Monitor and Check Experiments#
How to check the experiment configuration#
To check the configuration of the experiment, use the command:
autosubmit check EXPID
EXPID is the experiment identifier.
It checks experiment configuration and warns about any detected error or inconsistency. It is used to check if the script is well-formed. If any template has an inconsistency it will replace them for an empty value on the cmd generated. Options:
usage: autosubmit check [-h] [-nt] [-v] EXPID
check configuration for specified experiment
positional arguments:
EXPID experiment identifier
options:
-h, --help show this help message and exit
-nt, --notransitive Disable transitive reduction
-v, --update_version Update experiment version
Example:
autosubmit check cxxx
How to use check in running time:#
In jobs_cxxx.yml , you can set check(default true) to check the scripts during autosubmit run cxx.
There are two parameters related to check:
CHECK: Controls the mechanism that allows replacing an unused variable with an empty string ( %_% substitution). It is TRUE by default.
SHOW_CHECK_WARNINGS: For debugging purposes. It will print a lot of information regarding variables and substitution if it is set to TRUE.
CHECK: TRUE or FALSE or ON_SUBMISSION # Default is TRUE
SHOW_CHECK_WARNINGS: TRUE or FALSE # Default is FALSE
CHECK: TRUE # Static templates (existing on `autosubmit create`). Used to substitute empty variables
CHECK: ON_SUBMISSION # Dynamic templates (generated on running time). Used to substitute empty variables.
CHECK: FALSE # Used to disable this substitution.
SHOW_CHECK_WARNINGS: TRUE # Shows a LOT of information. Disabled by default.
For example:
LOCAL_SETUP:
FILE: filepath_that_exists
PLATFORM: LOCAL
WALLCLOCK: 05:00
CHECK: TRUE
SHOW_CHECK_WARNINGS: TRUE
...
SIM:
FILE: filepath_that_no_exists_until_setup_is_processed
PLATFORM: bsc_es
DEPENDENCIES: LOCAL_SETUP SIM-1
RUNNING: chunk
WALLCLOCK: 05:00
CHECK: ON_SUBMISSION
SHOW_CHECK_WARNINGS: FALSE
...
How to generate cmd files#
To generate the cmd files of the current non-active jobs experiment, it is possible to use the command:
autosubmit inspect EXPID
EXPID is the experiment identifier. Options:
usage: autosubmit inspect [-h] [-nt] [-f] [-cw] [-v] [-q]
[-fl LIST | -fc FILTER_CHUNKS | -fs {Any,READY,COMPLETED,WAITING,SUSPENDED,FAILED,UNKNOWN} | -ft FILTER_TYPE]
EXPID
Generate all .cmd files
positional arguments:
EXPID experiment identifier
options:
-h, --help show this help message and exit
-nt, --notransitive Disable transitive reduction
-f, --force Overwrite all cmd
-cw, --check_wrapper Generate possible wrapper in the current workflow
-v, --update_version Update experiment version
-q, --quick Only checks one job per each section
-fl LIST, --list LIST
Supply the list of job names to be filtered. Default = "Any". LIST = "b037_20101101_fc3_21_sim
b037_20111101_fc4_26_sim"
-fc FILTER_CHUNKS, --filter_chunks FILTER_CHUNKS
Supply the list of chunks to filter the list of jobs. Default = "Any". LIST = "[ 19601101 [ fc0 [1 2
3 4] fc1 [1] ] 19651101 [ fc0 [16-30] ] ]"
-fs {Any,READY,COMPLETED,WAITING,SUSPENDED,FAILED,UNKNOWN}, --filter_status {Any,READY,COMPLETED,WAITING,SUSPENDED,FAILED,UNKNOWN}
Select the original status to filter the list of jobs
-ft FILTER_TYPE, --filter_type FILTER_TYPE
Select the job type to filter the list of jobs
Examples:
with autosubmit.lock present or not:
autosubmit inspect cxxx
with autosubmit.lock present or not:
autosubmit inspect cxxx -f
without autosubmit.lock:
autosubmit inspect cxxx -fl [-fc,-fs or ft]
To generate cmd for wrappers:
autosubmit inspect cxxx -cw -f
With autosubmit.lock and no (-f) force, it will only generate all files that are not submitted.
