Difference between revisions of "MCProdWorkflow"

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==Introduction==
 
==Introduction==
−
This workflow is for production-style simulation jobs. It can be used for stage-1 jobs which start with a generator, or later simulation stages which start with the output files of previous stages.  It will result in the output files being concatenated and uploaded to tape and properly documented through the SAM database.  It is intended for cases where the output needs to be saved for more than a month or so, or that might be used by many collaborators, or needs to be carefully documented. If your work doesn't need to be uploaded or is more personal or temporary, you can follow the [[MCScrWorkflow|scratch workflow]] which does not concatenate or upload.  Most commonly this procedure would be part of a collaboration simulation effort and would be run out of the [[Mu2epro|mu2epro account]], but is can be run in a personal account.  
+
This workflow is for production-style simulation jobs. It can be used for stage-1 jobs which start with a generator, or later simulation stages which start with the output files of previous stages.  It can also be used for concatenation of a dataset.  The output may stay on disk, or the output files can be concatenated and uploaded to tape and properly documented through the SAM database.  Uploading is intended for cases where the output needs to be saved for more than a month or so, or that might be used by many collaborators, or needs to be carefully documented.   This process may be run out of the [[Mu2epro|mu2epro account]] for collaboration samples, or a personal account for personal samples.  
  
 
You will need to plan the project in some detail before starting this production workflow.
 
You will need to plan the project in some detail before starting this production workflow.
 
* the physics
 
* the physics
−
* the basic fcl to perform the job
+
* the basic fcl to perform the job, see [[SimulationFCL]] for the fcl patterns used in MDC2020.
 
* the output [[FileNames|dataset names]]
 
* the output [[FileNames|dataset names]]
 
* the [[JobPlan|job plan]] in terms of number and length of jobs, etc.
 
* the [[JobPlan|job plan]] in terms of number and length of jobs, etc.
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The basic steps, expanded below are  
 
The basic steps, expanded below are  
 
* prestage input files, if needed
 
* prestage input files, if needed
−
* generate a set of fcl files
+
* generate a set of fcl files, one for each job
−
* register the fcl dataset with SAM, and copy fcl files to dCache
+
* copy fcl files to dCache and optionally register the fcl dataset with SAM
−
* submit jobs
+
* submit jobs (after creating custom code tarball, if needed)
 
* check output and recover failed jobs
 
* check output and recover failed jobs
−
* concatenate output files, if needed, for each dataset
+
* optionally concatenate output files for each dataset
 
** generate a set of fcl files
 
** generate a set of fcl files
−
** register the fcl dataset with SAM, and copy fcl files to dCache
+
** copy fcl files to dCache and optionally register the fcl dataset with SAM
 
** submit jobs
 
** submit jobs
 
** check output and recover failed jobs
 
** check output and recover failed jobs
−
* upload output files
+
* optionally upload output files
−
* tar and upload log files
+
* optionally tar and upload log files
  
 
The <code>mu2egrid</code> and [[FileTools|related]] packages provide Mu2e-specific code
 
The <code>mu2egrid</code> and [[FileTools|related]] packages provide Mu2e-specific code
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  /mu2e/data/users/$USER/projects/my_project
 
  /mu2e/data/users/$USER/projects/my_project
 
and areas for the jobs main fcl
 
and areas for the jobs main fcl
−
  /mu2e/data/users/$USER/projects/my_project/fcl/job
+
  /mu2e/data/users/$USER/projects/project_name/job/fcl
 
and for each concatenation
 
and for each concatenation
−
  /mu2e/data/users/$USER/projects/my_project/fcl/output1
+
  /mu2e/data/users/$USER/projects/project_name/output1/fcl
  
 
For official collaboration work, the output will go to  
 
For official collaboration work, the output will go to  
 
  /pnfs/mu2e/persistent/users/mu2epro/workflow/project_name/STATUS
 
  /pnfs/mu2e/persistent/users/mu2epro/workflow/project_name/STATUS
 
for individual's work, the output will go to  
 
for individual's work, the output will go to  
−
  /pnfs/mu2e/persistent/users/$USER/workflow/project_name/STATUS
+
  /pnfs/mu2e/scratch/users/$USER/workflow/project_name/STATUS
 
where STATUS is  
 
where STATUS is  
 
* <code>outstage</code> for output from grid jobs
 
* <code>outstage</code> for output from grid jobs
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==Generate fcl ==
 
==Generate fcl ==
−
In this step you take a fcl file which works interactively to generate a simulation sample, and scale it up for the grid.  
+
In this step you take a fcl file which works interactively to generate a simulation sample (see [[SimulationFCL]] for the fcl patterns used in MDC2020), and scale it up for the grid.  
−
Please follow the [[GenerateFcl|instructions]] for generating fcl.  There are examples of a job which starts from a generator (stage 1) or a later stage that take input art files fro ma previous stage, as well as a fcl file.
+
Please follow the [[GenerateFcl|instructions]] for generating fcl from a template or example.  There are examples of a job which starts from a generator (stage 1) or a later stage that take input art files from a previous stage.
  
 
==Submit Jobs ==
 
==Submit Jobs ==
 +
If you are running code in a pre-built release on [[Cvmfs|cvmfs]], you can use that build directly on the grid nodes. If you are using locally-built code, please make a tarball of the code area with [[Muse]].  Next, please follow the [[SubmitJobs|instructions]] for submitting jobs.
  
