Project

General

Profile

User guide » History » Version 40

Herbert Greenlee, 01/12/2015 04:20 PM

1 1 Herbert Greenlee
{{toc}}
2 1 Herbert Greenlee
3 1 Herbert Greenlee
h1. Overview
4 1 Herbert Greenlee
5 4 Herbert Greenlee
Larsoft common batch and workflow tools are contained in ups product @larbatch@ (this redmine), which is built and distributed as part of @larsoft@.  Larbatch tools are built on top of Fermilab @jobsub_client@ batch submission tools.  For general information about jobsub_client and the Fermilab batch system, refer to articles on the "jobsub wiki":https://cdcvs.fnal.gov/redmine/projects/jobsub/wiki and the "fife wiki":https://cdcvs.fnal.gov/redmine/projects/fife/wiki/Getting_Started_on_GPCF.
6 3 Herbert Greenlee
7 3 Herbert Greenlee
No other part of larsoft is dependent on @larbatch@, and @larbatch@ is not setup as a dependent of the @larsoft@ umbrella ups product.  Rather, @larbatch@ is intended to be a dependent of experiment-specific ups products (see [[admin_guide|this article]] for instructions on configuring @larbatch@ for a specific experiment.
8 5 Herbert Greenlee
9 9 Herbert Greenlee
After setting up ups product @larbatch@, several executable scripts and python modules are available on the execution path and python path.  Here is a list of the more important ones.
10 9 Herbert Greenlee
11 11 Herbert Greenlee
* "project.py":https://cdcvs.fnal.gov/redmine/projects/larbatch/repository/revisions/develop/entry/scripts/project.py
12 10 Herbert Greenlee
An executable python script that is the the main entry point for user interation.  More information can be found below.  
13 9 Herbert Greenlee
14 11 Herbert Greenlee
* "project_utilities.py":https://cdcvs.fnal.gov/redmine/projects/larbatch/repository/revisions/develop/entry/python/project_utilities.py
15 10 Herbert Greenlee
A python module, imported by @project.py@, that implements some of the workflow functionality.  End users would not normally interact directly with this module.  However, a significant aspect of @project_utilities.py@ is that is supplies hooks for providing experiment-specific implementations of some functionality, as described in an [[admin_guide#Experiment-specific hooks|accompanying article]] on this wiki.
16 10 Herbert Greenlee
17 11 Herbert Greenlee
* "condor_lar.sh":https://cdcvs.fnal.gov/redmine/projects/larbatch/repository/revisions/develop/entry/scripts/condor_lar.sh
18 10 Herbert Greenlee
The main batch script.  @Condor_lar.sh@ is a general purpose script that manages a single invocation of an art framework program (@lar@ executable).  @Condor_lar.sh@ sets up the run-time environment, fetches input data, interacts with sam, and copies output data.  It is not intended that end users will directly invoke @condor_lar.sh@.  However, one can get a general idea of the features and capabilities of @condor_lar.sh@ by viewing the built-in documentation by typing "@condor_lar.sh -h@, or reading the file header. 
19 12 Herbert Greenlee
20 12 Herbert Greenlee
* "condor_start_project.sh":https://cdcvs.fnal.gov/redmine/projects/larbatch/repository/revisions/develop/entry/scripts/condor_start_project.sh
21 12 Herbert Greenlee
Batch script for starting a sam project.
22 12 Herbert Greenlee
23 12 Herbert Greenlee
* "condor_stop_project.sh":https://cdcvs.fnal.gov/redmine/projects/larbatch/repository/revisions/develop/entry/scripts/condor_stop_project.sh
24 12 Herbert Greenlee
Batch script for stopping a sam project.
25 13 Herbert Greenlee
26 17 Herbert Greenlee
h1. Using @project.py@
27 13 Herbert Greenlee
28 26 Herbert Greenlee
@Project.py@ is used in conjunction with a xml format project definition file (see [[user_guide#Project File Structure|below]]).  The concept of a project, as understood by @project.py@, and as defined by the project definition file, is a multistage linear processing chain involving a specified number of batch workers at each stage.
29 13 Herbert Greenlee
30 22 Herbert Greenlee
h2. Use cases
31 22 Herbert Greenlee
32 27 Herbert Greenlee
In a typical invocation of @project.py@, one specifies the project file (via option @--xml@), tha stage name (via option @--stage@), and one or more action options.  Here are some use cases for invoking @project.py@.
33 13 Herbert Greenlee
34 13 Herbert Greenlee
* @project.py -h@ or @project.py --help@
35 13 Herbert Greenlee
Print built-in help (lists all available command line options).
36 13 Herbert Greenlee
37 1 Herbert Greenlee
* @project.py -xh@ or @project.py --xmlhelp@
38 28 Herbert Greenlee
Print built-in xml help (lists all available elements that can be included in project definition file).
39 14 Herbert Greenlee
40 29 Herbert Greenlee
* @project.py --xml xml-name --status@
41 14 Herbert Greenlee
Print global summary status of the project.
42 14 Herbert Greenlee
43 29 Herbert Greenlee
* @project.py --xml xml-name --stage stage-name --submit@
44 14 Herbert Greenlee
Submit batch jobs for specified stage.
45 14 Herbert Greenlee
