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HTMLing READMES
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Robert Harrison
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contrib/workstations/workstations.html
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contrib/workstations/workstations.html
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<HTML>
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<HEAD>
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<TITLE>Notes on running NWChem on workstations and clusters</TITLE>
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</HEAD>
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<BODY BGCOLOR="FAEBD7">
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<P><IMG SRC="/msrc/home/d3g681/html/nwchem/nwchem_logo.gif" ALT="NWChem - computational chemistry on parallel computers">
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</P>
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<HR>
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<H1>Notes on running NWChem on workstations and clusters</H1>
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<P>Since these notes are generic to most workstations, it is impossible
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to be completely specific about the locations of files, etc. You will
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want to know where the nwchem and parallel executables reside. You
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may want to add this location to your shell's executable search path.
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<P>You may need to be aware of where the code expects to find the
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standard basis set library. The location is fixed at compile time and
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should have been set to something appropriate for your site. Without
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any special configuration, NWChem will look for the standard library
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in the source directory tree. This means that moving the source tree
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may confuse an existing executable. For most installations, however,
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we are configuring the library to live in the same directory as the
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nwchem and parallel executables. Should you run into problems in
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which NWChem cannot locate the standard basis library, you can easily
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work around it by using the "<TT>file</TT>" option on the basis set
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entry for each library basis set you need.
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<P>Since workstations vary widely in how much memory is available, the
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defaults may not be appropriate to your situation. It is advisable to
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check the defaults given in the manual and if necessary adjust them in
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the input deck. Remember that the memory specification is per
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process, so if you set the limit to 32 MB and run four processes on
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the machine, you'll use 128 MB in total.
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<H2>Single process</H2>
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<P>Single process execution is easy -- just invoke nwchem with the name
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of the input file as an argument: "<TT>nwchem input.nw</TT>".
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<H2>The "<TT>parallel</TT>" command for multiprocess execution</H2>
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<P>The "<TT>parallel</TT>" command is part of the TCGMSG (message
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passing) package, which NWChem uses to run jobs in parallel. The
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following description is largely cribbed from the TCGMSG README file
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(which can be found in the NWChem source tree). Explanations specific
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to NWChem follow it.
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<P> An auxiliary "process group" (aka PROCGRP) file controls the
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parallel execution. It is usually named with a "<TT>.p</TT>" suffix.
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The PROCGRP file can contain multiple lines, and comments are denoted
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by a "#" sign. Non-comment lines consist of the following fields,
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separated by white space:
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<PRE>
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<userid> <hostname> <nslave> <executable> <workdir>
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userid The username on the machine that will be executing the
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process.
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hostname The hostname of the machine to execute this process.
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If it is the same machine on which parallel was invoked
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the name must match the value returned by the command
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hostname. If a remote machine it must allow remote execution
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from this machine (see man pages for rlogin, rsh).
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nslave The total number of copies of this process to be executing
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on the specified machine. Only 'clusters' of identical processes
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specified in this fashion can use shared memory to communicate.
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If no shared memory is supported on machine <hostname> then
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only the value one (1) is valid (e.g. on the Cray).
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executable Full path name on the host <hostname> of the image to execute.
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If <hostname> is the local machine then a local path will
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suffice.
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workdir Full path name on the host <hostname> of the directory to
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work in. Processes execute a chdir() to this directory before
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returning from pbegin(). If specified as a '.' then remote
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processes will use the login directory on that machine and local
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processes (relative to where parallel was invoked) will use
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the current directory of parallel.
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</PRE>
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e.g.
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<PRE>
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harrison boys 3 /home/harrison/c/ipc/testf.x /tmp # my sun 4
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harrison dirac 3 /home/harrison/c/ipc/testf.x /tmp # ron's sun4
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harrison eyring 8 /usr5/harrison/c/ipc/testf.x /scratch # alliant fx/8
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</PRE>
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<P> The above PROCGRP file would put processes 0-2 on boys (executing
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<TT>testf.x</TT> in <TT>/tmp</TT>), 3-5 on dirac (executing
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<TT>testf.x</TT> in <TT>/tmp</TT>) and 6-13 on eyring (executing
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<TT>testf.x</TT> in <TT>/scratch</TT>). Processes on each machine use
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shared memory to communicate with each other, sockets otherwise.
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<P>To run NWChem using the parallel command, the comand line is
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"<TT>parallel procgrp input.nw</TT>". The first argument of
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<TT>parallel</TT> is the name of the PROCGRP file. <TT>Parallel</TT>
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automatically adds a "<TT>.p</TT>" to the end, so in this case it
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would look for a file named "<TT>procgrp.p</TT>". A common convention
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is to name the PROCGRP file "<TT>nwchem.p</TT>", but remember the
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actual executable to be invoked is specified within the PROCGRP file,
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not on the parallel command line. Remaining arguments to
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<TT>parallel</TT> are passed to the program being invoked, so we give
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then NWChem input deck "<TT>input.nw</TT>".
