NAME

       hmmpgmd_shard - sharded daemon for database search web services

SYNOPSIS

       hmmpgmd_shard [options]

DESCRIPTION

       The  hmmpgmd_shard  program  provides  a sharded version of the hmmpgmd program that we use internally to
       implement high-performance HMMER services that can be accessed via the internet.   See  the  hmmpgmd  man
       page  for  a  discussion  of  how  the base hmmpgmd program is used.  This man page discusses differences
       between hmmpgmd_shard and hmmpgmd.  The base hmmpgmd program loads the entirety of its database file into
       RAM on every worker node, in spite of the fact that each worker node searches a predictable  fraction  of
       the database(s) contained in that file when performing searches.  This wastes RAM, particularly when many
       worker nodes are used to accelerate searches of large databases.

       Hmmpgmd_shard  addresses  this by dividing protein sequence database files into shards.  Each worker node
       loads only 1/Nth of the database file, where N is the number of worker nodes attached to the master.  HMM
       database files are not sharded, meaning that every worker node will load the entire  database  file  into
       RAM.  Current HMM databases are much smaller than current protein sequence databases, and easily fit into
       the RAM of modern servers even without sharding.

       Hmmpgmd_shard  is  used  in  the  same  manner as hmmpgmd , except that it takes one additional argument:
       --num_shards <n> , which specifies the number of shards that protein databases will be divided into,  and
       defaults to 1 if unspecified.  This argument is only valid for the master node of a hmmpgmd system (i.e.,
       when  --master  is  passed  to the hmmpgmd program), and must be equal to the number of worker nodes that
       will connect to the master node.  Hmmpgmd_shard will signal an error if more than num_shards worker nodes
       attempt to connect to the master node or if a search is started when fewer than  num_shards  workers  are
       connected to the master.

OPTIONS

       -h     Help; print a brief reminder of command line usage and all available options.

       --master
              Run as the master server.

       --worker <s>
              Run as a worker, connecting to the master server that is running on IP address <s>.

       --cport <n>
              Port to use for communication between clients and the master server.  The default is 51371.

       --wport <n>
              Port to use for communication between workers and the master server.  The default is 51372.

       --ccncts <n>
              Maximum number of client connections to accept. The default is 16.

       --wcncts <n>
              Maximum number of worker connections to accept. The default is 32.

       --pid <f>
              Name of file into which the process id will be written.

       --seqdb <f>
              Name of the file (in hmmpgmd format) containing protein sequences.  The contents of this file will
              be cached for searches.

       --hmmdb <f>
              Name of the file containing protein HMMs. The contents of this file will be cached for searches.

       --cpu <n>
              Number of parallel threads to use (for --worker ).

       --num_shards <n>
              Number  of  shards to divide cached sequence database(s) into.  HMM databases are not sharded, due
              to their small size.  This option is only valid when the --master option is present, and  defaults
              to 1 if not specified.  Hmmpgmd_shard requires that the number of shards be equal to the number of
              worker  nodes,  and  will  give  errors  if more than num_shards workers attempt to connect to the
              master node or if a search is started with fewer than num_shards workers connected to the master.

SEE ALSO

       See hmmmpgmd(1) for a description of the base hmmpgmd command and how the daemon should be used.

       hmmer(1) for a master man page with a list of all the individual man pages  for  programs  in  the  HMMER
       package.

       For complete documentation, see the user guide that came with your HMMER distribution (Userguide.pdf); or
       see the HMMER web page (http://hmmer.org/).

COPYRIGHT

       Copyright (C) 2023 Howard Hughes Medical Institute.
       Freely distributed under the BSD open source license.

       For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source
       distribution, or see the HMMER web page (http://hmmer.org/).

AUTHOR

       http://eddylab.org

HMMER 3.4                                           Aug 2023                                    hmmpgmd_shard(1)