[GE users] [ANN] ruby queue : rq-2.3.1

Ara.T.Howard ara.t.howard at noaa.gov
Sun Dec 11 23:14:35 GMT 2005


URIS:

   http://codeforpeople.com/lib/ruby/rq/
   http://www.linuxjournal.com/article/7922
   http://raa.ruby-lang.org/project/rq/

HISTORY:

   ---
   2.3.1:
     - added 'stage' option to submit mode, which allows submission in a 'holding'
       state.  thanks to Juan.Fernandez at eu.Takata.com for this fix!

README:

   NAME
     rq v2.3.1

   SYNOPSIS
     rq (queue | export RQ_Q=q) mode [mode_args]* [options]*


   DESCRIPTION
     ruby queue (rq) is a tool used to create instant linux clusters by managing
     sqlite databases as nfs mounted priority work queues.  multiple instances of
     rq running from multiples hosts can work from these queues to distribute
     processing load to n nodes - bringing many dozens of otherwise powerful cpus
     to their knees with a single blow.  clearly this software should be kept out
     of the hands of free radicals, seti enthusiasts, and mr. jeff safran.

     the central concept of rq is that n nodes work in isolation to pull jobs from
     an central nfs mounted priority work queue in a synchronized fashion.  the
     nodes have absolutely no knowledge of each other and all communication if done
     via the queue meaning that, so long as the queue is available via nfs and a
     single node is running jobs from it, the system will continue to process jobs.
     there is no centralized process whatsoever - all nodes work to take jobs from
     the queue and run them as fast as possible.  this creates a system which load
     balances automatically and is robust in face of node failures.

     the first argument to any rq command is the name of the queue.  this name may
     be omitted if, and only if, the environment variable RQ_Q has been set to
     contain the absolute path of target queue.

     rq operates in one of the modes create, submit, resubmit, list, status,
     delete, update, query, execute, configure, snapshot, lock, backup, rotate,
     feed, or help.  depending on the mode of operation and the options used the
     meaning of 'mode_args' may change.

   MODES

     the following mode abbreviations exist

       c  => create
       s  => submit
       r  => resubmit
       l  => list
       ls => list
       t  => status
       d  => delete
       rm => delete
       u  => update
       q  => query
       e  => execute
       C  => configure
       S  => snapshot
       L  => lock
       b  => backup
       R  => rotate
       f  => feed
       h  => help

     not all modes have abbreviations

     create, c :

       create a queue.  the queue must be located on an nfs mounted file system
       visible from all nodes intended to run jobs from it.  nfs locking must be
       functional on this file system.

       examples :

         0) to create a queue
             ~ > rq /path/to/nfs/mounted/q create
           or simply
             ~ > rq /path/to/nfs/mounted/q c


     submit, s :

       submit jobs to a queue to be proccesed by a feeding node.  any 'mode_args'
       are taken as the command to run.  note that 'mode_args' are subject to shell
       expansion - if you don't understand what this means do not use this feature
       and pass jobs on stdin.

       when running in submit mode a file may by specified as a list of commands to
       run using the '--infile, -i' option.  this file is taken to be a newline
       separated list of commands to submit, blank lines and comments (#) are
       allowed.  if submitting a large number of jobs the input file method is
       MUCH, more efficient.  if no commands are specified on the command line rq
       automatically reads them from STDIN.  yaml formatted files are also allowed
       as input (http://www.yaml.org/) - note that the output of nearly all rq
       commands is valid yaml and may, therefore, be piped as input into the submit
       command.  the leading '---' of yaml file may not be omitted.

       when submitting the '--priority, -p' option can be used here to determine
       the priority of jobs.  priorities may be any whole number - zero is the
       default.  note that submission of a high priority job will NOT supplant
       currently running low priority jobs, but higher priority jobs WILL always
       migrate above lower priority jobs in the queue in order that they be run as
       soon as possible.  constant submission of high priority jobs may create a
       starvation situation whereby low priority jobs are never allowed to run.
       avoiding this situation is the responsibility of the user.  the only
       guaruntee rq makes regarding job execution is that jobs are executed in an
       'oldest highest priority' order and that running jobs are never supplanted.
       jobs submitted with the '--stage' option will not be run by any node and
       will remain in a 'holding' state until updated (see update mode) into the
       'pending' mode, this option allows jobs to entered, or staged, in the queue
       and made candidates for running at a later date.