−
Please follow the [[SubmitJobs|instructions]] for submitting jobs.
+
==Concatenate output datasets==
−
 
 
−
==Concatenate output dataset==
 
 
Some discussion and overview is available in [[JobPlan|job planning]] and [[Concatenate|concatenation]].  If you decide to concatenate the output datasets, for each dataset:
 
Some discussion and overview is available in [[JobPlan|job planning]] and [[Concatenate|concatenation]].  If you decide to concatenate the output datasets, for each dataset:
−
* [[GenerateFcl|generating]] a fcl file set, using the concatenation example
+
* [[GenerateFcl|generate]] a fcl file set, using the concatenation example
−
* [[SubmitJobs|submitting]] those fcl to the grid
+
* [[SubmitJobs|submit]] those fcl to the grid
  
 
This procedure is essentially the same as the main job: generate fcl, submit and recover jobs, and you will end up with the new datasets as output, and those will be uploaded in the next step.
 
This procedure is essentially the same as the main job: generate fcl, submit and recover jobs, and you will end up with the new datasets as output, and those will be uploaded in the next step.
  
−
Production datasets of the first stage of a simulation project often have the string '''g4s1''' in the dataset name, and we have been replacing this will '''cs1''' to create the concatenated dataset name.
+
In Production, and as a recommended convention for everyone, to create the concatenated dataset name, we add "-cat" to the description field in the name.
 +
 
 +
==Upload output files==
 +
Please see the background information on the [[Upload|upload page]] then follow the recipes in
 +
[[Upload#MC workflow, art files|MC art files section]].
 +
 
 +
==Archive log files==
 +
Please see the instructions on the [[Upload#MC workflow, log files|log files section]] of the [[Upload|upload page]].
 +
 
 +
[[Category:Computing]]
 +
[[Category:Workflows]]

Latest revision as of 21:25, 15 October 2021

Introduction

This workflow is for production-style simulation jobs. It can be used for stage-1 jobs which start with a generator, or later simulation stages which start with the output files of previous stages. It can also be used for concatenation of a dataset. The output may stay on disk, or the output files can be concatenated and uploaded to tape and properly documented through the SAM database. Uploading is intended for cases where the output needs to be saved for more than a month or so, or that might be used by many collaborators, or needs to be carefully documented. This process may be run out of the mu2epro account for collaboration samples, or a personal account for personal samples.

You will need to plan the project in some detail before starting this production workflow.

  • the physics
  • the basic fcl to perform the job, see SimulationFCL for the fcl patterns used in MDC2020.
  • the output dataset names
  • the job plan in terms of number and length of jobs, etc.

This page assumes that the user is familiar with the basic infrastructure and its references:

The basic steps, expanded below are

  • prestage input files, if needed
  • generate a set of fcl files, one for each job
  • copy fcl files to dCache and optionally register the fcl dataset with SAM
  • submit jobs (after creating custom code tarball, if needed)
  • check output and recover failed jobs
  • optionally concatenate output files for each dataset
    • generate a set of fcl files
    • copy fcl files to dCache and optionally register the fcl dataset with SAM
    • submit jobs
    • check output and recover failed jobs
  • optionally upload output files
  • optionally tar and upload log files

The mu2egrid and related packages provide Mu2e-specific code required for submitting jobs and manipulating files. Most scripts support the --help option. Look for the --dry-run and --verbose options to show what will be done without performing the action.

Directories

It is useful to have a working area: 

/mu2e/data/users/$USER/projects/my_project

and areas for the jobs main fcl 

/mu2e/data/users/$USER/projects/project_name/job/fcl

and for each concatenation 

/mu2e/data/users/$USER/projects/project_name/output1/fcl

For official collaboration work, the output will go to 

/pnfs/mu2e/persistent/users/mu2epro/workflow/project_name/STATUS

for individual's work, the output will go to 

/pnfs/mu2e/scratch/users/$USER/workflow/project_name/STATUS

where STATUS is

  • outstage for output from grid jobs
  • good for jobs that have been checked and passed
  • failed for jobs that have been checked and passed

Prestage input dataset

Prestaging makes sure the input dataset has been copied off tape to disk, so it is ready to use. If there is no input dataset, or it is known to be on disk (in scratch dCache for example) skip this step.

We recommend starting the prestaging as soon as possible since it can take several days. Please follow the prestage instructions on the input dataset.

Generate fcl

In this step you take a fcl file which works interactively to generate a simulation sample (see SimulationFCL for the fcl patterns used in MDC2020), and scale it up for the grid. Please follow the instructions for generating fcl from a template or example. There are examples of a job which starts from a generator (stage 1) or a later stage that take input art files from a previous stage.

Submit Jobs

If you are running code in a pre-built release on cvmfs, you can use that build directly on the grid nodes. If you are using locally-built code, please make a tarball of the code area with Muse. Next, please follow the instructions for submitting jobs.

Concatenate output datasets

Some discussion and overview is available in job planning and concatenation. If you decide to concatenate the output datasets, for each dataset:

  • generate a fcl file set, using the concatenation example
  • submit those fcl to the grid

This procedure is essentially the same as the main job: generate fcl, submit and recover jobs, and you will end up with the new datasets as output, and those will be uploaded in the next step.

In Production, and as a recommended convention for everyone, to create the concatenated dataset name, we add "-cat" to the description field in the name.

Upload output files

Please see the background information on the upload page then follow the recipes in MC art files section.

Archive log files

Please see the instructions on the log files section of the upload page.

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