Without autosubmit.lock, it will generate all unless filtered by -fl,fc,fs or ft.
To generate cmd only for a single job of the section :
autosubmit inspect cxxx -q
How to monitor an experiment#
To monitor the status of the experiment, use the command:
autosubmit monitor EXPID
EXPID is the experiment identifier.
Options:
usage: autosubmit monitor [-h] [-o {pdf,png,ps,svg,txt}] [-group_by {date,member,chunk,split,automatic}] [-expand EXPAND]
[-expand_status EXPAND_STATUS] [--hide_groups] [-cw]
[-fl LIST | -fc FILTER_CHUNKS | -fs {Any,READY,COMPLETED,WAITING,SUSPENDED,FAILED,UNKNOWN} | -ft FILTER_TYPE]
[--hide] [-txt | -txtlog] [-nt] [-v] [-p]
expid
plots specified experiment
positional arguments:
expid experiment identifier
options:
-h, --help show this help message and exit
-o {pdf,png,ps,svg,txt}, --output {pdf,png,ps,svg,txt}
chooses type of output for generated plot
-group_by {date,member,chunk,split,automatic}
Groups the jobs automatically or by date, member, chunk or split
-expand EXPAND Supply the list of dates/members/chunks to filter the list of jobs. Default = "Any". LIST = "[
19601101 [ fc0 [1 2 3 4] fc1 [1] ] 19651101 [ fc0 [16-30] ] ]"
-expand_status EXPAND_STATUS
Select the stat uses to be expanded
--hide_groups Hides the groups from the plot
-cw, --check_wrapper Generate possible wrapper in the current workflow
-fl LIST, --list LIST
Supply the list of job names to be filtered. Default = "Any". LIST = "b037_20101101_fc3_21_sim
b037_20111101_fc4_26_sim"
-fc FILTER_CHUNKS, --filter_chunks FILTER_CHUNKS
Supply the list of chunks to filter the list of jobs. Default = "Any". LIST = "[ 19601101 [ fc0 [1 2
3 4] fc1 [1] ] 19651101 [ fc0 [16-30] ] ]"
-fs {Any,READY,COMPLETED,WAITING,SUSPENDED,FAILED,UNKNOWN}, --filter_status {Any,READY,COMPLETED,WAITING,SUSPENDED,FAILED,UNKNOWN}
Select the original status to filter the list of jobs
-ft FILTER_TYPE, --filter_type FILTER_TYPE
Select the job type to filter the list of jobs
--hide hides plot window
-txt, --text Generates only txt status file
-txtlog, --txt_logfiles
Generates only txt status file(AS < 3.12b behaviour)
-nt, --notransitive Disable transitive reduction
-v, --update_version Update experiment version
-p, --profile Prints performance parameters of the execution of this command.
Example:
autosubmit monitor cxxx
The location where the user can find the generated plots with date and timestamp can be found below:
<experiments_directory>/<EXPID>/plot/<EXPID>_<DATE>_<TIME>.pdf
The location where the user can find the txt output containing the status of each job and the path to out and err log files.
<experiments_directory>/<EXPID>/status/<EXPID>_<DATE>_<TIME>.txt
Hint
Very large plots may be a problem for some pdf and image viewers. If you are having trouble with your usual monitoring tool, try using svg output and opening it with Google Chrome with the SVG Navigator extension installed.
In order to understand more the grouping options, please check Grouping jobs.
Grouping jobs#
Other than the filters, another option for large workflows is to group jobs. This option is available with the group_by keyword, which can receive the values {date,member,chunk,split,automatic}.
For the first 4 options, the grouping criteria is explicitly defined {date,member,chunk,split}.
In addition to that, it is possible to expand some dates/members/chunks that would be grouped either/both by status or/and by specifying the date/member/chunk not to group.
