SubmitJobs
Introduction
This page is part of the standard simulation workflow. It uses the jobsub product through the mu2eprodsys script from the mu2egrid product. Before this step, you should have prepared a set of fcl files for the job, and have them in a set of files, called fcllist.00, etc., in the example. Each of these files will drive one submission, or cluster. You should also have defined the Offline version (the filespec of the setup.sh file) to use in the project. This should be the same as the Offline you set up during fcl generation. If you are running custom-built code (instead of a fixed release on cvmfs), you will need to make a tarball of the code using gridexport.
Setup
It is advisable to start with a clean shell (no Offline setup),
because the jobsub_client package requires a different
Python version then Mu2e Offline.
mu2einit setup mu2egrid setup mu2efiletools
Job submission
The mu2eprodsys command is used to submit grid jobs. A single execution of mu2eprodsys submits a single Condor cluster of jobs. We have been asked to limit the size of clusters to 10,000 jobs. If the total number of jobs to be run exceeds 10,000, the list of fcl files should be split into several smaller files with each each file not exceeding 10,000 lines. One can use the Linux split -l command to do this. If the fcl files are in tarballs, each tarball should have fewer than 10,000 files.
The first required parameter points to the code using one of these two:
--setupthe setup script on cvmfs that determines which version of Offline to use if you are running a pre-built release available on cvmfs.--codethe path to the code tarball if you are using a custom-built release.
The other required parameters are:
--fcllistThe filespec of a file containing a list of fcl files, or the filespec of a tarball containing the fcl files.--dsconfAn user-defined string that will be used for the "configuration" field of output files.
Please review FileNames for guidance on choosing file names. The dsconf field here should reflect how the job is configured, in particular, if there are any non-standard detector or simulation settings. It may or may not be the the same as the fcl dataset dsconf, since one fcl dataset can be used to produce many very different output datasets by changing the geometry or simulation parameters.
Some other commonly-used options are:
--dsownerthe "owner" (in the dataset naming convention sense) of output datasets. Defaults to the user who runsmu2eprodsys, unless the user is "mu2epro". In the latter case--dsowneris set to "mu2e" to produce "official" datasets.--wfprojectcan be used to group results in the outstage area. The use of this option is highly recommended. For example,--wfproject=beamor--wfproject=cosmic.--expected-lifetimeshould be used to set an upper limit on the wallclock job duration. The value is passed directly tojobsub_submit, see its documentation for more information.--transfer-all-fileswill transfer all created files at the end of the job. The default is to only transfer *.art, *.root, *.json, and the log file.
Run mu2eprodsys --help to see all the options.
If you want to access additional nationwide opportunistic resources (at the cost of increased latency and possible complications) you can access the Open Science Grid (OSG).
If you plan to register the fcl files in SAM, you can submit the fcl file list before they are registered.
If you are approved by the management, you can run as a high priority user.
Outstage location
By default the outputs will be placed into
/pnfs/mu2e/scratch/users/$USER/workflow/$WFPROJECT/outstage/
where $USER is the submitter user name, and $WFPROJECT is specified by
the --wfproject parameter (the default is "default").
If --role=Production (see authentication) is used (default for the mu2epro user), the outputs will go into
/pnfs/mu2e/persistent/users/$USER/workflow/$WFPROJECT/outstage/
instead.
Each submission, or call to mu2eprosys creates one cluster of jobs. The number of jobs in the cluster is determined by how long the list is in the fcl list files. The script will print out a jobId like
Use job id 18497021.0@fifebatch2.fnal.gov to retrieve output
It is a good idea to save this so you can track this cluster.
Each submission will create a new directory in the outstage area, like
/pnfs/mu2e/scratch/users/$USER/workflow/$WFPROJECT/outstage/15503895.beam_p03_17_03_31_16_32_48_1490995968_0
in each directory will be subdirectories like 00 which serve to reduce the number of files in each directory, then in those directories are directories for each job, like 0000, and the job output is here.