       examples :

         0) submit the job ls to run on some feeding host

           ~ > rq q s ls

         1) submit the job ls to run on some feeding host, at priority 9

           ~ > rq -p9 q s ls

         2) submit 42000 jobs (quietly) from a command file, marking them as
            restartable should the node they are running on reboot.

           ~ > wc -l cmdfile
           42000
           ~ > rq q s --quiet --restartable < cmdfile

         3) submit 42 priority 9 jobs from a command file.

           ~ > wc -l cmdfile
           42
           ~ > rq -p9 q s < cmdfile

         4) submit 42 priority 9 jobs from a command file, marking them as
            'important' using the '--tag, -t' option.

           ~ > wc -l cmdfile
           42
           ~ > rq -p9 -timportant q s < cmdfile

         5) re-submit all the 'important' jobs (see 'query' section below)

           ~ > rq q query tag=important | rq q s

         6) re-submit all jobs which are already finished (see 'list' section
            below)

           ~ > rq q l f | rq q s


         7) stage the job wont_run_yet to the queue in a 'holding' state.  no
            feeder will run this job until it's state is upgraded to 'pending'

           ~ > rq q s --stage wont_run_yet


     resubmit, r :

       resubmit jobs back to a queue to be proccesed by a feeding node.  resubmit
       is essentially equivalent to submitting a job that is already in the queue
       as a new job and then deleting the original job except that using resubmit
       is atomic and, therefore, safer and more efficient.  read docs for delete
       and submit for more info.

       examples :

         0) resubmit job 42 to the queue.  afterwards


     list, l, ls :

       list mode lists jobs of a certain state or job id.  state may be one of
       pending, holding, running, finished, dead, or all.  any 'mode_args' that are
       numbers are taken to be job id's to list.

       states may be abbreviated to uniqueness, therefore the following shortcuts
       apply :

         p => pending
         h => holding
         r => running
         f => finished
         d => dead
         a => all

       examples :

         0) show everything in q
             ~ > rq q list all
           or
             ~ > rq q l all
           or
             ~ > export RQ_Q=q
             ~ > rq l

         1) show q's pending jobs
             ~ > rq q list pending

         2) show q's running jobs
             ~ > rq q list running

         3) show q's finished jobs
             ~ > rq q list finished

         4) show job id 42
             ~ > rq q l 42

         5) show q's holding jobs
             ~ > rq q list holding


     status, t :

       status mode shows the global state the queue.  there are no 'mode_args'.
       the meaning of each state is as follows:

         pending  => no feeder has yet taken this job
         holding  => a hold has been placed on this job, thus no feeder will start
                     it
         running  => a feeder has taken this job
         finished => a feeder has finished this job
         dead     => rq died while running a job, has restarted, and moved
                     this job to the dead state

       note that rq cannot move jobs into the dead state unless it has been
       restarted.  this is because no node has any knowledge of other nodes and
       cannot possibly know if a job was started on a node that died, or is simply
       taking a very long time.  only the node that dies, upon restart, can
       determine that is has jobs that 'were started before it started' and move
       these jobs into the dead state.  normally only a machine crash would cause a
       job to be placed into the dead state.  dead jobs are never automatically
       restarted, this is the responsibility of an operator.

       examples :

         0) show q's status

           ~ > rq q t


     delete, d :

       delete combinations of pending, holding, finished, dead, or jobs specified
       by jid.  the delete mode is capable of parsing the output of list and query
       modes, making it possible to create custom filters to delete jobs meeting
       very specific conditions.