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<P>Execution on remote workstations is initiated using
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<TT>rsh/rexec</TT> protocol. Users must have remote execution
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privileges enabled for <TT>parallel</TT> to work, this requires that
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the master workstation hostname appears in the slave's <TT>.rhosts</TT> files
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(see the man page, <TT>rsh(1)</TT>).
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<H3>Multiple processes -- single machine</H3>
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<P>If you have a multiprocessor workstation, you can run multiple
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processes using the shared memory regions. In this case, your PROCGRP
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file would have a single (non-comment) line with <TT><nslave></TT> indicating
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the number of processes you want to run. For example
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<PRE>
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gg502 bohr 12 /disk1/gg502/hpcci/nwchem .
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</PRE>
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which would run twelve processes of nwchem working in the current
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directory ("<TT>.</TT>" in Unix shorthand).
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<H3>Clustered workstations</H3>
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<P>In this case, your PROCGRP file will have multiple lines,
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generally one for each machine in your cluster. You must be able to
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<TT>rsh</TT> to each username/host you specify. Processes on
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different lines communicate via TCP/IP sockets. It is also possible
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to run multiple processes on individual nodes in a cluster. In this
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case, processes sharing a single host communicate internally by shared
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memmory and with processes on other machines via sockets.
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<P>The Global Array Toolkit sets up a process on each node in the
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cluster to act as a data server to facilitate answering off-processor
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requests for data. Consequently, the number of <TT><nslave></TT>
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specified on each line must be ONE MORE than the number of compute
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processes you want. For example,
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<PRE>
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gg502 bohr 8 /disk1/gg502/hpcci/nwchem /disk1/gg502/wrk
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gg502 coho 4 /scr/gg502/hpcci/nwchem /scr/gg502/wrk
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</PRE>
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would start 7 compute processes on bohr and 3 on coho, along with one
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data server on each for a total of twelve processes.
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<H2>Common problems</H2>
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<P>When running in parallel on workstations, NWChem uses shared memory
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and may use semaphores. If the run terminates abnormally (errors not
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trapped by the code itself, interrupted by the user, etc.) it may not
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release these resources back to the system. These are global
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resources, and it is possible for you and/or other users to exhaust
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them.
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<P>To see if you have any of these resources allocated, use the command
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"<TT>ipcs</TT>". You will see a table subdivieded into "Message Queues",
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"Shared Memory" and "Semaphores". The second column lists an id
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number which you can use to remove your claim on them with the "ipcrm"
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command. For example user gg502 would deallocate his resources described
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by the output of the <TT>ipcs</TT> command
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<PRE>
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IPC status from fermi as of Wed Aug 9 15:50:32 1995
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T ID KEY MODE OWNER GROUP
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Message Queues:
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Shared Memory:
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m 600 0x00000000 --rw-rw-rw- d3g681 101
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m 1302 0x00000000 --rw------- gg502 101
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m 903 0x00000000 --rw------- gg502 101
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m 1104 0x00000000 --rw------- gg502 101
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m 306 0x00000000 --rw------- gg502 101
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m 107 0x00000000 --rw------- gg502 101
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m 9 0x00000000 --rw------- gg502 101
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Semaphores:
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s 131 0x00000000 --ra------- gg502 101
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s 92 0x00000000 --ra------- gg502 101
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s 113 0x00000000 --ra------- gg502 101
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s 35 0x00000000 --ra------- gg502 101
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</PRE>
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by using the command
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<PRE>
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"ipcrm -m 1302 -m 903 -m 1104 -m 306 -m 107 -m 9 -s 131 -s 92 -s 113 -s 35"
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</PRE>
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A script (<TT>ipcreset</TT>) to simplify this procedure is provided by TCGMSG (see its README file).
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<P> You will not be able to remove someoneelse's resources unless you
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have sufficient privilige (i.e. root access).
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<H2>Caveats</H2>
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<P>Note that running multiple processes on a single processor machine is
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only useful for debugging purposes. You'll get faster turn around
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with production jobs by running them as a single process if you have
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only one processor available.
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<P>Running multiple processes on a single machine via a multi-line
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PROCGRP file (forcing them to communicate over sockets) is likewise
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less efficient than using the shared memory facilities with a one-line
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PROCGRP file specifying the desired number of <TT><nslave></TT>s.
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<P>Heterogeneous clusters (where all nodes are not the same type of
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hardware) are not generally supported by the current release of the
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Global Array Toolkit, and consequently by NWChem. If all machines
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involved use the same representation for data (big vs little endian,
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IEEE or other floating point, etc.) it will probably work, but
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otherwise it will not.
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<HR>
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<ADDRESS>Prepared by RJ Harrison: Email: nwchem-support@emsl.pnl.gov.</ADDRESS>
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</BODY></HTML>
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