The syntax used in this option is almost the same as for the filters, in the format of [ date1 [ member1 [ chunk1 chunk2 ] member2 [ chunk3 ... ] ... ] date2 [ member3 [ chunk1 ] ] ... ]
Important
The grouping option is also in autosubmit monitor, create, setstatus and recovery
Examples:
Consider the following workflow:
Group by date
-group_by=date
-group_by=date -expand="[ 20000101 ]"
-group_by=date -expand_status="FAILED RUNNING"
-group_by=date -expand="[ 20000101 ]" -expand_status="FAILED RUNNING"
Group by member
-group_by=member
-group_by=member -expand="[ 20000101 [ fc0 fc1 ] 20000202 [ fc0 ] ]"
-group_by=member -expand_status="FAILED QUEUING"
-group_by=member -expand="[ 20000101 [ fc0 fc1 ] 20000202 [ fc0 ] ]" -expand_status="FAILED QUEUING"
Group by chunk
-group_by=chunk
TODO: Add group_chunk.png figure.
Synchronize jobs
If there are jobs synchronized between members or dates, then a connection between groups is shown:
-group_by=chunk -expand="[ 20000101 [ fc0 [1 2] ] 20000202 [ fc1 [2] ] ]"
-group_by=chunk -expand_status="FAILED RUNNING"
-group_by=chunk -expand="[ 20000101 [ fc0 [1] ] 20000202 [ fc1 [1 2] ] ]" -expand_status="FAILED RUNNING"
Group by split
If there are chunk jobs that are split, the splits can also be grouped.
-group_by=split
Understanding the group status
If there are jobs with different status grouped together, the status of the group is determined as follows: If there is at least one job that failed, the status of the group will be FAILED. If there are no failures, but if there is at least one job running, the status will be RUNNING. The same idea applies following the hierarchy: SUBMITTED, QUEUING, READY, WAITING, SUSPENDED, UNKNOWN. If the group status is COMPLETED, it means that all jobs in the group were completed.
Automatic grouping
For the automatic grouping, the groups are created by collapsing the split->chunk->member->date that share the same status (following this hierarchy). The following workflow automatic created the groups 20000101_fc0, since all the jobs for this date and member were completed, 20000101_fc1_3, 20000202_fc0_2, 20000202_fc0_3 and 20000202_fc1, as all the jobs up to the respective group granularity share the same - waiting - status.
For example:
Especially in the case of monitoring an experiment with a very large number of chunks, it might be useful to hide the groups created automatically. This allows to better visualize the chunks in which there are jobs with different status, which can be a good indication that there is something currently happening within such chunks (jobs ready, submitted, running, queueing or failed).
-group_by=automatic --hide_groups
How to profile Autosubmit while monitoring an experiment#
Autosubmit offers the possibility to profile the execution of the monitoring process. To enable the
profiler, just add the --profile (or -p) flag to your autosubmit monitor command, as in
the following example:
autosubmit monitor --profile EXPID
Note
Remember that the purpose of this profiler is to measure the performance of Autosubmit, not the jobs it runs.
This profiler uses Python’s cProfile and psutil modules to generate a report with simple CPU and
memory metrics which will be displayed in your console after the command finishes, as in the example below:
The profiler output is also saved in <EXPID>/tmp/profile. There you will find two files, the
report in plain text format and a .prof binary which contains the CPU metrics. We highly recommend
using SnakeViz to visualize this file, as follows:
For more detailed documentation about the profiler, please visit this page.
How to get details about the experiment#
To get details about the experiment, use the command:
autosubmit describe [EXPID] [-u USERNAME]
EXPID is the experiment identifier, can be a list of expid separated by comma or spaces -u USERNAME is the username of the user who submitted the experiment.