       'mode_args' are the same as for list.

       note that it is NOT possible to delete a running job.  rq has a
       decentralized architechture which means that compute nodes are completely
       independant of one another; an extension is that there is no way to
       communicate the deletion of a running job from the queue the the node
       actually running that job.  it is not an error to force a job to die
       prematurely using a facility such as an ssh command spawned on the remote
       host to kill it.  once a job has been noted to have finished, whatever the
       exit status, it can be deleted from the queue.

       examples :

         0) delete all pending, finished, and dead jobs from a queue

           ~ > rq q d all

         1) delete all pending jobs from a queue

           ~ > rq q d p

         2) delete all finished jobs from a queue

           ~ > rq q d f

         3) delete jobs via hand crafted filter program

           ~ > rq q list | yaml_filter_prog | rq q d

           an example ruby filter program (you have to love this)

           require 'yaml'
           joblist = YAML::load STDIN
           y joblist.select{|job| job['command'] =~ /bombing_program/}

           this program reads the list of jobs (yaml) from stdin and then dumps
           only those jobs whose command matches 'bombing_program', which is
           subsequently piped to the delete command.


     update, u :

       update assumes all leading arguments are jids to update with subsequent
       key=value pairs.  currently only the 'command', 'priority', and 'tag' fields
       of pending jobs can be generically updated and the 'state' field may be
       toggled between pending and holding.

       examples:

         0) update the priority of job 42

           ~ > rq q update 42 priority=7

         1) update the priority of all pending jobs

           ~ > rq q update pending priority=7

         2) query jobs with a command matching 'foobar' and update their command
            to be 'barfoo'

           ~ > rq q q "command like '%foobar%'" |\
               rq q u command=barfoo

         3) place a hold on jid 2

           ~ > rq q u 2 state=holding

         4) place a hold on all jobs with tag=disk_filler

           ~ > rq q q tag=disk_filler | rq q u state=holding

         5) remove the hold on jid 2

           ~ > rq q u 2 state=pending


     query, q :

       query exposes the database more directly the user, evaluating the where
       clause specified on the command line (or read from STDIN).  this feature can
       be used to make a fine grained slection of jobs for reporting or as input
       into the delete command.  you must have a basic understanding of SQL syntax
       to use this feature, but it is fairly intuitive in this limited capacity.

       examples:

         0) show all jobs submitted within a specific 10 minute range

           ~ > rq q query "started >= '2004-06-29 22:51:00' and started < '2004-06-29 22:51:10'"

         1) shell quoting can be tricky here so input on STDIN is also allowed to
            avoid shell expansion

           ~ > cat constraints.txt
           started >= '2004-06-29 22:51:00' and
           started < '2004-06-29 22:51:10'

           ~ > rq q query < contraints.txt
             or (same thing)

           ~ > cat contraints.txt| rq q query


         2) this query output might then be used to delete those jobs

           ~ > cat contraints.txt | rq q q | rq q d

         3) show all jobs which are either finished or dead

           ~ > rq q q "state='finished' or state='dead'"

         4) show all jobs which have non-zero exit status

           ~ > rq q query exit_status!=0

         5) if you plan to query groups of jobs with some common feature consider
            using the '--tag, -t' feature of the submit mode which allows a user to
            tag a job with a user defined string which can then be used to easily
            query that job group

           ~ > rq q submit --tag=my_jobs < joblist
           ~ > rq q query tag=my_jobs


         6) in general all but numbers will need to be surrounded by single quotes
            unless the query is a 'simple' one.  a simple query is a query with no
            boolean operators, not quotes, and where every part of it looks like

               key op value

            with ** NO SPACES ** between key, op, and value.  if, and only if, the
            query is 'simple' rq will contruct the where clause appropriately.  the
            operators accepted, and their meanings, are

              =  : equivalence : sql =
              =~ : matches     : sql like
              !~ : not matches : sql not like

            match, in the context is ** NOT ** a regular expression but a sql style
            string match.  about all you need to know about sql matches is that the
            '%' char matches anything.  multiple simple queries will be joined with
            boolean 'and'

            this sounds confusing - it isn't.  here are some examples of simple
            queries

            6.a)
              query :
                rq q query tag=important

              where_clause :
                "( tag = 'important' )"

