPUT _d3d
BINOUT out:loc restart ~/palm/current_version/JOBS/$fname/OUTPUT _d3d
The mrun call for the initialization run of the job chain must look as follows:
mrun -h ibmh -d abcde -t 900 -r "d3# restart"
The specification of the environment variable write_binary, which must be assigned the value true, is essential. Only in this case the model writes binary-coded data for a possible restart run to the local file BINOUT at the end of the run. Then of course this output file must be stored on a permanent file with an appropriate file connection statement (last line of the example above). As you can see, both instructions (variable declaration and connection statements) are only carried out by mrun, if the character string restart is given for the option -r in the mrun call. Thus the example above can also be used if no restart runs are intended. In such cases the character string restart with the option -r can simply be omitted.
Only by the specification of write_binary=true the model is instructed to compute the remaining CPU time after each time step and 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 from the available job time (determined by the mrun option -t) and the time used so far by the job becomes smaller than the time given by the model variable termination_time_needed. With the variable termination_time_needed the user determines, how much time is needed for binary copying of the data for restart runs, as well as for the following data archiving and transfer of result data etc. (as long as this is part of the job). Thus, as soon as the remaining job time is less than termination_time_needed, the model stops the time step procedure and copies the data for a restart run to the local binary file BINOUT. The so-called initialization parameters are also written to this file (see chapter 4.0). In a last step the model produces another file with the local name CONTINUE_RUN. The presence of this file signals mrun the fact that a restart run must be started and leads to the start of an appropriate job.
During the initial phase of a restart run different actions than during the initial phase of an initial run of the model are neccessary. In this case the model must read in the binary data written by the preceding run at the beginning of the run. Beyond that it also reads the initialization parameters from this file. Therefore these do not need to be indicated in the parameter file (local name PARIN). If they are indicated nevertheless and if their value deviates from their value of the initial run, then this is ignored. There is exactly one exception to this rule: with the help of the initialization parameter initializing_actions it is determined 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 remarks make it clear that the model obviously needs two different parameter files (local name PARIN) for the case of job chains. One is needed for the initial run and contains all initialization parameters set by the user and the other one is needed for restart runs. The last one only contains the initialization parameter initializing_actions (also, initialization parameters with values different from the initial run may appear in this file, but they will be ignored), which must have the value “read_restart_data”. Therefore the user must produce two different parameter files if he wants to operate job chains. Since the model always expects the parameter file on the local file PARIN, two different file connection statements must be given for this file in the configuration file. One may be active only at the initial run, the other one only at restart runs. The mrun call for the initial run shown above activates the first of the two specified connection statements, because the character string d3# with the option -r coincides with the character string in the third column of the connection statement. Obviously the next statement must be active
PARIN in:job:npe d3f ~/palm/current_version/JOBS/$fname/INPUT _p3df
with the restart runs. Given that this statement only gets active if the option -r is given the value d3f and that the mrun call for this restart run is produced automatically (thus not by the user), mrun obviously has to replace "d3#" of the initial run with "d3f" within the call of this restart run. Actually, with restart runs all "#" characters within the strings given for the options -r , -i and -o are replaced by “f”.
For example, for the initial run the permanent file
and for restart runs the permanent file
is used. Only with restart runs the local file BININ is made available as input file, because the appropriate file connection statement also contains the character string "d3f" in the third column. This is logical and necessary since in BININ the binary data, produced by the model of the preceding job of the chain, are expected and the initial run does not need these data The permanent names of this input file (local name BININ) and the corresponding output file (local name BINOUT) are identical and read
However, after the file produced by the previous job was read in by the model and after at the local file BINOUT was produced at the end of the job, the restart job does not overwrite this permanent file (…/abcde_d3d) with the new data. Instead of that, it is examined whether already a permanent file with the name …/abcde_d3d exists when copying the output file (BINOUT) of mrun. If this is the case, BINOUT is copied to the file …/abcde_d3d.1. Even if this file is already present, …/abcde_d3d.2 is tried etc. For an input file the highest existing cycle of the respective permanent file is copied. In the example above this means: the initial run creates the permanent file …/abcde_d3d, the first restart run uses this file and creates …/abcde_d3d.1, the second restart run creates …/abcde_d3d.2 etc. After completion of the job chain the user can still access all files created by the jobs. This makes it possible for the user for example to restart the model run of a certain job of the job chain again.
Therefore restart jobs can not only be started automatically through mrun, but also manually by the user. This is necessary e.g. whenever after the end of a job chain it is decided that the simulation must be continued further, because the phenomenon which should be examined did not reach the desired state yet. In such cases the mrun options completely correspond to those of the initial call; simply the "#" characters in the arguments of options -r, -i and -o must be replaced by "f".
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