It displays information about the experiment. Currently it describes owner,description_date,model,branch and hpc
Options:
usage: autosubmit describe [-h] [-u USER] [-v] [EXPID]
Show details for specified experiment
positional arguments:
EXPID experiment identifier, can be a list of expid separated by comma or spaces
options:
-h, --help show this help message and exit
-u USER, --user USER username, default is current user or listed expid
-v, --update_version Update experiment version
Examples:
autosubmit describe cxxx
autosubmit describe "cxxx cyyy"
autosubmit describe cxxx,cyyy
autosubmit describe -u dbeltran
How to monitor job statistics#
The following command could be adopted to generate the plots for visualizing the jobs statistics of the experiment at any instance:
autosubmit stats EXPID
EXPID is the experiment identifier.
Options:
usage: autosubmit stats [-h] [-ft FILTER_TYPE] [-fp FILTER_PERIOD] [-o {pdf,png,ps,svg}] [--hide] [-nt] [-v] [-db] EXPID
plots statistics for specified experiment
positional arguments:
EXPID experiment identifier
options:
-h, --help show this help message and exit
-ft FILTER_TYPE, --filter_type FILTER_TYPE
Select the job type to filter the list of jobs
-fp FILTER_PERIOD, --filter_period FILTER_PERIOD
Select the period to filter jobs from current time to the past in number of hours back
-o {pdf,png,ps,svg}, --output {pdf,png,ps,svg}
type of output for generated plot
--hide hides plot window
-nt, --notransitive Disable transitive reduction
-v, --update_version Update experiment version
-db, --database Use database for statistics
Example:
autosubmit stats cxxx
The location where user can find the generated plots with date and timestamp can be found below:
<experiments_directory>/<EXPID>/plot/<EXPID>_statistics_<DATE>_<TIME>.pdf
For including the summaries:
autosubmit stats --section_summary --jobs_summary cxxx
The location will be:
<experiments_directory>/<EXPID>/stats/<EXPID>_section_summary_<DATE>_<TIME>.pdf
<experiments_directory>/<EXPID>/stats/<EXPID>_jobs_summary_<DATE>_<TIME>.pdf
Console output description#
Example:
Period: 2021-04-25 06:43:00 ~ 2021-05-07 18:43:00
Submitted (#): 37
Run (#): 37
Failed (#): 3
Completed (#): 34
Queueing time (h): 1.61
Expected consumption real (h): 2.75
Expected consumption CPU time (h): 3.33
Consumption real (h): 0.05
Consumption CPU time (h): 0.06
Consumption (%): 1.75
Where:
Period: Requested time frame.
Submitted: Total number of attempts that reached the SUBMITTED status.
Run: Total number of attempts that reached the RUNNING status.
Failed: Total number of FAILED attempts of running a job.
Completed: Total number of attempts that reached the COMPLETED status.
Queueing time (h): Sum of the time spent queuing by attempts that reached the COMPLETED status, in hours.
Expected consumption real (h): Sum of wallclock values for all jobs, in hours.
Expected consumption CPU time (h): Sum of the products of wallclock value and number of requested processors for each job, in hours.
Consumption real (h): Sum of the time spent running by all attempts of jobs, in hours.
Consumption CPU time (h): Sum of the products of the time spent running and number of requested processors for each job, in hours.
Consumption (%): Percentage of Consumption CPU time relative to Expected consumption CPU time.
Diagram output description#
The main stats output is a bar diagram. On this diagram, each job presents these values:
Queued (h): Sum of time spent queuing for COMPLETED attempts, in hours.
Run (h): Sum of time spent running for COMPLETED attempts, in hours.
Failed jobs (#): Total number of FAILED attempts.
Fail Queued (h): Sum of time spent queuing for FAILED attempts, in hours.
Fail Run (h): Sum of time spent running for FAILED attempts, in hours.
Max wallclock (h): Maximum wallclock value for all jobs in the plot.
Notice that the left scale of the diagram measures the time in hours, and the right scale measures the number of attempts.
Summaries output description#
Section summary
For each section, the following values are displayed:
Count: Number of completed or running jobs.
Queue Sum (h): Sum of time spent queuing for completed or running jobs, in hours.
Avg Queue (h): Average time spent queuing for completed or running jobs, in hours.