            6.b)
              query :
                rq q q priority=6 restartable=true

              where_clause :
                "( priority = 6 ) and ( restartable = 'true' )"

            6.c)
              query :
                rq q q command=~%bombing_job% runner=~%node_1%

              where_clause :
                "( command like '%bombing_job%') and (runner like '%node_1%')"


     execute, e :

       execute mode is to be used by expert users with a knowledge of sql syntax
       only.  it follows the locking protocol used by rq and then allows the user
       to execute arbitrary sql on the queue.  unlike query mode a write lock on
       the queue is obtained allowing a user to definitively shoot themselves in
       the foot.  for details on a queue's schema the file 'db.schema' in the queue
       directory should be examined.

         examples :

           0) list all jobs

             ~ > rq q execute 'select * from jobs'


     configure, C :

       this mode is not supported yet.


     snapshot, p :

       snapshot provides a means of taking a snapshot of the q. use this feature
       when many queries are going to be run; for example when attempting to figure
       out a complex pipeline command your test queries will not compete with the
       feeders for the queue's lock.  you should use this option whenever possible
       to avoid lock competition.

       examples:

         0) take a snapshot using default snapshot naming, which is made via the
            basename of the q plus '.snapshot'

           ~ > rq /path/to/nfs/q snapshot

         1) use this snapshot to chceck status

           ~ > rq ./q.snapshot status

         2) use the snapshot to see what's running on which host

           ~ > rq ./q.snapshot list running | grep `hostname`

       note that there is also a snapshot option - this option is not the same as
       the snapshot command.  the option can be applied to ANY command. if in
       effect then that command will be run on a snapshot of the database and the
       snapshot then immediately deleted.  this is really only useful if one were
       to need to run a command against a very heavily loaded queue and did not
       wish to wait to obtain the lock.  eg.

         0) get the status of a heavily loaded queue

           ~ > rq q t --snapshot

         1) same as above

           ~ > rq q t -s

       ** IMPORTANT **

         a really great way to hang all processing in your queue is to do this

           rq q list | less

         and then leave for the night.  you hold a read lock you won't release
         until less dies.  this is what snapshot is made for!  use it like

           rq q list -s | less

         now you've taken a snapshot of the queue to list so your locks affect no
         one.


     lock, L :

       lock the queue and then execute an arbitrary shell command.  lock mode uses
       the queue's locking protocol to safely obtain a lock of the specified type
       and execute a command on the user's behalf.  lock type must be one of

         (r)ead | (sh)ared | (w)rite | (ex)clusive

       examples :

         0) get a read lock on the queue and make a backup

           ~ > rq q L read -- cp -r q q.bak

           (the '--' is needed to tell rq to stop parsing command line
            options which allows the '-r' to be passed to the 'cp' command)

       ** IMPORTANT **

         this is another fantastic way to freeze your queue - use with care!


     backup, b :

       backup mode is exactly the same as getting a read lock on the queue and
       making a copy of it.  this mode is provided as a convenience.

         0) make a backup of the queue using default naming ( qname + timestamp + .bak )

           ~ > rq q b

         1) make a backup of the queue as 'q.bak'

           ~ > rq q b q.bak


     rotate, r :

       rotate mode is conceptually similar to log rolling.  normally the list of
       finished jobs will grow without bound in a queue unless they are manually
       deleted.  rotation is a method of trimming finished jobs from a queue
       without deleting them.  the method used is that the queue is copied to a
       'rotation'; all jobs that are dead or finished are deleted from the original
       queue and all pending and running jobs are deleted from the rotation.  in
       this way the rotation becomes a record of the queue's finished and dead jobs
       at the time the rotation was made.

