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FastBit IBIS Command Line Interface Document

IBIS [1] is an Implementation of Bitmap Indexing System named FastBit. This document explains the command line tool named ibis, which is a shorthand for Interactive Bitmap Index Search. Under FastBit, user data is organized into containers called tables and each table consists of an arbitrary number of rows and columns. In SQL algebra, the rows and columns are also called tuples and attributes. In this document, we will use the terms attribute and column interchangeably.

A table is physically organized into one or more data partitions, so that one column from a partition can comfortably fit in computer memory. Each data partition is stored in a directory on file systems and the command line tool ibis works with data directories.

• An example
• List of options
• Query statement syntax
• Sample output

An example

/home/kwu/bin/ibis -c /home/kwu/bin/ibis.rc -v
-q "select mchn, tmpr where ! (tmpr == 55 || tmpr == 60)"

The main option is -q which is followed by a query string. The basic syntax follows that of SQL, however, only the basic features of the SQL's select statement is implemented. Here we will first mention a few limitations that might cause non-descriptive failures of ibis.

• If two instance's of ibis are run at the same to create indexes, they may overwrite each other's output and produce something that is totally unusable.
• The computation of the functions SUM and AVG are performed using in the arithmetic supported on the type of the selected variable. For example, if variable a is an integer, the function SUM(a) will be computed using integer arithmetic. This may lead to overflow in certain cases. The same overflow problem affects both SUM and AVG.
• No multiple-table operations are supported. If multiple tables are specified, it will simply apply the same condition on all the tables. This is mostly used to split a large dataset into more manageable chunks.

The option -v tells ibis to be verbose. If this option is not supplied, only the number of hits and the result of the select clause are printed. The result of the select clause may be appended to a file instead of printed to standard output. To use this option specify '-output output-file'.

List of options

• -a[ppend] data_dir [to table_name]
  Take the data in the named directory and append it to the table with the specified name.

  Note: to specify a table name the keyword to must appear before the table name. If a table name is not specified, ibis attempt to use the meta tags contained in the table to generate a name. If no meta tags are found, it will generate a random name.

  More information about loading data can be found in dataLoading.html.

• -b[uild-index] [num-threads|indexing-option]
  Instruct FastBit to build indexes of all datasets known. Usually it builds indexes as needed, therefore there is no need to explicitly build indexes.

  The option -b may be followed by one of two arguments, an integer to indicate the number of simultaneous threads to use while building the indexes, or a string arguments to indicate the type of indexes to build. An indexing option string might look like "<binning nbins=1000/> <encoding range ncomp=2/>". More about the indexing options is available at indexSpec.html.

  To specify the number of threads and an indexing option, use two separate instances of -b option, such as,

  -b "<binning none/> <encoding interval-equality/>" -b 2
  

  Since building indexes is an expensive operation, FastBit by default only builds new indexe for a column if no index currently exists. To force FastBit to remove existing indexes and rebuild them from scratch, specify option -z in addition.

  Note: The numbre of threads to use depends heavily on the amount of memory available. Indexes are built one column of a data partition at a time. Each thread works one a column of a partition at any given time, and the index for the column is built completely in-memory before written to disk. If your data partitions are large, then each threads will require a lot of memory to complete it work. The default number of threads to use for index building is one (1).

• -c[onf] conf_file
  Specify a configuration file. If no configuration file is specified, it will look for a file named "ibis.rc" in the current working directory. If that file does not exist, it will also look at the environment variable named IBISRC. If the environment variable is defined, its value is taken to be the rc file. One of the most noticeable entries defined in the rc file is the "DataDir1" and "DataDir2" entries. They define the data directories used by IBIS. On UNIX systems, ibis will also recursively traverse the directories to find directory pairs with the same name and the matching -part.txt files. Each such pair defined a partition. If different data partitions have the same name, only the last one will be kept.

  Using a pair of directories for a data partition was intended to improve reliability and reduce the transition time when appending data. In most cases, it is fine to use only one directory for each data partition, in which case, one simply do not specify "DataDir2". More information about the configuration file is available in dataLoading.html.

