GenerateFcl
Introduction
This procedure is used to generate a set of fcl files, one for each job to be run in project. The fcl might drive a simulation project that starts with a generator, or a later stage of simulation starting with the art file output of an earlier stage, or a file concatenation project, or even an analysis project.
Preparation
A fcl file should be developed and verified
with interactive jobs before it is prepared for a grid job.
Several examples of simulation fcl files are under the JobConfig
subdirectory of Offline.
Using the fcl with the production system imposes
one extra requirement: all output files of the job should satisfy
the Mu2e naming conventions.
The values of the owner, configuration,
and sequencer fields used in the prepared fcl file are
not important, because they will be overridden later. The values of
data_tier, description,
and file_format will be used as is and must be set
correctly, please see file names for guidelines on how to use these fields.
Use the "art" extension ("file format") for framework
outputs (written by RootOutput modules) and "root"
for TFileService (ntuple and histogram) file output files.
Setup
Setup the utilities
setup mu2e source the appropriate Offline setup.sh file for your project setup mu2etools
The above makes the generate_fcl command available in your path.
Generating fcl
There are two invocation modes that require mutually exclusive sets of parameters
- For jobs with
EmptyEventinput source (events created by a generator) specify--run-numberthat will be used for all the generated fcl files--events-per-job--njobs
- Jobs with
RootInputsource (art files) require --inputsa file containing a list of all input data full filespecs--merge-factorhow many input files should be analyzed by a single job
The number of generated fcl files will be determined from the above inputs.
The following parameters are used to construct the names of fcl
files produced by the generate_fcl invocation.
Please see file names for guidelines on how to use these fields.
--descriptionthe "description" field of fcl file names--dsconfthe "configuration" field--dsownerthe "owner" field. This parameter defaults to the user who executesgenerate_fcl, but can be overridden. For example,--dsowner=mu2eshould be used to generate an official production dataset of fcl files.
The --old-seeds parameter can be used
for incremental generation of fcl datasets. For example, one can
generate a test batch of 1000 fcl files and run them through the
grid. If the result is satisfactory, and one wants to increase the
statistics to 10,000 jobs, care should be taken to guarantee the
uniqueness of random seeds across all the 10,000 jobs. Each run
of generate_fcl produces a text file that contains the
values of all random seeds used so far for the current set of jobs.
So when generate_fcl is used the second time to add
9,000 jobs to the dataset, one should use the file with 1000 seeds
from the first run for the --old-seeds parameter to
make sure those seeds are not re-used.
(Also, --first-subrun should be adjusted so that subrun
numbers do not repeat.) The second run will dump a list of 10,000
seeds, which can be used in a subsequent generation if a further
increase in statistics is desired. For the initial run you can
specify --old-seeds=/dev/null.
Run generate_fcl --help to see all the options.
Examples
Create a working dir. The data disk is a good place to work since we want fast response and some moderate space.
mkdir -p /mu2e/data/users/`whoami`/fclds/my_project_name cd /mu2e/data/users/`whoami`/fclds mkdir 20161121-my_project_name cd 20161121-my_project_name
Example 1 - generator
A first stage simulation job with no input files.
Prepare a template file. Usually it can be a single line file with just an include directive, in our case
#include "JobConfig/cd3/pions/pions_g4s1.fcl"
but one can also add e.g. geometry file overrides, or even write a
completely new fcl configuration and use it as a template.
In this example
we use template.fcl as the template file name.
Note that the include directive should specify include file pathname
relative to the Offline directory that you setup earlier. (More precisely, relative to
a directory listed in the FHICL_FILE_PATH.) Absolute filenames
do not work in fhicl #include.
