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The skimming tool has been generalized and externalized. The information below is obsolete and related to an old release. If possible, use a more recent release and get the corresponding documentation from the new TRAC server. |
The Skimmer is also known to GLAST people as the Data Server Back End or Skimmer Back End. It has a command-like interface which can be used directly from a linux shell. If you skim your data thanks to a web interface, you are going through an additional layer known as the Data Server Front End, or Skimmer Web Application, or Skimmer Front-End. Here, you will only find the documentation of the back-end tool with a command-like interface, which we will call simply skimmer, but maybe this can also help you to understand the front-end layer and its web interface.
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The basic task of the skimmer is to take Glast ROOT files, containing ROOT trees, and produce similar output files with a subset of branches and events. The search for ROOT data files to be skimmed is called here mining. The eventual non-copy of some branches is called pruning. The copy of only a subset of events is called cutting.
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As one can see in the steps given above, before the skimmer can proceed, it is collecting much information about the files to be skimmed, what they contain and what to extract. This is all tuned by some shell variables, and some of the information can come from an input ROOT CEL file (documented elsewhere) or from some textual parameter files, meant to be the textual flavor of the different subparts of a ROOT CEL.
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One will find below the description of the parameter files and shell variables which are meaningfull for a skimmer job.
Worth to note, for each of the official skimming step given previously, there is a SK_DEBUG_*
variable which can trigger the display of additionnal information about that specific step. Let's now see the details of each step.
The list of input data files can be obtained from different sources :
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SK_INPUT_CEL = "" SK_INPUT_FILE_LIST = "" SK_INPUT_TASK = "" SK_RUN_MIN = 0 SK_RUN_MAX = 0 SK_OUTPUT_FILE_LIST="" SK_DEBUG_FILE_LIST="false" |
When managing data such as recon, mc and/or digis, the skimmer sometimes needs to load the corresponding C++ shared libraries. It needs the ones which were used when generating the data, compiled with the correct release. The list of those shared libraries can be provided by the user in a dedicated file, whose name is defined by variable SK_INPUT_LIBRARY_LIST
. In this file, each line is the full path of a shared library, eventually prefixed by the data types associated with the library. If there is no such prefix, the library is to be loaded for any data type. Example of such a file :
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Instead of the file above, if the user knows about it, he can provide the data code release with the variable SK_EXPECTED_RELEASE
, and a set of directories where to search for the shared libraries, defined by SK_LIBRARY_DIRS
(which has a default value relevant for SLAC site). The latter is a ':' set of directories paths. SK_EXPECTED_RELEASE
should have the form <main_package>/<main_package>-<release>, as one can see in the example above. The exact names of the libraries for a given data type ar currently hardcoded, and described in the guide /Skimmer at SLAC/. For example, For each <dir> element in SK_LIBRARY_DIRS
, and a given <main_package> and a given <release>, the skimmer will look for <dir>/<main_package>/<main_package>-<release>/lib/libcommonRootData.so.
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SK_INPUT_LIBRARY_LIST="" SK_EXPECTED_RELEASE="" SK_LIBRARY_DIRS=""/nfs/farm/g/glast/u09/builds/rh9_gcc32:/nfs/farm/g/glast/u30/builds/rh9_gcc32:/afs/slac.stanford.edu/g/glast/ground/releases/rh9_gcc32opt" SK_OUTPUT_LIBRARY_LIST="" SK_DEBUG_LIBRARY_LIST="false" |
The list of selected events can be obtained from different sources :
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The expected content of the file defined by SK_INPUT_EVENT_LIST
is a simple list of pairs, one by line, where each pair is made of a run id followed by an event id. The "events" section header can be followed by two special comments which recall the number of events before and after the cut (this information is currently not used by the skimmer). For example :
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# #! CEL TXT 0.1 #! SECTION Events |
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SK_INPUT_CEL="" SK_INPUT_EVENT_LIST="" SK_TCUT_DATA_TYPE="merit" SK_TCUT="" SK_OUTPUT_EVENT_LIST="" SK_DEBUG_EVENT_LIST="false" |
The skimmer can also take into account a list of the branches to be activated or desactivated. This list is given through a file, whose full path is given by variable SK_INPUT_BRANCH_LIST
. Each line should contains a data type prefix, the name of the tree, a + or a -
(so to activate or desactivate respectively), and the specification of one or several branches (with the ROOT syntax). The lines are applied one after the other : you can desactivate all the branches of a given type with -*
, then activate the only ones of interest. There is a first implicit +*
for all the data types used in the skimming job (see SK_DATA_TYPES
in next section). So, all the data types which are not explicitly in the branch list will have all their branches activated. Here is an example of such file :
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SK_INPUT_BRANCH_LIST="" SK_OUTPUT_BRANCH_LIST="" SK_DEBUG_BRANCH_LIST=false |
We are now to the point where to say which types of data we want to skim. This is said by shell variable SK_DATA_TYPES
, which should be a ":" separated list of data types. The current recognized types can be found in the guide /Skimmer at SLAC/. If SK_DATA_TYPES
is empty, a default value of "merit:mc:digi:recon" will be used.
The skimmed files will be stored in the directory defined by shell variable SK_OUTOUTPUT_DIR
, in files called SK_OUTOUTPUT_FILE_BODY_<datatype>.root
. Yet, if they turned to be very big files, ROOT could automatically close the first file and open new ones, appending a rank number to the file name. The maximum bytes size of each ouput ROOT file can be changed with shell variable SK_MAX_FILE_SIZE
. If the value of 0 is given to this variable (this is the default), ROOT will use its own default value. Also, if the value is 0 and the job is merging all the events, the ROOT fast merging method will be used.
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If the events have been cut (thanks to SK_INPUT_EVENT_LIST
or SK_TCUT
) and SK_OUTPUT_CEL
is defined, no deep copy of data will take place. Instead, the skimmer will create a ROOT CEL file which is giving the list of valid files and entries for each relevant data type. In this case, the pruning of branches will not be applied. The relevant data types are the ones which have a branch giving the run id and a branch giving the event id. For other data types, the usual merging of files will take place, even if SK_OUTPUT_CEL
is defined, because the CEL format does not support yet such kind of data.
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SK_DATA_TYPES="merit:mc:digi:recon" SK_OUTOUTPUT_DIR=${PWD} SK_OUTOUTPUT_FILE_BODY=${SK_INPUT_TASK} SK_MAX_FILE_SIZE=0 SK_SKIP_SKIM=false SK_OUTPUT_CEL="" SK_DEBUG_SKIM=false |
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