• -d[atadir] data_dir [backup_dir]
  As an alternative to specify the data directories in a configuration file, one may specified them directly on the command line. The effect of "data_dir" and "backup_dir" are the same as "DataDir1" and "DataDir2" in the RC file.
• -e[stimation-only]
  Output a range for the number of hits rather than the exact number of hits. Note, the estimation is applicable to queries contain only simple range conditions without negation. Otherwise, the estimation may return 0 as both the upper and lower bound of the number of hits.
• -h[elp]
  Print a short usage statement.
• -i[nteractive]]
  Tell ibis to enter an interactive mode after finishing processing the command line arguments. In the interactive mode, the user may directly use the SELECT statement described below with the leading option -q. There are also a small number of other commands that can be used in the interactive mode. Type "help" in the interactive mode to see a list.
• -l[logfile] logfilename
  Redirect all messages printed out by ibis to the named file. The file is opened in append mode, therefore the existing content is preserved. The only message that may still be printed to standard output is something indicating the name of the message file.

  NOTE: this file contains the error messages and other information. If option -o is also specified, the file specified in that option will contain the results of select statements.

• -n[o-estimation]
  Forces ibis to evaluate the number of hits without first perform an estimation.

  NOTE: options -no-estimation and -estimation-only are mutually exclusive, the one that appears later will overwrite the one that appears early on the same command line.

• -o[utput] filename
  Tell ibis to append the result of select statements to the named file rather than to standard output. The output are coma-separated values.

  NOTE: Each set of results from a select statement will be preceded by a line of column names if the option appears as -output-[with-header] (the command line tool ibis only check till the second dash, nothing more). If multiple select statements are specified, a header line for each select statement is printed.

  NOTE: this file contains the results of the select statments only. Other messages, such as errors, progress information, and debug information, may be redirected with option -l.

• -p[rint] [Parts|Columns|Distributions|column-name [: conditions]]
  Print information about the tables known to ibis program.
• -q[uery] [SELECT ...] [FROM ...] WHERE ...
  On most systems the strings following -q must be quoted in order for them to be perceived as one argument.
• -r[id-check] [filename]
  This option will tells ibis to verify the RIDs can be used in queries of their own. If the optional file name is present, the RIDs will also be written into the named file.
• -s[quential-scan]
  For ibis to check the answer produced from the index operations with a sequence scan of the raw data.
• -t[=n]
  Instructs ibis to perform predefined self tests. If a positive integer is provided, it take the given number as the number of tests to perform.
• -v[=n]
  Any integer can be specified as the verbose level. Typically range are 1 -- 20. Use a negative number to mute ibis.

Query statement syntax

The command line tool ibis supports a limited version of the SQL select statement. It recognizes three key words, SELECT, FROM and WHERE. The key words are not case-sensitive, neither are the names of variables and functions described next.

The key word SELECT must be followed by a list of attribute names or one of the four functions AVG, MAX, MIN and SUM, separated by commas (,). The attribute names must be from the available datasets. If any name is not in the available dataset, IBIS treats it same as no attribute provided. If no attribute is provided, the SELECT key must not be used. In which case, only the number of hits would be printed. The four functions each take one argument that must be a column name of an available dataset. The variables not appearing in any functions are implicitly passed to a SQL 'GROUP BY' clause and the functions are defined on the groups defined by this implicit 'GROUP BY' clause. For example, the select clause 'SELECT mchn, avg(q20), min(snra)' will order the selected records according to machine name (mchn) and for each machine the average Q20 score and the minimum SNRA value will be computed. In the printout, the number of selected records is printed at the end. This is equivalent to adding 'count(*)' to the end of every (non-empty) select clause.

The key word FROM must be followed by a list of table names. Conceptually, the data under the management of IBIS are organized into tables; and each table must have a name. The table names may contain wild cards, '%' and '_', where '%' matches zero or more any characters and '_' matches exactly one character as in SQL "LIKE" expression. If no table name is specified, the key word FROM must not be used. In which case, all know data table would be queried.

The key word WHERE must be followed by a set of range conditions joined by logical operators 'AND', 'OR', 'XOR', and '!'. A range condition can be one-sided as "A = 5" or "B > 10", or two-sided as "10 <= B < 20." The supported operators are = (alternatively ==), <, <=, >, and >=. The range condition that involves only one attribute with constant bounds are known as simple conditions, which can be very efficiently processed by IBIS. A range condition can also involve multiple attributes, such as, "A < B <= 5", or even arithmetic expressions, such as, "sin(A) + fabs(B) < sqrt(cx*cx+cy*cy)". Note all one-argument and two-argument arithmetic functions available in math.h are supported. The key word WHERE and the conditions following it are essential to a query and can not be ommited.

