4.1. Rocoto Introductory Information
The tasks in the SRW Application are typically run using the Rocoto Workflow Manager (see Table 2.8 for default tasks). Rocoto is a Ruby program that communicates with the batch system on an HPC system to run and manage dependencies between the tasks. Rocoto submits jobs to the HPC batch system as the task dependencies allow and runs one instance of the workflow for a set of user-defined cycles. More information about Rocoto can be found on the Rocoto Wiki.
The SRW App workflow is defined in a Jinja-enabled Rocoto XML template called FV3LAM_wflow.xml,
which resides in the parm directory. When the generate_FV3LAM_wflow.py script is run,
the Unified Workflow set_template tool is called, and the parameters in the template file
are filled in. The completed file contains the workflow task names, parameters needed by the job scheduler,
and task interdependencies. The generated XML file is then copied to the experiment directory:
$EXPTDIR/FV3LAM_wflow.xml.
There are a number of Rocoto commands available to run and monitor the workflow; users can find more information in the complete Rocoto documentation. Descriptions and examples of commonly used commands are discussed below.
4.1.1. rocotorun
The rocotorun command is used to run the workflow by submitting tasks to the batch system. It will
automatically resubmit failed tasks and can recover from system outages without user intervention. The command takes the following format:
rocotorun -w /path/to/workflow/xml/file -d /path/to/workflow/database/file -v 10
where
-wspecifies the name of the workflow definition file. This must be an XML file.-dspecifies the name of the database file that stores the state of the workflow. The database file is a binary file created and used only by Rocoto. It does not need to exist when the command is initially run.-v(optional) specified level of verbosity. If no level is specified, a level of 1 is used.
From the $EXPTDIR directory, the rocotorun command for the workflow would be:
rocotorun -w FV3LAM_wflow.xml -d FV3LAM_wflow.db
Users will need to include the absolute or relative path to these files when running the command from another directory.
It is important to note that the rocotorun process is iterative; the command must be executed
many times before the entire workflow is completed, usually every 1-10 minutes. This command can be
placed in the user’s crontab, and cron will call it with a specified frequency. More information on
this command can be found in the Rocoto documentation.
The first time the rocotorun command is executed for a workflow, the files FV3LAM_wflow.db and
FV3LAM_wflow_lock.db are created. There is usually no need for the user to modify these files.
Each time this command is executed, the last known state of the workflow is read from the FV3LAM_wflow.db
file, the batch system is queried, jobs are submitted for tasks whose dependencies have been satisfied,
and the current state of the workflow is saved in FV3LAM_wflow.db. If there is a need to relaunch
the workflow from scratch, both database files can be deleted, and the workflow can be run by executing the rocotorun command
or the launch script (launch_FV3LAM_wflow.sh) multiple times.
4.1.2. rocotostat
rocotostat is a tool for querying the status of tasks in an active Rocoto workflow. Once the
workflow has been started with the rocotorun command, Rocoto can check the status of the
workflow using the rocotostat command:
rocotostat -w /path/to/workflow/xml/file -d /path/to/workflow/database/file
Executing this command will generate a workflow status table similar to the following:
CYCLE TASK JOBID STATE EXIT STATUS TRIES DURATION
===============================================================================================================
201907010000 make_grid 175805 QUEUED - 0 0.0
201907010000 make_orog - - - - -
201907010000 make_sfc_climo - - - - -
201907010000 get_extrn_ics druby://hfe01:36261 SUBMITTING - 0 0.0
201907010000 get_extrn_lbcs druby://hfe01:36261 SUBMITTING - 0 0.0
201907010000 make_ics_mem000 - - - - -
201907010000 make_lbcs_mem000 - - - - -
201907010000 run_fcst_mem000 - - - - -
201907010000 run_post__mem000_f000 - - - - -
201907010000 run_post__mem000_f001 - - - - -
201907010000 run_post__mem000_f002 - - - - -
201907010000 run_post__mem000_f003 - - - - -
201907010000 run_post__mem000_f004 - - - - -
201907010000 run_post__mem000_f005 - - - - -
201907010000 run_post__mem000_f006 - - - - -
This table indicates that the make_grid task was sent to the batch system and is now queued, while
the get_extrn_ics and get_extrn_lbcs tasks for the 201907010000 cycle are currently being
submitted to the batch system.
Note that issuing a rocotostat command without an intervening rocotorun command will not result in an
updated workflow status table; it will print out the same table. It is the rocotorun command that updates
the workflow database file (in this case FV3LAM_wflow.db, located in $EXPTDIR). The rocotostat command
reads the database file and prints the table to the screen. To see an updated table, the rocotorun command
must be executed followed by the rocotostat command.
