tricensus-mpi

TRICENSUS-MPI(1)              The Regina Handbook             TRICENSUS-MPI(1)



NAME
       tricensus-mpi - Distribute a triangulation census amongst several
       machines using MPI

SYNOPSIS
       tricensus-mpi [ -D, --depth=levels ] [ -x, --dryrun ] [ -2, --dim2 |
       -4, --dim4 ] [ -o, --orientable | -n, --nonorientable ] [ -f, --finite
       | -d, --ideal ] [ -m, --minimal | -M, --minprime | -N, --minprimep2 |
       -h, --minhyp ] [ -s, --sigs ] pairs-file output-file-prefix


CAUTION
       The MPI utilities in Regina are deprecated, and will be removed from
       Regina in a future release.  If you wish to parallelise the generation
       of a census, we recommend splitting up the input pairing files into
       chunks, and using typical queue systems (such as PBS) to parallelise.

DESCRIPTION
       Allows multiple processes, possibly running on a cluster of different
       machines, to collaborate in forming a census of 2-, 3- or 4-manifold
       triangulations.  Coordination is done through MPI (the Message Passing
       Interface), and the entire census is run as a single MPI job.  This
       program is well suited for high-performance clusters.

       The default behaviour is to enumerate 3-manifold triangulations.  If
       you wish to enumerate 2-manifold or 4-manifold triangulations instead,
       you must pass --dim2 or --dim4 respectively.

       To prepare a census for distribution amongst several processes or
       machines, the census must be split into smaller pieces.  Running
       tricensus with option --genpairs (which is very fast) will create a
       list of facet pairings (e.g., tetrahedron face pairings for 3-manifold
       triangulations, triangle edge pairings for 2-manifold triangulations,
       and so on).  Each facet pairing must be analysed in order to complete
       the census.

       The full list of facet pairings should be stored in a single file,
       which is passed on the command-line as pairs-file.  This file must
       contain one facet pairing per line, and each of these facet pairings
       must be in canonical form (i.e., must be a minimal representative of
       its isomorphism class).  The facet pairings generated by tricensus
       --genpairs are guaranteed to satisfy these conditions.

       The tricensus-mpi utility has two modes of operation: default mode, and
       subsearch mode.  These are explained separately under modes of
       operation below.

       In both modes, one MPI process acts as the controller and the remaining
       processes all act as slaves.  The controller reads the list of facet
       pairings from pairs-file, constructs a series of tasks based on these,
       and farms these tasks out to the slaves for processing.  Each slave
       processes one task at a time, asking the controller for a new task when
       it is finished with the previous one.

       At the end of each task, if any triangulations were found then the
       slave responsible will save these triangulations to an output file.
       The output file will have a name of the form output-file-prefix_p.rga
       in default mode or output-file-prefix_p-s.rga in subsearch mode.  Here
       output-file-prefix is passed on the command line, p is the number of
       the facet pairing being processed, and s is the number of the subsearch
       within that facet pairing (both facet pairings and subsearches are
       numbered from 1 upwards).  If no triangulations were found then the
       slave will not write any output file at all.

       The controller and slave processes all take the same tricensus-mpi
       options (excluding MPI-specific options, which are generally supplied
       by an MPI wrapper program such as mpirun or mpiexec).  The different
       roles of the processes are determined solely by their MPI process rank
       (the controller is always the process with rank 0).  It should
       therefore be possible to start all MPI processes by running a single
       command, as illustrated in the examples below.

       As the census progresses, the controller keeps a detailed log of each
       slave's activities, including how long each slave task has taken and
       how many triangulations have been found.  This log is written to the
       file output-file-prefix.log.  The utility tricensus-mpi-status can
       parse this log and produce a shorter human-readable summary.

              Important: It is highly recommended that you use the --sigs
              option.  This will keep output files small, and will
              significantly reduce the memory footprint of tricensus-mpi
              itself.

MODES OF OPERATION
       As discussed above, there are two basic modes of operation.  These are
       default mode (used when --depth is not passed), and subsearch mode
       (used when --depth is passed).

       • In default mode, the controller simply reads the list of facet
         pairings and gives each pairing to a slave for processing, one after
         another.

       • In subsearch mode, more work is pushed to the controller and the
         slave tasks are shorter.  Here the controller reads one facet pairing
         at a time and begins processing that facet pairing.  A fixed depth is
         supplied in the argument --depth; each time that depth is reached in
         the search tree, the subsearch from that point on is given as a task
         to the next idle slave.  Meanwhile the controller backtracks (as
         though the subsearch had finished) and continues, farming the next
         subsearch out when the given depth is reached again, and so on.