Now generate the files:
generate_fcl --description=my-test-s1 \
--dsconf=v0 \
--run=2700 \
--events=1000 \
--njobs=5 \
template.fcl
After the command completes, we will see something like
> ls 000 template.fcl seeds.gandr.my-test-s1.v0.Td6j.txt > ls 000 cnf.gandr.my-test-s1.v0.002700_00000000.fcl cnf.gandr.my-test-s1.v0.002700_00000002.fcl.json cnf.gandr.my-test-s1.v0.002700_00000000.fcl.json cnf.gandr.my-test-s1.v0.002700_00000003.fcl cnf.gandr.my-test-s1.v0.002700_00000001.fcl cnf.gandr.my-test-s1.v0.002700_00000003.fcl.json cnf.gandr.my-test-s1.v0.002700_00000001.fcl.json cnf.gandr.my-test-s1.v0.002700_00000004.fcl cnf.gandr.my-test-s1.v0.002700_00000002.fcl cnf.gandr.my-test-s1.v0.002700_00000004.fcl.json
The generated fcl files and their corresponding json files are written into subdirectories 000, 001, etc, with up to 1000 fcl files per subdirectory. Random number seeds used for all the fcl files have been dumped into the "seeds" file.
Example 2 - mixing
A digitization+reconstruction job on a conversion electron file, with background mixing.
Prepare a template file. We want to use
JobConfig/cd3/beam/dra_mix_baseline.fcl, but in many
Offline releases this file is, strictly speaking, not a valid fcl
because it references a variable bgHitFiles that is not
defined. (A legacy of the mu2eart way of running grid
jobs.) To fix that, we define the variable before including the
"baseline" file. This example template.fcl also
shows how to set names of output histogram files.
BEGIN_PROLOG bgHitFiles: @nil END_PROLOG #include "JobConfig/cd3/beam/dra_mix_baseline.fcl" services.TFileService.fileName: "nts.owner.my-ce-reco.ver.seq.root"
We also need a list of input files, and a list of background overlay files. We want to run 5 jobs with one input file per job, so we need to shorten the conversion list to have only 5 input files. We only need one background hits file per job, but there is no harm of listing more background overlay files than necessary, so we will use a complete detmix-cut dataset:
setup mu2efiletools mu2eDatasetFileList sim.mu2e.cd3-beam-g4s4-detconversion.v566.art | head -n 5 > inputs.txt mu2eDatasetFileList sim.mu2e.cd3-detmix-cut.v566b.art > backgrounds.txt
We are ready to generate the fcl dataset. Note the '@' symbol in the --aux parameter - it says that bgHitFiles should be devined in a PROLOG, as the included file expects instead of being appended at the end.
generate_fcl --desc=my-reco-test \
--dsconf=v0 \
--inputs=inputs.txt \
--merge=1 \
--aux=1:@bgHitFiles:backgrounds.txt \
template.fcl
Take a look:
> ls 000 backgrounds.txt template.fcl inputs.txt seeds.gandr.my-reco-test.v0.CRdP.txt > ls 000 cnf.gandr.my-reco-test.v0.004001_00000000.fcl cnf.gandr.my-reco-test.v0.004001_00000002.fcl.json cnf.gandr.my-reco-test.v0.004001_00000000.fcl.json cnf.gandr.my-reco-test.v0.004001_00000003.fcl cnf.gandr.my-reco-test.v0.004001_00000001.fcl cnf.gandr.my-reco-test.v0.004001_00000003.fcl.json cnf.gandr.my-reco-test.v0.004001_00000001.fcl.json cnf.gandr.my-reco-test.v0.004001_00000004.fcl cnf.gandr.my-reco-test.v0.004001_00000002.fcl cnf.gandr.my-reco-test.v0.004001_00000004.fcl.json
Test fcl
It is highly recommended to test a newly generated fcl file by running a small interactive job. Following up on Example 1 above, one can do
mkdir test cd test /usr/bin/time mu2e -c `ls ../000/*.fcl | head -1`
to run a full size job, or add a -n 10 option to the mu2e command line
to quickly make sure that there are no obvious problems with the configuration.