After issuing the rocotorun command several times (over the course of several minutes or longer, depending
on the grid size and computational resources available), the output of the rocotostat command should look like this:
CYCLE TASK JOBID STATE EXIT STATUS TRIES DURATION
===================================================================================================
201907010000 make_grid 175805 SUCCEEDED 0 1 10.0
201907010000 make_orog 175810 SUCCEEDED 0 1 27.0
201907010000 make_sfc_climo 175822 SUCCEEDED 0 1 38.0
201907010000 get_extrn_ics 175806 SUCCEEDED 0 1 37.0
201907010000 get_extrn_lbcs 175807 SUCCEEDED 0 1 53.0
201907010000 make_ics_mem000 175825 SUCCEEDED 0 1 99.0
201907010000 make_lbcs_mem000 175826 SUCCEEDED 0 1 90.0
201907010000 run_fcst_mem000 175937 RUNNING - 0 0.0
201907010000 run_post__mem000_f000 - - - - -
201907010000 run_post__mem000_f001 - - - - -
201907010000 run_post__mem000_f002 - - - - -
201907010000 run_post__mem000_f003 - - - - -
201907010000 run_post__mem000_f004 - - - - -
201907010000 run_post__mem000_f005 - - - - -
201907010000 run_post__mem000_f006 - - - - -
When the workflow runs to completion, all tasks will be marked as SUCCEEDED. The log file for each task
is located in $EXPTDIR/log. If any task fails, the corresponding log file can be checked for error
messages. Optional arguments for the rocotostat command can be found in the
Rocoto documentation.
4.1.3. rocotocheck
Sometimes, issuing a rocotorun command will not cause the next task to launch. rocotocheck is a
tool that can be used to query detailed information about a task or cycle in the Rocoto workflow. To
determine why a particular task has not been submitted, the rocotocheck command can be used
from the $EXPTDIR directory as follows:
rocotocheck -w FV3LAM_wflow.xml -d FV3LAM_wflow.db file -c <YYYYMMDDHHmm> -t <taskname>
where
-cis the cycle to query in YYYYMMDDHHmm format.-tis the task name (e.g.,make_grid,get_extrn_ics,run_fcst_mem000).
The cycle and task names appear in the first and second columns of the table output by rocotostat. Users will need to include the absolute or relative path to the workflow XML and database files when running the command from another directory.
A specific example is:
rocotocheck -w /Users/John.Doe/expt_dirs/test_community/FV3LAM_wflow.xml -d /Users/John.Doe/expt_dirs/test_community/FV3LAM_wflow.db -v 10 -c 201907010000 -t run_fcst_mem000
Running rocotocheck will result in output similar to the following:
Task: run_fcst_mem000
account: gsd-fv3
command: /scratch2/BMC/det/$USER/ufs-srweather-app/ush/load_modules_run_task.sh "run_fcst_mem000" "/scratch2/BMC/det/$USER/ufs-srweather-app/jobs/JREGIONAL_RUN_FCST"
cores: 24
final: false
jobname: run_FV3
join: /scratch2/BMC/det/$USER/expt_dirs/test_community/log/run_fcst_mem000_2019070100.log
maxtries: 3
name: run_fcst_mem000
nodes: 1:ppn=24
queue: batch
throttle: 9999999
walltime: 04:30:00
environment
CDATE ==> 2019070100
CYCLE_DIR ==> /scratch2/BMC/det/$USER/UFS_CAM/expt_dirs/test_community/2019070100
PDY ==> 20190701
SCRIPT_VAR_DEFNS_FP ==> /scratch2/BMC/det/$USER/expt_dirs/test_community/var_defns.sh
dependencies
AND is satisfied
make_ICS_surf_LBC0 of cycle 201907010000 is SUCCEEDED
make_LBC1_to_LBCN of cycle 201907010000 is SUCCEEDED
Cycle: 201907010000
Valid for this task: YES
State: active
Activated: 2019-10-29 18:13:10 UTC
Completed: -
Expired: -
Job: 513615
State: DEAD (FAILED)
Exit Status: 1
Tries: 3
Unknown count: 0
Duration: 58.0
This output shows that although all dependencies for this task are satisfied (see the dependencies section, highlighted above),
it cannot run because its maxtries value (highlighted) is 3. Rocoto will attempt to launch it at most 3 times,
and it has already been tried 3 times (note the Tries value, also highlighted).
The output of the rocotocheck command is often useful in determining whether the dependencies for a given task
have been met. If not, the dependencies section in the output of rocotocheck will indicate this by stating that a
dependency “is NOT satisfied”.
4.1.4. rocotorewind
rocotorewind is a tool that attempts to undo the effects of running a task. It is commonly used to rerun part
of a workflow that has failed. If a task fails to run (the STATE is DEAD) and needs to be restarted, the rocotorewind
command will rerun tasks in the workflow. The command line options are the same as those described for rocotocheck
(in Section 4.1.3), and the general usage statement looks like this:
rocotorewind -w /path/to/workflow/xml/file -d /path/to/workflow/database/ file -c <YYYYMMDDHHmm> -t <taskname>
Running this command will edit the Rocoto database file FV3LAM_wflow.db to remove evidence that the job has been run.
rocotorewind is recommended over rocotoboot for restarting a task, since rocotoboot will force a specific
task to run, ignoring all dependencies and throttle limits. The throttle limit, denoted by the variable cyclethrottle
in the FV3LAM_wflow.xml file, limits how many cycles can be active at one time. An example of how to use the rocotorewind
command to rerun the forecast task from $EXPTDIR is:
rocotorewind -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 201907010000 -t run_fcst_mem000
4.1.5. rocotoboot
rocotoboot will force a specific task of a cycle in a Rocoto workflow to run. All dependencies and throttle
limits are ignored, and it is generally recommended to use rocotorewind instead. An example of how to
use this command to rerun the make_ics task from $EXPTDIR is:
rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 201907010000 -t make_ics