         0) rotate a queue using default rotation name

           ~ > rq q rotate

         1) rotate a queue naming the rotation

           ~ > rq q rotate q.rotation

         2) a crontab entry like this could be used to rotate a queue daily

           59 23 * * * rq q rotate `date +q.%Y%m%d`


     feed, f :

       take jobs from the queue and run them on behalf of the submitter as quickly
       as possible.  jobs are taken from the queue in an 'oldest highest priority'
       first order.

       feeders can be run from any number of nodes allowing you to harness the CPU
       power of many nodes simoultaneously in order to more effectively clobber
       your network, anoy your sysads, and set output raids on fire.

       the most useful method of feeding from a queue is to do so in daemon mode so
       that if the process loses it's controling terminal it will not exit when you
       exit your terminal session.  use the '--daemon, -d' option to accomplish
       this.  by default only one feeding process per host per queue is allowed to
       run at any given moment.  because of this it is acceptable to start a feeder
       at some regular interval from a cron entry since, if a feeder is alreay
       running, the process will simply exit and otherwise a new feeder will be
       started.  in this way you may keep feeder processing running even acroess
       machine reboots without requiring sysad intervention to add an entry to the
       machine's startup tasks.


       examples :

         0) feed from a queue verbosely for debugging purposes, using a minimum and
            maximum polling time of 2 and 4 respectively.  you would NEVER specify
            polling times this brief except for debugging purposes!!!

           ~ > rq q feed -v4 -m2 -M4

         1) same as above, but viewing the executed sql as it is sent to the
            database

           ~ > RQ_SQL_DEBUG=1 rq q f -v4 -m2 -M4

         2) feed from a queue in daemon mode - logging to /home/ahoward/rq.log

           ~ > rq q f -d -l/home/ahoward/rq.log

            log rolling in daemon mode is automatic so your logs should never need
            to be deleted to prevent disk overflow.

         3) use something like this sample crontab entry to keep a feeder running
            forever - it attempts to (re)start every fifteen minutes but exits if
            another process is already feeding.

           #
           # your crontab file - sample only
           #

           */15 * * * * /full/path/to/bin/rq /full/path/to/nfs/mounted/q f -d -l/home/username/cfq.log -q

           the '--quiet, -q' here tells rq to exit quietly (no STDERR)
           when another process is found to already be feeding so that no cron
           message would be sent under these conditions.


     start :

       the start mode is equivalent to running the feed mode except the --daemon is
       implied so the process instantly goes into the background.  also, if no log
       (--log) is specified in start mode a default one is used.  the default is

         ENV['HOME'] + '/' + File::basename(queue) + '.log'

       the crontab line above could just as well be

         */15 * * * * /full/path/to/bin/rq /full/path/to/nfs/mounted/q start -q

       with the resulting log ending up in ~/q.log

       examples :

         0) start a daemon process feeding from q

           ~ > rq q start


     shutdown :

       tell a running feeder to finish any pending jobs and then to exit.  this is
       equivalent to sending signal 'SIGTERM' to the process - this is what using
       'kill pid' does by default.

       examples :

         0) stop a feeding process, if any, that is feeding from q.  allow all jobs
            to be finished first.

           ~ > rq q shutdown

       ** VERY IMPORTANT **

         if you are keeping your feeder alive with a crontab entry you'll need to
         comment it out before doing this or else it will simply re-start!!!

     stop :

       tell any running feeder to stop NOW.  this sends signal 'SIGKILL' (-9) to
       the feeder process.  the same warning as for shutdown applies!!!

       examples :

         0) stop a feeding process, if any, that is feeding from q.  allow NO jobs
            to be finished first - exit instantly.

           ~ > rq q stop


     feeder :

       show the pid, if any, of the feeder

       ~ > rq q feeder

         feeder <15366>


     help, h :

       this message

       examples :

         0) get this message

           ~> rq q help
           or
           ~> rq help


   NOTES
     - realize that your job is going to be running on a remote host and this has
       implications.  paths, for example, should be absolute, not relative.
       specifically the submitted job script must be visible from all hosts
       currently feeding from a queue as must be the input and output
       files/directories.

     - jobs are currently run under the bash shell using the --login option.
       therefore any settings in your .bashrc will apply - specifically your PATH
       setting.  you should not, however, rely on jobs running with any given
       environment.