Examples
An example using a code tarball from Gridexport and a tarball of fcl files:
mu2eprodsys \
--fcllist=/pnfs/mu2e/scratch/users/rlc/${FCLLIST}.tgz \
--clustername=00 \
--wfproject=geant_181203_new_0 \
--dsconf=geant_181203 --dsowner=rlc \
--disk=10GB --memory=1950MB --expected-lifetime=6h \
--code=/pnfs/mu2e/resilient/users/rlc/gridexport/tmp.ZD43mR9OB3/Code.tar.bz
An example using a pre-compiled release on cvmfs and a local text file of fcl file names:
mu2eprodsys --setup=/cvmfs/mu2e.opensciencegrid.org/Offline/v5_6_7/SLF6/prof/Offline/setup.sh \ --wfpro=pion-test \ --fcllist=fcllist.00 \ --dsconf=v567 \ --expected-lifetime=5h
An example from production, using xrootd input
mu2eprodsys \ --fcllist=fcllist.01 \ --clustername=$FCLLIST \ --wfproject=MDC2018_DS-cosmic-mix_i-cat_1 \ --setup=/cvmfs/mu2e.opensciencegrid.org/Offline/v7_5_4/SLF7/prof/Offline/setup.sh \ --dsconf=MDC2018i --dsowner=mu2e \ --disk=30GB --memory=2GB --expected-lifetime=3h \ --xrootd
Note that for mu2eprodsys and jobsub, the memory is labeled, for example, as "2400MB", but it actually limited by MiB, 2400*1024*1024
Monitoring
You can use the mu2e_clusters script from the mu2egrid package, or
the jobsub_q command, to check the status of your jobs.
If you see that some jobs
are on hold (the "H" state), look for HoldReason in the output of
jobsub_q --long --jobid <jobid>. If you see a PERIODIC_HOLD message, that means the job
tried to use more resources (memory/disk/time) than you asked for.
jobsub_rm the offending jobs and re-submit after
adjusting the requirements. If HoldReason is not a
PERIODIC_HOLD, open a servicedesk ticket.
See the operation links page for links to useful monitors, in particular mu2e grafana. If the jobs go on hold, the pages called "Why are my jobs held?" will tell you which resource limits you violated.
Checking output
The mu2eClusterCheckAndMove script from the
mu2efiletools package can be used to separate
"good" and "failed" jobs. One does not have to wait
until all jobs complete;
mu2eClusterCheckAndMove can be run periodically
on job outputs in the outstage area.
cd .../workflow/$WFPROJECT/outstage
mu2eClusterCheckAndMove 15503895.beam_p03_17_03_31_16_32_48_1490995968_0 >& \
$WORKDIR/cam_`date +"%y_%m_%d_%H_%M_%S_%s"`.log &
After running the mu2eClusterCheckAndMove script,
in the output area are there will be three directories:
.../workflow/$WFPROJECT/outstage .../workflow/$WFPROJECT/good .../workflow/$WFPROJECT/failed
As they are checked, job directories are moved from "outstage" into "good" and "failed" subdirectories, as needed. The script prints a summary of the results.
Two frequently used options:
--timecutThe script will not look at job outputs that are "too fresh" and may still be written out. The default minimal age is 7200 seconds. If you know that all jobs in the cluster have finished, you can set--timecutto a small value instead of waiting for 2 hours before checking the results.--nosamBy default the script talks to SAM to ensure that there are no duplicate jobs. Because of glitches in grid running, sometimes one gets more than one copy of files for the same jobs. However if the original fcl files have not been registered with SAM, the uniquiness check can not be performed. This obviously means if you are registering the fcl files in SAM, you don't want to run this script before that registration is done.
Recovering jobs
If the fcl dataset was declared in SAM, then you can use the following
method to make a list of jobs to recover.
After all jobs from the current submission have completed and processed
with the mu2eClusterCheckAndMove script, so that
outstage area is empty,
SAM will have a record of all "good" jobs from that attempt.
Continuing with the pion example, one can run
mu2eMissingJobs --fclds=cnf.gandr.my-test-s1.v0.fcl --dsconf=v567 > failed-jobs.txt
then use the list of failed jobs to re-submit them
with mu2eprodsys. Here, --dsconf is the value used at for the same switch at submission (and --dsowner, if non-default). It is important to set these consistently throughout the submission and recovery process. The fcl dataset name is the dataset of the fcl files in the submission, and was set in the generate fcl step - it may or may not have the same dsconf.
If the fcl dataset was not registered in SAM, then you need to make
a list of job directories in the good directory, find
missing entries, and construct a new fcl file list from that.
Return to workflow
At the end of this procedure, you should have a complete set of output files in the good
subdirectory of the output area.