       The modes can be visualised as follows.  For each facet pairing,
       consider the corresponding recursive search as a large search tree.  In
       default mode, the entire tree is processed at once as a single slave
       task.  In subsearch mode, each subtree rooted at the given depth is
       processed as a separate slave task (and all processing between the root
       and the given depth is done by the controller).

       The main difference between the different modes of operation is the
       lengths of the slave tasks, which can have a variety of effects.

       • In default mode the slave tasks are quite long.  This means the
         parallelisation can become very poor towards the end of the census,
         with some slaves sitting idle for a long time as they wait for the
         remaining slaves to finish.

       • As we move to subsearch mode with increasing depth, the slave tasks
         become shorter and the slaves' finish times will be closer together
         (thus avoiding the idle slave inefficiency described above).
         Moreover, with a more refined subsearch, the progress information
         stored in the log will be more detailed, giving a better idea of how
         long the census has to go.  On the other hand, more work is pushed to
         the single-process controller (risking a bottleneck if the depth is
         too great, with slaves now sitting idle as they wait for new tasks).
         In addition the MPI overhead is greater, and the number of output
         files can become extremely large.

       In the end, experimentation is the best way to decide whether to run in
       subsearch mode and at what depth.  Be aware of the option --dryrun,
       which can give a quick overview of the search space (and in particular,
       show how many subsearches are required for each facet pairing at any
       given depth).

OPTIONS
       The census options accepted by tricensus-mpi are identical to the
       options for tricensus See the tricensus reference for details.

       Some options from tricensus are not available here (e.g., tetrahedra
       and boundary options), since these must be supplied earlier on when
       generating the initial list of facet pairings.

       There are new options specific to tricensus-mpi, which are as follows.

       -D, --depth=levels
              Indicates that subsearch mode should be used (instead of default
              mode).  The argument levels specifies at what depth in the
              search tree processing should pass from the controller to a new
              slave task.

              The given depth must be strictly positive (running at depth zero
              is equivalent to running in default mode).

              See the modes of operation section above for further
              information, as well as hints on choosing a good value for
              levels.

       -x, --dryrun
              Specifies that a fast dry run should be performed, instead of a
              full census.

              In a dry run, each time a slave accepts a task it will
              immediately mark it as finished with no triangulations found.
              The behaviour of the controller remains unchanged.

              The result will be an empty census.  The benefit of a dry run is
              the log file it produces, which will show precisely how facet
              pairings would be divided into subsearches in a real census run.
              In particular, the log file will show how many subsearches each
              facet pairing produces (the utility tricensus-mpi-status can
              help extract this information from the log).

              At small subsearch depths, a dry run should be extremely fast.
              As the depth increases however, the dry run will become slower
              due to the extra work given to the controller.

              This option is only useful in subsearch mode (it can be used in
              default mode, but the results are uninteresting).  See the modes
              of operation section above for further details.

EXAMPLES
       Suppose we wish to form a census of all 6-tetrahedron closed non-
       orientable 3-manifold triangulations, optimised for prime minimal
       P2-irreducible triangulations (so some non-prime, non-minimal or non-
       P2-irreducible triangulations may be omitted).

       We begin by using tricensus to generate a full list of face pairings.

           example$ tricensus --genpairs -t 6 -i > 6.pairs
           Total face pairings: 97
           example$

       We now use tricensus-mpi to run the distributed census.  A wrapper
       program such as mpirun or mpiexec can generally be used to start the
       MPI processes, though this depends on your specific MPI implementation.
       The following command runs a distributed census on 10 processors using
       the MPICH implementation of MPI.

           example$ mpirun -np 10 /usr/bin/tricensus-mpi -Nnf 6.pairs 6-nor
           example$

       The current state of processing is kept in the controller log
       6-nor.log.  You can watch this log with the help of tricensus-mpi-
       status.

           example$ tricensus-mpi-status 6-nor.log
           Pairing 1: done, 0 found
           ...
           Pairing 85: done, 0 found
           Pairing 86: done, 7 found
           Pairing 87: running
           Pairing 88: running
           Still running, 15 found, last activity: Wed Jun 10 05:57:34 2009
           example$

       Once the census is finished, the resulting triangulations will be saved
       in files such as 6-nor_8.rga, 6-nor_86.rga and so on.

MACOS X AND WINDOWS USERS
       This utility is not shipped with the drag-and-drop app bundle for
       MacOS X or with the Windows installer.

SEE ALSO
       censuslookup, regconcat, sigcensus, tricensus, tricensus-mpi-status,
       regina-gui.

AUTHOR
       This utility was written by Benjamin Burton <bab@maths.uq.edu.au>.
       Many people have been involved in the development of Regina; see the
       users' handbook for a full list of credits.



                               14 December 2016               TRICENSUS-MPI(1)