46 29 Herbert Greenlee
* @project.py --xml xml-name --stage stage-name --check@
47 15 Herbert Greenlee
Check results from specified stage (identifies failed jobs).  This action assumes that the art program produces an artroot output file.  
48 14 Herbert Greenlee
49 29 Herbert Greenlee
* @project.py --xml xml-name --stage stage-name --checkana@
50 15 Herbert Greenlee
Check results from specified stage (identifies failed jobs).  This version of the check action skips some checks done by @--check@ that only make sense if the art program produces an artroot output file.  Use this action to check results from an analyzer-only art program.
51 14 Herbert Greenlee
52 29 Herbert Greenlee
* @project.py --xml xml-name --stage stage-name --makeup@
53 14 Herbert Greenlee
Submit makeup jobs for failed jobs, as identified by a previous @--check@ or @--checkana@ action.
54 14 Herbert Greenlee
55 29 Herbert Greenlee
* @project.py --xml xml-name --stage stage-name --clean@
56 14 Herbert Greenlee
Delete output for the specified stage and later stages.  This option can be combined with @--submit@.
57 14 Herbert Greenlee
58 29 Herbert Greenlee
* @project.py --xml xml-name --stage stage-name --declare@
59 14 Herbert Greenlee
Declare successful artroot files to sam.
60 14 Herbert Greenlee
61 29 Herbert Greenlee
* @project.py --xml xml-name --stage stage-name --upload@
62 14 Herbert Greenlee
Upload successful artroot files to enstore.
63 14 Herbert Greenlee
64 29 Herbert Greenlee
* @project.py --xml xml-name --stage stage-name --define@
65 1 Herbert Greenlee
Create sam dataset definition.
66 1 Herbert Greenlee
67 29 Herbert Greenlee
* @project.py --xml xml-name --stage stage-name --audit@
68 1 Herbert Greenlee
Check the completeness and correctness of a processing stage using sam parentage information.  For this action to work, input and output files must be must be declared to sam.
69 1 Herbert Greenlee
70 1 Herbert Greenlee
h1. Project File Structure
71 26 Herbert Greenlee
72 38 Herbert Greenlee
The general structure of the project file is that it contains a single root element of type "@project@" (enclosed in "@<project name=project-name>...</project>@").  Inside the project element, there can be option elements and one or more stage elements (enclosed in "@<stage name=stage-name>...</stage>@."  Stage elements can contain their own option elements.  Each stage element defines a group of batch jobs that are submitted together by a single invocation of @jobsub_submit@.
73 15 Herbert Greenlee
74 39 Herbert Greenlee
h2. Examples
75 16 Herbert Greenlee
76 39 Herbert Greenlee
Example XML project files used by microboone from ubutil product can be found "here.":https://cdcvs.fnal.gov/redmine/projects/ubutil/repository/revisions/master/show/xml/mcc5.0
77 1 Herbert Greenlee
78 21 Herbert Greenlee
h2. Internal documentation
79 21 Herbert Greenlee
80 21 Herbert Greenlee
Refer to header of "project.py":https://cdcvs.fnal.gov/redmine/projects/larbatch/repository/revisions/develop/entry/scripts/project.py or type @"project.py --xmlhelp"@.
81 21 Herbert Greenlee
82 23 Herbert Greenlee
h2. XML header section
83 1 Herbert Greenlee
84 23 Herbert Greenlee
The initial lines of an XML project file should follow a standard pattern.  Here is a typical example header.
85 1 Herbert Greenlee
86 23 Herbert Greenlee
<pre>
87 23 Herbert Greenlee
<?xml version="1.0"?>
88 23 Herbert Greenlee
<!DOCTYPE project [
89 23 Herbert Greenlee
<!ENTITY release "v02_05_01">
90 23 Herbert Greenlee
<!ENTITY file_type "mc">
91 23 Herbert Greenlee
<!ENTITY run_type "physics">
92 23 Herbert Greenlee
<!ENTITY name "prod_eminus_0.1-2.0GeV_isotropic_uboone">
93 23 Herbert Greenlee
<!ENTITY tag "mcc5.0">
94 23 Herbert Greenlee
]>
95 23 Herbert Greenlee
</pre>
96 23 Herbert Greenlee
97 23 Herbert Greenlee
The significance of the header elements are as follows.
98 23 Herbert Greenlee
99 23 Herbert Greenlee
* The XML version
100 33 Herbert Greenlee
Copy the above version line exactly, namely,
101 32 Herbert Greenlee
<pre>
102 32 Herbert Greenlee
<?xml version="1.0"?>
103 32 Herbert Greenlee
</pre>
104 23 Herbert Greenlee
105 24 Herbert Greenlee
* The document type (DOCTYPE keyword).
106 34 Herbert Greenlee
The argument following the DOCTYPE keyword specifies the "root element" of the XML file, and should always be "@project@."
107 24 Herbert Greenlee
108 24 Herbert Greenlee
* Entity definitions
109 40 Herbert Greenlee
Entity definitions, which occur inside the DOCTYPE section, are XML aliases.  Any string that occurs repeatedly inside an XML file is a candidate for being defined as an entity.  Entities can be substituted inside the the body of the XML file by enclosing the entity name inside @&...;@ (e.g. @&release;@).
110 23 Herbert Greenlee
111 21 Herbert Greenlee
112 21 Herbert Greenlee
h2. Global options
113 21 Herbert Greenlee
114 21 Herbert Greenlee
h2. Project Block
115 21 Herbert Greenlee
116 21 Herbert Greenlee
h2. Stage Blocks