     - you need to consider __CAREFULLY__ what the ramifications of having multiple
       instances of your program all potentially running at the same time will be.
       for instance, it is beyond the scope of rq to ensure multiple instances of a
       given program will not overwrite each others output files.  coordination
       of programs is left entirely to the user.

     - the list of finished jobs will grow without bound unless you sometimes
       delete some (all) of them.  the reason for this is that rq cannot know when
       the user has collected the exit_status of a given job, and so keeps this
       information in the queue forever until instructed to delete it.  if you have
       collected the exit_status of you job(s) it is not an error to then delete
       that job from the finished list - the information is kept for your
       informational purposes only.  in a production system it would be normal to
       periodically save, and then delete, all finished jobs.

     - know that it is a VERY bad idea to spawn several dozen process all
       reading/writing huge output files to a single NFS server.  use this paradigm
       instead

         copy data locally from input space
         work on date
         move data to output space

       the vsftp daemon is an excellent utility to have running on hosts in your
       cluster so anonymous ftp can be used to get/put data.

     - know that nfs locking is very, very easy to break with firewalls put in
       place by over zealous system administrators.  be postive not only that nfs
       locking works, but that lock recovery server/client crash or reboot works as
       well.  http://nfs.sourceforge.net/ is the place to learn about NFS.  my
       experience thus far is that there are ZERO properly configured NFS
       installations in the world.  please test yours.  contact me for a simple
       script which can assist you.  donations of beer may be required.

   ENVIRONMENT
     RQ_Q: set to the full path of nfs mounted queue

       the queue argument to all commands may be omitted if, and only if, the
       environment variable 'RQ_Q' contains the full path to the q.  eg.

         ~ > export RQ_Q=/full/path/to/my/q

       this feature can save a considerable amount of typing for those weak of
       wrist.

   DIAGNOSTICS
    success : $? == 0
    failure : $? != 0

   CREDITS
     - kim baugh       : patient tester and design input
     - jeff safran     : the guy can break anything
     - chris elvidge   : made it possible
     - trond myklebust : tons of help with nfs
     - jamis buck      : for writing the sqlite bindings for ruby
     - _why            : for writing yaml for ruby
     - matz            : for writing ruby

   AUTHOR
     ara.t.howard at noaa.gov

   BUGS
    0 < bugno && bugno <= 42

    reports to ara.t.howard at noaa.gov

   OPTIONS
     --priority=priority, -p
           modes <submit> : set the job(s) priority - lowest(0) .. highest(n) -
           (default 0)
     --tag=tag, -t
           modes <submit> : set the job(s) user data tag
     --runner=runner
           modes <submit> : set the job(s) required runner(s)
     --restartable
           modes <submit> : set the job(s) to be restartable on node reboot
     --stage
           modes <submit> : set the job(s) initial state to be holding (default
           pending)
     --infile=infile
           modes <submit> : infile
     --quiet, -q
           modes <submit, feed> : do not echo submitted jobs, fail silently if
           another process is already feeding
     --daemon, -D
           modes <feed> : spawn a daemon
     --max_feed=max_feed
           modes <feed> : the maximum number of concurrent jobs run
     --retries=retries
           modes <feed> : specify transaction retries
     --min_sleep=min_sleep
           modes <feed> : specify min sleep
     --max_sleep=max_sleep
           modes <feed> : specify max sleep
     --snapshot, -s
           operate on snapshot of queue
     --verbosity=verbostiy, -v
           0|fatal < 1|error < 2|warn < 3|info < 4|debug - (default info)
     --log=path, -l
           set log file - (default stderr)
     --log_age=log_age
           daily | weekly | monthly - what age will cause log rolling (default
           nil)
     --log_size=log_size
           size in bytes - what size will cause log rolling (default nil)
     --help, -h
           this message
     --version
           show version number


enjoy.

-a
-- 
===============================================================================
| ara [dot] t [dot] howard [at] noaa [dot] gov
| all happiness comes from the desire for others to be happy.  all misery
| comes from the desire for oneself to be happy.
| -- bodhicaryavatara
===============================================================================


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