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) 2020 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