Run Sum (h): Sum of time spent running for completed or running jobs, in hours.
Avg Run (h): Average time spent running for completed or running jobs, in hours.
CSV files are also generated with the same information, in the same directory as the PDFs.
Jobs summary
For each job completed or running, the following values are displayed:
Queue Time (h): Time spent queuing for the job, in hours.
Run Time (h): Time spent running for the job, in hours.
Status: Status of the job.
CSV files are also generated with the same information, in the same directory as the PDFs.
Custom statistics#
Although Autosubmit saves several statistics about your experiment, as the queueing time for each job, how many failures per job, etc.
The user also might be interested in adding his particular statistics to the Autosubmit stats report (`autosubmit stats EXPID`).
The allowed format for this feature is the same as the Autosubmit configuration files: INI style. For example:
COUPLING:
LOAD_BALANCE: 0.44
RECOMMENDED_PROCS_MODEL_A: 522
RECOMMENDED_PROCS_MODEL_B: 418
The location where user can put this stats is in the file:
<experiments_directory>/<EXPID>/tmp/<EXPID>_GENERAL_STATS
Hint
If it is not yet created, you can manually create the file: `expid_GENERAL_STATS` inside the `tmp` folder.
How to extract information about the experiment parameters#
This procedure allows you to extract the experiment variables that you want.
The command can be called with:
autosubmit report EXPID -t "absolute_file_path"
Alternatively it also can be called as follows:
autosubmit report EXPID
Or combined as follows:
autosubmit report EXPID -t "absolute_file_path"
Options:
usage: autosubmit report [-h] [-t TEMPLATE] [-all] [-fp FOLDER_PATH] [-p] [-v] EXPID
Show metrics..
positional arguments:
EXPID experiment identifier
options:
-h, --help show this help message and exit
-t TEMPLATE, --template TEMPLATE
Supply the metric template.
-all, --show_all_parameters
Writes a file containing all parameters
-fp FOLDER_PATH, --folder_path FOLDER_PATH
Allows to select a non-default folder.
-p, --placeholders disables the substitution of placeholders by -
-v, --update_version Update experiment version
Autosubmit parameters are encapsulated by %_%, once you know how the parameter is called you can create a template similar to the one as follows:
- **CHUNKS:** %NUMCHUNKS% - %CHUNKSIZE% %CHUNKSIZEUNIT%
- **VERSION:** %VERSION%
- **MODEL_RES:** %MODEL_RES%
- **PROCS:** %XIO_NUMPROC% / %NEM_NUMPROC% / %IFS_NUMPROC% / %LPJG_NUMPROC% / %TM5_NUMPROC_X% / %TM5_NUMPROC_Y%
- **PRODUCTION_EXP:** %PRODUCTION_EXP%
- **OUTCLASS:** %BSC_OUTCLASS% / %CMIP6_OUTCLASS%
This will be understood by Autosubmit and the result would be similar to:
- CHUNKS: 2 - 1 month
- VERSION: trunk
- MODEL_RES: LR
- PROCS: 96 / 336 / - / - / 1 / 45
- PRODUCTION_EXP: FALSE
- OUTCLASS: reduced / -
Although it depends on the experiment.
If the parameter doesn’t exists, it will be returned as ‘-’ while if the parameter is declared but empty it will remain empty
HPCQUEUE: bsc_es
HPCARCH: marenostrum4
LOCAL_TEMP_DIR: /home/dbeltran/experiments/ASlogs
NUMCHUNKS: 1
PROJECT_ORIGIN: https://earth.bsc.es/gitlab/es/auto-ecearth3.git
MARENOSTRUM4_HOST: mn1.bsc.es
NORD3_QUEUE: bsc_es
NORD3_ARCH: nord3
CHUNKSIZEUNIT: month
MARENOSTRUM4_LOGDIR: /gpfs/scratch/bsc32/bsc32070/a01w/LOG_a01w
PROJECT_COMMIT:
SCRATCH_DIR: /gpfs/scratch
HPCPROJ: bsc32
NORD3_BUDG: bsc32