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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 The information below is obsolete and related to an old release.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.
The skimmer is only usable on linux. For what concerns the external tools, skimmer v6r0 v6r1 depends on :
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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A skimming job is organized as a sequence of steps. All but the two last one ones are preparation steps, which are analyzing the shell variables defined by the user, the textual parameter files he is providing, and establish what to skim. Currently, the steps are :
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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.
All kinds of parameter files can contain any number of empty lines and comments starting with "#". The lines starting with "#!" are called special comments. The first special comment in any parameter file should express the global file format release, currently "CEL TXT 0.1". The second special comment should be of the form "SECTION <name>", where <name> depends on the kind of information in the rest of the file. For example, if the file contain the list of input data files, <name> will be "Files". Several examples will be given below.
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 :
SK_INPUT_CEL
.SK_INPUT_FILE_LIST
.SK_INPUT_TASK
. One and only Only one of those three
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In the case of Pipeline I products, sources will be used for a given job. The variables SK_INPUT_FILE_LIST
and SK_INPUT_TASK
is enough and should not be defined at the same time. If defined, the variable SK_INPUT_CEL
will only be used if both SK_INPUT_FILE_LIST
and SK_INPUT_TASK
are empty. In future releases, we could try to intersect the sets defined by SK_INPUT_FILE_LIST
and SK_INPUT_CEL
, but we are not yet sure it is useful and usable.
In the case of Pipeline I products, SK_INPUT_TASK
is enough and should be any of the tasks recognized by the Pipeline I Oracle Database. On top of that, one can select a subset of the task runs through the shell variables SK_RUN_MIN
and SK_RUN_MAX
. If the value of SK_RUN_MAX
is 0
, all any of the tasks recognized by the Pipeline I Oracle Database. On top of that, one can select a subset of the task runs through the shell variables SK_RUN_MIN
and SK_RUN_MAX
. If the value of SK_RUN_MAX
is 0
, all the runs will be taken into consideration.
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Whatever the source for the list of input data files, one can obtain a copy of this list when giving a value to SK_OUTPUT_FILE_LIST
. This list is restrained to the files whose at least one entry has been kept after skimming. The ouput format is the same as the input format above. After a skimming, one can copy the output file defined by SK_OUTPUT_FILE_LIST
, edit it freely and reuse the copy later as a SK_INPUT_FILE_LIST
. It is not recommended to use the same single file for both input and ouput, because the file defined by SK_OUTPUT_FILE_LIST
is always overwritten, and you could easily loose your modifications.
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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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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 :
SK_INPUT_CEL
.SK_INPUT_EVENT_CELLIST
.From a textual file made by the user : the format is given below, and the file path is given thanks to variable SK_TCUT
and SK_TCUT_DATA_TYPE
. The syntax of SK_TCUT
should be the ROOT one. Currently, the only valid value for SK_TCUT_DATA_TYPE
is merit
.Only one of those three sources will be used for a given job. The variables SK_INPUT_EVENT_LIST
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and SK_TCUT
should not be defined at the same time. If defined, the variable SK_INPUT_CEL
will only be used if both SK_INPUT_EVENT_LIST
and SK_TCUT
are empty. In future releases, we could try to intersect the sets defined by SK_INPUT_EVENT_LIST
, SK_TCUT
and SK_INPUT_CEL
, but we are not yet sure it is useful and usable.
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 |
In the case you do want to keep all the entries, i.e. to merge the input data files, you should not give any kind of cut to the skimmer : SK_INPUT_CEL
, SK_INPUT_EVENT_LIST
and SK_TCUT
should be empty. SK_INPUT_CEL
, SK_INPUT_EVENT_LIST
and SK_TCUT
should be empty.
It In theory, we should also be able to combine any number of those cuts above, but this is not yet implemented. Currently, you must define either an input CEL, or a textual file, or a cut. Also, it is not yet possible to define a TCut
which is going through several data types, but it will be studied as soon as we have several possible values for SK_TCUT_DATA_TYPE
.
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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.
If the value of SK_SKIP_SKIM
is "true", no real skimming will take place. This is useful when someone only want to generate some of the parameter files defined by SK_OUTPUT_FILE_LIST
, SK_OUTPUT_LIBRARY_LIST
, SK_OUTPUT_EVENT_LIST
or SK_OUTPUT_BRANCH_LIST
.
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.
Here are the default values of the shell variables for this section :
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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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