Local test
This is an example of how to run one section of mu2eprodsys grid job locally. It comes from v4_00_02, so other versions may need tweaks.
export EXPERIMENT="mu2e" export MU2EGRID_MU2ESETUP="/cvmfs/mu2e.opensciencegrid.org/setupmu2e-art.sh" export IFDH_VERSION="v2_1_0" export MU2EGRID_ERRORDELAY="1" export MU2EGRID_INPUTLIST="filelist-test-10fast" export MU2EGRID_DIR="/mu2e/app/home/mu2epro/test/products/mu2egrid/v4_00_02" export MU2EGRID_USERSETUP="/mu2e/app/users/rlc/head/Offline/setup.sh" export MU2EGRID_CLUSTERNAME="00" export MU2EGRID_DHTOOLS_VERSION="v1_13" export MU2EGRID_SAM_WEB_CLIENT_VERSION="v2_0" export MU2EGRID_DSOWNER="mu2e" export MU2EGRID_TRANSFER_ALL="0" export MU2EGRID_DSCONF="0000a" export MU2EGRID_WFOUTSTAGE="/pnfs/mu2e/persistent/users/mu2epro/workflow/grid_pwd_test_2/outstage" export MU2EGRID_MU2EBINTOOLS_VERSION="v1_01_06" export MU2EGRID_SUBMITTER="mu2epro" export PROCESS=0 export CLUSTER=100 export TMPDIR=$PWD export CONDOR_DIR_INPUT="$PWD" rm -rf $MU2EGRID_WFOUTSTAGE rm -rf mu2egridInDir localFileDefs err.log out.log mu2eprodsys_errmsg* ifdh_* ./mu2eprodsys.sh > out.log 2> err.log
MiB, MB, 1000KiB and the Grid Memory Watchdog
This section has the secret decoder ring for the many different memory units you will encounter while managing your jobs. For extra confusion, not all software correctly describes the units its uses. First, the standard definitions from https://en.wikipedia.org/wiki/Kilobyte
| 1 kB | = 1,000 bytes |
| 1 MB | = 1,000,000 bytes |
| 1 KiB | = 1024 bytes |
| 1 MiB | = 1024*1024 bytes |
and so on for GB/GiB, TB/TiB etc.
There is another unit that appears in some places: 1000KiB which is sometimes erroneously written as either MB or MiB.
First the units that are done correctly. The art end-of-job memory report looks like:
MemReport ---------- Memory summary [base-10 MB] ------ MemReport VmPeak = 2964.03 VmHWM = 2240.32
It is really in MB, properly defined, and art goes out of its way to say so. Note that "VmHWM" means "Virtual Memory High Water Mark".
If you look in your grid log file, the first line after the output from art looks like:
136.42user 4.12system 2:25.97elapsed 96%CPU (0avgtext+0avgdata 2188076maxresident)k
Here "k" means 1024 bytes and "max resident" means "Maximum Resident set size". This means the same thing as VmHWM. You can cross-check this with the reported value of VmHWM; they usually agree to a few in the first decimal place. Why are they not exactly equal? While the two metrics measure the same thing they do so at different times.
Both of the above numbers come from /proc/self/status, which reports both the current value of the resident set size plus the maximum value over the job. The reported value is the maximum over the job.
The Condor software used by the grid has a memory watchdog that periodically asks each running grid process for the current value of its resident set size (summed over all subprocesses and threads if that is relevant). It does not ask for the maximum resident set size over the processes so it will almost always miss the peak. If the value found by Condor is above the memory limit requested when you submit your job, then the grid management software will stop your job and put it into a hold state. At this time the only thing that you can do is to end the job using:
jobsub_rm --jobid=<id of your grid process>
and resubmit it with a larger memory request, by adding this option to mu2eprodsys
--memory="nnnnMB"
where nnnn is a number that the grid group tells us is actually in MiB; however we have some counter examples and are discussing the the Fermilab grid support team.
As best I can reverse engineer the watchdog looks up memory use in units of KiB. When your grid job completes, it includes a summary of the Min, Max and average memory use. These numbers are labeled as being in MiB, which I believe is correct. The number reported in the email is always consistent with the largest value found by the watchdog.
You can see the reports from the memory watchdog using jobsub_fetchlog. Note that the values are labelled as being in kB but they are actually in KiB.