The select clause may also contain arithmetic expressions, e.g.,

-q "select pressure, sqrt(vx*vx+vy*vy+vz*vz) where temperature > 1000"

Sample output

ibis::part::readTDC (Tue Jun 14 03:30:32 2005 UTC) --- failed to open file "/home/xhe/TRAC/tmp/dir1/-part.txt" -- No such file or directory
buildTables: directory /home/xhe/TRAC/tmp/dir1 does not contain a valid -part.txt file or contains an empty table.
Make sure the parameter Number_of_events has the correct value
Completed construction of an ibis::part named 200506.
1766540 records each with 36 attributes


./ibis: batch mode, log level 1

Tables:
200506

Query:
select mchn, tmpr where ! (tmpr == 55 or tmpr == 60)

doQuery (Tue Jun 14 03:31:13 2005 UTC) --- processing query ! (tmpr == 55 or tmpr == 60) on table 200506
query[LT55J4AkJu400000]::setWhereClause -- WHERE "! (tmpr == 55 or tmpr == 60)"
query[LT55J4AkJu400000]::setSelectClause -- SELECT mchn,tmpr
ibis::column[200506.Tmpr](INT)::readIndex -- the basic index was read (/home/xhe/TRAC/tmp/dir1/200506) in 0 sec(CPU), 0.00101352 sec(elapsed)
query[LT55J4AkJu400000]::estimate -- time to compute the bounds: 0.01 sec(CPU), 0.00476098 sec(elapsed).
query[LT55J4AkJu400000]::estimate -- # of hits for query "! (tmpr == 55 or tmpr == 60)" is 0
doQuery (Tue Jun 14 03:31:13 2005 UTC) --- number of hits in [0, 0]
query[LT55J4AkJu400000]::evaluate -- time to compute the 15744 hits: 0 sec(CPU), 0.000848532 sec(elapsed).
query[LT55J4AkJu400000]::evaluate -- user kwu SELECT mchn,tmpr FROM 200506 WHERE ! (tmpr == 55 or tmpr == 60) ==> 15744 hit(s).
doQuery (Tue Jun 14 03:31:13 2005 UTC) --- number of hits = 15744
doQuery:: evaluate(! (tmpr == 55 or tmpr == 60)) took 0.00626969 sec(elapsed)
ibis::part[200506]::getRIDs -- number of RIDs (0) does not match the size of the mask (1766540)
Tue Jun 14 03:31:13 2005 UTC
Warning -- query[LT55J4AkJu400000]::getRIDs -- got 0 row IDs from table 200506, expected 15744
ibis::part[200506]::getRIDs -- number of RIDs (0) does not match the size of the mask (1766540)
ibis::column[200506.MCHN](KEY)::readIndex -- the basic index was read (/home/xhe/TRAC/tmp/dir1/200506) in 0 sec(CPU), 0.000895739 sec(elapsed)
Query LT55J4AkJu400000 produces 32 distinct tuples of columns mchn,tmpr
MegaBACE # MB424 -128 
MegaBACE # MB424 -120 
MegaBACE # MB424 -112 
MegaBACE # MB424 -104 
MegaBACE # MB424 -96 
MegaBACE # MB424 -88 
MegaBACE # MB424 -80 
MegaBACE # MB424 -72 
MegaBACE # MB424 -64 
MegaBACE # MB424 -56 
MegaBACE # MB424 -48 
MegaBACE # MB424 -40 
MegaBACE # MB424 -32 
MegaBACE # MB424 -24 
MegaBACE # MB424 -16 
MegaBACE # MB424 -8 
MegaBACE # MB424 0 
MegaBACE # MB424 8 
MegaBACE # MB424 16 
MegaBACE # MB424 24 
MegaBACE # MB424 32 
MegaBACE # MB424 40 
MegaBACE # MB424 48 
MegaBACE # MB424 56 
MegaBACE # MB424 64 
MegaBACE # MB424 72 
MegaBACE # MB424 80 
MegaBACE # MB424 88 
MegaBACE # MB424 96 
MegaBACE # MB424 104 
MegaBACE # MB424 112 
MegaBACE # MB424 120 
Cleaning up table 200506
Cleaning up the file manager
Total pages accessed through read(unistd.h) is 145

The number of hits is printed in the following line

query[LT55J4AkJu400000]::evaluate -- user ... ==> 15744 hit(s).

The SELECT clause produced the output with the following heading.

Query LT55J4AkJu400000 produces 32 distinct tuples of columns mchn,tmpr

In this particular case, it prints the machine name with the abnormal temperature, 'MegaBACE # MB 424', and the abnormal temperature values, which incidentally all appears to be multiple of 8.

Endnotes

1. FastBit IBIS has been released as open source software under LGPL license. You may download a free copy from FastBit download page.
2. Additional documentation about FastBit can be found on-line at FastBit website. Questions may be directed to [email protected] (free subscription required, click here).